chemical

Bindings for core::chemical namespace

class pyrosetta.rosetta.core.chemical.AA

Bases: pybind11_object

enumeration for amino acids and nucleotides types with the total number as num_aa_types

Members:

aa_none

aa_ala

first_l_aa

aa_cys

aa_asp

aa_glu

aa_phe

aa_gly

aa_his

aa_ile

aa_lys

aa_leu

aa_met

aa_asn

aa_pro

aa_gln

aa_arg

aa_ser

aa_thr

aa_val

aa_trp

aa_tyr

num_canonical_aas

na_ade

first_DNA_aa

na_cyt

na_gua

na_thy

last_DNA_aa

na_rgu

na_rad

na_rcy

na_ura

aa_dal

first_D_aa

aa_dcs

aa_das

aa_dgu

aa_dph

aa_dhi

aa_dil

aa_dly

aa_dle

aa_dme

aa_dan

aa_dpr

aa_dgn

aa_dar

aa_dse

aa_dth

aa_dva

aa_dtr

aa_dty

last_D_aa

aa_b3a

first_beta3_aa

aa_b3c

aa_b3d

aa_b3e

aa_b3f

aa_b3g

aa_b3h

aa_b3i

aa_b3k

aa_b3l

aa_b3m

aa_b3n

aa_b3p

aa_b3q

aa_b3r

aa_b3s

aa_b3t

aa_b3v

aa_b3w

aa_b3y

aa_b3cisACPC

aa_b3transACPC

aa_b3cisACHC

last_beta3_aa

aa_b2a

first_beta2_aa

last_beta2_aa

na_lra

na_lrc

na_lrg

na_lur

ou3_ala

first_oligourea

ou3_cys

ou3_asp

ou3_glu

ou3_phe

ou3_gly

ou3_his

ou3_ile

ou3_lys

ou3_leu

ou3_met

ou3_asn

ou3_pro

ou3_gln

ou3_arg

ou3_ser

ou3_thr

ou3_val

ou3_trp

ou3_tyr

ou3_aib

last_oligourea

aa_h2o

aa_vrt

aa_unp

aa_unk

num_aa_types

aa_ala = <AA.aa_ala: 1>
aa_arg = <AA.aa_arg: 15>
aa_asn = <AA.aa_asn: 12>
aa_asp = <AA.aa_asp: 3>
aa_b2a = <AA.aa_b2a: 71>
aa_b3a = <AA.aa_b3a: 48>
aa_b3c = <AA.aa_b3c: 49>
aa_b3cisACHC = <AA.aa_b3cisACHC: 70>
aa_b3cisACPC = <AA.aa_b3cisACPC: 68>
aa_b3d = <AA.aa_b3d: 50>
aa_b3e = <AA.aa_b3e: 51>
aa_b3f = <AA.aa_b3f: 52>
aa_b3g = <AA.aa_b3g: 53>
aa_b3h = <AA.aa_b3h: 54>
aa_b3i = <AA.aa_b3i: 55>
aa_b3k = <AA.aa_b3k: 56>
aa_b3l = <AA.aa_b3l: 57>
aa_b3m = <AA.aa_b3m: 58>
aa_b3n = <AA.aa_b3n: 59>
aa_b3p = <AA.aa_b3p: 60>
aa_b3q = <AA.aa_b3q: 61>
aa_b3r = <AA.aa_b3r: 62>
aa_b3s = <AA.aa_b3s: 63>
aa_b3t = <AA.aa_b3t: 64>
aa_b3transACPC = <AA.aa_b3transACPC: 69>
aa_b3v = <AA.aa_b3v: 65>
aa_b3w = <AA.aa_b3w: 66>
aa_b3y = <AA.aa_b3y: 67>
aa_cys = <AA.aa_cys: 2>
aa_dal = <AA.aa_dal: 29>
aa_dan = <AA.aa_dan: 39>
aa_dar = <AA.aa_dar: 42>
aa_das = <AA.aa_das: 31>
aa_dcs = <AA.aa_dcs: 30>
aa_dgn = <AA.aa_dgn: 41>
aa_dgu = <AA.aa_dgu: 32>
aa_dhi = <AA.aa_dhi: 34>
aa_dil = <AA.aa_dil: 35>
aa_dle = <AA.aa_dle: 37>
aa_dly = <AA.aa_dly: 36>
aa_dme = <AA.aa_dme: 38>
aa_dph = <AA.aa_dph: 33>
aa_dpr = <AA.aa_dpr: 40>
aa_dse = <AA.aa_dse: 43>
aa_dth = <AA.aa_dth: 44>
aa_dtr = <AA.aa_dtr: 46>
aa_dty = <AA.aa_dty: 47>
aa_dva = <AA.aa_dva: 45>
aa_gln = <AA.aa_gln: 14>
aa_glu = <AA.aa_glu: 4>
aa_gly = <AA.aa_gly: 6>
aa_h2o = <AA.aa_h2o: 97>
aa_his = <AA.aa_his: 7>
aa_ile = <AA.aa_ile: 8>
aa_leu = <AA.aa_leu: 10>
aa_lys = <AA.aa_lys: 9>
aa_met = <AA.aa_met: 11>
aa_none = <AA.aa_none: 0>
aa_phe = <AA.aa_phe: 5>
aa_pro = <AA.aa_pro: 13>
aa_ser = <AA.aa_ser: 16>
aa_thr = <AA.aa_thr: 17>
aa_trp = <AA.aa_trp: 19>
aa_tyr = <AA.aa_tyr: 20>
aa_unk = <AA.aa_unk: 100>
aa_unp = <AA.aa_unp: 99>
aa_val = <AA.aa_val: 18>
aa_vrt = <AA.aa_vrt: 98>
first_DNA_aa = <AA.na_ade: 21>
first_D_aa = <AA.aa_dal: 29>
first_beta2_aa = <AA.aa_b2a: 71>
first_beta3_aa = <AA.aa_b3a: 48>
first_l_aa = <AA.aa_ala: 1>
first_oligourea = <AA.ou3_ala: 76>
last_DNA_aa = <AA.na_thy: 24>
last_D_aa = <AA.aa_dty: 47>
last_beta2_aa = <AA.aa_b2a: 71>
last_beta3_aa = <AA.aa_b3cisACHC: 70>
last_oligourea = <AA.ou3_aib: 96>
na_ade = <AA.na_ade: 21>
na_cyt = <AA.na_cyt: 22>
na_gua = <AA.na_gua: 23>
na_lra = <AA.na_lra: 72>
na_lrc = <AA.na_lrc: 73>
na_lrg = <AA.na_lrg: 74>
na_lur = <AA.na_lur: 75>
na_rad = <AA.na_rad: 26>
na_rcy = <AA.na_rcy: 27>
na_rgu = <AA.na_rgu: 25>
na_thy = <AA.na_thy: 24>
na_ura = <AA.na_ura: 28>
property name
num_aa_types = <AA.aa_unk: 100>
num_canonical_aas = <AA.aa_tyr: 20>
ou3_aib = <AA.ou3_aib: 96>
ou3_ala = <AA.ou3_ala: 76>
ou3_arg = <AA.ou3_arg: 90>
ou3_asn = <AA.ou3_asn: 87>
ou3_asp = <AA.ou3_asp: 78>
ou3_cys = <AA.ou3_cys: 77>
ou3_gln = <AA.ou3_gln: 89>
ou3_glu = <AA.ou3_glu: 79>
ou3_gly = <AA.ou3_gly: 81>
ou3_his = <AA.ou3_his: 82>
ou3_ile = <AA.ou3_ile: 83>
ou3_leu = <AA.ou3_leu: 85>
ou3_lys = <AA.ou3_lys: 84>
ou3_met = <AA.ou3_met: 86>
ou3_phe = <AA.ou3_phe: 80>
ou3_pro = <AA.ou3_pro: 88>
ou3_ser = <AA.ou3_ser: 91>
ou3_thr = <AA.ou3_thr: 92>
ou3_trp = <AA.ou3_trp: 94>
ou3_tyr = <AA.ou3_tyr: 95>
ou3_val = <AA.ou3_val: 93>
property value
class pyrosetta.rosetta.core.chemical.APolarHydrogenFilter

Bases: pybind11_object

The filter responsible for all apolar hydrogens.

assign(self: pyrosetta.rosetta.core.chemical.APolarHydrogenFilter, : pyrosetta.rosetta.core.chemical.APolarHydrogenFilter) → pyrosetta.rosetta.core.chemical.APolarHydrogenFilter

C++: core::chemical::APolarHydrogenFilter::operator=(const class core::chemical::APolarHydrogenFilter &) –> class core::chemical::APolarHydrogenFilter &

class pyrosetta.rosetta.core.chemical.AcceptorAtomFilter

Bases: pybind11_object

The filter responsible for obtaining all acceptor atoms.

assign(self: pyrosetta.rosetta.core.chemical.AcceptorAtomFilter, : pyrosetta.rosetta.core.chemical.AcceptorAtomFilter) → pyrosetta.rosetta.core.chemical.AcceptorAtomFilter

C++: core::chemical::AcceptorAtomFilter::operator=(const class core::chemical::AcceptorAtomFilter &) –> class core::chemical::AcceptorAtomFilter &

class pyrosetta.rosetta.core.chemical.AddAtom

Bases: PatchOperation

add an atom to ResidueType

adds_atoms(self: pyrosetta.rosetta.core.chemical.AddAtom) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::AddAtom::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

add an atom

C++: core::chemical::AddAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddAtom, : pyrosetta.rosetta.core.chemical.AddAtom) → pyrosetta.rosetta.core.chemical.AddAtom

C++: core::chemical::AddAtom::operator=(const class core::chemical::AddAtom &) –> class core::chemical::AddAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddAtom) → str

Return the name of this PatchOperation (“AddAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddAtomAlias

Bases: PatchOperation

A patch operation for adding an atom alias to a ResidueType.

See residue_io.cc for a description of atom aliases.

Atom aliases were graciously added to Rosetta by Rocco Moretti.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.AddAtomAlias) → pyrosetta.rosetta.utility.vector1_std_string

Return a list of all atom names that this operation adds (as aliases).

All of the aliases for an atom must be offered as options to the ResidueTypeFinder.

C++: core::chemical::AddAtomAlias::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddAtomAlias, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::AddAtomAlias::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddAtomAlias, : pyrosetta.rosetta.core.chemical.AddAtomAlias) → pyrosetta.rosetta.core.chemical.AddAtomAlias

C++: core::chemical::AddAtomAlias::operator=(const class core::chemical::AddAtomAlias &) –> class core::chemical::AddAtomAlias &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddAtomAlias) → str

Return the name of this PatchOperation (“AddAtomAlias”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddAtomAlias::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddBond

Bases: PatchOperation

add a bond to ResidueType

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddBond, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

add a bond

C++: core::chemical::AddBond::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddBond, : pyrosetta.rosetta.core.chemical.AddBond) → pyrosetta.rosetta.core.chemical.AddBond

C++: core::chemical::AddBond::operator=(const class core::chemical::AddBond &) –> class core::chemical::AddBond &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddBond) → str

Return the name of this PatchOperation (“AddBond”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddBond::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddBondType

Bases: PatchOperation

A patch operation for adding a specific type of bond to a ResidueType.

See residue_io.cc for a description of bond types.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddBondType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::AddBondType::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddBondType, : pyrosetta.rosetta.core.chemical.AddBondType) → pyrosetta.rosetta.core.chemical.AddBondType

C++: core::chemical::AddBondType::operator=(const class core::chemical::AddBondType &) –> class core::chemical::AddBondType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddBondType) → str

Return the name of this PatchOperation (“AddBondType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddBondType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddChi

Bases: PatchOperation

Add a chi angle to ResidueType.

Added by Andy M. Chen in June 2009

This is needed for PTMs, which often result in one or more extra chi angles.

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Add a chi angle.

C++: core::chemical::AddChi::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddChi, : pyrosetta.rosetta.core.chemical.AddChi) → pyrosetta.rosetta.core.chemical.AddChi

C++: core::chemical::AddChi::operator=(const class core::chemical::AddChi &) –> class core::chemical::AddChi &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddChi) → str

Return the name of this PatchOperation (“AddChi”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddChi::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddChiRotamer

Bases: PatchOperation

Add a rotamer sample to a chi angle of the ResidueType.

Added by Andy M. Chen in June 2009

This is needed for PTMs.

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddChiRotamer, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Add a rotamer sample.

C++: core::chemical::AddChiRotamer::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddChiRotamer, : pyrosetta.rosetta.core.chemical.AddChiRotamer) → pyrosetta.rosetta.core.chemical.AddChiRotamer

C++: core::chemical::AddChiRotamer::operator=(const class core::chemical::AddChiRotamer &) –> class core::chemical::AddChiRotamer &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddChiRotamer) → str

Return the name of this PatchOperation (“AddChiRotamer”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddChiRotamer::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddConnect

Bases: PatchOperation

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddConnect, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

add a property

C++: core::chemical::AddConnect::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddConnect, : pyrosetta.rosetta.core.chemical.AddConnect) → pyrosetta.rosetta.core.chemical.AddConnect

C++: core::chemical::AddConnect::operator=(const class core::chemical::AddConnect &) –> class core::chemical::AddConnect &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnect, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

C++: core::chemical::AddConnect::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddConnect) → str

Return the name of this PatchOperation (“AddConnect”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddConnect::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt

Bases: PatchOperation

add a connect and tracking virt to the atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::AddConnectAndTrackingVirt::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, : pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt) → pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt

C++: core::chemical::AddConnectAndTrackingVirt::operator=(const class core::chemical::AddConnectAndTrackingVirt &) –> class core::chemical::AddConnectAndTrackingVirt &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

C++: core::chemical::AddConnectAndTrackingVirt::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt) → str

Return the name of this PatchOperation (“AddConnectAndTrackingVirt”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddConnectAndTrackingVirt::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton

Bases: PatchOperation

add a connect to the atom, delete child proton

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::AddConnectDeleteChildProton::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, : pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton) → pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton

C++: core::chemical::AddConnectDeleteChildProton::operator=(const class core::chemical::AddConnectDeleteChildProton &) –> class core::chemical::AddConnectDeleteChildProton &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

C++: core::chemical::AddConnectDeleteChildProton::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton) → str

Return the name of this PatchOperation (“AddConnectDeleteChildProton”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddConnectDeleteChildProton::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddProperty

Bases: PatchOperation

add a property to ResidueType

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.AddProperty) → str

Which property, if any, is added.

C++: core::chemical::AddProperty::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.AddProperty) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::AddProperty::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddProperty, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

add a property

C++: core::chemical::AddProperty::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddProperty, : pyrosetta.rosetta.core.chemical.AddProperty) → pyrosetta.rosetta.core.chemical.AddProperty

C++: core::chemical::AddProperty::operator=(const class core::chemical::AddProperty &) –> class core::chemical::AddProperty &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddProperty) → str

Return the name of this PatchOperation (“AddProperty”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddProperty::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AddProtonChi

Bases: PatchOperation

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AddProtonChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

add a proton chi angle

C++: core::chemical::AddProtonChi::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AddProtonChi, : pyrosetta.rosetta.core.chemical.AddProtonChi) → pyrosetta.rosetta.core.chemical.AddProtonChi

C++: core::chemical::AddProtonChi::operator=(const class core::chemical::AddProtonChi &) –> class core::chemical::AddProtonChi &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AddProtonChi) → str

Return the name of this PatchOperation (“AddProtonChi”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AddProtonChi::name() const –> std::string

class pyrosetta.rosetta.core.chemical.Adduct

Bases: pybind11_object

Description of optional single-atom residue adducts

adduct_name(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to adduct_name string

C++: core::chemical::Adduct::adduct_name() const –> const std::string &

assign(self: pyrosetta.rosetta.core.chemical.Adduct, : pyrosetta.rosetta.core.chemical.Adduct) → pyrosetta.rosetta.core.chemical.Adduct

C++: core::chemical::Adduct::operator=(const class core::chemical::Adduct &) –> class core::chemical::Adduct &

atom_charge(self: pyrosetta.rosetta.core.chemical.Adduct) → float

C++: core::chemical::Adduct::atom_charge() const –> double

atom_name(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to atom_name string

C++: core::chemical::Adduct::atom_name() const –> const std::string &

atom_type_name(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to atom type string

C++: core::chemical::Adduct::atom_type_name() const –> const std::string &

d(self: pyrosetta.rosetta.core.chemical.Adduct) → float

C++: core::chemical::Adduct::d() const –> double

mm_atom_type_name(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to mm type string

C++: core::chemical::Adduct::mm_atom_type_name() const –> const std::string &

phi(self: pyrosetta.rosetta.core.chemical.Adduct) → float

accessor for Adduct geometric info

C++: core::chemical::Adduct::phi() const –> double

stub_atom(self: pyrosetta.rosetta.core.chemical.Adduct, atm: int) → str

const accessor to stub_atom strings by index

C++: core::chemical::Adduct::stub_atom(const int) const –> const std::string &

stub_atom1(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to stub_atom1 name string

C++: core::chemical::Adduct::stub_atom1() const –> const std::string &

stub_atom2(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to stub_atom2 name string

C++: core::chemical::Adduct::stub_atom2() const –> const std::string &

stub_atom3(self: pyrosetta.rosetta.core.chemical.Adduct) → str

accessor to stub_atom3 name string

C++: core::chemical::Adduct::stub_atom3() const –> const std::string &

theta(self: pyrosetta.rosetta.core.chemical.Adduct) → float

C++: core::chemical::Adduct::theta() const –> double

class pyrosetta.rosetta.core.chemical.Ancestor

Bases: pybind11_object

Change the parent, grandparent, or great-grandparent of an atom

Members:

anc_parent

anc_grandparent

anc_greatgrandparent

anc_grandparent = <Ancestor.anc_grandparent: 1>
anc_greatgrandparent = <Ancestor.anc_greatgrandparent: 2>
anc_parent = <Ancestor.anc_parent: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.AppendMainchainAtom

Bases: PatchOperation

add a mainchain atom after the last mainchain atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom to be the last mainchain atom

C++: core::chemical::AppendMainchainAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom, : pyrosetta.rosetta.core.chemical.AppendMainchainAtom) → pyrosetta.rosetta.core.chemical.AppendMainchainAtom

C++: core::chemical::AppendMainchainAtom::operator=(const class core::chemical::AppendMainchainAtom &) –> class core::chemical::AppendMainchainAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom) → str

Return the name of this PatchOperation (“AppendMainchainAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AppendMainchainAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.AromaticAtomFilter

Bases: pybind11_object

The filter responsible for all aromatic atoms.

assign(self: pyrosetta.rosetta.core.chemical.AromaticAtomFilter, : pyrosetta.rosetta.core.chemical.AromaticAtomFilter) → pyrosetta.rosetta.core.chemical.AromaticAtomFilter

C++: core::chemical::AromaticAtomFilter::operator=(const class core::chemical::AromaticAtomFilter &) –> class core::chemical::AromaticAtomFilter &

class pyrosetta.rosetta.core.chemical.Atom

Bases: pybind11_object

This class contains the “chemical” information for atoms in a MutableResidueType. This does not contain the actual xyz coordinates of the atom, (which are found in core/conformation/Atom.hh) It is also not used for the plain ResidueType class, which holds the corresponding information intenrally. This class should contain the information that’s associated with the atom, calculated from other info. (Do that in the MutableResidueType -> ResidueType transition. )

chemical::Atoms are stored in chemical::MutableResidueType (within its ResidueGraph);

conformation::Atoms are stored in conformation::Residue

absolute_stereochemistry(self: pyrosetta.rosetta.core.chemical.Atom) → str

Return the absolute stereochemistry (R/S designation) of this stereocenter.

C++: core::chemical::Atom::absolute_stereochemistry() const –> char

add_bonded_orbital(self: pyrosetta.rosetta.core.chemical.Atom, orbital_index: int) → None

C++: core::chemical::Atom::add_bonded_orbital(unsigned long) –> void

assign(self: pyrosetta.rosetta.core.chemical.Atom, : pyrosetta.rosetta.core.chemical.Atom) → pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::Atom::operator=(const class core::chemical::Atom &) –> class core::chemical::Atom &

atom_type_index(self: pyrosetta.rosetta.core.chemical.Atom) → int

C++: core::chemical::Atom::atom_type_index() const –> const unsigned long &

bonded_orbitals(self: pyrosetta.rosetta.core.chemical.Atom) → pyrosetta.rosetta.utility.vector1_unsigned_long

Which orbital indicies are attached to this atom?

C++: core::chemical::Atom::bonded_orbitals() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

charge(*args, **kwargs)

Overloaded function.

  1. charge(self: pyrosetta.rosetta.core.chemical.Atom) -> float

C++: core::chemical::Atom::charge() const –> const double &

  1. charge(self: pyrosetta.rosetta.core.chemical.Atom, charge: float) -> None

C++: core::chemical::Atom::charge(const double &) –> void

element(self: pyrosetta.rosetta.core.chemical.Atom) → pyrosetta.rosetta.core.chemical.element.Elements

Convenience function to go directly to the element enum

C++: core::chemical::Atom::element() const –> enum core::chemical::element::Elements

element_type(*args, **kwargs)

Overloaded function.

  1. element_type(self: pyrosetta.rosetta.core.chemical.Atom) -> core::chemical::Element

C++: core::chemical::Atom::element_type() const –> class std::shared_ptr<const class core::chemical::Element>

  1. element_type(self: pyrosetta.rosetta.core.chemical.Atom, element: core::chemical::Element) -> None

C++: core::chemical::Atom::element_type(class std::shared_ptr<const class core::chemical::Element>) –> void

formal_charge(*args, **kwargs)

Overloaded function.

  1. formal_charge(self: pyrosetta.rosetta.core.chemical.Atom) -> int

C++: core::chemical::Atom::formal_charge() const –> const int &

  1. formal_charge(self: pyrosetta.rosetta.core.chemical.Atom, charge: int) -> None

C++: core::chemical::Atom::formal_charge(int) –> void

gasteiger_atom_type(*args, **kwargs)

Overloaded function.

  1. gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.Atom) -> core::chemical::gasteiger::GasteigerAtomTypeData

C++: core::chemical::Atom::gasteiger_atom_type() const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>

  1. gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.Atom, gasteiger_atom_type: core::chemical::gasteiger::GasteigerAtomTypeData) -> None

C++: core::chemical::Atom::gasteiger_atom_type(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>) –> void

greek_distance(*args, **kwargs)

Overloaded function.

  1. greek_distance(self: pyrosetta.rosetta.core.chemical.Atom) -> pyrosetta.rosetta.core.chemical.GreekDistance

How far (in Greek letters) is this atom from the primary functional group of the molecule?

C++: core::chemical::Atom::greek_distance() const –> enum core::chemical::GreekDistance

  1. greek_distance(self: pyrosetta.rosetta.core.chemical.Atom, setting: pyrosetta.rosetta.core.chemical.GreekDistance) -> None

Set how far (in Greek letters) this atom is from the primary functional group of the molecule.

C++: core::chemical::Atom::greek_distance(const enum core::chemical::GreekDistance) –> void

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.Atom, property: str) -> bool

Generic property access.

IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

C++: core::chemical::Atom::has_property(const std::string &) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.Atom, property: pyrosetta.rosetta.core.chemical.AtomProperty) -> bool

Generic property access.

IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

C++: core::chemical::Atom::has_property(const enum core::chemical::AtomProperty) const –> bool

icoor(*args, **kwargs)

Overloaded function.

  1. icoor(self: pyrosetta.rosetta.core.chemical.Atom) -> core::chemical::MutableICoorRecord

The ICoor record for this residue – may be null.

C++: core::chemical::Atom::icoor() const –> class std::shared_ptr<const class core::chemical::MutableICoorRecord>

  1. icoor(self: pyrosetta.rosetta.core.chemical.Atom, icoor_record: core::chemical::MutableICoorRecord) -> None

C++: core::chemical::Atom::icoor(class std::shared_ptr<const class core::chemical::MutableICoorRecord>) –> void

ideal_xyz(*args, **kwargs)

Overloaded function.

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.Atom) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::Atom::ideal_xyz() const –> const class numeric::xyzVector<double> &

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.Atom, ideal_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::Atom::ideal_xyz(const class numeric::xyzVector<double> &) –> void

is_actcoord(*args, **kwargs)

Overloaded function.

  1. is_actcoord(self: pyrosetta.rosetta.core.chemical.Atom) -> bool

Is this atom part of the action coordinate centers?

The geometric center of all atoms listed as actcoords are the residue’s “action coordinate” (for pair energy)

C++: core::chemical::Atom::is_actcoord() const –> const bool &

  1. is_actcoord(self: pyrosetta.rosetta.core.chemical.Atom, setting: bool) -> None

C++: core::chemical::Atom::is_actcoord(bool) –> void

is_backbone(*args, **kwargs)

Overloaded function.

  1. is_backbone(self: pyrosetta.rosetta.core.chemical.Atom) -> bool

C++: core::chemical::Atom::is_backbone() const –> const bool &

  1. is_backbone(self: pyrosetta.rosetta.core.chemical.Atom, setting: bool) -> None

C++: core::chemical::Atom::is_backbone(bool) –> void

is_fake(self: pyrosetta.rosetta.core.chemical.Atom) → bool

Return true if this represents a fake/mock atom.

C++: core::chemical::Atom::is_fake() const –> bool

is_hydrogen(self: pyrosetta.rosetta.core.chemical.Atom) → bool

C++: core::chemical::Atom::is_hydrogen() const –> bool

is_virtual(*args, **kwargs)

Overloaded function.

  1. is_virtual(self: pyrosetta.rosetta.core.chemical.Atom, setting: bool) -> None

Set whether or not this atom is virtual.

C++: core::chemical::Atom::is_virtual(bool) –> void

  1. is_virtual(self: pyrosetta.rosetta.core.chemical.Atom) -> bool

Get whether or not this atom is virtual.

C++: core::chemical::Atom::is_virtual() const –> bool

mm_name(*args, **kwargs)

Overloaded function.

  1. mm_name(self: pyrosetta.rosetta.core.chemical.Atom) -> str

C++: core::chemical::Atom::mm_name() const –> const std::string &

  1. mm_name(self: pyrosetta.rosetta.core.chemical.Atom, name: str) -> None

C++: core::chemical::Atom::mm_name(const std::string &) –> void

name(self: pyrosetta.rosetta.core.chemical.Atom) → str

C++: core::chemical::Atom::name() const –> const std::string &

properties(self: pyrosetta.rosetta.core.chemical.Atom) → core::chemical::AtomProperties
Access the collection of properties for this Atom.

IMPORTANT – This only looks at manually set properties, not any automatically derived ones.

C++: core::chemical::Atom::properties() const –> const class core::chemical::AtomProperties &

reset_all_properies(self: pyrosetta.rosetta.core.chemical.Atom, setting: core::chemical::AtomProperties) → None

Discard all the current properties, and set the the passed values.

C++: core::chemical::Atom::reset_all_properies(const class core::chemical::AtomProperties &) –> void

set_absolute_stereochemistry(self: pyrosetta.rosetta.core.chemical.Atom, setting: str) → None

Set the absolute stereochemistry (R/S designation) of this stereocenter.

C++: core::chemical::Atom::set_absolute_stereochemistry(const char) –> void

set_bonded_orbitals(self: pyrosetta.rosetta.core.chemical.Atom, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::chemical::Atom::set_bonded_orbitals(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_property(*args, **kwargs)

Overloaded function.

  1. set_property(self: pyrosetta.rosetta.core.chemical.Atom, property: str, setting: bool) -> None

C++: core::chemical::Atom::set_property(const std::string &, const bool) –> void

  1. set_property(self: pyrosetta.rosetta.core.chemical.Atom, property: pyrosetta.rosetta.core.chemical.AtomProperty, setting: bool) -> None

C++: core::chemical::Atom::set_property(const enum core::chemical::AtomProperty, const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.Atom, out: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of chemical::Atom for debugging purposes.

C++: core::chemical::Atom::show(std::ostream &) const –> void

  1. show(self: pyrosetta.rosetta.core.chemical.Atom) -> None

Generate string representation of chemical::Atom to std::cout for debugging purposes.

C++: core::chemical::Atom::show() const –> void

class pyrosetta.rosetta.core.chemical.AtomICoor

Bases: pybind11_object

A basic class containing info of internal coordinates needed for building an atom within a ResidueType

In atom tree, each atom is defined by its internal coordinates, which include a bond distance, a bond angle and a torsion angle. Of course, all these internal coordinates are only meaningful in the context of three reference (stub) atoms. AtomICoor information is stored in the residue param files and some terms are defined as following: - bond distance d_ is that between the atom to be built (child) and stub_atom1 (parent) - bond angle theta_ is that defined by child-parent-stub2(angle) - torsion angle phi_ is that defined by child-parent-stub2-stub3(torsion)

assign(self: pyrosetta.rosetta.core.chemical.AtomICoor, : pyrosetta.rosetta.core.chemical.AtomICoor) → pyrosetta.rosetta.core.chemical.AtomICoor

C++: core::chemical::AtomICoor::operator=(const class core::chemical::AtomICoor &) –> class core::chemical::AtomICoor &

build(*args, **kwargs)

Overloaded function.

  1. build(self: pyrosetta.rosetta.core.chemical.AtomICoor, rsd: core::conformation::Residue, conformation: core::conformation::Conformation) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::AtomICoor::build(const class core::conformation::Residue &, const class core::conformation::Conformation &) const –> class numeric::xyzVector<double>

  1. build(self: pyrosetta.rosetta.core.chemical.AtomICoor, rsd_type: core::chemical::ResidueType) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::AtomICoor::build(const class core::chemical::ResidueType &) const –> class numeric::xyzVector<double>

  1. build(self: pyrosetta.rosetta.core.chemical.AtomICoor, rsd: core::conformation::Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t

WARNING: Slightly dangerous function intended for black magic use only.

Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom’s locations, as opposed to being retrieved from connected residues via a conformation.

C++: core::chemical::AtomICoor::build(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

built_atom(self: pyrosetta.rosetta.core.chemical.AtomICoor) → str

The name of the atom being built by this icoor

C++: core::chemical::AtomICoor::built_atom() const –> const std::string &

d(self: pyrosetta.rosetta.core.chemical.AtomICoor) → float

C++: core::chemical::AtomICoor::d() const –> double

depends_on_a_true_index(self: pyrosetta.rosetta.core.chemical.AtomICoor, atomvect: pyrosetta.rosetta.utility.vector1_bool) → bool
Given a Boolean vector corresponding to atom indices, determine whether any of the stub

indices depends on one of the atoms that are “true”.

Called by ResidueType::update_polymer_dependent_groups() when figuring out which atoms depend on atoms that depend on a connection.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::AtomICoor::depends_on_a_true_index(const class utility::vector1<bool, class std::allocator<bool> > &) const –> bool

depends_on_polymer_lower(self: pyrosetta.rosetta.core.chemical.AtomICoor) → bool

Is this icoor immediately dependent on LOWER?

Returns true if stub atom 1, 2, or 3 is LOWER.

C++: core::chemical::AtomICoor::depends_on_polymer_lower() const –> bool

depends_on_polymer_upper(self: pyrosetta.rosetta.core.chemical.AtomICoor) → bool

Is this icoor immediately dependent on UPPER?

Returns true if stub atom 1, 2, or 3 is UPPER.

C++: core::chemical::AtomICoor::depends_on_polymer_upper() const –> bool

depends_on_residue_connection(*args, **kwargs)

Overloaded function.

  1. depends_on_residue_connection(self: pyrosetta.rosetta.core.chemical.AtomICoor, connid: int) -> bool

Returns true if any of the stub atoms is the specified connection ID.

C++: core::chemical::AtomICoor::depends_on_residue_connection(const unsigned long) const –> bool

  1. depends_on_residue_connection(self: pyrosetta.rosetta.core.chemical.AtomICoor) -> bool

Returns true if any of the stub atoms is a connection ID.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::AtomICoor::depends_on_residue_connection() const –> bool

is_internal(self: pyrosetta.rosetta.core.chemical.AtomICoor) → bool

C++: core::chemical::AtomICoor::is_internal() const –> bool

phi(self: pyrosetta.rosetta.core.chemical.AtomICoor) → float

accessor to stub_atom1 ICoorAtomID

C++: core::chemical::AtomICoor::phi() const –> double

show(self: pyrosetta.rosetta.core.chemical.AtomICoor, : pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::AtomICoor::show(std::ostream &) const –> void

stub_atom(self: pyrosetta.rosetta.core.chemical.AtomICoor, atm: int) → pyrosetta.rosetta.core.chemical.ICoorAtomID

accessor to stub_atom ICoorAtomID

C++: core::chemical::AtomICoor::stub_atom(const int) –> class core::chemical::ICoorAtomID &

stub_atom1(self: pyrosetta.rosetta.core.chemical.AtomICoor) → pyrosetta.rosetta.core.chemical.ICoorAtomID

C++: core::chemical::AtomICoor::stub_atom1() const –> const class core::chemical::ICoorAtomID &

stub_atom2(self: pyrosetta.rosetta.core.chemical.AtomICoor) → pyrosetta.rosetta.core.chemical.ICoorAtomID

accessor to stub_atom2 ICoorAtomID

C++: core::chemical::AtomICoor::stub_atom2() const –> const class core::chemical::ICoorAtomID &

stub_atom3(self: pyrosetta.rosetta.core.chemical.AtomICoor) → pyrosetta.rosetta.core.chemical.ICoorAtomID

accessor to stub_atom3 ICoorAtomID

C++: core::chemical::AtomICoor::stub_atom3() const –> const class core::chemical::ICoorAtomID &

theta(self: pyrosetta.rosetta.core.chemical.AtomICoor) → float

C++: core::chemical::AtomICoor::theta() const –> double

class pyrosetta.rosetta.core.chemical.AtomProperties

Bases: pybind11_object

This is a container class for storing properties specific to a ResidueType’s atoms. These properties belong to a particular ResidueType’s Atoms; they do not belong to an AtomType. chemical::Atoms store both AtomTypes and AtomProperties.

assign(self: pyrosetta.rosetta.core.chemical.AtomProperties, object_to_copy: pyrosetta.rosetta.core.chemical.AtomProperties) → pyrosetta.rosetta.core.chemical.AtomProperties

C++: core::chemical::AtomProperties::operator=(const class core::chemical::AtomProperties &) –> class core::chemical::AtomProperties &

get_list_of_properties(self: pyrosetta.rosetta.core.chemical.AtomProperties) → pyrosetta.rosetta.utility.vector1_std_string

Generate and return a list of strings representing the properties of this Atom.

C++: core::chemical::AtomProperties::get_list_of_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.AtomProperties, property: pyrosetta.rosetta.core.chemical.AtomProperty) -> bool

Get whether or not this Atom has the requested property.

C++: core::chemical::AtomProperties::has_property(const enum core::chemical::AtomProperty) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.AtomProperties, property: str) -> bool

Get whether or not this Atom has the requested property by string.

C++: core::chemical::AtomProperties::has_property(const std::string &) const –> bool

set_property(*args, **kwargs)

Overloaded function.

  1. set_property(self: pyrosetta.rosetta.core.chemical.AtomProperties, property: pyrosetta.rosetta.core.chemical.AtomProperty, setting: bool) -> None

Set the status of the given property for this Atom.

C++: core::chemical::AtomProperties::set_property(const enum core::chemical::AtomProperty, const bool) –> void

  1. set_property(self: pyrosetta.rosetta.core.chemical.AtomProperties, property: str, setting: bool) -> None

Set the status of the given property for this Atom by string.

C++: core::chemical::AtomProperties::set_property(const std::string &, const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.AtomProperties) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.AtomProperties, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of AtomProperties for debugging purposes.

C++: core::chemical::AtomProperties::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.chemical.AtomPropertiesManager

Bases: SingletonBase_core_chemical_AtomPropertiesManager_t

This class is a singleton and manages AtomProperties enum mappings.

static get_instance() → core::chemical::AtomPropertiesManager

C++: utility::SingletonBase<core::chemical::AtomPropertiesManager>::get_instance() –> class core::chemical::AtomPropertiesManager *

static property_from_string(property: str) → pyrosetta.rosetta.core.chemical.AtomProperty

C++: core::chemical::AtomPropertiesManager::property_from_string(const std::string &) –> const enum core::chemical::AtomProperty &

static string_from_property(property: pyrosetta.rosetta.core.chemical.AtomProperty) → str

C++: core::chemical::AtomPropertiesManager::string_from_property(const enum core::chemical::AtomProperty) –> const std::string &

class pyrosetta.rosetta.core.chemical.AtomProperty

Bases: pybind11_object

Enumerators for all the properties that can be assigned to a chemical::Atom.

Members:

NO_ATOM_PROPERTY

FIRST_ATOM_PROPERTY

H_DONOR

H_ACCEPTOR

POLAR_HYDROGEN

AROMATIC_HYDROGEN

HAS_ORBITALS

VIRTUAL_ATOM

REPULSIVE

AROMATIC_CARBON_WITH_FREE_VALENCE

N_ATOM_PROPERTIES

AROMATIC_CARBON_WITH_FREE_VALENCE = <AtomProperty.AROMATIC_CARBON_WITH_FREE_VALENCE: 9>
AROMATIC_HYDROGEN = <AtomProperty.AROMATIC_HYDROGEN: 5>
FIRST_ATOM_PROPERTY = <AtomProperty.FIRST_ATOM_PROPERTY: 1>
HAS_ORBITALS = <AtomProperty.HAS_ORBITALS: 6>
H_ACCEPTOR = <AtomProperty.H_ACCEPTOR: 3>
H_DONOR = <AtomProperty.H_DONOR: 2>
NO_ATOM_PROPERTY = <AtomProperty.NO_ATOM_PROPERTY: 0>
N_ATOM_PROPERTIES = <AtomProperty.AROMATIC_CARBON_WITH_FREE_VALENCE: 9>
POLAR_HYDROGEN = <AtomProperty.POLAR_HYDROGEN: 4>
REPULSIVE = <AtomProperty.REPULSIVE: 8>
VIRTUAL_ATOM = <AtomProperty.VIRTUAL_ATOM: 7>
property name
property value
class pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t

C++: core::chemical::AtomRefMapping<unsigned long, void *>::operator=(const class core::chemical::AtomRefMapping<unsigned long, void *> &) –> class core::chemical::AtomRefMapping<unsigned long, void *> &

clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → None

C++: core::chemical::AtomRefMapping<unsigned long, void *>::clear() –> void

count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, key: int) → bool

C++: core::chemical::AtomRefMapping<unsigned long, void *>::count(const unsigned long &) const –> bool

empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → bool

C++: core::chemical::AtomRefMapping<unsigned long, void *>::empty() const –> bool

erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, in: int) → None

C++: core::chemical::AtomRefMapping<unsigned long, void *>::erase(const unsigned long &) –> void

identity(*args, **kwargs)

Overloaded function.

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, setting: bool) -> None

C++: core::chemical::AtomRefMapping<unsigned long, void *>::identity(bool) –> void

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) -> bool

C++: core::chemical::AtomRefMapping<unsigned long, void *>::identity() const –> bool

invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → capsule

C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalid_entry() const –> void *const &

invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → int

C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalid_key() const –> const unsigned long &

invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, in: int) → None

C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalidate(const unsigned long &) –> void

reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t

C++: core::chemical::AtomRefMapping<unsigned long, void *>::reverse() const –> class core::chemical::AtomRefMapping<void *, unsigned long>

reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, out: capsule) → int

C++: core::chemical::AtomRefMapping<unsigned long, void *>::reverse_lookup(void *const &) const –> const unsigned long &

show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, output: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::AtomRefMapping<unsigned long, void *>::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t

C++: core::chemical::AtomRefMapping<void *, unsigned long>::operator=(const class core::chemical::AtomRefMapping<void *, unsigned long> &) –> class core::chemical::AtomRefMapping<void *, unsigned long> &

clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → None

C++: core::chemical::AtomRefMapping<void *, unsigned long>::clear() –> void

count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, key: capsule) → bool

C++: core::chemical::AtomRefMapping<void *, unsigned long>::count(void *const &) const –> bool

empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → bool

C++: core::chemical::AtomRefMapping<void *, unsigned long>::empty() const –> bool

erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, in: capsule) → None

C++: core::chemical::AtomRefMapping<void *, unsigned long>::erase(void *const &) –> void

identity(*args, **kwargs)

Overloaded function.

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, setting: bool) -> None

C++: core::chemical::AtomRefMapping<void *, unsigned long>::identity(bool) –> void

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) -> bool

C++: core::chemical::AtomRefMapping<void *, unsigned long>::identity() const –> bool

invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → int

C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalid_entry() const –> const unsigned long &

invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → capsule

C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalid_key() const –> void *const &

invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, in: capsule) → None

C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalidate(void *const &) –> void

reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) → core::chemical::AtomRefMapping<unsigned long, void*>

C++: core::chemical::AtomRefMapping<void *, unsigned long>::reverse() const –> class core::chemical::AtomRefMapping<unsigned long, void *>

reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, out: int) → capsule

C++: core::chemical::AtomRefMapping<void *, unsigned long>::reverse_lookup(const unsigned long &) const –> void *const &

show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, output: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::AtomRefMapping<void *, unsigned long>::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

C++: core::chemical::AtomRefMapping<void *, void *>::operator=(const class core::chemical::AtomRefMapping<void *, void *> &) –> class core::chemical::AtomRefMapping<void *, void *> &

clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → None

C++: core::chemical::AtomRefMapping<void *, void *>::clear() –> void

count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, key: capsule) → bool

C++: core::chemical::AtomRefMapping<void *, void *>::count(void *const &) const –> bool

empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → bool

C++: core::chemical::AtomRefMapping<void *, void *>::empty() const –> bool

erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, in: capsule) → None

C++: core::chemical::AtomRefMapping<void *, void *>::erase(void *const &) –> void

identity(*args, **kwargs)

Overloaded function.

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, setting: bool) -> None

C++: core::chemical::AtomRefMapping<void *, void *>::identity(bool) –> void

  1. identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) -> bool

C++: core::chemical::AtomRefMapping<void *, void *>::identity() const –> bool

invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → capsule

C++: core::chemical::AtomRefMapping<void *, void *>::invalid_entry() const –> void *const &

invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → capsule

C++: core::chemical::AtomRefMapping<void *, void *>::invalid_key() const –> void *const &

invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, in: capsule) → None

C++: core::chemical::AtomRefMapping<void *, void *>::invalidate(void *const &) –> void

reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) → pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t

C++: core::chemical::AtomRefMapping<void *, void *>::reverse() const –> class core::chemical::AtomRefMapping<void *, void *>

reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, out: capsule) → capsule

C++: core::chemical::AtomRefMapping<void *, void *>::reverse_lookup(void *const &) const –> void *const &

show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, output: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::AtomRefMapping<void *, void *>::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.chemical.AtomType

Bases: pybind11_object

basic atom type

name, element, certain properties and parameters

add_property(self: pyrosetta.rosetta.core.chemical.AtomType, property: str) → None

set standard property to true, or set the specified hybridization

C++: core::chemical::AtomType::add_property(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.chemical.AtomType, : pyrosetta.rosetta.core.chemical.AtomType) → pyrosetta.rosetta.core.chemical.AtomType

C++: core::chemical::AtomType::operator=(const class core::chemical::AtomType &) –> class core::chemical::AtomType &

atom_has_orbital(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

atom has an orbital attached

C++: core::chemical::AtomType::atom_has_orbital() const –> bool

atom_type_name(self: pyrosetta.rosetta.core.chemical.AtomType) → str
Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB.

You want pose.residue(i).atom_name(j) for that.

C++: core::chemical::AtomType::atom_type_name() const –> std::string

clear_properties(self: pyrosetta.rosetta.core.chemical.AtomType) → None

set all standard properties to false, set hybridization to UNKNOWN_HYBRID, and clear extra properties

C++: core::chemical::AtomType::clear_properties() –> void

element(self: pyrosetta.rosetta.core.chemical.AtomType) → str

returns the one- or two-letter element type

C++: core::chemical::AtomType::element() const –> std::string

extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, index: int) → float

return an additional, non-hardcoded property

C++: core::chemical::AtomType::extra_parameter(const unsigned long) const –> double

get_all_properties(self: pyrosetta.rosetta.core.chemical.AtomType) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::AtomType::get_all_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >

hybridization(self: pyrosetta.rosetta.core.chemical.AtomType) → pyrosetta.rosetta.core.chemical.Hybridization

retrieve an atom’s hybridization status.

C++: core::chemical::AtomType::hybridization() const –> const enum core::chemical::Hybridization &

is_acceptor(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a hydrogen bond acceptor

C++: core::chemical::AtomType::is_acceptor() const –> bool

is_aromatic(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is aromatic

C++: core::chemical::AtomType::is_aromatic() const –> bool

is_donor(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a hydrogen bond donor

C++: core::chemical::AtomType::is_donor() const –> bool

is_h2o(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a water

C++: core::chemical::AtomType::is_h2o() const –> bool

is_haro(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

is the H atom aromatic?

C++: core::chemical::AtomType::is_haro() const –> bool

is_heavyatom(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a heavy atom

C++: core::chemical::AtomType::is_heavyatom() const –> bool

is_hydrogen(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a hydrogen atom

C++: core::chemical::AtomType::is_hydrogen() const –> bool

is_polar_hydrogen(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

whether atom is a polar hydrogen atom

C++: core::chemical::AtomType::is_polar_hydrogen() const –> bool

is_repulsive(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

is atom type repulsive (REPL, REPLS, HREPS)

C++: core::chemical::AtomType::is_repulsive() const –> bool

is_virtual(self: pyrosetta.rosetta.core.chemical.AtomType) → bool

is atom type virtual?

C++: core::chemical::AtomType::is_virtual() const –> bool

lj_radius(self: pyrosetta.rosetta.core.chemical.AtomType) → float

Lennard-Jones 6-12 potential parameter – atom radius

There are two functionally identical versions of the Lennard-Jones potential:

E ~ 4eps(sigma1/d)^12 - (sigma1/d)^6 and

and

E ~ eps(sigma2/d)^12 - 2*(sigma2/d)^6

where sigma1 and sigma2 represent two different interpretations of the radius. eps represents the depth of the potential well. Sigma1 represents the distance between the two atoms where the Lennard-Jones energy is 0, i.e. where a collision is just forming/resolving. Sigma2 represents the distance between the two atoms where the derivative of the Lennard-Jones energy is 0, i.e. the minimum of the well depth.

In rosetta, we mean sigma2 when we talk about radii, but PyMOL usually sets the radii to sigma1.

If you see two atoms overlapping using the Rosetta radii, they’re not necessarily in collision. They are just not at their minimum value.

The distances are related as sigma2 = 2^(1.0/6)*sigma1; sigma2 ~= 1.22*sigma1

C++: core::chemical::AtomType::lj_radius() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.chemical.AtomType) → float

Lennard-Jones 6-12 potential parameter – well depth

C++: core::chemical::AtomType::lj_wdepth() const –> double

lk_dgfree(self: pyrosetta.rosetta.core.chemical.AtomType) → float

Lazaridis and Karplus solvation parameter – dgfree

C++: core::chemical::AtomType::lk_dgfree() const –> double

lk_lambda(self: pyrosetta.rosetta.core.chemical.AtomType) → float

Lazaridis and Karplus solvation parameter – lambda

C++: core::chemical::AtomType::lk_lambda() const –> double

lk_volume(self: pyrosetta.rosetta.core.chemical.AtomType) → float

Lazaridis and Karplus solvation parameter – volume

C++: core::chemical::AtomType::lk_volume() const –> double

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.AtomType, setting: str) -> None

C++: core::chemical::AtomType::name(const std::string &) –> void

  1. name(self: pyrosetta.rosetta.core.chemical.AtomType) -> str

Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB.

You want pose.residue(i).atom_name(j) for that.

C++: core::chemical::AtomType::name() const –> const std::string &

print(self: pyrosetta.rosetta.core.chemical.AtomType, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::AtomType::print(std::ostream &) const –> void

set_all_extra_parameters(self: pyrosetta.rosetta.core.chemical.AtomType, extra_parameters: pyrosetta.rosetta.utility.vector1_double) → None

all the extra parameters at once

C++: core::chemical::AtomType::set_all_extra_parameters(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, index: int, setting: float) → None

return an additional, non-hardcoded property

C++: core::chemical::AtomType::set_extra_parameter(const unsigned long, const double) –> void

set_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, param: str, setting: float) → None

set LJ and LK solvation parameter for this atom type

C++: core::chemical::AtomType::set_parameter(const std::string &, const double) –> void

set_property(self: pyrosetta.rosetta.core.chemical.AtomType, property: str, setting: bool) → None

set relevant properties for this atom type hh

C++: core::chemical::AtomType::set_property(const std::string &, const bool) –> void

class pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, : pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO) → pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO

C++: core::chemical::AtomTypeDatabaseIO::operator=(const class core::chemical::AtomTypeDatabaseIO &) –> class core::chemical::AtomTypeDatabaseIO &

get_all_atom_types_in_database(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::AtomTypeDatabaseIO::get_all_atom_types_in_database(class std::shared_ptr<class utility::sql_database::session>) const –> class utility::vector1<std::string, class std::allocator<std::string > >

initialize(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) → None

write the schema

C++: core::chemical::AtomTypeDatabaseIO::initialize(class std::shared_ptr<class utility::sql_database::session>) const –> void

write_atom_type_set_to_database(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, atom_type_set: core::chemical::AtomTypeSet, db_session: utility::sql_database::session) → None

C++: core::chemical::AtomTypeDatabaseIO::write_atom_type_set_to_database(const class core::chemical::AtomTypeSet &, class std::shared_ptr<class utility::sql_database::session>) const –> void

write_schema_to_db(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) → None

generate the table schemas and write them to the database

C++: core::chemical::AtomTypeDatabaseIO::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.core.chemical.AtomTypeSet

Bases: pybind11_object

a set of AtomTypes

a vector of pointers each of which points to an AtomType and the vector index is looked up by an atom_name string in a map

add_parameters_from_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) → None

additional file I/O

C++: core::chemical::AtomTypeSet::add_parameters_from_file(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, : pyrosetta.rosetta.core.chemical.AtomTypeSet) → pyrosetta.rosetta.core.chemical.AtomTypeSet

C++: core::chemical::AtomTypeSet::operator=(const class core::chemical::AtomTypeSet &) –> class core::chemical::AtomTypeSet &

atom_type_index(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, atom_type_name: str) → int

lookup the atom_type by the atom_type_name string

C++: core::chemical::AtomTypeSet::atom_type_index(const std::string &) const –> int

directory(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) → str

Get the source directory, eg to open an additional file in that directory

C++: core::chemical::AtomTypeSet::directory() const –> const std::string &

extra_parameter_index(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, name: str) → int

SLOW

C++: core::chemical::AtomTypeSet::extra_parameter_index(const std::string &) const –> int

extra_parameter_indices(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) → pyrosetta.rosetta.std.map_std_string_int

C++: core::chemical::AtomTypeSet::extra_parameter_indices() const –> const class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > > &

has_atom(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, atom_type_name: str) → bool

Check if atom is present

C++: core::chemical::AtomTypeSet::has_atom(const std::string &) const –> bool

has_extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, name: str) → bool

C++: core::chemical::AtomTypeSet::has_extra_parameter(const std::string &) const –> bool

mode(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) → pyrosetta.rosetta.core.chemical.TypeSetMode

The mode of the AtomTypeSet

C++: core::chemical::AtomTypeSet::mode() const –> enum core::chemical::TypeSetMode

n_atomtypes(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) → int

number of atom types in the set

C++: core::chemical::AtomTypeSet::n_atomtypes() const –> unsigned long

name(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) → str

the name of the AtomTypeSet

C++: core::chemical::AtomTypeSet::name() const –> std::string

read_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) → None

file I/O

C++: core::chemical::AtomTypeSet::read_file(const std::string &) –> void

read_meta_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) → None
Read in meta information from the given file

Meta information is info about the AtomTypeSet as a whole

C++: core::chemical::AtomTypeSet::read_meta_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.AutomorphismIterator

Bases: pybind11_object

Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations.

Common automorphisms include flipping a phenyl ring (think Phe chi2) or rotating a methyl group (or CF3, if you don’t care about H). However, they can be much more complicated than that, and some cannot be imitated by rotation about a bond. Examples include labeling a -CF3 clockwise vs. counterclockwise, or swapping the -CF3 branches of -C(CF3)2R. See the ligand of PDB 1PQC for a reasonably complex example.

Formally, a graph automorphism is an isomorphism of that graph with itself: given a graph G(V,E) and a mapping M that relabels the vertices according to M(v) -> v’, then M is an automorphism iff (M(u),M(v)) is an edge if and only if (u,v) is an edge. If the vertices are “colored” (in our case, have atom types), it must also be true that M(v) and v have the same color, for all v in V.

Thus you can re-label a phenyl ring

2 3 6 5 6 3

1 4 or 1 4 but not 1 4

6 5 2 3 2 5

because in the last case, there are new bonds 6-3 and 2-5, and missing bonds 6-5 and 2-3.

See also: OpenEye’s OEChem library and its OERMSD() function.

next(self: pyrosetta.rosetta.core.chemical.AutomorphismIterator) → pyrosetta.rosetta.utility.vector1_unsigned_long
Returns the next automorphism for this residue type

as a vector that maps “old” atom indices to “new” atom indices. Returns an empty vector when no more automorphisms remain.

C++: core::chemical::AutomorphismIterator::next() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

class pyrosetta.rosetta.core.chemical.Bond

Bases: pybind11_object

basic chemical Bond

name, element, certain properties and parameters from .params file

GetMaximumElectrons(self: pyrosetta.rosetta.core.chemical.Bond) → int

C++: core::chemical::Bond::GetMaximumElectrons() const –> unsigned long

GetMinimumElectrons(self: pyrosetta.rosetta.core.chemical.Bond) → int

C++: core::chemical::Bond::GetMinimumElectrons() const –> unsigned long

GetNumberOfElectrons(self: pyrosetta.rosetta.core.chemical.Bond) → int

C++: core::chemical::Bond::GetNumberOfElectrons() const –> unsigned long

GetSDAltFileID(self: pyrosetta.rosetta.core.chemical.Bond) → int

C++: core::chemical::Bond::GetSDAltFileID() const –> unsigned long

GetSDFileID(self: pyrosetta.rosetta.core.chemical.Bond) → int

C++: core::chemical::Bond::GetSDFileID() const –> unsigned long

IsBondInRing(self: pyrosetta.rosetta.core.chemical.Bond) → bool

C++: core::chemical::Bond::IsBondInRing() const –> bool

IsBondOrderKnown(self: pyrosetta.rosetta.core.chemical.Bond) → bool

C++: core::chemical::Bond::IsBondOrderKnown() const –> bool

SetSDFType(self: pyrosetta.rosetta.core.chemical.Bond, SDF_ID: int) → None

Reset the internal data such that it matches the appropriate value for the SDF datatype.

Substitution (taken from) for BCL’s FindBondTypeFromSDFInfo( const std::size_t &SDF_ID)

C++: core::chemical::Bond::SetSDFType(const unsigned long) –> void

aromaticity(*args, **kwargs)

Overloaded function.

  1. aromaticity(self: pyrosetta.rosetta.core.chemical.Bond, aroma: pyrosetta.rosetta.core.chemical.BondAromaticity) -> None

C++: core::chemical::Bond::aromaticity(enum core::chemical::BondAromaticity) –> void

  1. aromaticity(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondAromaticity

C++: core::chemical::Bond::aromaticity() const –> enum core::chemical::BondAromaticity

bond_name(*args, **kwargs)

Overloaded function.

  1. bond_name(self: pyrosetta.rosetta.core.chemical.Bond, bond_name: pyrosetta.rosetta.core.chemical.BondName) -> None

C++: core::chemical::Bond::bond_name(enum core::chemical::BondName) –> void

  1. bond_name(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondName

/ Getters

C++: core::chemical::Bond::bond_name() const –> enum core::chemical::BondName

conjugability(*args, **kwargs)

Overloaded function.

  1. conjugability(self: pyrosetta.rosetta.core.chemical.Bond, conjug: pyrosetta.rosetta.core.chemical.BondConjugability) -> None

C++: core::chemical::Bond::conjugability(enum core::chemical::BondConjugability) –> void

  1. conjugability(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondConjugability

C++: core::chemical::Bond::conjugability() const –> enum core::chemical::BondConjugability

cut_bond(*args, **kwargs)

Overloaded function.

  1. cut_bond(self: pyrosetta.rosetta.core.chemical.Bond, cut_bond: bool) -> None

C++: core::chemical::Bond::cut_bond(bool) –> void

  1. cut_bond(self: pyrosetta.rosetta.core.chemical.Bond) -> bool

C++: core::chemical::Bond::cut_bond() const –> bool

is_fake(self: pyrosetta.rosetta.core.chemical.Bond) → bool

Return true if this bond represents a non-physical bond

C++: core::chemical::Bond::is_fake() const –> bool

isometry(*args, **kwargs)

Overloaded function.

  1. isometry(self: pyrosetta.rosetta.core.chemical.Bond, isom: pyrosetta.rosetta.core.chemical.BondIsometry) -> None

C++: core::chemical::Bond::isometry(enum core::chemical::BondIsometry) –> void

  1. isometry(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondIsometry

C++: core::chemical::Bond::isometry() const –> enum core::chemical::BondIsometry

order(*args, **kwargs)

Overloaded function.

  1. order(self: pyrosetta.rosetta.core.chemical.Bond, order: pyrosetta.rosetta.core.chemical.BondOrder) -> None

C++: core::chemical::Bond::order(enum core::chemical::BondOrder) –> void

  1. order(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondOrder

C++: core::chemical::Bond::order() const –> enum core::chemical::BondOrder

print(self: pyrosetta.rosetta.core.chemical.Bond, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::Bond::print(std::ostream &) const –> void

ringness(*args, **kwargs)

Overloaded function.

  1. ringness(self: pyrosetta.rosetta.core.chemical.Bond, ring: pyrosetta.rosetta.core.chemical.BondRingness) -> None

C++: core::chemical::Bond::ringness(enum core::chemical::BondRingness) –> void

  1. ringness(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondRingness

C++: core::chemical::Bond::ringness() const –> enum core::chemical::BondRingness

class pyrosetta.rosetta.core.chemical.BondAromaticity

Bases: pybind11_object

Proper aromaticity implies participation in a 4n+2 electron ring system.

For simple single-double alternation, see conjugatable bond.

Members:

UnknownAromaticity

NonaromaticBond

IsAromaticBond

IsAromaticBond = <BondAromaticity.IsAromaticBond: 2>
NonaromaticBond = <BondAromaticity.NonaromaticBond: 1>
UnknownAromaticity = <BondAromaticity.UnknownAromaticity: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.BondConjugability

Bases: pybind11_object

As with the BCL, bond conjugability is more about the atom types on

either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems

Members:

UnknownConjugability

NotConjugableBond

ConjugableBond

ConjugableBond = <BondConjugability.ConjugableBond: 2>
NotConjugableBond = <BondConjugability.NotConjugableBond: 1>
UnknownConjugability = <BondConjugability.UnknownConjugability: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.BondIsometry

Bases: pybind11_object

Members:

UnknownIsometry

NoBondIsometry

EIsometry

ZIsometry

EIsometry = <BondIsometry.EIsometry: 2>
NoBondIsometry = <BondIsometry.NoBondIsometry: 1>
UnknownIsometry = <BondIsometry.UnknownIsometry: 0>
ZIsometry = <BondIsometry.ZIsometry: 3>
property name
property value
class pyrosetta.rosetta.core.chemical.BondName

Bases: pybind11_object

Members:

UnknownBond

SingleBond

DoubleBond

TripleBond

AromaticBond

OrbitalBond

PseudoBond

AromaticBond = <BondName.AromaticBond: 4>
DoubleBond = <BondName.DoubleBond: 2>
OrbitalBond = <BondName.OrbitalBond: 5>
PseudoBond = <BondName.PseudoBond: 99>
SingleBond = <BondName.SingleBond: 1>
TripleBond = <BondName.TripleBond: 3>
UnknownBond = <BondName.UnknownBond: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.BondOrder

Bases: pybind11_object

Members:

UnknownBondOrder

SingleBondOrder

DoubleBondOrder

TripleBondOrder

OrbitalBondOrder

DeleteBondOrder

PseudoBondOrder

DeleteBondOrder = <BondOrder.DeleteBondOrder: 5>
DoubleBondOrder = <BondOrder.DoubleBondOrder: 2>
OrbitalBondOrder = <BondOrder.OrbitalBondOrder: 4>
PseudoBondOrder = <BondOrder.PseudoBondOrder: 99>
SingleBondOrder = <BondOrder.SingleBondOrder: 1>
TripleBondOrder = <BondOrder.TripleBondOrder: 3>
UnknownBondOrder = <BondOrder.UnknownBondOrder: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.BondRingness

Bases: pybind11_object

Members:

UnknownRingness

BondNotInRing

BondInRing

BondInRing = <BondRingness.BondInRing: 2>
BondNotInRing = <BondRingness.BondNotInRing: 1>
UnknownRingness = <BondRingness.UnknownRingness: 0>
property name
property value
class pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets

Bases: CacheableData

A (Pose-cacheable) container for ResidueTypeSets

assign(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, src: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) → pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets

C++: core::chemical::CacheableResidueTypeSets::operator=(const class core::chemical::CacheableResidueTypeSets &) –> class core::chemical::CacheableResidueTypeSets &

clear(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) → None

C++: core::chemical::CacheableResidueTypeSets::clear() –> void

clone(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::chemical::CacheableResidueTypeSets::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_res_type_set(*args, **kwargs)

Overloaded function.

  1. get_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) -> core::chemical::PoseResidueTypeSet

  2. get_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> core::chemical::PoseResidueTypeSet

Return a ResidueTypeSet of the appropriate type, non-const version

If one doesn’t already exist, return a null pointer.

C++: core::chemical::CacheableResidueTypeSets::get_res_type_set(enum core::chemical::TypeSetMode) –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

has_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) → bool

Do we have a ‘mode’ ResidueTypeSet already instantiated?

C++: core::chemical::CacheableResidueTypeSets::has_res_type_set(enum core::chemical::TypeSetMode) const –> bool

set_res_type_set(*args, **kwargs)

Overloaded function.

  1. set_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, rts: core::chemical::PoseResidueTypeSet) -> None

  2. set_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, rts: core::chemical::PoseResidueTypeSet, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> None

Replace the current ResidueTypeSet of the given mode with the given RTS.

If mode is INVALID_t (the recommended default) the mode will be autodetermined from the rts.

C++: core::chemical::CacheableResidueTypeSets::set_res_type_set(class std::shared_ptr<class core::chemical::PoseResidueTypeSet>, enum core::chemical::TypeSetMode) –> void

class pyrosetta.rosetta.core.chemical.ChangeAncestory

Bases: PatchOperation

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ChangeAncestory, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

change the ancestory, but leave the icoors intact.

C++: core::chemical::ChangeAncestory::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ChangeAncestory, : pyrosetta.rosetta.core.chemical.ChangeAncestory) → pyrosetta.rosetta.core.chemical.ChangeAncestory

C++: core::chemical::ChangeAncestory::operator=(const class core::chemical::ChangeAncestory &) –> class core::chemical::ChangeAncestory &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ChangeAncestory) → str

Return the name of this PatchOperation (“ChangeAncestory”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ChangeAncestory::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ChangeBondType

Bases: PatchOperation

A patch operation for changing the bond type of a given bond.

See residue_io.cc for a description of bond types.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ChangeBondType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::ChangeBondType::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ChangeBondType, : pyrosetta.rosetta.core.chemical.ChangeBondType) → pyrosetta.rosetta.core.chemical.ChangeBondType

C++: core::chemical::ChangeBondType::operator=(const class core::chemical::ChangeBondType &) –> class core::chemical::ChangeBondType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ChangeBondType) → str

Return the name of this PatchOperation (“ChangeBondType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ChangeBondType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ChemicalManager

Bases: SingletonBase_core_chemical_ChemicalManager_t

a class managing different sets of atom_type_set and residue_type_set

make it as a singleton class so that atom_type_set and residue_type_set are only

input and initialized once. They can be later retrieved by querying this class.

atom_type_set(*args, **kwargs)

Overloaded function.

  1. atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, type_set_type: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.AtomTypeSet

query atom_type_set by mode

C++: core::chemical::ChemicalManager::atom_type_set(enum core::chemical::TypeSetMode) –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

  1. atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) -> pyrosetta.rosetta.core.chemical.AtomTypeSet

query atom_type_set by a name tag

C++: core::chemical::ChemicalManager::atom_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

element_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) → core::chemical::ElementSet

query atom_type_set by a name tag

C++: core::chemical::ChemicalManager::element_set(const std::string &) –> class std::shared_ptr<const class core::chemical::ElementSet>

gasteiger_atom_type_set(*args, **kwargs)

Overloaded function.

  1. gasteiger_atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager) -> core::chemical::gasteiger::GasteigerAtomTypeSet

  2. gasteiger_atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) -> core::chemical::gasteiger::GasteigerAtomTypeSet

query gasteiger_atom_type_set by a name tag

C++: core::chemical::ChemicalManager::gasteiger_atom_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

static get_instance() → core::chemical::ChemicalManager

C++: utility::SingletonBase<core::chemical::ChemicalManager>::get_instance() –> class core::chemical::ChemicalManager *

has_residue_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) → bool

Check if residue_type_set is instantiated…

C++: core::chemical::ChemicalManager::has_residue_type_set(const std::string &) –> bool

ideal_bond_length_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) → core::chemical::IdealBondLengthSet

query ideal_bond_lengths

C++: core::chemical::ChemicalManager::ideal_bond_length_set(const std::string &) –> class std::shared_ptr<const class core::chemical::IdealBondLengthSet>

mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) → core::chemical::MMAtomTypeSet

query mm_atom_type_set by a name tag

C++: core::chemical::ChemicalManager::mm_atom_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

orbital_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) → core::chemical::orbitals::OrbitalTypeSet

query orbital_type_set by a name tag

C++: core::chemical::ChemicalManager::orbital_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

residue_type_set(*args, **kwargs)

Overloaded function.

  1. residue_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, type_set_type: pyrosetta.rosetta.core.chemical.TypeSetMode) -> core::chemical::ResidueTypeSet

query residue_type_set by a type

If you have access to a Pose/Conformation, you probably don’t want to use this function. The Conformation can have custom ResidueTypeSets which add additional ResidueTypes to the ResidueTypeSet. Instead, use the residue_type_set_for_*() function on the pose. Those will fall back to this function if there isn’t a custom ResidueTypeSet.

C++: core::chemical::ChemicalManager::residue_type_set(enum core::chemical::TypeSetMode) –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

  1. residue_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) -> core::chemical::ResidueTypeSet

query residue_type_set by a name tag

C++: core::chemical::ChemicalManager::residue_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

class pyrosetta.rosetta.core.chemical.ChiralFlipAtoms

Bases: PatchOperation

Execute chiral flip (primarily: at CA)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the NCAA rotamer library path in the residue type

C++: core::chemical::ChiralFlipAtoms::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms, : pyrosetta.rosetta.core.chemical.ChiralFlipAtoms) → pyrosetta.rosetta.core.chemical.ChiralFlipAtoms

C++: core::chemical::ChiralFlipAtoms::operator=(const class core::chemical::ChiralFlipAtoms &) –> class core::chemical::ChiralFlipAtoms &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms) → str

Return the name of this PatchOperation (“ChiralFlipAtoms”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ChiralFlipAtoms::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ChiralFlipNaming

Bases: PatchOperation

Execute chiral flip (primarily: at CA)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) → bool

C++: core::chemical::ChiralFlipNaming::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the NCAA rotamer library path in the residue type

C++: core::chemical::ChiralFlipNaming::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming, : pyrosetta.rosetta.core.chemical.ChiralFlipNaming) → pyrosetta.rosetta.core.chemical.ChiralFlipNaming

C++: core::chemical::ChiralFlipNaming::operator=(const class core::chemical::ChiralFlipNaming &) –> class core::chemical::ChiralFlipNaming &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) → bool

This patch operaton DOES result in a new base residue type.

C++: core::chemical::ChiralFlipNaming::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) → bool

Generates a new aa

C++: core::chemical::ChiralFlipNaming::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) → str

Return the name of this PatchOperation (“ChiralFlipNaming”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ChiralFlipNaming::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ClearChiRotamers

Bases: PatchOperation

A patch operation for clearing all rotamer bins from the chi of a ResidueType.

This is useful if one has redefined a chi.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::ClearChiRotamers::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers, : pyrosetta.rosetta.core.chemical.ClearChiRotamers) → pyrosetta.rosetta.core.chemical.ClearChiRotamers

C++: core::chemical::ClearChiRotamers::operator=(const class core::chemical::ClearChiRotamers &) –> class core::chemical::ClearChiRotamers &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers) → str

Return the name of this PatchOperation (“ClearChiRotamers”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ClearChiRotamers::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton

Bases: PatchOperation

Add a connection to the residue’s sulfur and make a virtual proton to track the position of the connection atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ConnectSulfurAndMakeVirtualProton::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, : pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton) → pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton

C++: core::chemical::ConnectSulfurAndMakeVirtualProton::operator=(const class core::chemical::ConnectSulfurAndMakeVirtualProton &) –> class core::chemical::ConnectSulfurAndMakeVirtualProton &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

C++: core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton) → str

Return the name of this PatchOperation (“ConnectSulfurAndMakeVirtualProton”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ConnectSulfurAndMakeVirtualProton::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteActCoordAtom

Bases: PatchOperation

Delete an act coord atom

Added by Andrew M. Watkins in April 2015

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::DeleteActCoordAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom, : pyrosetta.rosetta.core.chemical.DeleteActCoordAtom) → pyrosetta.rosetta.core.chemical.DeleteActCoordAtom

C++: core::chemical::DeleteActCoordAtom::operator=(const class core::chemical::DeleteActCoordAtom &) –> class core::chemical::DeleteActCoordAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom) → str

Return the name of this PatchOperation (“DeleteActCoordAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteActCoordAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteAtom

Bases: PatchOperation

delete an atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

delete an atom from ResidueType rsd

C++: core::chemical::DeleteAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteAtom, : pyrosetta.rosetta.core.chemical.DeleteAtom) → pyrosetta.rosetta.core.chemical.DeleteAtom

C++: core::chemical::DeleteAtom::operator=(const class core::chemical::DeleteAtom &) –> class core::chemical::DeleteAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.DeleteAtom) → str

C++: core::chemical::DeleteAtom::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteAtom) → str

Return the name of this PatchOperation (“DeleteAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteChildProton

Bases: PatchOperation

delete child proton

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteChildProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::DeleteChildProton::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteChildProton, : pyrosetta.rosetta.core.chemical.DeleteChildProton) → pyrosetta.rosetta.core.chemical.DeleteChildProton

C++: core::chemical::DeleteChildProton::operator=(const class core::chemical::DeleteChildProton &) –> class core::chemical::DeleteChildProton &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteChildProton) → str

Return the name of this PatchOperation (“DeleteChildProton”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteChildProton::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom

Bases: PatchOperation

Delete a metal binding atom

Added by Andrew M. Watkins in April 2015

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::DeleteMetalbindingAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom, : pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom) → pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom

C++: core::chemical::DeleteMetalbindingAtom::operator=(const class core::chemical::DeleteMetalbindingAtom &) –> class core::chemical::DeleteMetalbindingAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom) → str

Return the name of this PatchOperation (“DeleteMetalbindingAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteMetalbindingAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteProperty

Bases: PatchOperation

delete a property from ResidueType

Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM’s (e.g. methylation) Rewritten by Vikram K. Mulligan on 25 Aug. 2016 to use enums wherever possible for speed.

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteProperty, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

delete a property

C++: core::chemical::DeleteProperty::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteProperty, : pyrosetta.rosetta.core.chemical.DeleteProperty) → pyrosetta.rosetta.core.chemical.DeleteProperty

C++: core::chemical::DeleteProperty::operator=(const class core::chemical::DeleteProperty &) –> class core::chemical::DeleteProperty &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.DeleteProperty) → str

Which property, if any, is deleted.

C++: core::chemical::DeleteProperty::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.DeleteProperty) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

Returns NO_PROPERTY if this PatchOperation deletes a custom, on-the-fly property.

C++: core::chemical::DeleteProperty::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteProperty) → str

Return the name of this PatchOperation (“DeleteProperty”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteProperty::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteTerminalChi

Bases: PatchOperation

Delete terminal chi angle

Added by Andrew M. Watkins in April 2015

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

redefine a chi angle

C++: core::chemical::DeleteTerminalChi::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi, : pyrosetta.rosetta.core.chemical.DeleteTerminalChi) → pyrosetta.rosetta.core.chemical.DeleteTerminalChi

C++: core::chemical::DeleteTerminalChi::operator=(const class core::chemical::DeleteTerminalChi &) –> class core::chemical::DeleteTerminalChi &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi) → str

Return the name of this PatchOperation (“DeleteTerminalChi”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteTerminalChi::name() const –> std::string

class pyrosetta.rosetta.core.chemical.DeleteVariantType

Bases: PatchOperation

A patch operation for deleting a VariantType from a ResidueType.

Labonte <JWLabonte.edu>

Vikram K. Mulligan (vmullig.edu) – modified to primarily use enums instead of strings.

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.DeleteVariantType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::DeleteVariantType::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.DeleteVariantType, : pyrosetta.rosetta.core.chemical.DeleteVariantType) → pyrosetta.rosetta.core.chemical.DeleteVariantType

C++: core::chemical::DeleteVariantType::operator=(const class core::chemical::DeleteVariantType &) –> class core::chemical::DeleteVariantType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) → str

Which variant, if any, is deleted.

C++: core::chemical::DeleteVariantType::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::DeleteVariantType::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) → str

Return the name of this PatchOperation (“DeleteVariantType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::DeleteVariantType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ElectronConfiguration

Bases: pybind11_object

describes the electron configuration of atoms

Describes the electron configuration of an atom on quantum chemistry level.

class AngularMomentumQuantumNumber

Bases: pybind11_object

Members:

e_S

e_P

e_D

e_F

MaxAngularMomentumQuantumNumber

MaxAngularMomentumQuantumNumber = <AngularMomentumQuantumNumber.MaxAngularMomentumQuantumNumber: 4>
e_D = <AngularMomentumQuantumNumber.e_D: 2>
e_F = <AngularMomentumQuantumNumber.e_F: 3>
e_P = <AngularMomentumQuantumNumber.e_P: 1>
e_S = <AngularMomentumQuantumNumber.e_S: 0>
property name
property value
static AngularMomentumQuantumNumber_strings() → pyrosetta.rosetta.std.vector_std_string

C++: core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber_strings() –> const class std::vector<std::string, class std::allocator<std::string > > &

MaxAngularMomentumQuantumNumber = <AngularMomentumQuantumNumber.MaxAngularMomentumQuantumNumber: 4>
MaxPrincipleQuantumNumber = <PrincipalQuantumNumber.MaxPrincipleQuantumNumber: 7>
class PrincipalQuantumNumber

Bases: pybind11_object

Members:

e_1

e_2

e_3

e_4

e_5

e_6

e_7

MaxPrincipleQuantumNumber

MaxPrincipleQuantumNumber = <PrincipalQuantumNumber.MaxPrincipleQuantumNumber: 7>
e_1 = <PrincipalQuantumNumber.e_1: 0>
e_2 = <PrincipalQuantumNumber.e_2: 1>
e_3 = <PrincipalQuantumNumber.e_3: 2>
e_4 = <PrincipalQuantumNumber.e_4: 3>
e_5 = <PrincipalQuantumNumber.e_5: 4>
e_6 = <PrincipalQuantumNumber.e_6: 5>
e_7 = <PrincipalQuantumNumber.e_7: 6>
property name
property value
static PrincipalQuantumNumber_strings() → pyrosetta.rosetta.std.vector_std_string

C++: core::chemical::ElectronConfiguration::PrincipalQuantumNumber_strings() –> const class std::vector<std::string, class std::allocator<std::string > > &

assign(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, : pyrosetta.rosetta.core.chemical.ElectronConfiguration) → pyrosetta.rosetta.core.chemical.ElectronConfiguration

C++: core::chemical::ElectronConfiguration::operator=(const class core::chemical::ElectronConfiguration &) –> class core::chemical::ElectronConfiguration &

e_1 = <PrincipalQuantumNumber.e_1: 0>
e_2 = <PrincipalQuantumNumber.e_2: 1>
e_3 = <PrincipalQuantumNumber.e_3: 2>
e_4 = <PrincipalQuantumNumber.e_4: 3>
e_5 = <PrincipalQuantumNumber.e_5: 4>
e_6 = <PrincipalQuantumNumber.e_6: 5>
e_7 = <PrincipalQuantumNumber.e_7: 6>
e_D = <AngularMomentumQuantumNumber.e_D: 2>
e_F = <AngularMomentumQuantumNumber.e_F: 3>
e_P = <AngularMomentumQuantumNumber.e_P: 1>
e_S = <AngularMomentumQuantumNumber.e_S: 0>
static get_angular_momentum_quantum_number(STR: str) → pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber

AngularMomentumQuantumNumber as string

NUM the AngularMomentumQuantumNumber desired

AngularMomentumQuantumNumber as string

C++: core::chemical::ElectronConfiguration::get_angular_momentum_quantum_number(const std::string &) –> enum core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber

static get_descriptor(*args, **kwargs)

Overloaded function.

  1. get_descriptor(NUM: pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber) -> str

PrincipalQuantumNumber as string

the PrincipalQuantumNumber desired

the PrincipalQuantumNumber as string

C++: core::chemical::ElectronConfiguration::get_descriptor(const enum core::chemical::ElectronConfiguration::PrincipalQuantumNumber &) –> const std::string &

  1. get_descriptor(NUM: pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber) -> str

AngularMomentumQuantumNumber as string

the AngularMomentumQuantumNumber desired

the AngularMomentumQuantumNumber as string

C++: core::chemical::ElectronConfiguration::get_descriptor(const enum core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber &) –> const std::string &

static get_principal_quantum_number(STR: str) → pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber

PrincipalQuantumNumber from string

NUM the PrincipalQuantumNumber desired

PrincipalQuantumNumber as string

C++: core::chemical::ElectronConfiguration::get_principal_quantum_number(const std::string &) –> enum core::chemical::ElectronConfiguration::PrincipalQuantumNumber

max_valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

the maximum number of electrons in SP orbitals for the noble gas in this period

C++: core::chemical::ElectronConfiguration::max_valence_electrons_sp() const –> unsigned long

read(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, ISTREAM: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.std.istream

read from std::istream

input stream

istream which was read from

C++: core::chemical::ElectronConfiguration::read(std::istream &) –> std::istream &

unpaired_valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

return the number of valence electrons in SP orbitals

C++: core::chemical::ElectronConfiguration::unpaired_valence_electrons_sp() const –> unsigned long

valence_electrons_p(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

number ValenceElectrons in the pi valence orbitals

C++: core::chemical::ElectronConfiguration::valence_electrons_p() const –> unsigned long

valence_electrons_s(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

return number ValenceElectrons in the sigma valence orbitals

C++: core::chemical::ElectronConfiguration::valence_electrons_s() const –> unsigned long

valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

number valence_electrons_sp

C++: core::chemical::ElectronConfiguration::valence_electrons_sp() const –> unsigned long

valence_electrons_spd(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) → int

number valence_electrons_spd

C++: core::chemical::ElectronConfiguration::valence_electrons_spd() const –> unsigned long

write(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, OSTREAM: pyrosetta.rosetta.std.ostream) → pyrosetta.rosetta.std.ostream

write to std::ostream

output stream

number of indentations

ostream which was written to

C++: core::chemical::ElectronConfiguration::write(std::ostream &) const –> std::ostream &

class pyrosetta.rosetta.core.chemical.Element

Bases: pybind11_object

stores element properties

This is a low level helper class to store element properties

Clone(self: pyrosetta.rosetta.core.chemical.Element) → pyrosetta.rosetta.core.chemical.Element

virtual copy constructor

C++: core::chemical::Element::Clone() const –> class std::shared_ptr<class core::chemical::Element>

CovalentRadius = <Properties.CovalentRadius: 1>
Mass = <Properties.Mass: 0>
NumberOfProperties = <Properties.NumberOfProperties: 3>
class Properties

Bases: pybind11_object

enum properties for element types

Members:

Mass

CovalentRadius

VDWaalsRadius

NumberOfProperties

CovalentRadius = <Properties.CovalentRadius: 1>
Mass = <Properties.Mass: 0>
NumberOfProperties = <Properties.NumberOfProperties: 3>
VDWaalsRadius = <Properties.VDWaalsRadius: 2>
property name
property value
VDWaalsRadius = <Properties.VDWaalsRadius: 2>
assign(self: pyrosetta.rosetta.core.chemical.Element, : pyrosetta.rosetta.core.chemical.Element) → pyrosetta.rosetta.core.chemical.Element

C++: core::chemical::Element::operator=(const class core::chemical::Element &) –> class core::chemical::Element &

element(self: pyrosetta.rosetta.core.chemical.Element) → pyrosetta.rosetta.core.chemical.element.Elements

The element enumeration

C++: core::chemical::Element::element() const –> enum core::chemical::element::Elements

get_atomic_number(self: pyrosetta.rosetta.core.chemical.Element) → int

atomic number

atomic number

C++: core::chemical::Element::get_atomic_number() const –> unsigned long

get_chemical_name(self: pyrosetta.rosetta.core.chemical.Element) → str

GetChemicalName

full chemical name

C++: core::chemical::Element::get_chemical_name() const –> const std::string &

get_chemical_symbol(self: pyrosetta.rosetta.core.chemical.Element) → str

GetChemicalSymbol

chemical symbol one or two letters as AtomName

C++: core::chemical::Element::get_chemical_symbol() const –> const std::string &

get_electron_configuration(self: pyrosetta.rosetta.core.chemical.Element) → pyrosetta.rosetta.core.chemical.ElectronConfiguration

electron configuration

the ElectronConfiguration

C++: core::chemical::Element::get_electron_configuration() const –> const class core::chemical::ElectronConfiguration &

get_index(self: pyrosetta.rosetta.core.chemical.Element) → int
Get the index of this element in the parent Element set

Will be zero if it’s not a member.

C++: core::chemical::Element::get_index() const –> unsigned long

get_main_group(self: pyrosetta.rosetta.core.chemical.Element) → int

main Group #

C++: core::chemical::Element::get_main_group() const –> unsigned long

get_period(self: pyrosetta.rosetta.core.chemical.Element) → int

Period

C++: core::chemical::Element::get_period() const –> unsigned long

get_property(self: pyrosetta.rosetta.core.chemical.Element, PROPERTY: pyrosetta.rosetta.core.chemical.Element.Properties) → float

element type property as core::Real

the property desired

the property as core::Real

C++: core::chemical::Element::get_property(const enum core::chemical::Element::Properties &) const –> double

static get_property_name(PROPERTY: pyrosetta.rosetta.core.chemical.Element.Properties) → str

element type property as string

the property desired

the property as string

C++: core::chemical::Element::get_property_name(const enum core::chemical::Element::Properties &) –> const std::string &

is_conjugatable(self: pyrosetta.rosetta.core.chemical.Element) → bool

tell whether this element type can participate in a conjugated system

true if this element can participate in a common conjugated system Specifically tests if the element has 1-4 valence electrons in P orbitals

C++: core::chemical::Element::is_conjugatable() const –> bool

is_fake(self: pyrosetta.rosetta.core.chemical.Element) → bool

Return true unless the element actually exists in the periodic table.

C++: core::chemical::Element::is_fake() const –> bool

read(self: pyrosetta.rosetta.core.chemical.Element, ISTREAM: pyrosetta.rosetta.std.istream) → pyrosetta.rosetta.std.istream

read from std::istream

input stream

istream which was read from

C++: core::chemical::Element::read(std::istream &) –> std::istream &

set_index(self: pyrosetta.rosetta.core.chemical.Element, setting: int) → None

C++: core::chemical::Element::set_index(unsigned long) –> void

weight(self: pyrosetta.rosetta.core.chemical.Element) → float

This is legacy code from old element set

Return the full name of the Element

C++: core::chemical::Element::weight() const –> double

write(self: pyrosetta.rosetta.core.chemical.Element, OSTREAM: pyrosetta.rosetta.std.ostream) → pyrosetta.rosetta.std.ostream

write to std::ostream

output stream

ostream which was written to

C++: core::chemical::Element::write(std::ostream &) const –> std::ostream &

class pyrosetta.rosetta.core.chemical.ElementSet

Bases: pybind11_object

A set of Bcl Elements

This class contains a vector of pointers each of which points to an Element and the vector index is looked up by an element_name string in a map.

assign(self: pyrosetta.rosetta.core.chemical.ElementSet, : pyrosetta.rosetta.core.chemical.ElementSet) → pyrosetta.rosetta.core.chemical.ElementSet

C++: core::chemical::ElementSet::operator=(const class core::chemical::ElementSet &) –> class core::chemical::ElementSet &

contains_element_type(self: pyrosetta.rosetta.core.chemical.ElementSet, element_symbol: str) → bool

Check if there is an element_type associated with an element_symbol string

C++: core::chemical::ElementSet::contains_element_type(const std::string &) const –> bool

element(*args, **kwargs)

Overloaded function.

  1. element(self: pyrosetta.rosetta.core.chemical.ElementSet, ele: pyrosetta.rosetta.core.chemical.element.Elements) -> pyrosetta.rosetta.core.chemical.Element

Lookup the element index by the element enum;

C++: core::chemical::ElementSet::element(enum core::chemical::element::Elements) const –> class std::shared_ptr<const class core::chemical::Element>

  1. element(self: pyrosetta.rosetta.core.chemical.ElementSet, element_symbol: str) -> pyrosetta.rosetta.core.chemical.Element

Lookup the element object by the element_symbol string

C++: core::chemical::ElementSet::element(const std::string &) const –> class std::shared_ptr<const class core::chemical::Element>

element_index(*args, **kwargs)

Overloaded function.

  1. element_index(self: pyrosetta.rosetta.core.chemical.ElementSet, ele: pyrosetta.rosetta.core.chemical.element.Elements) -> int

Lookup the element index by the element enum

C++: core::chemical::ElementSet::element_index(enum core::chemical::element::Elements) const –> unsigned long

  1. element_index(self: pyrosetta.rosetta.core.chemical.ElementSet, element_symbol: str) -> int

Lookup the element index by the element_symbol string

C++: core::chemical::ElementSet::element_index(const std::string &) const –> unsigned long

n_elements(self: pyrosetta.rosetta.core.chemical.ElementSet) → int

Number of elements in the set

C++: core::chemical::ElementSet::n_elements() const –> unsigned long

name(self: pyrosetta.rosetta.core.chemical.ElementSet) → str

What the ChemicalManager knows this as, if relevant

C++: core::chemical::ElementSet::name() const –> const std::string &

read_file(self: pyrosetta.rosetta.core.chemical.ElementSet, filename: str) → None

Load the ElementSet from a file

C++: core::chemical::ElementSet::read_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet

Bases: ResidueTypeSet

A collection of ResidueType defined

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.AtomTypeSet

C++: core::chemical::ResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

The list of ResidueTypes that don’t have any patches, but can be patched.

C++: core::chemical::ResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

database_directory(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet) → str

accessor for database_directory

C++: core::chemical::GlobalResidueTypeSet::database_directory() const –> const std::string &

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ElementSet

C++: core::chemical::ResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>

generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, interchangeability_group: str) → bool
Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated))

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const std::string &, const std::string &) const –> bool

generates_patched_residue_type_with_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, name3: str) → bool
Check if a base type (like “SER”) generates any types with another name3 (like “SEP”)

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3(const std::string &, const std::string &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)

Overloaded function.

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants

The number of variants must match exactly. Variants can be custom variants. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants, making exceptions for some variants.

The number of variants must match exactly. Variants can be custom variants, but exceptions must

be standard types, listed in VariantType.hh.

(It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_by_basetype(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Given a base residue type, desired variants, and undesired variants, retrieve a list

of cached ResidueTypeCOPs. If not cached, generate the data and cache them.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

A list of ResidueTypeCOPs matching the desired variants, with the desired base type.

This function is threadsafe. Caching and retrieveal are handled with a ReadWriteMutex.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Gets all non-patched types with the given aa type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_aa(enum core::chemical::AA) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name1(char) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name3(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_d_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, l_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

Given a D-residue, get its L-equivalent.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not a D-residue. Preserves variant types. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Works for L-amino acids and L-peptoids (peptoids with chiral “L” sidechains”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeSet::get_d_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_l_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, d_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType
Given an L-residue, get its D-equivalent.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not an L-residue. Preserves variant types.

Works for D-amino acids and D-peptoids (peptoids with chiral “D” sidechains”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeSet::get_l_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_mirrored_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, original_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType
Given a residue, get its mirror-image type.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Returns the same residue if this is an ACHIRAL type (e.g. gly), the D-equivalent for an L-residue, the L-equivalent of a D-residue, or NULL if this is an L-residue with no D-equivalent (or a D- with no L-equivalent). Preserves variant types.

C++: core::chemical::ResidueTypeSet::get_mirrored_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t
Get the patches corresponding to a patch name.

Will get both regular an metapatches

C++: core::chemical::ResidueTypeSet::get_patches(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

get_representative_type_aa(*args, **kwargs)

Overloaded function.

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given aa type and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_base_name(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name1 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name3 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_custom_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_added(*args, **kwargs)

Overloaded function.

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) -> pyrosetta.rosetta.core.chemical.ResidueType

Query a variant ResidueType by its base ResidueType and VariantType

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) -> pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → pyrosetta.rosetta.core.chemical.ResidueType
return the residuetype we get from variant rsd type after removing the desired variant type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ResidueTypeSet

C++: core::chemical::ResidueTypeSet::get_self_ptr() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t

C++: core::chemical::ResidueTypeSet::get_self_weak_ptr() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>

has_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
Does this ResidueTypeSet have ResidueTypes with the given interchangeability group?

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_interchangeability_group(const std::string &) const –> bool

has_metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool

Do we have this metapatch?

C++: core::chemical::ResidueTypeSet::has_metapatch(const std::string &) const –> bool

has_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
query if a ResidueType of the unique residue id (name) is present.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name(const std::string &) const –> bool

has_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → bool
query if any ResidueTypes in the set have a “name3” that matches the input name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name3(const std::string &) const –> bool

merge_split_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::io::MergeAndSplitBehaviorManager

accessor for merge/split behavior manager

C++: core::chemical::ResidueTypeSet::merge_split_behavior_manager() const –> const class core::chemical::io::MergeAndSplitBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → core::chemical::Metapatch

C++: core::chemical::ResidueTypeSet::metapatch(const std::string &) const –> class std::shared_ptr<const class core::chemical::Metapatch>

metapatch_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches, index by name.

C++: core::chemical::ResidueTypeSet::metapatch_map() const –> const class std::map<std::string, class std::shared_ptr<const class core::chemical::Metapatch>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class core::chemical::Metapatch> > > > &

metapatches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches

C++: core::chemical::ResidueTypeSet::metapatches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Metapatch>, class std::allocator<class std::shared_ptr<const class core::chemical::Metapatch> > >

mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::MMAtomTypeSet

C++: core::chemical::ResidueTypeSet::mm_atom_type_set() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.TypeSetMode

The type of the ResidueTypeSet

The difference between a ResidueTypeSet name and a ResidueTypeSet mode is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same mode. The mode specifies what compatibility class (full atom, centroid) the ResidueTypeSet has.

C++: core::chemical::ResidueTypeSet::mode() const –> enum core::chemical::TypeSetMode

name(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet) → str

name of the residue type set (may be empty)

The difference between a ResidueTypeSet name and a ResidueTypeSet category is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same category. The type specifies what compatibility class (full atom, centroid) the ResidueTypeSet has. Generally speaking, the name should only be used when interacting with the user.

C++: core::chemical::GlobalResidueTypeSet::name() const –> const std::string &

name_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
query ResidueType by its unique residue id. Note for derived classes: this

method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

since within a ResidueTypeSet, each residue id must be unique, this method only returns one residue type or it exits (the program!) without a match.

C++: core::chemical::ResidueTypeSet::name_map(const std::string &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Get ResidueType by exact name, returning COP. Will return null pointer

for no matches. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::name_mapOP(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

orbital_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::orbitals::OrbitalTypeSet

C++: core::chemical::ResidueTypeSet::orbital_type_set() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

patch_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t

the patches, index by name.

C++: core::chemical::ResidueTypeSet::patch_map() const –> const class std::map<std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > > > > > &

patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t

the patches

C++: core::chemical::ResidueTypeSet::patches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

The list of ResidueTypes which shouldn’t get patches applied to them

C++: core::chemical::ResidueTypeSet::unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

class pyrosetta.rosetta.core.chemical.GreekDistance

Bases: pybind11_object

Enumerators for the Greek distance from the atom with the functional group of highest priority.

Members:

PRIMARY_ATOM

ALPHA_ATOM

BETA_ATOM

GAMMA_ATOM

DELTA_ATOM

EPSILON_ATOM

ZETA_ATOM

ETA_ATOM

THETA_ATOM

IOTA_ATOM

KAPPA_ATOM

LAMBDA_ATOM

MU_ATOM

NU_ATOM

XI_ATOM

OMICRON_ATOM

PI_ATOM

SIGMA_ATOM

TAU_ATOM

UPSILON_ATOM

PHI_ATOM

CHI_ATOM

PSI_ATOM

NA_GREEK_DISTANCE

ALPHA_ATOM = <GreekDistance.ALPHA_ATOM: 1>
BETA_ATOM = <GreekDistance.BETA_ATOM: 2>
CHI_ATOM = <GreekDistance.CHI_ATOM: 21>
DELTA_ATOM = <GreekDistance.DELTA_ATOM: 4>
EPSILON_ATOM = <GreekDistance.EPSILON_ATOM: 5>
ETA_ATOM = <GreekDistance.ETA_ATOM: 7>
GAMMA_ATOM = <GreekDistance.GAMMA_ATOM: 3>
IOTA_ATOM = <GreekDistance.IOTA_ATOM: 9>
KAPPA_ATOM = <GreekDistance.KAPPA_ATOM: 10>
LAMBDA_ATOM = <GreekDistance.LAMBDA_ATOM: 11>
MU_ATOM = <GreekDistance.MU_ATOM: 12>
NA_GREEK_DISTANCE = <GreekDistance.NA_GREEK_DISTANCE: 1023>
NU_ATOM = <GreekDistance.NU_ATOM: 13>
OMICRON_ATOM = <GreekDistance.OMICRON_ATOM: 15>
PHI_ATOM = <GreekDistance.PHI_ATOM: 20>
PI_ATOM = <GreekDistance.PI_ATOM: 16>
PRIMARY_ATOM = <GreekDistance.PRIMARY_ATOM: 0>
PSI_ATOM = <GreekDistance.PSI_ATOM: 22>
SIGMA_ATOM = <GreekDistance.SIGMA_ATOM: 17>
TAU_ATOM = <GreekDistance.TAU_ATOM: 18>
THETA_ATOM = <GreekDistance.THETA_ATOM: 8>
UPSILON_ATOM = <GreekDistance.UPSILON_ATOM: 19>
XI_ATOM = <GreekDistance.XI_ATOM: 14>
ZETA_ATOM = <GreekDistance.ZETA_ATOM: 6>
property name
property value
class pyrosetta.rosetta.core.chemical.HeavyAtomFilter

Bases: pybind11_object

The filter responsible for obtaining all heavy atoms.

assign(self: pyrosetta.rosetta.core.chemical.HeavyAtomFilter, : pyrosetta.rosetta.core.chemical.HeavyAtomFilter) → pyrosetta.rosetta.core.chemical.HeavyAtomFilter

C++: core::chemical::HeavyAtomFilter::operator=(const class core::chemical::HeavyAtomFilter &) –> class core::chemical::HeavyAtomFilter &

class pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter

Bases: pybind11_object

The filter responsible for finding heavy atoms with hydrogens.

assign(self: pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter, : pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter) → pyrosetta.rosetta.core.chemical.HeavyAtomWithHydrogensFilter

C++: core::chemical::HeavyAtomWithHydrogensFilter::operator=(const class core::chemical::HeavyAtomWithHydrogensFilter &) –> class core::chemical::HeavyAtomWithHydrogensFilter &

class pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter

Bases: pybind11_object

The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them.

assign(self: pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter, : pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter) → pyrosetta.rosetta.core.chemical.HeavyAtomWithPolarHydrogensFilter

C++: core::chemical::HeavyAtomWithPolarHydrogensFilter::operator=(const class core::chemical::HeavyAtomWithPolarHydrogensFilter &) –> class core::chemical::HeavyAtomWithPolarHydrogensFilter &

class pyrosetta.rosetta.core.chemical.Hybridization

Bases: pybind11_object

Members:

SP2_HYBRID

SP3_HYBRID

RING_HYBRID

UNKNOWN_HYBRID

HYBRID_MAX

HYBRID_MAX = <Hybridization.UNKNOWN_HYBRID: 4>
RING_HYBRID = <Hybridization.RING_HYBRID: 3>
SP2_HYBRID = <Hybridization.SP2_HYBRID: 1>
SP3_HYBRID = <Hybridization.SP3_HYBRID: 2>
UNKNOWN_HYBRID = <Hybridization.UNKNOWN_HYBRID: 4>
property name
property value
class pyrosetta.rosetta.core.chemical.HydrogenAtomFilter

Bases: pybind11_object

The filter responsible for all hydrogens.

assign(self: pyrosetta.rosetta.core.chemical.HydrogenAtomFilter, : pyrosetta.rosetta.core.chemical.HydrogenAtomFilter) → pyrosetta.rosetta.core.chemical.HydrogenAtomFilter

C++: core::chemical::HydrogenAtomFilter::operator=(const class core::chemical::HydrogenAtomFilter &) –> class core::chemical::HydrogenAtomFilter &

class pyrosetta.rosetta.core.chemical.ICoorAtomID

Bases: pybind11_object

Atom ‘s ID in internal coordinates in a ResidueType

assign(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, : pyrosetta.rosetta.core.chemical.ICoorAtomID) → pyrosetta.rosetta.core.chemical.ICoorAtomID

C++: core::chemical::ICoorAtomID::operator=(const class core::chemical::ICoorAtomID &) –> class core::chemical::ICoorAtomID &

atom_id(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rsd: core::conformation::Residue, conformation: core::conformation::Conformation) → core::id::AtomID

This ICoorAtomID (for the given residue) corresponds to which id::AtomID in the conformation?

C++: core::chemical::ICoorAtomID::atom_id(const class core::conformation::Residue &, const class core::conformation::Conformation &) const –> class core::id::AtomID

atomno(*args, **kwargs)

Overloaded function.

  1. atomno(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) -> int

get ICoorAtomID atomno

C++: core::chemical::ICoorAtomID::atomno() const –> unsigned long

  1. atomno(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, atomno_in: int) -> None

set ICoorAtomID atomno

C++: core::chemical::ICoorAtomID::atomno(const int) –> void

buildable(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rsd: core::conformation::Residue, conformation: core::conformation::Conformation) → bool
Can valid coordinates be built for this ICoorAtomID,

given the residue and conformation?

C++: core::chemical::ICoorAtomID::buildable(const class core::conformation::Residue &, const class core::conformation::Conformation &) const –> bool

is_connect(*args, **kwargs)

Overloaded function.

  1. is_connect(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, connid: int) -> bool

Returns true if this is the specified connection id

C++: core::chemical::ICoorAtomID::is_connect(const unsigned long) const –> bool

  1. is_connect(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) -> bool

Returns true if this is a connection.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ICoorAtomID::is_connect() const –> bool

is_internal(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) → bool

C++: core::chemical::ICoorAtomID::is_internal() const –> bool

is_polymer_lower(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) → bool

C++: core::chemical::ICoorAtomID::is_polymer_lower() const –> bool

is_polymer_upper(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) → bool

C++: core::chemical::ICoorAtomID::is_polymer_upper() const –> bool

name(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rt: core::chemical::ResidueType) → str
Returns the string representation which will build this ICoorAtomID

(e.g. atom name, UPPER, LOWER, CONN*

C++: core::chemical::ICoorAtomID::name(const class core::chemical::ResidueType &) const –> std::string

type(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

get ICoordAtomID type

C++: core::chemical::ICoorAtomID::type() const –> const enum core::chemical::ICoordAtomIDType &

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rsd: core::conformation::Residue, conformation: core::conformation::Conformation) -> pyrosetta.rosetta.numeric.xyzVector_double_t

What is the coordinates corresponding to this ICoorAtomID,

for the given residue and conformation

C++: core::chemical::ICoorAtomID::xyz(const class core::conformation::Residue &, const class core::conformation::Conformation &) const –> const class numeric::xyzVector<double> &

  1. xyz(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rsd_type: core::chemical::ResidueType) -> pyrosetta.rosetta.numeric.xyzVector_double_t

What is the coordinates corresponding to this ICoorAtomID,

for the given idealized ResidueType

C++: core::chemical::ICoorAtomID::xyz(const class core::chemical::ResidueType &) const –> class numeric::xyzVector<double>

  1. xyz(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, rsd: core::conformation::Residue) -> pyrosetta.rosetta.numeric.xyzVector_double_t

WARNING: Slightly dangerous function intended for black magic use only.

Rebuilds atom location from stub atoms. If stub atom are not internal atoms, their location will be rebuilt from their residue stub atom’s locations, as opposed to being retrieved from connected residues via a conformation.

C++: core::chemical::ICoorAtomID::xyz(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.core.chemical.ICoordAtomIDType

Bases: pybind11_object

  • INTERNAL: atoms which inherently belong to this ResidueType

  • POLYMER_LOWER: atom at the polymer lower connection, such as backbone C in

the previous residue (N-term side) - POLYMER_UPPER: atom at the polymer upper connection, such as backbone N in the next residue (C-term side) - CONNECT: atoms from a non-adjacent residue which connect to this residue by non-polymer connection, such as disulfide

If you add anything to this enum, be sure to update the string_to_icoord_type() function.

Members:

INTERNAL

POLYMER_LOWER

POLYMER_UPPER

CONNECT

CONNECT = <ICoordAtomIDType.CONNECT: 4>
INTERNAL = <ICoordAtomIDType.INTERNAL: 1>
POLYMER_LOWER = <ICoordAtomIDType.POLYMER_LOWER: 2>
POLYMER_UPPER = <ICoordAtomIDType.POLYMER_UPPER: 3>
property name
property value
class pyrosetta.rosetta.core.chemical.IdealBondLengthSet

Bases: pybind11_object

A set of Elements

This class contains a vector of pointers each of which points to an Element and the vector index is looked up by an element_name string in a map.

assign(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, : pyrosetta.rosetta.core.chemical.IdealBondLengthSet) → pyrosetta.rosetta.core.chemical.IdealBondLengthSet

C++: core::chemical::IdealBondLengthSet::operator=(const class core::chemical::IdealBondLengthSet &) –> class core::chemical::IdealBondLengthSet &

contains_bond_length(*args, **kwargs)

Overloaded function.

  1. contains_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_name1: str, atom_type_name2: str) -> bool

Check if an ideal bond length is known for this pair of atom types…

C++: core::chemical::IdealBondLengthSet::contains_bond_length(const std::string &, const std::string &) const –> bool

  1. contains_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_index1: int, atom_type_index2: int) -> bool

C++: core::chemical::IdealBondLengthSet::contains_bond_length(int, int) const –> bool

get_bond_length(*args, **kwargs)

Overloaded function.

  1. get_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_name1: str, atom_type_name2: str) -> float

Lookup the element index by the element_symbol string

C++: core::chemical::IdealBondLengthSet::get_bond_length(const std::string &, const std::string &) const –> double

  1. get_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_index1: int, atom_type_index2: int) -> float

C++: core::chemical::IdealBondLengthSet::get_bond_length(const int, const int) const –> double

print_all_bond_lengths(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet) → None

Print all of the symbols of all of the Elements in the set. Usefull for debuging.

C++: core::chemical::IdealBondLengthSet::print_all_bond_lengths() –> void

read_file(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, filename: str) → None

Load the IdealBondLengthSet from a file

C++: core::chemical::IdealBondLengthSet::read_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.MMAtomType

Bases: pybind11_object

Basic MM atom type

Simple class for holding the name and the LJ properties of a Charmm molecular mechanics atom type. Borrows heavily and functions similarly to the rosetta atom type class, AtomType

lj_radius(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the LJ radius of the atom type

C++: core::chemical::MMAtomType::lj_radius() const –> double

lj_radius_sq(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the squared LJ radius of the atom type

C++: core::chemical::MMAtomType::lj_radius_sq() const –> double

lj_three_bond_radius(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the LJ radius for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_radius() const –> double

lj_three_bond_radius_sq(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the squaredLJ radius for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_radius_sq() const –> double

lj_three_bond_wdepth(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the LJ well depth for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_wdepth() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float

Return the LJ well depth of the atom type

C++: core::chemical::MMAtomType::lj_wdepth() const –> double

name(self: pyrosetta.rosetta.core.chemical.MMAtomType) → str

Return the name of the MMAtomType

C++: core::chemical::MMAtomType::name() const –> const std::string &

set_parameter(self: pyrosetta.rosetta.core.chemical.MMAtomType, param: str, setting: float) → None

set LJ and LK solvation parameter for this atom type

C++: core::chemical::MMAtomType::set_parameter(const std::string &, const double) –> void

class pyrosetta.rosetta.core.chemical.MMAtomTypeSet

Bases: pybind11_object

A set of MMAtomTypes

This class contains a vector of pointers each of which points to an MMAtomType and the vector index is looked up by an atom_name string in a map.

assign(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, : pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → pyrosetta.rosetta.core.chemical.MMAtomTypeSet

C++: core::chemical::MMAtomTypeSet::operator=(const class core::chemical::MMAtomTypeSet &) –> class core::chemical::MMAtomTypeSet &

atom_type_index(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, atom_type_name: str) → int

Lookup the atom_type by the atom_type_name string

C++: core::chemical::MMAtomTypeSet::atom_type_index(const std::string &) const –> int

contains_atom_type(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, atom_type_name: str) → bool

Check if there is an atom_type associated with an atom_type_name string

C++: core::chemical::MMAtomTypeSet::contains_atom_type(const std::string &) const –> bool

n_atomtypes(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → int

Number of MM atom types in the set

C++: core::chemical::MMAtomTypeSet::n_atomtypes() const –> unsigned long

name(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → str

What the ChemicalManager knows this as, if relevant

C++: core::chemical::MMAtomTypeSet::name() const –> const std::string &

print_all_types(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → None

Print all of the names of all of the MMAtomTypes in the set. Usefull for debuging.

C++: core::chemical::MMAtomTypeSet::print_all_types() –> void

read_file(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, filename: str) → None

Load the MMAtomTypeSet from a file

C++: core::chemical::MMAtomTypeSet::read_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.Metapatch

Bases: pybind11_object

A class patching basic ResidueType to create variant types, containing multiple PatchCase

applies_to(self: pyrosetta.rosetta.core.chemical.Metapatch, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → bool

can I operate on this residue type?

C++: core::chemical::Metapatch::applies_to(const class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.Metapatch, : pyrosetta.rosetta.core.chemical.Metapatch) → pyrosetta.rosetta.core.chemical.Metapatch

C++: core::chemical::Metapatch::operator=(const class core::chemical::Metapatch &) –> class core::chemical::Metapatch &

atoms(self: pyrosetta.rosetta.core.chemical.Metapatch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::Metapatch::atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_one_patch(self: pyrosetta.rosetta.core.chemical.Metapatch, atom_name: str) → core::chemical::Patch

C++: core::chemical::Metapatch::get_one_patch(const std::string &) const –> class std::shared_ptr<const class core::chemical::Patch>

meets_requirements(self: pyrosetta.rosetta.core.chemical.Metapatch, r: pyrosetta.rosetta.core.chemical.ResidueType, i: int) → bool

C++: core::chemical::Metapatch::meets_requirements(const class core::chemical::ResidueType &, unsigned long) const –> bool

name(self: pyrosetta.rosetta.core.chemical.Metapatch) → str

unique name of this patch, eg Nter-simple, Cter-full, Phospho, … ?

C++: core::chemical::Metapatch::name() const –> const std::string &

read_file(self: pyrosetta.rosetta.core.chemical.Metapatch, filename: str) → None

constructor from file

C++: core::chemical::Metapatch::read_file(const std::string &) –> void

types(self: pyrosetta.rosetta.core.chemical.Metapatch) → pyrosetta.rosetta.utility.vector1_std_string

the variant types created by applying this patch

C++: core::chemical::Metapatch::types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

class pyrosetta.rosetta.core.chemical.MutableChiRecord

Bases: pybind11_object

A class containing bundled info about chis

add_chi_rotamer(self: pyrosetta.rosetta.core.chemical.MutableChiRecord, mean: float, sdev: float) → None

C++: core::chemical::MutableChiRecord::add_chi_rotamer(const double, const double) –> void

chi_atoms(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → pyrosetta.rosetta.utility.vector1_void_*

C++: core::chemical::MutableChiRecord::chi_atoms() const –> const class utility::vector1<void *, class std::allocator<void *> > &

chi_rotamers(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → pyrosetta.rosetta.utility.vector1_std_pair_double_double_t

C++: core::chemical::MutableChiRecord::chi_rotamers() const –> const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &

clear_chi_rotamers(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → None

C++: core::chemical::MutableChiRecord::clear_chi_rotamers() –> void

is_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → bool

C++: core::chemical::MutableChiRecord::is_proton_chi() const –> bool

proton_chi_extra_samples(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::MutableChiRecord::proton_chi_extra_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

proton_chi_samples(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) → pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::MutableChiRecord::proton_chi_samples() const –> const class utility::vector1<double, class std::allocator<double> > &

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.MutableChiRecord, old_to_new: pyrosetta.rosetta.std.map_void_ * _void_ * _std_less_void__star__t_std_allocator_std_pair_void__star_const_void__star__t) → None

Update the internal VDs based on the provide mapping

C++: core::chemical::MutableChiRecord::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> void

set_chi_rotamers(self: pyrosetta.rosetta.core.chemical.MutableChiRecord, rots: pyrosetta.rosetta.utility.vector1_std_pair_double_double_t) → None

C++: core::chemical::MutableChiRecord::set_chi_rotamers(const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &) –> void

set_proton_chi(*args, **kwargs)

Overloaded function.

  1. set_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableChiRecord) -> None

  2. set_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableChiRecord, setting: bool) -> None

C++: core::chemical::MutableChiRecord::set_proton_chi(bool) –> void

  1. set_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableChiRecord, dihedral_samples: pyrosetta.rosetta.utility.vector1_double, extra_samples: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::chemical::MutableChiRecord::set_proton_chi(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.core.chemical.MutableICoorRecord

Bases: pybind11_object

A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType

This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor.

In atom tree, each atom is defined by its internal coordinates, which include a bond distance, a bond angle and a torsion angle. Of course, all these internal coordinates are only meaningful in the context of three reference (stub) atoms. MutableICoorRecord information is stored in the residue param files and some terms are defined as following: - bond distance d_ is that between the atom to be built (child) and stub_atom1 (parent) - bond angle theta_ is that defined by child-parent-stub2(angle) - torsion angle phi_ is that defined by child-parent-stub2-stub3(torsion)

assign(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, : pyrosetta.rosetta.core.chemical.MutableICoorRecord) → pyrosetta.rosetta.core.chemical.MutableICoorRecord

C++: core::chemical::MutableICoorRecord::operator=(const class core::chemical::MutableICoorRecord &) –> class core::chemical::MutableICoorRecord &

build(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, rsd_type: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.numeric.xyzVector_double_t

Build the location of the built atom, given the other atoms in the residue type.

C++: core::chemical::MutableICoorRecord::build(const class core::chemical::MutableResidueType &) const –> class numeric::xyzVector<double>

static build_xyz(stub: str, restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.numeric.xyzVector_double_t

Given a stub designation (atom name, UPPER/LOWER/CONN, etc.) find the coordinate from the MutableResidueType

C++: core::chemical::MutableICoorRecord::build_xyz(const std::string &, const class core::chemical::MutableResidueType &) –> class numeric::xyzVector<double>

buildable(*args, **kwargs)

Overloaded function.

  1. buildable(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, rsd_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> bool

  2. buildable(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, rsd_type: pyrosetta.rosetta.core.chemical.MutableResidueType, verbose: bool) -> bool

Can valid coordinates be built for this MutableICoorRecord, given the residue type?

C++: core::chemical::MutableICoorRecord::buildable(const class core::chemical::MutableResidueType &, bool) const –> bool

d(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → float

C++: core::chemical::MutableICoorRecord::d() const –> double

phi(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → float

accessor to stub_atom1 ICoorAtomID

C++: core::chemical::MutableICoorRecord::phi() const –> double

show(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::MutableICoorRecord::show(std::ostream &) const –> void

stub_atom(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, atm: int) → str

accessor to stub_atom ICoorAtomID

C++: core::chemical::MutableICoorRecord::stub_atom(const int) const –> const std::string &

stub_atom1(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → str

C++: core::chemical::MutableICoorRecord::stub_atom1() const –> const std::string &

stub_atom2(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → str

C++: core::chemical::MutableICoorRecord::stub_atom2() const –> const std::string &

stub_atom3(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → str

C++: core::chemical::MutableICoorRecord::stub_atom3() const –> const std::string &

stub_type(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, atm: int) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

accessor to stub_type ICoorAtomID

C++: core::chemical::MutableICoorRecord::stub_type(const int) const –> enum core::chemical::ICoordAtomIDType

stub_type1(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

C++: core::chemical::MutableICoorRecord::stub_type1() const –> enum core::chemical::ICoordAtomIDType

stub_type2(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

C++: core::chemical::MutableICoorRecord::stub_type2() const –> enum core::chemical::ICoordAtomIDType

stub_type3(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

C++: core::chemical::MutableICoorRecord::stub_type3() const –> enum core::chemical::ICoordAtomIDType

theta(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord) → float

C++: core::chemical::MutableICoorRecord::theta() const –> double

xyz(self: pyrosetta.rosetta.core.chemical.MutableICoorRecord, stubno: int, restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.numeric.xyzVector_double_t

Given a the stub designation (1/2/3) find the coordinate from the MutableResidueType

C++: core::chemical::MutableICoorRecord::xyz(unsigned long, const class core::chemical::MutableResidueType &) const –> class numeric::xyzVector<double>

class pyrosetta.rosetta.core.chemical.MutableResidueConnection

Bases: pybind11_object

A simple class marking atoms at inter-residue connections.

Each residue type specifies some number of positions at which it is expecting to form a chemical bond with another residue. Think of them as ports: they are parts of the residue where there are chemical bonds beyond the intra-residue chemical bonds are expected – places where they can be chemically linked to the outside world. The MutableResidueConnection class stores the information for available connections for the MutableResidueType object.

assign(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection, : pyrosetta.rosetta.core.chemical.MutableResidueConnection) → pyrosetta.rosetta.core.chemical.MutableResidueConnection

C++: core::chemical::MutableResidueConnection::operator=(const class core::chemical::MutableResidueConnection &) –> class core::chemical::MutableResidueConnection &

icoor(*args, **kwargs)

Overloaded function.

  1. icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection) -> pyrosetta.rosetta.core.chemical.MutableICoorRecord

get atom’s AtomICoor

C++: core::chemical::MutableResidueConnection::icoor() const –> const class core::chemical::MutableICoorRecord &

  1. icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection, ic: pyrosetta.rosetta.core.chemical.MutableICoorRecord) -> None

set atom’s AtomICoor

C++: core::chemical::MutableResidueConnection::icoor(const class core::chemical::MutableICoorRecord &) –> void

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection, old_to_new: pyrosetta.rosetta.std.map_void_ * _void_ * _std_less_void__star__t_std_allocator_std_pair_void__star_const_void__star__t) → None

Update the internal VDs based on the provide mapping

C++: core::chemical::MutableResidueConnection::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> void

vertex(*args, **kwargs)

Overloaded function.

  1. vertex(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection) -> capsule

get the vetex associated with this residue connection

C++: core::chemical::MutableResidueConnection::vertex() const –> void *

  1. vertex(self: pyrosetta.rosetta.core.chemical.MutableResidueConnection, vertex: capsule) -> None

set the vertex of this residue connection

C++: core::chemical::MutableResidueConnection::vertex(void *const) –> void

class pyrosetta.rosetta.core.chemical.MutableResidueType

Bases: ResidueTypeBase

A class for defining a type of residue, modifiable version

This class contains the “chemical” information for residues. A MutableResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. MutableResidueTypes are normally generated through .params files, which are read from the database chemical/residue_types. However, there are several other ways of generating this class, and the MutableResidueTypes can even be modified during the run (hence their name).

The MutableResidueType differs from a plain ResidueType in that it’s constructed to be modifiable. It’s also not intented to be used itself (aside from ResidueType modification). Instead, the typical usage is to convert a MutableResidueType into a plain ResidueType.

Another MutableResidueType/ResidueType distinction is that in a MutableResidueType the atom information is encoded in a molecular graph which should make it easier to add/remove/modify atoms. These atoms are referred to primarily by their “vertex desciptor” in the graph, which should be invariant to insertion/deletion/etc. While MutableResidueType does has a minimal sense of atom indexing, this is not the primary way to identify atoms, and will not be robust to addition/deletion of atoms.

To actually use a MutableResidueType for a simulation, you need to create a plain ResidueType from it. At this point all of the derived data will be calculated and converted to a more efficient struct-of-arrays format.

aa(*args, **kwargs)

Overloaded function.

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const enum core::chemical::AA &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const std::string &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be “aa_unk”.

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

C++: core::chemical::ResidueTypeBase::aa() const –> const enum core::chemical::AA &

actcoord_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.utility.vector1_void_*

get descriptors for atoms used to define actcoord

C++: core::chemical::MutableResidueType::actcoord_atoms() const –> class utility::vector1<void *, class std::allocator<void *> >

add_actcoord_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: str) → None

add an atom to the list for calculating actcoord center

C++: core::chemical::MutableResidueType::add_actcoord_atom(const std::string &) –> void

add_adduct(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: pyrosetta.rosetta.core.chemical.Adduct) → None

C++: core::chemical::ResidueTypeBase::add_adduct(class core::chemical::Adduct &) –> void

add_atom(*args, **kwargs)

Overloaded function.

  1. add_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str, atom_type_name: str, mm_atom_type_name: str, charge: float) -> capsule

add an atom into this residue

Will return the vertex descriptor of the added atom.

C++: core::chemical::MutableResidueType::add_atom(const std::string &, const std::string &, const std::string &, const double) –> void *

  1. add_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> capsule

  2. add_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) -> capsule

add an atom into this residue, with just the name.

Will return the vertex descriptor of the added atom.

C++: core::chemical::MutableResidueType::add_atom(const std::string &) –> void *

  1. add_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: pyrosetta.rosetta.core.chemical.Atom, icoor: core::chemical::MutableICoorRecord) -> capsule

C++: core::chemical::MutableResidueType::add_atom(const class core::chemical::Atom &, const class core::chemical::MutableICoorRecord &) –> void *

add_atom_alias(self: pyrosetta.rosetta.core.chemical.MutableResidueType, rosetta_atom: str, alias: str) → None

Add an alias name for an atom.

C++: core::chemical::MutableResidueType::add_atom_alias(const std::string &, const std::string &) –> void

add_bond(*args, **kwargs)

Overloaded function.

  1. add_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, atom_name2: str) -> None

  2. add_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, atom_name2: str, bondLabel: pyrosetta.rosetta.core.chemical.BondName) -> None

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

C++: core::chemical::MutableResidueType::add_bond(const std::string &, const std::string &, enum core::chemical::BondName) –> void

  1. add_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: capsule, atom2: capsule) -> None

  2. add_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: capsule, atom2: capsule, bondLabel: pyrosetta.rosetta.core.chemical.BondName) -> None

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

C++: core::chemical::MutableResidueType::add_bond(void *, void *, enum core::chemical::BondName) –> void

add_canonical_atom_alias(self: pyrosetta.rosetta.core.chemical.MutableResidueType, rosetta_atom: str, alias: str) → None

store canonical to alias mapping

C++: core::chemical::MutableResidueType::add_canonical_atom_alias(const std::string &, const std::string &) –> void

add_chi(*args, **kwargs)

Overloaded function.

  1. add_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int, atom1: capsule, atom2: capsule, atom3: capsule, atom4: capsule) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::MutableResidueType::add_chi(const unsigned long, void *, void *, void *, void *) –> void

  1. add_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: capsule, atom2: capsule, atom3: capsule, atom4: capsule) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::MutableResidueType::add_chi(void *, void *, void *, void *) –> void

  1. add_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::MutableResidueType::add_chi(const unsigned long, const std::string &, const std::string &, const std::string &, const std::string &) –> void

  1. add_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) -> None

Add a chi (side-chain) angle defined by four atoms to the end of the list of chis.

C++: core::chemical::MutableResidueType::add_chi(const std::string &, const std::string &, const std::string &, const std::string &) –> void

add_chi_rotamer(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int, mean: float, sdev: float) → None

Add a rotamer bin for a given chi.

C++: core::chemical::MutableResidueType::add_chi_rotamer(const unsigned long, const double, const double) –> void

add_chi_rotamer_to_last_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, mean: float, sdev: float) → None

Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this MutableResidueType.

C++: core::chemical::MutableResidueType::add_chi_rotamer_to_last_chi(const double, const double) –> void

add_cut_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, atom_name2: str) → None

add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond

C++: core::chemical::MutableResidueType::add_cut_bond(const std::string &, const std::string &) –> void

add_metalbinding_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) → None
Add an atom to the list of atoms that can potentially form a bond to a metal ion.

Note that the atom must exist in the residue type (the function checks for this at runtime).

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::MutableResidueType::add_metalbinding_atom(const std::string &) –> void

add_metapatch_connect(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: str) → None

C++: core::chemical::MutableResidueType::add_metapatch_connect(const std::string &) –> void

add_nu(self: pyrosetta.rosetta.core.chemical.MutableResidueType, nu_index: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) → None

Add a nu (internal cyclic) angle defined by four atoms.

C++: core::chemical::MutableResidueType::add_nu(const unsigned long, const std::string &, const std::string &, const std::string &, const std::string &) –> void

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: float) → None

Add a numeric property.

C++: core::chemical::ResidueTypeBase::add_numeric_property(const std::string &, double) –> void

add_orbital(self: pyrosetta.rosetta.core.chemical.MutableResidueType, orbital_name: str, orbital_type_name: str) → None

add an orbital onto a residue based upon atom

C++: core::chemical::MutableResidueType::add_orbital(std::string &, std::string &) –> void

add_orbital_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, orbital_name: str) → None

add an orbital bond between an atom and an orbital.

NOTE!!!!! This is indexed based upon atoms, not orbitals. That means that in your params file you must have the atom as the first and orbital as the second.

C++: core::chemical::MutableResidueType::add_orbital_bond(const std::string &, const std::string &) –> void

add_property(*args, **kwargs)

Overloaded function.

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Add a property to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_property(const std::string &) –> void

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Add a property to this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::add_property(const enum core::chemical::ResidueProperty) –> void

add_residue_connection(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) → int

add a non-polymeric ResidueConnection

For polymeric connections, see set_lower_connect() and set_upper_connect() Doesn’t set the ideal geometry – maybe it should?

C++: core::chemical::MutableResidueType::add_residue_connection(const std::string &) –> unsigned long

add_ring(*args, **kwargs)

Overloaded function.

  1. add_ring(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int, ring_atoms: pyrosetta.rosetta.utility.vector1_std_string) -> None

  2. add_ring(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int, ring_atoms: pyrosetta.rosetta.utility.vector1_std_string, saturation_type: pyrosetta.rosetta.core.chemical.rings.RingSaturationType) -> None

Add a ring definition.

C++: core::chemical::MutableResidueType::add_ring(const unsigned long, const class utility::vector1<std::string, class std::allocator<std::string > > &, const enum core::chemical::rings::RingSaturationType) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: str) → None

Add a string property.

C++: core::chemical::ResidueTypeBase::add_string_property(const std::string &, std::string) –> void

add_variant_type(*args, **kwargs)

Overloaded function.

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Add a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_variant_type(const enum core::chemical::VariantType) –> void

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Add a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::add_variant_type(const std::string &) –> void

all_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.utility.vector1_void_*
Convenience function for iterating over all the atoms

e.g. for ( VA atm: restype->all_atoms() ) {

C++: core::chemical::MutableResidueType::all_atoms() const –> const class utility::vector1<void *, class std::allocator<void *> > &

assign(self: pyrosetta.rosetta.core.chemical.MutableResidueType, src: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.core.chemical.MutableResidueType

Copies <src> into the MutableResidueType

C++: core::chemical::MutableResidueType::operator=(const class core::chemical::MutableResidueType &) –> class core::chemical::MutableResidueType &

assign_internal_coordinates(*args, **kwargs)

Overloaded function.

  1. assign_internal_coordinates(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

Assign internal coordinates from the set ideal xyz coordinates.

Note that it currently does not obey mainchain designations or cut bonds.

C++: core::chemical::MutableResidueType::assign_internal_coordinates() –> void

  1. assign_internal_coordinates(self: pyrosetta.rosetta.core.chemical.MutableResidueType, new_root: capsule) -> None

Function to assign internal coordinates from bonding patterns

Note that it currently does not work well with polymers.

C++: core::chemical::MutableResidueType::assign_internal_coordinates(void *) –> void

assign_neighbor_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Figure out what the “center” atom of the residue is from current coordinates

Assumes that all the ideal_xyz values have been set

C++: core::chemical::MutableResidueType::assign_neighbor_atom() –> void

atom(*args, **kwargs)

Overloaded function.

  1. atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_vd: capsule) -> pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::MutableResidueType::atom(void *const) –> class core::chemical::Atom &

  1. atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) -> pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::MutableResidueType::atom(const std::string &) –> class core::chemical::Atom &

atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::atom_alias(const std::string &) const –> const std::string &

atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

atom_base(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule) → capsule
The atom base is the distance atom the atom is bonded to.

If the specified atom doesn’t have valid ICOOR record yet, this function will return a null vertex

C++: core::chemical::MutableResidueType::atom_base(void *const) const –> void *

atom_index(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vd: capsule) → int

Get an integer value for the atom (the index for all_atoms())

This is provided purely for a convenience in matching up external vector entries Use all_atoms() directly for normal iteration over atoms Will return 0 if the vd isn’t in the MutableResidueType.

C++: core::chemical::MutableResidueType::atom_index(void *const &) const –> unsigned long

atom_iterators(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → Tuple[std::_List_iterator<void*>, std::_List_iterator<void*>]

C++: core::chemical::MutableResidueType::atom_iterators() const –> struct std::pair<struct std::_List_iterator<void *>, struct std::_List_iterator<void *> >

atom_name(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vd: capsule) → str
get atom name by vertex descriptor

IMPORTANT NOTE: Atoms don’t necessarily have names!

C++: core::chemical::MutableResidueType::atom_name(void *const) const –> const std::string &

atom_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vd: capsule) → pyrosetta.rosetta.core.chemical.AtomType

Get the chemical atom_type for this atom

C++: core::chemical::MutableResidueType::atom_type(void *const) const –> const class core::chemical::AtomType &

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by reference the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set() const –> const class core::chemical::AtomTypeSet &

atom_type_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by const pointer the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set_ptr() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

atom_vertex(self: pyrosetta.rosetta.core.chemical.MutableResidueType, name: str) → capsule

get the vertex descriptor from the name of the atom.

C++: core::chemical::MutableResidueType::atom_vertex(const std::string &) const –> void *

atoms_are_bonded(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: str, atom2: str) → bool

C++: core::chemical::MutableResidueType::atoms_are_bonded(const std::string &, const std::string &) const –> bool

autodetermine_chi_bonds(*args, **kwargs)

Overloaded function.

  1. autodetermine_chi_bonds(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. autodetermine_chi_bonds(self: pyrosetta.rosetta.core.chemical.MutableResidueType, max_proton_chi_samples: int) -> None

Regenerate the rotatable chi bonds from the internal graph structure.

If the number of proton chi samples would exceed max_proton_chi_samples, don’t add extra sampling to proton chis. As a special case, if this is zero don’t add any proton chi sampling at all.

Requires that Icoor and atom base records are up-to-date, and that ring bonds have been annotated.

C++: core::chemical::MutableResidueType::autodetermine_chi_bonds(unsigned long) –> void

backbone_aa(*args, **kwargs)

Overloaded function.

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

AA to use for backbone scoring

C++: core::chemical::ResidueTypeBase::backbone_aa(const std::string &) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

Set AA to use for backbone scoring directly (without string conversion).

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::backbone_aa(const enum core::chemical::AA) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

C++: core::chemical::ResidueTypeBase::backbone_aa() const –> const enum core::chemical::AA &

base_analogue(*args, **kwargs)

Overloaded function.

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for base-specific generalization (can be more

forgiving than na_analogue for new NA backbones)

C++: core::chemical::ResidueTypeBase::base_analogue(const std::string &) –> void

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for base features

C++: core::chemical::ResidueTypeBase::base_analogue() const –> const enum core::chemical::AA &

base_name(*args, **kwargs)

Overloaded function.

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

Get this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name() const –> const std::string &

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, base_name_in: str) -> None

Set this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name(const std::string &) –> void

bond(*args, **kwargs)

Overloaded function.

  1. bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vd1: capsule, vd2: capsule) -> pyrosetta.rosetta.core.chemical.Bond

C++: core::chemical::MutableResidueType::bond(void *, void *) –> class core::chemical::Bond &

  1. bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: str, atom2: str) -> pyrosetta.rosetta.core.chemical.Bond

C++: core::chemical::MutableResidueType::bond(const std::string &, const std::string &) –> class core::chemical::Bond &

bonded_heavyatoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) → pyrosetta.rosetta.utility.vector1_void_*

Get the atoms bonded to the specified atom, if they’re annotated as heavyatoms.

This is recalculated each time the function is called.

C++: core::chemical::MutableResidueType::bonded_heavyatoms(void *const &) const –> class utility::vector1<void *, class std::allocator<void *> >

bonded_hydrogens(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) → pyrosetta.rosetta.utility.vector1_void_*

Get the atoms bonded to the specified atom, if they’re annotated as hydrogens.

This is recalculated each time the function is called.

C++: core::chemical::MutableResidueType::bonded_hydrogens(void *const &) const –> class utility::vector1<void *, class std::allocator<void *> >

bonded_neighbors(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) → pyrosetta.rosetta.utility.vector1_void_*

Get the atoms bonded to the specified atom.

This is recalculated each time the function is called.

C++: core::chemical::MutableResidueType::bonded_neighbors(void *const &) const –> class utility::vector1<void *, class std::allocator<void *> >

canonical_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::canonical_atom_alias(const std::string &) const –> const std::string &

canonical_atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::canonical_atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

change_bond_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name1: str, atom_name2: str, new_bond_label: pyrosetta.rosetta.core.chemical.BondName) → None

Change the bond type of the given bond from one type to another.

Acts like a bond deletion + bond add, rather than a change.

C++: core::chemical::MutableResidueType::change_bond_type(const std::string &, const std::string &, const enum core::chemical::BondName) –> void

chi_atom_vds(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_void_*

VDs of the atoms which are used to define a given chi angle (chino)

C++: core::chemical::MutableResidueType::chi_atom_vds(const unsigned long) const –> const class utility::vector1<void *, class std::allocator<void *> > &

chi_rotamers(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_std_pair_double_double_t

all rotamers bins (mean, std) for a given chi angle

C++: core::chemical::MutableResidueType::chi_rotamers(const unsigned long) const –> const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &

chi_valid(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → bool

Will return if the chi is currently valid.

C++: core::chemical::MutableResidueType::chi_valid(const unsigned long) const –> bool

clear_chi_rotamers(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chi_no: int) → None

Delete all of the chi rotamer bins from the specified chi for this MutableResidueType.

C++: core::chemical::MutableResidueType::clear_chi_rotamers(const unsigned long) –> void

clear_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

C++: core::chemical::MutableResidueType::clear_icoor() –> void

clear_orbitals(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

clear orbitals

C++: core::chemical::MutableResidueType::clear_orbitals() –> void

clone(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.core.chemical.MutableResidueType

make a copy

C++: core::chemical::MutableResidueType::clone() const –> class std::shared_ptr<class core::chemical::MutableResidueType>

custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

Get a list of custom VariantType strings for this ResidueTypeBase (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::custom_variant_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

defined_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_Adduct

get the adducts defined for this residue

C++: core::chemical::ResidueTypeBase::defined_adducts() const –> const class utility::vector1<class core::chemical::Adduct, class std::allocator<class core::chemical::Adduct> > &

defines_custom_rama_prepro_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → bool
Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_

defined for this ResidueTypeBase (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

C++: core::chemical::ResidueTypeBase::defines_custom_rama_prepro_map(const bool) const –> bool

delete_actcoord_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) → None
Remove an atom from the list of act coord atoms

(used in patching when it kills the valence that is thus used)

Andrew Watkins (amw579.edu)

C++: core::chemical::MutableResidueType::delete_actcoord_atom(const std::string &) –> void

delete_atom(*args, **kwargs)

Overloaded function.

  1. delete_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, name: str) -> None

Remove the atom from the ResidueType

C++: core::chemical::MutableResidueType::delete_atom(const std::string &) –> void

  1. delete_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) -> None

Remove the atom from the ResidueType

C++: core::chemical::MutableResidueType::delete_atom(void *) –> void

delete_atom_alias(*args, **kwargs)

Overloaded function.

  1. delete_atom_alias(self: pyrosetta.rosetta.core.chemical.MutableResidueType, alias: str) -> None

  2. delete_atom_alias(self: pyrosetta.rosetta.core.chemical.MutableResidueType, alias: str, error: bool) -> None

Remove a given alias name for an atom.

If error is true, raise error if the alias can’t be found

C++: core::chemical::MutableResidueType::delete_atom_alias(const std::string &, bool) –> void

delete_bond(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom1: capsule, atom2: capsule) → None

Delete a bond between the two atoms.

Note that this might leave dangling atoms.

C++: core::chemical::MutableResidueType::delete_bond(void *, void *) –> void

delete_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → None

Deletes a given chi, potentially renumbering the remaining chis

C++: core::chemical::MutableResidueType::delete_chi(const unsigned long) –> void

delete_child_proton(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: str) → None

C++: core::chemical::MutableResidueType::delete_child_proton(const std::string &) –> void

delete_metalbinding_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) → None
Remove an atom from the list of atoms that can potentially form a bond to a metal ion

(used in patching when it kills the valence that is thus used)

Andrew Watkins (amw579.edu)

C++: core::chemical::MutableResidueType::delete_metalbinding_atom(const std::string &) –> void

delete_nu(self: pyrosetta.rosetta.core.chemical.MutableResidueType, nu_index: int) → None

Deletes a given nu, potentially renumbering the remaining nus

C++: core::chemical::MutableResidueType::delete_nu(const unsigned long) –> void

delete_property(*args, **kwargs)

Overloaded function.

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Delete a property of this ResidueType.

C++: core::chemical::ResidueTypeBase::delete_property(const std::string &) –> void

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Delete a property of this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::delete_property(const enum core::chemical::ResidueProperty) –> void

delete_residue_connection(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule) → None

Remove all connections (both polymeric and otherwise) for an atom

C++: core::chemical::MutableResidueType::delete_residue_connection(void *) –> void

delete_ring(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int) → None

Deletes a given ring, potentially renumbering the remaining ring

C++: core::chemical::MutableResidueType::delete_ring(const unsigned long) –> void

delete_terminal_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

delete terminal chi angle

C++: core::chemical::MutableResidueType::delete_terminal_chi() –> void

dump_vd_info(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

C++: core::chemical::MutableResidueType::dump_vd_info() const –> void

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by reference the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set() const –> const class core::chemical::ElementSet &

element_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by const pointer the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set_ptr() const –> class std::shared_ptr<const class core::chemical::ElementSet>

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Turn on the ability to create VariantTypes “on-the-fly”.

C++: core::chemical::ResidueTypeBase::enable_custom_variant_types() –> void

fill_ideal_xyz_from_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Assign ideal_xyz coordinates from icoor records.

C++: core::chemical::MutableResidueType::fill_ideal_xyz_from_icoor() –> void

force_nbr_atom_orient(*args, **kwargs)

Overloaded function.

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient() const –> bool

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, force_orient: bool) -> None

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient(bool) –> void

gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::gasteiger::GasteigerAtomTypeSet

C++: core::chemical::ResidueTypeBase::gasteiger_atom_typeset() const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

get_atom_name_to_vd_map(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.std.map_std_string_void_*_std_allocator_std_pair_const_std_string_void__star__t
Get access to the atom_name-to-vd map.

Provided only for MutableResidueType->ResidueType conversion

C++: core::chemical::MutableResidueType::get_atom_name_to_vd_map() const –> const class std::map<std::string, void *, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, void *> > > &

get_base_type_cop(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

Get a pointer to this ResidueType’s base ResidueType.

Returns NULL if base_type_cop_ is NULL. (Difference from ResidueType behavior!)

C++: core::chemical::MutableResidueType::get_base_type_cop() const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → str

Gets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::get_disulfide_atom_name() const –> const std::string &

get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::ResidueTypeBase::get_metal_binding_atoms() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

get_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → float

Get a numeric property, if it exists.

C++: core::chemical::ResidueTypeBase::get_numeric_property(const std::string &) const –> double

get_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(const bool) const –> const std::string &

get_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(const bool) const –> const std::string &

get_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → str

Get a string property, if it exists.

C++: core::chemical::ResidueTypeBase::get_string_property(const std::string &) const –> std::string

has(*args, **kwargs)

Overloaded function.

  1. has(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) -> bool

is this atom present in this residue?

C++: core::chemical::MutableResidueType::has(const std::string &) const –> bool

  1. has(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vd: capsule) -> bool

is this vertex descriptor present in this residue?

C++: core::chemical::MutableResidueType::has(void *const) const –> bool

has_orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) → bool

is this orbital present in this residue?

C++: core::chemical::ResidueTypeBase::has_orbital(const std::string &) const –> bool

has_orbital_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this residue type define orbital types?

C++: core::chemical::ResidueTypeBase::has_orbital_types() const –> bool

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> bool

Generic property access.

C++: core::chemical::ResidueTypeBase::has_property(const std::string &) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Generic property access, by ResidueProperty.

C++: core::chemical::ResidueTypeBase::has_property(const enum core::chemical::ResidueProperty) const –> bool

has_variant_type(*args, **kwargs)

Overloaded function.

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Generic variant access.

C++: core::chemical::ResidueTypeBase::has_variant_type(const enum core::chemical::VariantType) const –> bool

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> bool

Generic variant access by string.

C++: core::chemical::ResidueTypeBase::has_variant_type(const std::string &) const –> bool

icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule) → core::chemical::MutableICoorRecord

MutableICoorRecord of an atom

C++: core::chemical::MutableResidueType::icoor(void *const) const –> class std::shared_ptr<const class core::chemical::MutableICoorRecord>

interchangeability_group(*args, **kwargs)

Overloaded function.

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our interchangeability-group id. Used to

determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag.

C++: core::chemical::ResidueTypeBase::interchangeability_group() const –> std::string

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: str) -> None

set our interchangeability-group id

C++: core::chemical::ResidueTypeBase::interchangeability_group(const std::string &) –> void

is_DNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is DNA?

C++: core::chemical::ResidueTypeBase::is_DNA() const –> bool

is_RNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is RNA?

C++: core::chemical::ResidueTypeBase::is_RNA() const –> bool

is_achiral_backbone(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an achiral backbone?

C++: core::chemical::ResidueTypeBase::is_achiral_backbone() const –> bool

is_achiral_sidechain(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this have an achiral sidechain?

Includes gly and aib, and most (but not all) peptoids.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_achiral_sidechain() const –> bool

is_backbone_heavyatom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) → bool

C++: core::chemical::MutableResidueType::is_backbone_heavyatom(void *) const –> bool

is_base_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Is this ResidueType a base type?

C++: core::chemical::MutableResidueType::is_base_type() const –> bool

is_d_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-amino acid?

C++: core::chemical::ResidueTypeBase::is_d_aa() const –> bool

is_d_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-RNA?

C++: core::chemical::ResidueTypeBase::is_d_rna() const –> bool

is_l_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-amino acid?

C++: core::chemical::ResidueTypeBase::is_l_aa() const –> bool

is_l_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-RNA?

C++: core::chemical::ResidueTypeBase::is_l_rna() const –> bool

is_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Get whether this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_metapatched() const –> bool

is_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is peptoid?

C++: core::chemical::ResidueTypeBase::is_peptoid() const –> bool

is_polymer(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is polymer?

C++: core::chemical::ResidueTypeBase::is_polymer() const –> bool

is_protein(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is protein?

C++: core::chemical::ResidueTypeBase::is_protein() const –> bool

is_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → bool

number of proton chis

C++: core::chemical::MutableResidueType::is_proton_chi(const unsigned long) const –> bool

is_r_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “R” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_r_peptoid() const –> bool

is_s_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “S” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_s_peptoid() const –> bool

low_ring_conformers(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int) → pyrosetta.rosetta.utility.vector1_std_string

Low-energy ring conformers for the given ring

C++: core::chemical::MutableResidueType::low_ring_conformers(const unsigned long) const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

lower_connect(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → core::chemical::MutableResidueConnection

C++: core::chemical::MutableResidueType::lower_connect() const –> const class core::chemical::MutableResidueConnection &

lower_connect_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → capsule

index number of the atom which connects to the lower connection

C++: core::chemical::MutableResidueType::lower_connect_atom() const –> void *

lower_connect_id(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

C++: core::chemical::MutableResidueType::lower_connect_id() const –> unsigned long

lowest_ring_conformer(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int) → str

Lowest-energy ring conformer for the given ring

C++: core::chemical::MutableResidueType::lowest_ring_conformer(const unsigned long) const –> const std::string &

mainchain_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.utility.vector1_void_*

indices of all mainchain atoms

C++: core::chemical::MutableResidueType::mainchain_atoms() const –> const class utility::vector1<void *, class std::allocator<void *> > &

mainchain_potentials_match(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, other: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Do the rama_prepro mainchain torsion potentials of this residue match another?

C++: core::chemical::ResidueTypeBase::mainchain_potentials_match(const class core::chemical::ResidueTypeBase &) const –> bool

mm_atom_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::MMAtomTypeSet

C++: core::chemical::ResidueTypeBase::mm_atom_types_ptr() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.TypeSetMode

C++: core::chemical::ResidueTypeBase::mode() const –> enum core::chemical::TypeSetMode

n_nus(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

Return number of nu (internal ring) angles.

C++: core::chemical::MutableResidueType::n_nus() const –> unsigned long

n_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of orbitals

C++: core::chemical::ResidueTypeBase::n_orbitals() const –> unsigned long

n_polymeric_residue_connections(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

The number of polymeric residue connections.

C++: core::chemical::MutableResidueType::n_polymeric_residue_connections() const –> unsigned long

n_possible_residue_connections(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

number of ResidueConnections, counting polymeric residue connections

C++: core::chemical::MutableResidueType::n_possible_residue_connections() const –> unsigned long

n_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

number of proton chis

C++: core::chemical::MutableResidueType::n_proton_chi() const –> unsigned long

n_residue_connections_for_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atomid: capsule) → int
//

How many inter-residue chemical bonds does a particular atom form?

C++: core::chemical::MutableResidueType::n_residue_connections_for_atom(void *const) const –> unsigned long

n_rings(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

Return the number of rings in this residue.

C++: core::chemical::MutableResidueType::n_rings() const –> unsigned long

n_virtual_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and

can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::MutableResidueType::n_virtual_atoms() const –> unsigned long

na_analogue(*args, **kwargs)

Overloaded function.

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for fragment sampling and some scoring purposes

C++: core::chemical::ResidueTypeBase::na_analogue(const std::string &) –> void

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for fragment sampling/scoring.

C++: core::chemical::ResidueTypeBase::na_analogue() const –> const enum core::chemical::AA &

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our (unique) residue name

C++: core::chemical::ResidueTypeBase::name() const –> const std::string &

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our (unique) residue name

C++: core::chemical::ResidueTypeBase::name(const std::string &) –> void

name1(*args, **kwargs)

Overloaded function.

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 1letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name3 string.

C++: core::chemical::ResidueTypeBase::name1() const –> char

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, code: str) -> None

set our 1letter code

C++: core::chemical::ResidueTypeBase::name1(const char) –> void

name3(*args, **kwargs)

Overloaded function.

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 3letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The “name3” is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

C++: core::chemical::ResidueTypeBase::name3() const –> const std::string &

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our 3letter code

C++: core::chemical::ResidueTypeBase::name3(const std::string &) –> void

natoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int
number of atoms

Note: Don’t use this to iterate over atoms – use the vector returned by all_atoms() instead.

C++: core::chemical::MutableResidueType::natoms() const –> unsigned long

nbonds(*args, **kwargs)

Overloaded function.

  1. nbonds(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> int

number of bonds

C++: core::chemical::MutableResidueType::nbonds() const –> unsigned long

  1. nbonds(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule) -> int

number of bonds for given atom

C++: core::chemical::MutableResidueType::nbonds(void *) const –> unsigned long

nbr_atom(*args, **kwargs)

Overloaded function.

  1. nbr_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str) -> None

set nbr_atom used to define residue-level neighbors

C++: core::chemical::MutableResidueType::nbr_atom(const std::string &) –> void

  1. nbr_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, vertex: capsule) -> None

set nbr_atom used to define residue-level neighbors

C++: core::chemical::MutableResidueType::nbr_atom(void *) –> void

nbr_radius(*args, **kwargs)

Overloaded function.

  1. nbr_radius(self: pyrosetta.rosetta.core.chemical.MutableResidueType, radius: float) -> None

set nbr_radius_ used to define residue-level neighbors

C++: core::chemical::MutableResidueType::nbr_radius(const double) –> void

  1. nbr_radius(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> float

get nbr_radius_ used to define residue-level neighbors

C++: core::chemical::MutableResidueType::nbr_radius() const –> double

nbr_vertex(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → capsule

get VD used to define residue-level neighbors

C++: core::chemical::MutableResidueType::nbr_vertex() const –> void *

nchi(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

number of chi angles

C++: core::chemical::MutableResidueType::nchi() const –> unsigned long

net_formal_charge(*args, **kwargs)

Overloaded function.

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> int

Get the nominal net formal charge on this residue type.

This may not match the sum of the formal charges on the atoms

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge() const –> long

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, charge_in: int) -> None

Set the nominal net formal charge on this residue type.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge(long) –> void

nheavyatoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

number of heavy atoms

C++: core::chemical::MutableResidueType::nheavyatoms() const –> unsigned long

nu_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType, nu_index: int) → pyrosetta.rosetta.utility.vector1_void_*

C++: core::chemical::MutableResidueType::nu_atoms(const unsigned long) const –> const class utility::vector1<void *, class std::allocator<void *> > &

number_bonded_heavyatoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atomvd: capsule) → int

indicates how many heavyatom bonded neighbors an atom has, graph version

C++: core::chemical::MutableResidueType::number_bonded_heavyatoms(void *) const –> unsigned long

number_bonded_hydrogens(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atomvd: capsule) → int

indicates how many proton bonded neighbors an atom has

C++: core::chemical::MutableResidueType::number_bonded_hydrogens(void *) const –> unsigned long

orbital(*args, **kwargs)

Overloaded function.

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const unsigned long) const –> const class core::chemical::Orbital &

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const std::string &) const –> const class core::chemical::Orbital &

orbital_index(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → int

get orbital index by name

C++: core::chemical::ResidueTypeBase::orbital_index(const std::string &) const –> unsigned long

orbital_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) → core::chemical::orbitals::OrbitalType

C++: core::chemical::ResidueTypeBase::orbital_type(const unsigned long) const –> const class core::chemical::orbitals::OrbitalType &

orbital_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::orbitals::OrbitalTypeSet

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueTypeBase::orbital_types_ptr() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

placeholder_clone(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.core.chemical.MutableResidueType

make a copy

C++: core::chemical::MutableResidueType::placeholder_clone() const –> class std::shared_ptr<class core::chemical::MutableResidueType>

properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.ResidueProperties

Access the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::properties() const –> const class core::chemical::ResidueProperties &

proton_chi_extra_samples_for_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_double
The proton chi extra samples

Important - this takes the full chi numbering (not proton chi numbering)

C++: core::chemical::MutableResidueType::proton_chi_extra_samples_for_chi(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

proton_chi_samples_for_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_double
The proton chi samples

Important - this takes the full chi numbering (not proton chi numbering)

C++: core::chemical::MutableResidueType::proton_chi_samples_for_chi(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

redefine_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) → None

redefine a chi angle based on four atoms

C++: core::chemical::MutableResidueType::redefine_chi(const unsigned long, const std::string &, const std::string &, const std::string &, const std::string &) –> void

remap_pdb_atom_names(*args, **kwargs)

Overloaded function.

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, rename: bool) -> None

Turn on geometry-based atom renaming when loading this residue type from PDB files

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names(bool) –> void

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Are we using geometry-based atom renaming when loading this residue type from PDB

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names() const –> bool

remove_variant_type(*args, **kwargs)

Overloaded function.

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Remove a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const enum core::chemical::VariantType) –> void

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Remove a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const std::string &) –> void

rename_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule, name: str) → None

Rename the atom, updating the ResidueType-internal data mapping

C++: core::chemical::MutableResidueType::rename_atom(void *, const std::string &) –> void

report_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

C++: core::chemical::ResidueTypeBase::report_adducts() const –> void

reset_base_type_cop(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Reset the base type COP to be null. This implies that this ResidueTypeBase is a base type.

C++: core::chemical::MutableResidueType::reset_base_type_cop() –> void

reset_bond_distance_to_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: str, d: float) → None

Reset the bond distance to an atom whose internal coordinates have already been set.

C++: core::chemical::MutableResidueType::reset_bond_distance_to_atom(const std::string &, const double) –> void

reset_mainchain_torsion_potential_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set the names of the mainchain torsion potential maps to use to “”.

Also resets the mainchain torsion potential filename strings.

C++: core::chemical::ResidueTypeBase::reset_mainchain_torsion_potential_names() –> void

residue_connect_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, resconn_id: int) → capsule

C++: core::chemical::MutableResidueType::residue_connect_atom(const unsigned long) const –> void *

residue_connection(self: pyrosetta.rosetta.core.chemical.MutableResidueType, i: int) → core::chemical::MutableResidueConnection

Get a ResidueConection.

C++: core::chemical::MutableResidueType::residue_connection(const unsigned long) –> class core::chemical::MutableResidueConnection &

residue_connection_is_polymeric(self: pyrosetta.rosetta.core.chemical.MutableResidueType, resconn_id: int) → bool

C++: core::chemical::MutableResidueType::residue_connection_is_polymeric(const unsigned long) const –> bool

ring_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int) → pyrosetta.rosetta.utility.vector1_void_*

C++: core::chemical::MutableResidueType::ring_atoms(const unsigned long) const –> const class utility::vector1<void *, class std::allocator<void *> > &

ring_saturation_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int) → pyrosetta.rosetta.core.chemical.rings.RingSaturationType

Return the saturation level of this residue’s nth cycle.

C++: core::chemical::MutableResidueType::ring_saturation_type(const unsigned long) const –> enum core::chemical::rings::RingSaturationType

root_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → capsule

get root_atom used as the base of the icoor tree.

C++: core::chemical::MutableResidueType::root_atom() const –> void *

rotamer_library_specification(*args, **kwargs)

Overloaded function.

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, : core::chemical::rotamers::RotamerLibrarySpecification) -> None

C++: core::chemical::ResidueTypeBase::rotamer_library_specification(class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>) –> void

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> core::chemical::rotamers::RotamerLibrarySpecification

C++: core::chemical::ResidueTypeBase::rotamer_library_specification() const –> class std::shared_ptr<const class core::chemical::rotamers::RotamerLibrarySpecification>

rotamer_library_specification_nonconst(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::rotamers::RotamerLibrarySpecification

Nonconst access to the RotamerLibrarySpecification.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst() –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

set_adduct_flag(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: bool) → None

C++: core::chemical::ResidueTypeBase::set_adduct_flag(bool) –> void

set_atom_type(*args, **kwargs)

Overloaded function.

  1. set_atom_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, name: str, atom_type_name: str) -> None

set atom type

C++: core::chemical::MutableResidueType::set_atom_type(const std::string &, const std::string &) –> void

  1. set_atom_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule, atom_type_name: str) -> None

Set atom type, correctly updating internal state.

This method also sets/updates the atom’s element and the residue’s mass.

C++: core::chemical::MutableResidueType::set_atom_type(void *, const std::string &) –> void

set_backbone_heavyatom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, name: str) → None

set an atom as backbone heavy atom

When converted to a plain ResidueType, backbone atoms will be placed first. This is differenct from the mainchain atoms below, as the mainchain is a subset of the backbone

C++: core::chemical::MutableResidueType::set_backbone_heavyatom(const std::string &) –> void

set_base_type_cop(self: pyrosetta.rosetta.core.chemical.MutableResidueType, new_base_type: pyrosetta.rosetta.core.chemical.ResidueType) → None

Set the base type COP. This implies that this ResidueTypeBase is NOT a base type.

C++: core::chemical::MutableResidueType::set_base_type_cop(class std::shared_ptr<const class core::chemical::ResidueType>) –> void

set_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, n: str) → None

Sets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::set_disulfide_atom_name(const std::string &) –> void

set_gasteiger_atom_type(*args, **kwargs)

Overloaded function.

  1. set_gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom_name: str, gasteiger_atom_type_name: str) -> None

set gasteiger atom type

C++: core::chemical::MutableResidueType::set_gasteiger_atom_type(const std::string &, const std::string &) –> void

  1. set_gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: capsule, gasteiger_atom_type_name: str) -> None

set gasteiger atom type

C++: core::chemical::MutableResidueType::set_gasteiger_atom_type(void *, const std::string &) –> void

set_gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::gasteiger::GasteigerAtomTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>) –> void

set_icoor(*args, **kwargs)

Overloaded function.

  1. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str) -> None

  2. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str, update_xyz: bool) -> None

set MutableICoorRecord for an atom

phi and theta are in radians

C++: core::chemical::MutableResidueType::set_icoor(const std::string &, const double, const double, const double, const std::string &, const std::string &, const std::string &, const bool) –> void

  1. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: capsule, stub_atom2: capsule, stub_atom3: capsule) -> None

  2. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: capsule, stub_atom2: capsule, stub_atom3: capsule, update_xyz: bool) -> None

set MutableICoorRecord for an atom, vertex descriptor version

phi and theta are in radians

C++: core::chemical::MutableResidueType::set_icoor(void *const &, const double, const double, const double, void *const &, void *const &, void *const &, const bool) –> void

  1. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str) -> None

  2. set_icoor(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str, update_xyz: bool) -> None

set MutableICoorRecord for an atom, vertex descriptor version

phi and theta are in radians

C++: core::chemical::MutableResidueType::set_icoor(void *const &, const double, const double, const double, const std::string &, const std::string &, const std::string &, const bool) –> void

set_ideal_xyz(*args, **kwargs)

Overloaded function.

  1. set_ideal_xyz(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: str, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::MutableResidueType::set_ideal_xyz(const std::string &, const class numeric::xyzVector<double> &) –> void

  1. set_ideal_xyz(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm: capsule, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::MutableResidueType::set_ideal_xyz(void *, const class numeric::xyzVector<double> &) –> void

set_low_energy_ring_conformers(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int, conformers: pyrosetta.rosetta.utility.vector1_std_string) → None

Set this cyclic residue’s low-energy ring conformers for the nth ring by IUPAC name.

C++: core::chemical::MutableResidueType::set_low_energy_ring_conformers(const unsigned long, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_lower_connect_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm_name: str) → None

set the atom which connects to the lower connection

C++: core::chemical::MutableResidueType::set_lower_connect_atom(const std::string &) –> void

set_lowest_energy_ring_conformer(self: pyrosetta.rosetta.core.chemical.MutableResidueType, ring_num: int, conformer: str) → None

Set this cyclic residue’s lowest-energy ring conformer for the nth ring by IUPAC name.

C++: core::chemical::MutableResidueType::set_lowest_energy_ring_conformer(const unsigned long, const std::string &) –> void

set_mainchain_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType, mainchain: pyrosetta.rosetta.utility.vector1_void_*) → None
set indices of all mainchain atoms

TODO Should we make sure that mainchain atoms are also backbones?

C++: core::chemical::MutableResidueType::set_mainchain_atoms(const class utility::vector1<void *, class std::allocator<void *> > &) –> void

set_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set that this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::set_metapatched() –> void

set_orbital_icoor_id(self: pyrosetta.rosetta.core.chemical.MutableResidueType, orbital: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str) → None

set OrbitalICoor for an orbital

C++: core::chemical::MutableResidueType::set_orbital_icoor_id(const std::string &, const double, const double, const double, const std::string &, const std::string &, const std::string &) –> void

set_orbital_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::orbitals::OrbitalTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_orbital_typeset(class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>) –> void

set_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, properties: pyrosetta.rosetta.core.chemical.ResidueProperties) → None

Set the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::set_properties(class std::shared_ptr<class core::chemical::ResidueProperties>) –> void

set_proton_chi(self: pyrosetta.rosetta.core.chemical.MutableResidueType, chino: int, dihedral_samples: pyrosetta.rosetta.utility.vector1_double, extra_samples: pyrosetta.rosetta.utility.vector1_double) → None
Annotate a given chi as a proton chi, and set the sampling behavior

If the chi is already listed as a proton chi, change the sampling behavior

C++: core::chemical::MutableResidueType::set_proton_chi(unsigned long, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str, pre_proline_position: bool) → None

Set the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_mainchain_torsion_potential_name(const std::string &, const bool) –> void

set_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, filename_in: str, pre_proline_position: bool) → None

Set the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_map_file_name(const std::string &, const bool) –> void

set_shadowing_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atom: str, atom_being_shadowed: str) → None

C++: core::chemical::MutableResidueType::set_shadowing_atom(const std::string &, const std::string &) –> void

set_upper_connect_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType, atm_name: str) → None

set the atom which connects to the upper connection

C++: core::chemical::MutableResidueType::set_upper_connect_atom(const std::string &) –> void

shadow_atoms(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.std.map_void_*_void_*_std_less_void__star__t_std_allocator_std_pair_void__star_const_void__star__t

C++: core::chemical::MutableResidueType::shadow_atoms() const –> const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.MutableResidueType, output: pyrosetta.rosetta.std.ostream) -> None

  3. show(self: pyrosetta.rosetta.core.chemical.MutableResidueType, output: pyrosetta.rosetta.std.ostream, output_atomic_details: bool) -> None

Generate string representation of MutableResidueType for debugging purposes.

C++: core::chemical::MutableResidueType::show(std::ostream &, bool) const –> void

show_all_atom_names(self: pyrosetta.rosetta.core.chemical.MutableResidueType, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::MutableResidueType::show_all_atom_names(std::ostream &) const –> void

strip_rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Remove any rotamer library specifications attached to this ResidueTypeBase.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::strip_rotamer_library_specification() –> void

update_atom_type_set(self: pyrosetta.rosetta.core.chemical.MutableResidueType, setting: core::chemical::AtomTypeSet) → None
Change which atom type set this MutableResidueType points to

WARNING - While this tries to switch over the atom types, it will null out any that don’t have exact name correspondences. You NEED to go through and manually reset the types on all atoms. Exposed for black-magic use only.

C++: core::chemical::MutableResidueType::update_atom_type_set(class std::shared_ptr<const class core::chemical::AtomTypeSet>) –> void

upper_connect(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → core::chemical::MutableResidueConnection

C++: core::chemical::MutableResidueType::upper_connect() const –> const class core::chemical::MutableResidueConnection &

upper_connect_atom(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → capsule

index number of the atom which connects to the upper connection

C++: core::chemical::MutableResidueType::upper_connect_atom() const –> void *

upper_connect_id(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → int

C++: core::chemical::MutableResidueType::upper_connect_id() const –> unsigned long

validate_residue_type(self: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool
Run checks on this MutableResidueType, checking to make sure it’s okay.

Return true on success and false on failure (Intended usage is within something like a debug_assert())

C++: core::chemical::MutableResidueType::validate_residue_type() const –> bool

variant_type_enums(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Get a vector of VariantType enums for this ResidueTypeBase.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::variant_type_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

get all the variant types for this ResidueTypeBase

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants.

– rhiju (merging roccomoretti/restypeset_fiddle)

C++: core::chemical::ResidueTypeBase::variant_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions

Bases: PatchOperation

Set the mainchain torsion indices that a noncanonical rotamer library depends upon.

Vikram K. Mulligan (vmullig.edu).

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Set the mainchain torsion indices that a noncanonical rotamer library depends upon.

C++: core::chemical::NCAARotLibBBTorsions::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions, : pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions) → pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions

C++: core::chemical::NCAARotLibBBTorsions::operator=(const class core::chemical::NCAARotLibBBTorsions &) –> class core::chemical::NCAARotLibBBTorsions &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions) → str

Return the name of this PatchOperation (“NCAARotLibBBTorsions”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::NCAARotLibBBTorsions::name() const –> std::string

class pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins

Bases: PatchOperation

Set the number of rotamer bins per chi for an NCAA that is not in dunbrack.

Vikram K. Mulligan (vmullig.edu).

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Set the number of rotamer bins per chi for an NCAA.

C++: core::chemical::NCAARotLibNumRotamerBins::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins, : pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins) → pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins

C++: core::chemical::NCAARotLibNumRotamerBins::operator=(const class core::chemical::NCAARotLibNumRotamerBins &) –> class core::chemical::NCAARotLibNumRotamerBins &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins) → str

Return the name of this PatchOperation (“NCAARotLibNumRotamerBins”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::NCAARotLibNumRotamerBins::name() const –> std::string

class pyrosetta.rosetta.core.chemical.NCAARotLibPath

Bases: PatchOperation

set the path to a rotamer library for an NCAA that is not in dunbrack

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibPath, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the NCAA rotamer library path in the residue type

C++: core::chemical::NCAARotLibPath::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibPath, : pyrosetta.rosetta.core.chemical.NCAARotLibPath) → pyrosetta.rosetta.core.chemical.NCAARotLibPath

C++: core::chemical::NCAARotLibPath::operator=(const class core::chemical::NCAARotLibPath &) –> class core::chemical::NCAARotLibPath &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.NCAARotLibPath) → str

Return the name of this PatchOperation (“NCAARotLibPath”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::NCAARotLibPath::name() const –> std::string

class pyrosetta.rosetta.core.chemical.Orbital

Bases: pybind11_object

basic chemical atom

name, element, certain properties and parameters from .params file

assign(self: pyrosetta.rosetta.core.chemical.Orbital, : pyrosetta.rosetta.core.chemical.Orbital) → pyrosetta.rosetta.core.chemical.Orbital

C++: core::chemical::Orbital::operator=(const class core::chemical::Orbital &) –> class core::chemical::Orbital &

icoor(*args, **kwargs)

Overloaded function.

  1. icoor(self: pyrosetta.rosetta.core.chemical.Orbital) -> pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

C++: core::chemical::Orbital::icoor() –> class core::chemical::orbitals::ICoorOrbitalData &

  1. icoor(self: pyrosetta.rosetta.core.chemical.Orbital, icoor: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) -> None

C++: core::chemical::Orbital::icoor(const class core::chemical::orbitals::ICoorOrbitalData &) –> void

ideal_xyz(*args, **kwargs)

Overloaded function.

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.Orbital) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::Orbital::ideal_xyz() const –> const class numeric::xyzVector<double> &

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.Orbital, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::Orbital::ideal_xyz(const class numeric::xyzVector<double> &) –> void

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.Orbital) -> str

C++: core::chemical::Orbital::name() const –> const std::string &

  1. name(self: pyrosetta.rosetta.core.chemical.Orbital, name: str) -> None

C++: core::chemical::Orbital::name(const std::string &) –> void

new_icoor(*args, **kwargs)

Overloaded function.

  1. new_icoor(self: pyrosetta.rosetta.core.chemical.Orbital) -> pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

C++: core::chemical::Orbital::new_icoor() –> class core::chemical::orbitals::ICoorOrbitalData &

  1. new_icoor(self: pyrosetta.rosetta.core.chemical.Orbital, new_icoor: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) -> None

C++: core::chemical::Orbital::new_icoor(const class core::chemical::orbitals::ICoorOrbitalData &) –> void

orbital_type_index(*args, **kwargs)

Overloaded function.

  1. orbital_type_index(self: pyrosetta.rosetta.core.chemical.Orbital) -> int

C++: core::chemical::Orbital::orbital_type_index() const –> const unsigned long &

  1. orbital_type_index(self: pyrosetta.rosetta.core.chemical.Orbital, atom_type_index: int) -> None

C++: core::chemical::Orbital::orbital_type_index(const unsigned long &) –> void

print(self: pyrosetta.rosetta.core.chemical.Orbital, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::Orbital::print(std::ostream &) const –> void

class pyrosetta.rosetta.core.chemical.Patch

Bases: pybind11_object

A class patching basic ResidueType to create variant types, containing multiple PatchCase

add_case(self: pyrosetta.rosetta.core.chemical.Patch, pcase: pyrosetta.rosetta.core.chemical.PatchCase) → None

Add a patch case to this patch.

C++: core::chemical::Patch::add_case(class std::shared_ptr<class core::chemical::PatchCase>) –> void

add_custom_type(self: pyrosetta.rosetta.core.chemical.Patch, custom_type: str) → None

Add a custom VariantType to the list that this patch applies.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::add_custom_type(const std::string &) –> void

add_type(self: pyrosetta.rosetta.core.chemical.Patch, type: pyrosetta.rosetta.core.chemical.VariantType) → None

Add a VariantType to the list that this patch applies.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::add_type(const enum core::chemical::VariantType) –> void

adds_atoms(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

returns list of added atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::adds_atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_properties(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

returns list of added property names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::adds_properties(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_properties_enums(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty

Returns list of added properties, by enum. Useful for identifying patches that go with PDB residues.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::adds_properties_enums(const class core::chemical::ResidueType &) const –> class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> >

applies_to(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

can I operate on this residue type?

C++: core::chemical::Patch::applies_to(const class core::chemical::ResidueTypeBase &) const –> bool

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  2. apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.MutableResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::Patch::apply(const class core::chemical::ResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  2. apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.MutableResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.MutableResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::Patch::apply(const class core::chemical::MutableResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::MutableResidueType>

assign(self: pyrosetta.rosetta.core.chemical.Patch, : pyrosetta.rosetta.core.chemical.Patch) → pyrosetta.rosetta.core.chemical.Patch

C++: core::chemical::Patch::operator=(const class core::chemical::Patch &) –> class core::chemical::Patch &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

Does the patch potentially change the connections for the given atom on the ResidueType

C++: core::chemical::Patch::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

custom_types(self: pyrosetta.rosetta.core.chemical.Patch) → pyrosetta.rosetta.utility.vector1_std_string

The custom variant types added by this patch.

This must be a vector of strings, since the custom types are generated at runtime and can’t be enumerated at compile time.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::custom_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

deletes_atoms(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_properties(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted property names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_properties(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_properties_enums(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty

returns list of deleted property enums, useful for identifying patches that go with PDB residues.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::deletes_properties_enums(const class core::chemical::ResidueType &) const –> class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> >

deletes_variants(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted variant names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_variants(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_variants_by_enum(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Returns list of deleted VariantTypes. Doesn’t support on-the-fly VariantTypes.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::Patch::deletes_variants_by_enum(const class core::chemical::ResidueType &) const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

generates_aa(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.AA

returns new AA, if changed.

C++: core::chemical::Patch::generates_aa(const class core::chemical::ResidueType &) const –> enum core::chemical::AA

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.Patch) → bool

Is this a special patch that expands the list of base residue types?

C++: core::chemical::Patch::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → str

returns new interchangeability_group, if changed. Only one new interchangeability_group allowed.

C++: core::chemical::Patch::generates_interchangeability_group(const class core::chemical::ResidueType &) const –> std::string

generates_new_name3(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → str

returns new name3, if changed. Only one new name3 allowed.

C++: core::chemical::Patch::generates_new_name3(const class core::chemical::ResidueType &) const –> std::string

is_metapatch(self: pyrosetta.rosetta.core.chemical.Patch) → bool

Is this a metapatch?

C++: core::chemical::Patch::is_metapatch() const –> bool

name(self: pyrosetta.rosetta.core.chemical.Patch) → str

unique name of this patch, eg Nter-simple, Cter-full, Phospho, … ?

C++: core::chemical::Patch::name() const –> const std::string &

patched_name(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → str
Returns the name of the residueType after applying the patch

(Theoretical - doesn’t actually check if the patch would be applied.)

C++: core::chemical::Patch::patched_name(const class core::chemical::ResidueTypeBase &) const –> std::string

read_file(self: pyrosetta.rosetta.core.chemical.Patch, filename: str) → None

constructor from file

C++: core::chemical::Patch::read_file(const std::string &) –> void

replaces(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

do I replace this residue type?

C++: core::chemical::Patch::replaces(const class core::chemical::ResidueTypeBase &) const –> bool

replaces_residue_type(self: pyrosetta.rosetta.core.chemical.Patch, replaces: bool) → None

C++: core::chemical::Patch::replaces_residue_type(bool) –> void

set_name(self: pyrosetta.rosetta.core.chemical.Patch, name: str) → None

C++: core::chemical::Patch::set_name(const std::string &) –> void

set_selector(self: pyrosetta.rosetta.core.chemical.Patch, selector: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → None

C++: core::chemical::Patch::set_selector(const class core::chemical::ResidueTypeSelector &) –> void

types(*args, **kwargs)

Overloaded function.

  1. types(self: pyrosetta.rosetta.core.chemical.Patch) -> pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

The variant types created by applying this patch

Use custom_types() for a vector of strings of custom types.

C++: core::chemical::Patch::types() const –> const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &

  1. types(self: pyrosetta.rosetta.core.chemical.Patch, types: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> None

Set the variant types created by applying this patch.

For custom variant types, use the add_custom_type() function, which takes a string.

C++: core::chemical::Patch::types(const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) –> void

class pyrosetta.rosetta.core.chemical.PatchCase

Bases: pybind11_object

A single case of a patch, eg proline Nterminus is a case of NtermProteinFull

add_operation(self: pyrosetta.rosetta.core.chemical.PatchCase, operation: core::chemical::PatchOperation) → None

add one more operation in this PatchCase

C++: core::chemical::PatchCase::add_operation(class std::shared_ptr<class core::chemical::PatchOperation>) –> void

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string

returns list of added atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::PatchCase::adds_atoms() const –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_properties(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string

returns list of added property names, useful for identifying patches that go with PDB residues

C++: core::chemical::PatchCase::adds_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_properties_enums(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty

Returns list of added property enums. Useful for identifying patches that go with PDB residues.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::PatchCase::adds_properties_enums() const –> class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> >

applies_to(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

whether the PatchCase is applicable to this ResidueType?

C++: core::chemical::PatchCase::applies_to(const class core::chemical::ResidueTypeBase &) const –> bool

apply(*args, **kwargs)

Overloaded function.

  1. apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  2. apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.MutableResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::PatchCase::apply(const class core::chemical::ResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.MutableResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

  2. apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.MutableResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.MutableResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::PatchCase::apply(const class core::chemical::MutableResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::MutableResidueType>

assign(self: pyrosetta.rosetta.core.chemical.PatchCase, : pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.core.chemical.PatchCase

C++: core::chemical::PatchCase::operator=(const class core::chemical::PatchCase &) –> class core::chemical::PatchCase &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

Can the patch case change the connections for atom on the ResidueType?

C++: core::chemical::PatchCase::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atoms(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::PatchCase::deletes_atoms() const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_properties(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted property names, useful for identifying patches that go with PDB residues

C++: core::chemical::PatchCase::deletes_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_properties_enums(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty

Returns list of deleted property enums. Useful for identifying patches that go with PDB residues.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::PatchCase::deletes_properties_enums() const –> class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> >

deletes_variants(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string

returns list of deleted variant names, useful for identifying patches that go with PDB residues

C++: core::chemical::PatchCase::deletes_variants() const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_variants_by_enum(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Returns list of deleted VariantTypes. Doesn’t support on-the-fly VariantTypes.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::PatchCase::deletes_variants_by_enum() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchCase) → bool

Does this PatchCase result in a new base residue type?

C++: core::chemical::PatchCase::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchCase) → str

returns interchangeability group, if set.

C++: core::chemical::PatchCase::generates_interchangeability_group() const –> std::string

generates_new_name3(self: pyrosetta.rosetta.core.chemical.PatchCase) → str

returns new name3, if changed

C++: core::chemical::PatchCase::generates_new_name3() const –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchCase) → bool

C++: core::chemical::PatchCase::may_change_aa() const –> bool

selector(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

to which ResidueTypes this PatchCase applies to?

C++: core::chemical::PatchCase::selector() –> class core::chemical::ResidueTypeSelector &

set_selector(self: pyrosetta.rosetta.core.chemical.PatchCase, selector: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → None

C++: core::chemical::PatchCase::set_selector(const class core::chemical::ResidueTypeSelector &) –> void

class pyrosetta.rosetta.core.chemical.PatchOperation

Bases: pybind11_object

A single operation that needs to be applied in a residue patch

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.PatchOperation, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Returns true to signal failure, false to indicate success.

C++: core::chemical::PatchOperation::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.PatchOperation

C++: core::chemical::PatchOperation::operator=(const class core::chemical::PatchOperation &) –> class core::chemical::PatchOperation &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Returns the name of the patch operation. Useful for debugging.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::PatchOperation::name() const –> std::string

class pyrosetta.rosetta.core.chemical.PatchOperationCreator

Bases: pybind11_object

The PatchOperationCreator is responsible for creating a PatchOperation from input line(s)

assign(self: pyrosetta.rosetta.core.chemical.PatchOperationCreator, : pyrosetta.rosetta.core.chemical.PatchOperationCreator) → pyrosetta.rosetta.core.chemical.PatchOperationCreator

C++: core::chemical::PatchOperationCreator::operator=(const class core::chemical::PatchOperationCreator &) –> class core::chemical::PatchOperationCreator &

create_operation(self: pyrosetta.rosetta.core.chemical.PatchOperationCreator, line: str, input: pyrosetta.rosetta.std.istream, atomic_charge_reassignments: pyrosetta.rosetta.std.map_std_string_double) → pyrosetta.rosetta.core.chemical.PatchOperation

Return a new mover.

C++: core::chemical::PatchOperationCreator::create_operation(const std::string &, std::istream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) const –> class std::shared_ptr<class core::chemical::PatchOperation>

keyname(self: pyrosetta.rosetta.core.chemical.PatchOperationCreator) → str

Return the tag name associated with this factory.

C++: core::chemical::PatchOperationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.PatchOperationFactory

Bases: SingletonBase_core_chemical_PatchOperationFactory_t

factory_register(self: pyrosetta.rosetta.core.chemical.PatchOperationFactory, creator: pyrosetta.rosetta.core.chemical.PatchOperationCreator) → None

C++: core::chemical::PatchOperationFactory::factory_register(class std::shared_ptr<class core::chemical::PatchOperationCreator>) –> void

static get_instance() → core::chemical::PatchOperationFactory

C++: utility::SingletonBase<core::chemical::PatchOperationFactory>::get_instance() –> class core::chemical::PatchOperationFactory *

newPatchOperation(self: pyrosetta.rosetta.core.chemical.PatchOperationFactory, tag: str, line: str, input: pyrosetta.rosetta.std.istream, atomic_charge_reassignments: pyrosetta.rosetta.std.map_std_string_double) → pyrosetta.rosetta.core.chemical.PatchOperation

Create a mover given its identifying string, the full line, and the istream advanced to after the tag.

C++: core::chemical::PatchOperationFactory::newPatchOperation(const std::string &, const std::string &, std::istream &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) const –> class std::shared_ptr<class core::chemical::PatchOperation>

class pyrosetta.rosetta.core.chemical.PolarHydrogenFilter

Bases: pybind11_object

The filter responsible for all polar hydrogens.

assign(self: pyrosetta.rosetta.core.chemical.PolarHydrogenFilter, : pyrosetta.rosetta.core.chemical.PolarHydrogenFilter) → pyrosetta.rosetta.core.chemical.PolarHydrogenFilter

C++: core::chemical::PolarHydrogenFilter::operator=(const class core::chemical::PolarHydrogenFilter &) –> class core::chemical::PolarHydrogenFilter &

class pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

Bases: ResidueTypeSet

A ResidueTypeSet which can be cached in the Pose

add_base_residue_type(*args, **kwargs)

Overloaded function.

  1. add_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, new_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: core::chemical::PoseResidueTypeSet::add_base_residue_type(class std::shared_ptr<class core::chemical::MutableResidueType>) –> void

  1. add_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filename: str) -> None

C++: core::chemical::PoseResidueTypeSet::add_base_residue_type(const std::string &) –> void

add_patches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, patch_filenames: pyrosetta.rosetta.utility.vector1_std_string, metapatch_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::chemical::PoseResidueTypeSet::add_patches(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

add_unpatchable_residue_type(*args, **kwargs)

Overloaded function.

  1. add_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, new_type: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

C++: core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type(class std::shared_ptr<class core::chemical::MutableResidueType>) –> void

  1. add_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filename: str) -> None

C++: core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type(const std::string &) –> void

atom_type_set(*args, **kwargs)

Overloaded function.

  1. atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.AtomTypeSet

C++: core::chemical::PoseResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

  1. atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::atom_type_set(class std::shared_ptr<const class core::chemical::AtomTypeSet>) –> void

base_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

the residues with no patches applied

C++: core::chemical::PoseResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

clone(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.core.chemical.PoseResidueTypeSet

C++: core::chemical::PoseResidueTypeSet::clone() const –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>

default_rts(*args, **kwargs)

Overloaded function.

  1. default_rts(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, setting: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

Set the default fall-back ResidueTypeSet

C++: core::chemical::PoseResidueTypeSet::default_rts(class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

  1. default_rts(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

What is the default fall-back ResidueTypesSet

C++: core::chemical::PoseResidueTypeSet::default_rts() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

element_set(*args, **kwargs)

Overloaded function.

  1. element_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ElementSet

C++: core::chemical::PoseResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>

  1. element_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, elements: pyrosetta.rosetta.core.chemical.ElementSet) -> None

C++: core::chemical::PoseResidueTypeSet::element_set(class std::shared_ptr<const class core::chemical::ElementSet>) –> void

generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, base_residue_name: str, interchangeability_group: str) → bool

Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated))

C++: core::chemical::PoseResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const std::string &, const std::string &) const –> bool

generates_patched_residue_type_with_name3(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, base_residue_name: str, name3: str) → bool

Check if a base type (like “SER”) generates any types with another name3 (like “SEP”)

C++: core::chemical::PoseResidueTypeSet::generates_patched_residue_type_with_name3(const std::string &, const std::string &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)

Overloaded function.

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants, making exceptions for some variants.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants, but exceptions must be standard types, listed in VariantType.hh. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_by_basetype(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Given a base residue type, desired variants, and undesired variants, retrieve a list

of cached ResidueTypeCOPs. If not cached, generate the data and cache them.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

A list of ResidueTypeCOPs matching the desired variants, with the desired base type.

This function is threadsafe. Caching and retrieveal are handled with a ReadWriteMutex.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Gets all non-patched types with the given aa type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_aa(enum core::chemical::AA) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name1(char) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name3(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_d_equivalent(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, l_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::PoseResidueTypeSet::get_d_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_l_equivalent(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, d_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::PoseResidueTypeSet::get_l_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_mirrored_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, original_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::PoseResidueTypeSet::get_mirrored_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t
Get the patches corresponding to a patch name.

Will get both regular an metapatches

C++: core::chemical::ResidueTypeSet::get_patches(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

get_representative_type_aa(*args, **kwargs)

Overloaded function.

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given aa type and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_base_name(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name1 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name3 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_custom_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_added(*args, **kwargs)

Overloaded function.

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) -> pyrosetta.rosetta.core.chemical.ResidueType

Query a variant ResidueType by its base ResidueType and VariantType

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) -> pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → pyrosetta.rosetta.core.chemical.ResidueType
return the residuetype we get from variant rsd type after removing the desired variant type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ResidueTypeSet

C++: core::chemical::ResidueTypeSet::get_self_ptr() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t

C++: core::chemical::ResidueTypeSet::get_self_weak_ptr() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>

has_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
Does this ResidueTypeSet have ResidueTypes with the given interchangeability group?

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_interchangeability_group(const std::string &) const –> bool

has_metapatch(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → bool

Do we have this metapatch?

C++: core::chemical::PoseResidueTypeSet::has_metapatch(const std::string &) const –> bool

has_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
query if a ResidueType of the unique residue id (name) is present.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name(const std::string &) const –> bool

has_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → bool
query if any ResidueTypes in the set have a “name3” that matches the input name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name3(const std::string &) const –> bool

merge_split_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::io::MergeAndSplitBehaviorManager

accessor for merge/split behavior manager

C++: core::chemical::ResidueTypeSet::merge_split_behavior_manager() const –> const class core::chemical::io::MergeAndSplitBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.Metapatch

C++: core::chemical::PoseResidueTypeSet::metapatch(const std::string &) const –> class std::shared_ptr<const class core::chemical::Metapatch>

metapatch_map(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches, index by name.

C++: core::chemical::PoseResidueTypeSet::metapatch_map() const –> const class std::map<std::string, class std::shared_ptr<const class core::chemical::Metapatch>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class core::chemical::Metapatch> > > > &

metapatches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches

C++: core::chemical::PoseResidueTypeSet::metapatches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Metapatch>, class std::allocator<class std::shared_ptr<const class core::chemical::Metapatch> > >

mm_atom_type_set(*args, **kwargs)

Overloaded function.

  1. mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.MMAtomTypeSet

C++: core::chemical::PoseResidueTypeSet::mm_atom_type_set() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

  1. mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::mm_atom_type_set(class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> void

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.TypeSetMode

The type of the ResidueTypeSet

The difference between a ResidueTypeSet name and a ResidueTypeSet mode is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same mode. The mode specifies what compatibility class (full atom, centroid) the ResidueTypeSet has.

C++: core::chemical::ResidueTypeSet::mode() const –> enum core::chemical::TypeSetMode

name_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
query ResidueType by its unique residue id. Note for derived classes: this

method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

since within a ResidueTypeSet, each residue id must be unique, this method only returns one residue type or it exits (the program!) without a match.

C++: core::chemical::ResidueTypeSet::name_map(const std::string &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Get ResidueType by exact name, returning COP. Will return null pointer

for no matches. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::name_mapOP(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

orbital_type_set(*args, **kwargs)

Overloaded function.

  1. orbital_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> core::chemical::orbitals::OrbitalTypeSet

C++: core::chemical::PoseResidueTypeSet::orbital_type_set() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

  1. orbital_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, orbital_types: core::chemical::orbitals::OrbitalTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::orbital_type_set(class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>) –> void

patch_map(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t

the patches, index by name.

C++: core::chemical::PoseResidueTypeSet::patch_map() const –> const class std::map<std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > > > > > &

patches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t

the patches

C++: core::chemical::PoseResidueTypeSet::patches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

read_files_for_base_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::chemical::PoseResidueTypeSet::read_files_for_base_residue_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

read_files_for_unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: core::chemical::PoseResidueTypeSet::read_files_for_unpatchable_residue_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

remove_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → None

C++: core::chemical::PoseResidueTypeSet::remove_base_residue_type(const std::string &) –> void

remove_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → None

C++: core::chemical::PoseResidueTypeSet::remove_unpatchable_residue_type(const std::string &) –> void

set_merge_split_behavior_manager(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mbm: core::chemical::io::MergeAndSplitBehaviorManager) → None

C++: core::chemical::PoseResidueTypeSet::set_merge_split_behavior_manager(class std::shared_ptr<const class core::chemical::io::MergeAndSplitBehaviorManager>) –> void

unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

the residues with no patches applied

C++: core::chemical::PoseResidueTypeSet::unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

class pyrosetta.rosetta.core.chemical.PrependMainchainAtom

Bases: PatchOperation

add a mainchain atom before the first mainchain atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.PrependMainchainAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom to be the first mainchain atom

C++: core::chemical::PrependMainchainAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.PrependMainchainAtom, : pyrosetta.rosetta.core.chemical.PrependMainchainAtom) → pyrosetta.rosetta.core.chemical.PrependMainchainAtom

C++: core::chemical::PrependMainchainAtom::operator=(const class core::chemical::PrependMainchainAtom &) –> class core::chemical::PrependMainchainAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.PrependMainchainAtom) → str

Return the name of this PatchOperation (“PrependMainchainAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::PrependMainchainAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.RamaPreproFilename

Bases: PatchOperation

Set the filenames for RamaPrePro scoring tables.

Vikram K. Mulligan (vmullig.edu)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.RamaPreproFilename, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Set the RamaPrepro library paths in the residue type.

C++: core::chemical::RamaPreproFilename::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RamaPreproFilename, : pyrosetta.rosetta.core.chemical.RamaPreproFilename) → pyrosetta.rosetta.core.chemical.RamaPreproFilename

C++: core::chemical::RamaPreproFilename::operator=(const class core::chemical::RamaPreproFilename &) –> class core::chemical::RamaPreproFilename &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.RamaPreproFilename) → str

Return the name of this PatchOperation (“RamaPreproFilename”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::RamaPreproFilename::name() const –> std::string

class pyrosetta.rosetta.core.chemical.RamaPreproResname

Bases: PatchOperation

Set the residue name for RamaPrePro scoring tables.

This is the name in the scoring table AND the reference string used to look up the table. Should be unique.

Vikram K. Mulligan (vmullig.edu)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.RamaPreproResname, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Set the RamaPrepro reference string in the residue type.

C++: core::chemical::RamaPreproResname::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RamaPreproResname, : pyrosetta.rosetta.core.chemical.RamaPreproResname) → pyrosetta.rosetta.core.chemical.RamaPreproResname

C++: core::chemical::RamaPreproResname::operator=(const class core::chemical::RamaPreproResname &) –> class core::chemical::RamaPreproResname &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.RamaPreproResname) → str

Return the name of this PatchOperation (“RamaPreproResname”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::RamaPreproResname::name() const –> std::string

class pyrosetta.rosetta.core.chemical.RealFilter

Bases: pybind11_object

A filtered graph that doesn’t contain fake/virtual atoms and fake/virtual bonds.

assign(self: pyrosetta.rosetta.core.chemical.RealFilter, : pyrosetta.rosetta.core.chemical.RealFilter) → pyrosetta.rosetta.core.chemical.RealFilter

C++: core::chemical::RealFilter::operator=(const class core::chemical::RealFilter &) –> class core::chemical::RealFilter &

class pyrosetta.rosetta.core.chemical.RedefineChi

Bases: PatchOperation

Redefine a chi angle

Added by Andy M. Chen in June 2009 This is needed for certain PTMs

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.RedefineChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

redefine a chi angle

C++: core::chemical::RedefineChi::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RedefineChi, : pyrosetta.rosetta.core.chemical.RedefineChi) → pyrosetta.rosetta.core.chemical.RedefineChi

C++: core::chemical::RedefineChi::operator=(const class core::chemical::RedefineChi &) –> class core::chemical::RedefineChi &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.RedefineChi) → str

Return the name of this PatchOperation (“RedefineChi”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::RedefineChi::name() const –> std::string

class pyrosetta.rosetta.core.chemical.RefConvert_std_string_t

Bases: pybind11_object

static convert(: pyrosetta.rosetta.core.chemical.ResidueTypeBase, ref: str) → str

C++: core::chemical::RefConvert<std::string >::convert(const class core::chemical::ResidueTypeBase &, const std::string &) –> std::string

static identity_pass_through(ref: str, : str) → str

C++: core::chemical::RefConvert<std::string >::identity_pass_through(const std::string &, const std::string &) –> const std::string &

static invalid() → str

C++: core::chemical::RefConvert<std::string >::invalid() –> const std::string &

class pyrosetta.rosetta.core.chemical.RefConvert_unsigned_long_t

Bases: pybind11_object

static convert(: pyrosetta.rosetta.core.chemical.ResidueType, ref: int) → int

C++: core::chemical::RefConvert<unsigned long>::convert(const class core::chemical::ResidueType &, const unsigned long &) –> unsigned long

static identity_pass_through(ref: int, : int) → int

C++: core::chemical::RefConvert<unsigned long>::identity_pass_through(const unsigned long &, const unsigned long &) –> const unsigned long &

static invalid() → int

C++: core::chemical::RefConvert<unsigned long>::invalid() –> const unsigned long &

class pyrosetta.rosetta.core.chemical.RefConvert_void__star__t

Bases: pybind11_object

static convert(: pyrosetta.rosetta.core.chemical.MutableResidueType, ref: capsule) → capsule

C++: core::chemical::RefConvert<void *>::convert(const class core::chemical::MutableResidueType &, void *const &) –> void *

static identity_pass_through(ref: capsule, : capsule) → capsule

C++: core::chemical::RefConvert<void *>::identity_pass_through(void *const &, void *const &) –> void *const &

static invalid() → capsule

C++: core::chemical::RefConvert<void *>::invalid() –> void *const &

class pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications

Bases: PatchOperation

Remove existing rotamer specifications (of any type).

Vikram K. Mulligan (vmullig.edu)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Strip all RotamerSpecifications from the ResidueType.

C++: core::chemical::RemoveRotamerSpecifications::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications, : pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications) → pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications

C++: core::chemical::RemoveRotamerSpecifications::operator=(const class core::chemical::RemoveRotamerSpecifications &) –> class core::chemical::RemoveRotamerSpecifications &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications) → str

Return the name of this PatchOperation (“RemoveRotamerSpecifications”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::RemoveRotamerSpecifications::name() const –> std::string

class pyrosetta.rosetta.core.chemical.RenameAtom

Bases: PatchOperation

rename atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.RenameAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::RenameAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RenameAtom, : pyrosetta.rosetta.core.chemical.RenameAtom) → pyrosetta.rosetta.core.chemical.RenameAtom

C++: core::chemical::RenameAtom::operator=(const class core::chemical::RenameAtom &) –> class core::chemical::RenameAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.RenameAtom) → str

Return the name of this PatchOperation (“RenameAtom”).

C++: core::chemical::RenameAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom

Bases: PatchOperation

replace a mainchain atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom to be the last mainchain atom

C++: core::chemical::ReplaceMainchainAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom, : pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom) → pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom

C++: core::chemical::ReplaceMainchainAtom::operator=(const class core::chemical::ReplaceMainchainAtom &) –> class core::chemical::ReplaceMainchainAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom) → str

Return the name of this PatchOperation (“ReplaceMainchainAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceMainchainAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine

Bases: PatchOperation

replace proton with bromine

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithBromine::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine

C++: core::chemical::ReplaceProtonWithBromine::operator=(const class core::chemical::ReplaceProtonWithBromine &) –> class core::chemical::ReplaceProtonWithBromine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine) → str

Return the name of this PatchOperation (“ReplaceProtonWithBromine”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithBromine::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine

Bases: PatchOperation

replace proton with chlorine

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithChlorine::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine

C++: core::chemical::ReplaceProtonWithChlorine::operator=(const class core::chemical::ReplaceProtonWithChlorine &) –> class core::chemical::ReplaceProtonWithChlorine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine) → str

Return the name of this PatchOperation (“ReplaceProtonWithChlorine”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithChlorine::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl

Bases: PatchOperation

replace proton with ethyl

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithEthyl::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl

C++: core::chemical::ReplaceProtonWithEthyl::operator=(const class core::chemical::ReplaceProtonWithEthyl &) –> class core::chemical::ReplaceProtonWithEthyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl) → str

Return the name of this PatchOperation (“ReplaceProtonWithEthyl”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithEthyl::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine

Bases: PatchOperation

replace proton with fluorine

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithFluorine::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine

C++: core::chemical::ReplaceProtonWithFluorine::operator=(const class core::chemical::ReplaceProtonWithFluorine &) –> class core::chemical::ReplaceProtonWithFluorine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine) → str

Return the name of this PatchOperation (“ReplaceProtonWithFluorine”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithFluorine::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl

Bases: PatchOperation

replace proton with hydroxyl

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithHydroxyl::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl

C++: core::chemical::ReplaceProtonWithHydroxyl::operator=(const class core::chemical::ReplaceProtonWithHydroxyl &) –> class core::chemical::ReplaceProtonWithHydroxyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl) → str

Return the name of this PatchOperation (“ReplaceProtonWithHydroxyl”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithHydroxyl::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine

Bases: PatchOperation

replace proton with iodine

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithIodine::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine

C++: core::chemical::ReplaceProtonWithIodine::operator=(const class core::chemical::ReplaceProtonWithIodine &) –> class core::chemical::ReplaceProtonWithIodine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine) → str

Return the name of this PatchOperation (“ReplaceProtonWithIodine”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithIodine::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy

Bases: PatchOperation

replace proton with methoxy

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithMethoxy::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy

C++: core::chemical::ReplaceProtonWithMethoxy::operator=(const class core::chemical::ReplaceProtonWithMethoxy &) –> class core::chemical::ReplaceProtonWithMethoxy &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy) → str

Return the name of this PatchOperation (“ReplaceProtonWithMethoxy”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithMethoxy::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl

Bases: PatchOperation

replace proton with methyl

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithMethyl::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl

C++: core::chemical::ReplaceProtonWithMethyl::operator=(const class core::chemical::ReplaceProtonWithMethyl &) –> class core::chemical::ReplaceProtonWithMethyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl) → str

Return the name of this PatchOperation (“ReplaceProtonWithMethyl”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithMethyl::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl

Bases: PatchOperation

replace proton with trifluoromethyl

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::ReplaceProtonWithTrifluoromethyl::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl

C++: core::chemical::ReplaceProtonWithTrifluoromethyl::operator=(const class core::chemical::ReplaceProtonWithTrifluoromethyl &) –> class core::chemical::ReplaceProtonWithTrifluoromethyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl) → str

Return the name of this PatchOperation (“ReplaceProtonWithTrifluoromethyl”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ReplaceProtonWithTrifluoromethyl::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ResConnID

Bases: pybind11_object

The ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue’s index and the ResidueConnection index.

assign(self: pyrosetta.rosetta.core.chemical.ResConnID, : pyrosetta.rosetta.core.chemical.ResConnID) → pyrosetta.rosetta.core.chemical.ResConnID

C++: core::chemical::ResConnID::operator=(const class core::chemical::ResConnID &) –> class core::chemical::ResConnID &

connid(*args, **kwargs)

Overloaded function.

  1. connid(self: pyrosetta.rosetta.core.chemical.ResConnID) -> int

C++: core::chemical::ResConnID::connid() const –> unsigned long

  1. connid(self: pyrosetta.rosetta.core.chemical.ResConnID, conn_id: int) -> None

C++: core::chemical::ResConnID::connid(unsigned long) –> void

incomplete(self: pyrosetta.rosetta.core.chemical.ResConnID) → bool

C++: core::chemical::ResConnID::incomplete() const –> bool

mark_incomplete(self: pyrosetta.rosetta.core.chemical.ResConnID) → None

C++: core::chemical::ResConnID::mark_incomplete() –> void

resid(*args, **kwargs)

Overloaded function.

  1. resid(self: pyrosetta.rosetta.core.chemical.ResConnID) -> int

C++: core::chemical::ResConnID::resid() const –> unsigned long

  1. resid(self: pyrosetta.rosetta.core.chemical.ResConnID, res_id: int) -> None

C++: core::chemical::ResConnID::resid(unsigned long) –> void

class pyrosetta.rosetta.core.chemical.ResetBondLength

Bases: PatchOperation

A patch operation for resetting the length of a bond within a ResidueType.

This is useful for when an atom is rehybridized within a patch file.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.ResetBondLength, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::ResetBondLength::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ResetBondLength, : pyrosetta.rosetta.core.chemical.ResetBondLength) → pyrosetta.rosetta.core.chemical.ResetBondLength

C++: core::chemical::ResetBondLength::operator=(const class core::chemical::ResetBondLength &) –> class core::chemical::ResetBondLength &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.ResetBondLength) → str

Return the name of this PatchOperation (“ResetBondLength”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResetBondLength::name() const –> std::string

class pyrosetta.rosetta.core.chemical.ResidueConnection

Bases: pybind11_object

A simple class marking atoms at inter-residue connections.

Each residue type specifies some number of positions at which it is expecting to form a chemical bond with another residue. Think of them as ports: they are parts of the residue where there are chemical bonds beyond the intra-residue chemical bonds are expected – places where they can be chemically linked to the outside world. A conformation::Residue will require that its ResidueConnections be fulfilled by other Residues – the ResConnID class describes how two residues are connected: e.g., the third ResConnID for residue 10 would say “I connect to residue 58 at residue 58’s third residue connection” if residue 10 and residue 58 were disulfide bonded as the disulfide connection id is “3” for two mid-protein cystine residues. The advantages of separating ResidueConnections from atoms themselves are that 1) it allows multiple residue connections to stem from the same atom – useful for single-atom residues, such as coordinated metals (Zn, Mg), and 2) it allows one residue to change its set of atoms without invalidating the bond information (e.g. the atom index) on its partner. For example, if a chain-break were placed between residues 57 and 58, then residue 58 will get an extra C-prev virtual atom, and the index of SG will change. Residue 10, if it had recorded the SG index would have to find SG’s new index. If instead, the connection point is represented simply as connection point 3, and if the new residue type (the chainbreak disulfide residue) has the same number of residue connections as the original residue type (it will!) then nothing about residue 10 needs to be updated.

assign(self: pyrosetta.rosetta.core.chemical.ResidueConnection, : pyrosetta.rosetta.core.chemical.ResidueConnection) → pyrosetta.rosetta.core.chemical.ResidueConnection

C++: core::chemical::ResidueConnection::operator=(const class core::chemical::ResidueConnection &) –> class core::chemical::ResidueConnection &

atomno(*args, **kwargs)

Overloaded function.

  1. atomno(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> int

get atom index number

C++: core::chemical::ResidueConnection::atomno() const –> int

  1. atomno(self: pyrosetta.rosetta.core.chemical.ResidueConnection, atomno_in: int) -> None

set atom index number

C++: core::chemical::ResidueConnection::atomno(const unsigned long) –> void

icoor(*args, **kwargs)

Overloaded function.

  1. icoor(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> pyrosetta.rosetta.core.chemical.AtomICoor

get atom’s AtomICoor

C++: core::chemical::ResidueConnection::icoor() const –> const class core::chemical::AtomICoor &

  1. icoor(self: pyrosetta.rosetta.core.chemical.ResidueConnection, ic: pyrosetta.rosetta.core.chemical.AtomICoor) -> None

set atom’s AtomICoor

C++: core::chemical::ResidueConnection::icoor(const class core::chemical::AtomICoor &) –> void

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> int

C++: core::chemical::ResidueConnection::index() const –> int

  1. index(self: pyrosetta.rosetta.core.chemical.ResidueConnection, index_in: int) -> None

C++: core::chemical::ResidueConnection::index(int) –> void

class pyrosetta.rosetta.core.chemical.ResidueDatabaseIO

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, : pyrosetta.rosetta.core.chemical.ResidueDatabaseIO) → pyrosetta.rosetta.core.chemical.ResidueDatabaseIO

C++: core::chemical::ResidueDatabaseIO::operator=(const class core::chemical::ResidueDatabaseIO &) –> class core::chemical::ResidueDatabaseIO &

get_all_residues_in_database(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, db_session: pyrosetta.rosetta.utility.sql_database.session) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::ResidueDatabaseIO::get_all_residues_in_database(class std::shared_ptr<class utility::sql_database::session>) –> class utility::vector1<std::string, class std::allocator<std::string > >

get_version(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO) → float

C++: core::chemical::ResidueDatabaseIO::get_version() –> double

initialize(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, db_session: pyrosetta.rosetta.utility.sql_database.session) → None

write the schema

C++: core::chemical::ResidueDatabaseIO::initialize(class std::shared_ptr<class utility::sql_database::session>) –> void

read_residuetype_from_database(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet, elements: pyrosetta.rosetta.core.chemical.ElementSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, orbital_atom_types: core::chemical::orbitals::OrbitalTypeSet, residue_type_set_name: str, residue_type_name: str, db_session: pyrosetta.rosetta.utility.sql_database.session) → pyrosetta.rosetta.core.chemical.MutableResidueType

C++: core::chemical::ResidueDatabaseIO::read_residuetype_from_database(class std::shared_ptr<const class core::chemical::AtomTypeSet>, class std::shared_ptr<const class core::chemical::ElementSet>, class std::shared_ptr<const class core::chemical::MMAtomTypeSet>, class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>, const std::string &, const std::string &, class std::shared_ptr<class utility::sql_database::session>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

write_residuetype_to_database(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, residue_type_set_name: str, res_type: pyrosetta.rosetta.core.chemical.ResidueType, db_session: pyrosetta.rosetta.utility.sql_database.session) → None

C++: core::chemical::ResidueDatabaseIO::write_residuetype_to_database(const std::string &, const class core::chemical::ResidueType &, class std::shared_ptr<class utility::sql_database::session>) –> void

write_schema_to_db(self: pyrosetta.rosetta.core.chemical.ResidueDatabaseIO, db_session: pyrosetta.rosetta.utility.sql_database.session) → None

generate the table schemas and write them to the database

C++: core::chemical::ResidueDatabaseIO::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void

class pyrosetta.rosetta.core.chemical.ResidueProperties

Bases: pybind11_object

This is a container class for the large assortment of properties associated with ResidueTypes. It prevents ResidueType from becoming cluttered with an over-abundance of properties and related methods.

This is the first step in a major refactor of how properties are handled in Rosetta. For now, I have just gathered all the properties related code into one place, so that changes to the system can be more readily made. Previous behavior has been maintained. In the future, I have several ideas for further improvements. ~Labonte

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, tag: str, value: float) → None

Add a numeric property.

C++: core::chemical::ResidueProperties::add_numeric_property(const std::string &, const double) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, tag: str, value: str) → None

Add a string property.

C++: core::chemical::ResidueProperties::add_string_property(const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.core.chemical.ResidueProperties, : pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.core.chemical.ResidueProperties

C++: core::chemical::ResidueProperties::operator=(const class core::chemical::ResidueProperties &) –> class core::chemical::ResidueProperties &

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → None

Turn on the ability to create VariantTypes “on-the-fly”.

Custom” VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

C++: core::chemical::ResidueProperties::enable_custom_variant_types() –> void

get_list_of_custom_variants(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string

Return a list of custom VariantTypes only for this ResidueType.

C++: core::chemical::ResidueProperties::get_list_of_custom_variants() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_list_of_custom_variants_by_reference(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string

Get a const-access reference to the list of custom VariantType strings for this ResidueType.

This will not include enum-based standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueProperties::get_list_of_custom_variants_by_reference() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

get_list_of_properties(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string

Generate and return a list of strings representing the properties of this ResidueType.

C++: core::chemical::ResidueProperties::get_list_of_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_list_of_variant_enums(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Return a list of VariantType enums for this ResidueType.

This will not include custom, string-based variant types generated on the fly.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueProperties::get_list_of_variant_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

get_list_of_variants(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string

Generate and return a list of strings representing the VariantTypes of this ResidueType.

This will include both custom, string-based variants made on-the-fly AND the standard variants that are enumerated.

C++: core::chemical::ResidueProperties::get_list_of_variants() const –> class utility::vector1<std::string, class std::allocator<std::string > >

static get_property_from_string(property: str) → pyrosetta.rosetta.core.chemical.ResidueProperty

Static constant data access

Get the ResidueProperty enum value from the corresponding string. This public static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it’s a handy function for other code to use (VKM, 22 July 2015).

Returns core::chemical::NO_PROPERTY if the string can’t be parsed.

C++: core::chemical::ResidueProperties::get_property_from_string(const std::string &) –> const enum core::chemical::ResidueProperty &

static get_string_from_property(property: pyrosetta.rosetta.core.chemical.ResidueProperty) → str

Get a string from the corresponding ResidueProperty enum value.

This public static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it’s a handy function for other code to use (VKM, 22 July 2015).

This function should be used to iterate through all property names. This can be done as follows: for( core::Size i(1); i<=static_cast<core::Size>( core::chemcial::N_PROPERTIES ); ++i ) {

std::string const name( core::chemical::ResidueProperties::get_string_from_property( static_cast< core::chemical::ResidueProperty >(i) ) ); // Do something with the name here.

}

C++: core::chemical::ResidueProperties::get_string_from_property(const enum core::chemical::ResidueProperty) –> const std::string &

static get_string_from_variant(variant: pyrosetta.rosetta.core.chemical.VariantType) → str
Get a string from the corresponding VariantType enum value.

This public static class method is defined in VariantType_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script.

C++: core::chemical::ResidueProperties::get_string_from_variant(const enum core::chemical::VariantType) –> const std::string &

static get_variant_from_string(variant: str) → pyrosetta.rosetta.core.chemical.VariantType
Get the VariantType enum value from the corresponding string.

This public static class method is defined in VariantType_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script.

C++: core::chemical::ResidueProperties::get_variant_from_string(const std::string &) –> const enum core::chemical::VariantType &

has_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → bool

Does this ResidueType contain additional VariantTypes than the standard list?

C++: core::chemical::ResidueProperties::has_custom_variant_types() const –> bool

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Get whether or not this ResidueType has the requested property.

C++: core::chemical::ResidueProperties::has_property(const enum core::chemical::ResidueProperty) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: str) -> bool

Get whether or not this ResidueType has the requested property by string.

C++: core::chemical::ResidueProperties::has_property(const std::string &) const –> bool

is_variant_type(*args, **kwargs)

Overloaded function.

  1. is_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Get whether or not this ResidueType is of the requested VariantType.

C++: core::chemical::ResidueProperties::is_variant_type(const enum core::chemical::VariantType) const –> bool

  1. is_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: str) -> bool

Get whether or not this ResidueType is of the requested VariantType by string.

C++: core::chemical::ResidueProperties::is_variant_type(const std::string &) const –> bool

numeric_properties(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.std.map_std_string_double

C++: core::chemical::ResidueProperties::numeric_properties() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

set_parent_name(self: pyrosetta.rosetta.core.chemical.ResidueProperties, setting: str) → None

Set the name of the owning ResidueType, for diagnostic purposes.

C++: core::chemical::ResidueProperties::set_parent_name(const std::string &) –> void

set_property(*args, **kwargs)

Overloaded function.

  1. set_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: pyrosetta.rosetta.core.chemical.ResidueProperty, setting: bool) -> None

Set the status of the given property for this ResidueType.

C++: core::chemical::ResidueProperties::set_property(const enum core::chemical::ResidueProperty, const bool) –> void

  1. set_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: str, setting: bool) -> None

Set the status of the given property for this ResidueType by string.

C++: core::chemical::ResidueProperties::set_property(const std::string &, const bool) –> void

set_variant_type(*args, **kwargs)

Overloaded function.

  1. set_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: pyrosetta.rosetta.core.chemical.VariantType, setting: bool) -> None

Set the status of a given VariantType for this ResidueType.

C++: core::chemical::ResidueProperties::set_variant_type(const enum core::chemical::VariantType, const bool) –> void

  1. set_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: str, setting: bool) -> None

Set the status of a given VariantType for this ResidueType by string.

C++: core::chemical::ResidueProperties::set_variant_type(const std::string &, const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.ResidueProperties) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.ResidueProperties, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of ResidueProperties for debugging purposes.

C++: core::chemical::ResidueProperties::show(std::ostream &) const –> void

string_properties(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.std.map_std_string_std_string

C++: core::chemical::ResidueProperties::string_properties() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

class pyrosetta.rosetta.core.chemical.ResidueProperty

Bases: pybind11_object

Enumerators for all the properties that can be assigned to a ResidueType.

Members:

NO_PROPERTY

FIRST_PROPERTY

POLYMER

LIGAND

PROTEIN

CANONICAL_AA

CANONICAL_NUCLEIC

DNA

RNA

TNA

PNA

PEPTOID

OLIGOUREA

ARAMID

ORTHO_ARAMID

META_ARAMID

PARA_ARAMID

PRE_METHYLENE_ORTHO_ARAMID

PRE_METHYLENE_META_ARAMID

PRE_METHYLENE_PARA_ARAMID

POST_METHYLENE_ORTHO_ARAMID

POST_METHYLENE_META_ARAMID

POST_METHYLENE_PARA_ARAMID

PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID

PRE_METHYLENE_POST_METHYLENE_META_ARAMID

PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID

CARBOHYDRATE

LIPID

TERPENE

NUCLEOTIDE_DIPHOSPHATE

SRI

TRIAZOLE_LINKER

METAL

SURFACE

WATER

TP3

VIRTUALIZABLE_BY_PACKER

SOLVENT

VIRTUAL_RESIDUE

VRT1

INVERTED_VIRTUAL_RESIDUE

LOWER_TERMINUS

UPPER_TERMINUS

BRANCH_POINT

TERMINUS

LOWERTERM_TRUNC

UPPERTERM_TRUNC

COARSE

ADDUCT

SC_ORBITALS

FRAGMENT

UPPERTERM_CAP

LOWERTERM_CAP

POLAR

HYDROPHOBIC

CHARGED

NEGATIVE_CHARGE

POSITIVE_CHARGE

AROMATIC

ALIPHATIC

CYCLIC

BETA_BRANCHED_SIDECHAIN

METALBINDING

SIDECHAIN_THIOL

DISULFIDE_BONDED

ELECTROPHILE

SIDECHAIN_AMINE

N_METHYLATED

MEMBRANE

PHOSPHONATE

PHOSPHONATE_UPPER

ACETYLATED_NTERMINUS

METHYLATED_CTERMINUS

DIMETHYLATED_CTERMINUS

ALPHA_AA

BETA_AA

GAMMA_AA

L_AA

D_AA

ACHIRAL_BACKBONE

ACHIRAL_SIDECHAIN

R_PEPTOID

S_PEPTOID

TAUTOMER

PURINE

PYRIMIDINE

L_RNA

D_RNA

METHYLATED_NA

TRIOSE

TETROSE

PENTOSE

HEXOSE

HEPTOSE

OCTOSE

NONOSE

ALDOSE

KETOSE

L_SUGAR

D_SUGAR

OXIROSE

OXETOSE

FURANOSE

PYRANOSE

SEPTANOSE

ALPHA_SUGAR

BETA_SUGAR

SIALIC_ACID

C1_MODIFIED

C2_MODIFIED

C3_MODIFIED

C4_MODIFIED

C5_MODIFIED

C6_MODIFIED

C7_MODIFIED

C8_MODIFIED

C9_MODIFIED

GLYCOSIDE

ALDONIC_ACID

URONIC_ACID

DEOXY_SUGAR

AMINO_SUGAR

ACETYLAMINO_SUGAR

GLYCOLYLAMINO_SUGAR

ACETYL_SUGAR

BUTYRYL_SUGAR

LACTYL_SUGAR

R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

PHOSPHORYLATED_SUGAR

SULFATED_SUGAR

SULFOAMINO_SUGAR

THIO_SUGAR

C_METHYLATED_SUGAR

PROPARGYL_SUGAR

FLUORO_SUGAR

METHYL_SUGAR

PHOSPHATE

SPINLABEL

DIAMAGNETIC

PARAMAGNETIC

N_PROPERTIES

ACETYLAMINO_SUGAR = <ResidueProperty.ACETYLAMINO_SUGAR: 121>
ACETYLATED_NTERMINUS = <ResidueProperty.ACETYLATED_NTERMINUS: 70>
ACETYL_SUGAR = <ResidueProperty.ACETYL_SUGAR: 123>
ACHIRAL_BACKBONE = <ResidueProperty.ACHIRAL_BACKBONE: 78>
ACHIRAL_SIDECHAIN = <ResidueProperty.ACHIRAL_SIDECHAIN: 79>
ADDUCT = <ResidueProperty.ADDUCT: 47>
ALDONIC_ACID = <ResidueProperty.ALDONIC_ACID: 117>
ALDOSE = <ResidueProperty.ALDOSE: 95>
ALIPHATIC = <ResidueProperty.ALIPHATIC: 58>
ALPHA_AA = <ResidueProperty.ALPHA_AA: 73>
ALPHA_SUGAR = <ResidueProperty.ALPHA_SUGAR: 104>
AMINO_SUGAR = <ResidueProperty.AMINO_SUGAR: 120>
ARAMID = <ResidueProperty.ARAMID: 12>
AROMATIC = <ResidueProperty.AROMATIC: 57>
BETA_AA = <ResidueProperty.BETA_AA: 74>
BETA_BRANCHED_SIDECHAIN = <ResidueProperty.BETA_BRANCHED_SIDECHAIN: 60>
BETA_SUGAR = <ResidueProperty.BETA_SUGAR: 105>
BRANCH_POINT = <ResidueProperty.BRANCH_POINT: 42>
BUTYRYL_SUGAR = <ResidueProperty.BUTYRYL_SUGAR: 124>
C1_MODIFIED = <ResidueProperty.C1_MODIFIED: 107>
C2_MODIFIED = <ResidueProperty.C2_MODIFIED: 108>
C3_MODIFIED = <ResidueProperty.C3_MODIFIED: 109>
C4_MODIFIED = <ResidueProperty.C4_MODIFIED: 110>
C5_MODIFIED = <ResidueProperty.C5_MODIFIED: 111>
C6_MODIFIED = <ResidueProperty.C6_MODIFIED: 112>
C7_MODIFIED = <ResidueProperty.C7_MODIFIED: 113>
C8_MODIFIED = <ResidueProperty.C8_MODIFIED: 114>
C9_MODIFIED = <ResidueProperty.C9_MODIFIED: 115>
CANONICAL_AA = <ResidueProperty.CANONICAL_AA: 4>
CANONICAL_NUCLEIC = <ResidueProperty.CANONICAL_NUCLEIC: 5>
CARBOHYDRATE = <ResidueProperty.CARBOHYDRATE: 25>
CHARGED = <ResidueProperty.CHARGED: 54>
COARSE = <ResidueProperty.COARSE: 46>
CYCLIC = <ResidueProperty.CYCLIC: 59>
C_METHYLATED_SUGAR = <ResidueProperty.C_METHYLATED_SUGAR: 131>
DEOXY_SUGAR = <ResidueProperty.DEOXY_SUGAR: 119>
DIAMAGNETIC = <ResidueProperty.DIAMAGNETIC: 137>
DIMETHYLATED_CTERMINUS = <ResidueProperty.DIMETHYLATED_CTERMINUS: 72>
DISULFIDE_BONDED = <ResidueProperty.DISULFIDE_BONDED: 63>
DNA = <ResidueProperty.DNA: 6>
D_AA = <ResidueProperty.D_AA: 77>
D_RNA = <ResidueProperty.D_RNA: 86>
D_SUGAR = <ResidueProperty.D_SUGAR: 98>
ELECTROPHILE = <ResidueProperty.ELECTROPHILE: 64>
FIRST_PROPERTY = <ResidueProperty.FIRST_PROPERTY: 1>
FLUORO_SUGAR = <ResidueProperty.FLUORO_SUGAR: 133>
FRAGMENT = <ResidueProperty.FRAGMENT: 49>
FURANOSE = <ResidueProperty.FURANOSE: 101>
GAMMA_AA = <ResidueProperty.GAMMA_AA: 75>
GLYCOLYLAMINO_SUGAR = <ResidueProperty.GLYCOLYLAMINO_SUGAR: 122>
GLYCOSIDE = <ResidueProperty.GLYCOSIDE: 116>
HEPTOSE = <ResidueProperty.HEPTOSE: 92>
HEXOSE = <ResidueProperty.HEXOSE: 91>
HYDROPHOBIC = <ResidueProperty.HYDROPHOBIC: 53>
INVERTED_VIRTUAL_RESIDUE = <ResidueProperty.INVERTED_VIRTUAL_RESIDUE: 39>
KETOSE = <ResidueProperty.KETOSE: 96>
LACTYL_SUGAR = <ResidueProperty.LACTYL_SUGAR: 125>
LIGAND = <ResidueProperty.LIGAND: 2>
LIPID = <ResidueProperty.LIPID: 26>
LOWERTERM_CAP = <ResidueProperty.LOWERTERM_CAP: 51>
LOWERTERM_TRUNC = <ResidueProperty.LOWERTERM_TRUNC: 44>
LOWER_TERMINUS = <ResidueProperty.LOWER_TERMINUS: 40>
L_AA = <ResidueProperty.L_AA: 76>
L_RNA = <ResidueProperty.L_RNA: 85>
L_SUGAR = <ResidueProperty.L_SUGAR: 97>
MEMBRANE = <ResidueProperty.MEMBRANE: 67>
METAL = <ResidueProperty.METAL: 31>
METALBINDING = <ResidueProperty.METALBINDING: 61>
META_ARAMID = <ResidueProperty.META_ARAMID: 14>
METHYLATED_CTERMINUS = <ResidueProperty.METHYLATED_CTERMINUS: 71>
METHYLATED_NA = <ResidueProperty.METHYLATED_NA: 87>
METHYL_SUGAR = <ResidueProperty.METHYL_SUGAR: 134>
NEGATIVE_CHARGE = <ResidueProperty.NEGATIVE_CHARGE: 55>
NONOSE = <ResidueProperty.NONOSE: 94>
NO_PROPERTY = <ResidueProperty.NO_PROPERTY: 0>
NUCLEOTIDE_DIPHOSPHATE = <ResidueProperty.NUCLEOTIDE_DIPHOSPHATE: 28>
N_METHYLATED = <ResidueProperty.N_METHYLATED: 66>
N_PROPERTIES = <ResidueProperty.PARAMAGNETIC: 138>
OCTOSE = <ResidueProperty.OCTOSE: 93>
OLIGOUREA = <ResidueProperty.OLIGOUREA: 11>
ORTHO_ARAMID = <ResidueProperty.ORTHO_ARAMID: 13>
OXETOSE = <ResidueProperty.OXETOSE: 100>
OXIROSE = <ResidueProperty.OXIROSE: 99>
PARAMAGNETIC = <ResidueProperty.PARAMAGNETIC: 138>
PARA_ARAMID = <ResidueProperty.PARA_ARAMID: 15>
PENTOSE = <ResidueProperty.PENTOSE: 90>
PEPTOID = <ResidueProperty.PEPTOID: 10>
PHOSPHATE = <ResidueProperty.PHOSPHATE: 135>
PHOSPHONATE = <ResidueProperty.PHOSPHONATE: 68>
PHOSPHONATE_UPPER = <ResidueProperty.PHOSPHONATE_UPPER: 69>
PHOSPHORYLATED_SUGAR = <ResidueProperty.PHOSPHORYLATED_SUGAR: 127>
PNA = <ResidueProperty.PNA: 9>
POLAR = <ResidueProperty.POLAR: 52>
POLYMER = <ResidueProperty.FIRST_PROPERTY: 1>
POSITIVE_CHARGE = <ResidueProperty.POSITIVE_CHARGE: 56>
POST_METHYLENE_META_ARAMID = <ResidueProperty.POST_METHYLENE_META_ARAMID: 20>
POST_METHYLENE_ORTHO_ARAMID = <ResidueProperty.POST_METHYLENE_ORTHO_ARAMID: 19>
POST_METHYLENE_PARA_ARAMID = <ResidueProperty.POST_METHYLENE_PARA_ARAMID: 21>
PRE_METHYLENE_META_ARAMID = <ResidueProperty.PRE_METHYLENE_META_ARAMID: 17>
PRE_METHYLENE_ORTHO_ARAMID = <ResidueProperty.PRE_METHYLENE_ORTHO_ARAMID: 16>
PRE_METHYLENE_PARA_ARAMID = <ResidueProperty.PRE_METHYLENE_PARA_ARAMID: 18>
PRE_METHYLENE_POST_METHYLENE_META_ARAMID = <ResidueProperty.PRE_METHYLENE_POST_METHYLENE_META_ARAMID: 23>
PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID = <ResidueProperty.PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID: 22>
PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID = <ResidueProperty.PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID: 24>
PROPARGYL_SUGAR = <ResidueProperty.PROPARGYL_SUGAR: 132>
PROTEIN = <ResidueProperty.PROTEIN: 3>
PURINE = <ResidueProperty.PURINE: 83>
PYRANOSE = <ResidueProperty.PYRANOSE: 102>
PYRIMIDINE = <ResidueProperty.PYRIMIDINE: 84>
R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <ResidueProperty.R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 126>
RNA = <ResidueProperty.RNA: 7>
R_PEPTOID = <ResidueProperty.R_PEPTOID: 80>
SC_ORBITALS = <ResidueProperty.SC_ORBITALS: 48>
SEPTANOSE = <ResidueProperty.SEPTANOSE: 103>
SIALIC_ACID = <ResidueProperty.SIALIC_ACID: 106>
SIDECHAIN_AMINE = <ResidueProperty.SIDECHAIN_AMINE: 65>
SIDECHAIN_THIOL = <ResidueProperty.SIDECHAIN_THIOL: 62>
SOLVENT = <ResidueProperty.SOLVENT: 36>
SPINLABEL = <ResidueProperty.SPINLABEL: 136>
SRI = <ResidueProperty.SRI: 29>
SULFATED_SUGAR = <ResidueProperty.SULFATED_SUGAR: 128>
SULFOAMINO_SUGAR = <ResidueProperty.SULFOAMINO_SUGAR: 129>
SURFACE = <ResidueProperty.SURFACE: 32>
S_PEPTOID = <ResidueProperty.S_PEPTOID: 81>
TAUTOMER = <ResidueProperty.TAUTOMER: 82>
TERMINUS = <ResidueProperty.TERMINUS: 43>
TERPENE = <ResidueProperty.TERPENE: 27>
TETROSE = <ResidueProperty.TETROSE: 89>
THIO_SUGAR = <ResidueProperty.THIO_SUGAR: 130>
TNA = <ResidueProperty.TNA: 8>
TP3 = <ResidueProperty.TP3: 34>
TRIAZOLE_LINKER = <ResidueProperty.TRIAZOLE_LINKER: 30>
TRIOSE = <ResidueProperty.TRIOSE: 88>
UPPERTERM_CAP = <ResidueProperty.UPPERTERM_CAP: 50>
UPPERTERM_TRUNC = <ResidueProperty.UPPERTERM_TRUNC: 45>
UPPER_TERMINUS = <ResidueProperty.UPPER_TERMINUS: 41>
URONIC_ACID = <ResidueProperty.URONIC_ACID: 118>
VIRTUALIZABLE_BY_PACKER = <ResidueProperty.VIRTUALIZABLE_BY_PACKER: 35>
VIRTUAL_RESIDUE = <ResidueProperty.VIRTUAL_RESIDUE: 37>
VRT1 = <ResidueProperty.VRT1: 38>
WATER = <ResidueProperty.WATER: 33>
property name
property value
class pyrosetta.rosetta.core.chemical.ResidueType

Bases: ResidueTypeBase

A class for defining a type of residue

This class contains the “chemical” information for residues as well as the ideal xyz and internal coordinates for a residue (generated xyz coordinates are found in core/conformation/Residue.hh). A ResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. ResidueTypes are generated through .params files, which are read from the database chemical/residue_types. For ligands, a parameter has to be provided to rosetta through the -extra_res_fa flag. Primary data are set through the residue_io.cc class. The primary data that are set are: atoms, mmatoms, orbitals, and properties of the particular ResidueType. These properties can be modified through patches, which create new ResidueTypes, and are controlled through PatchOperations.cc.

When a ResidueType is initially created, it’s created as a MutableResidueType, which represents the data as an atom graph, which facilitates atomistic modification. This class (the plain ResidueType class) is a “finalized” version of the ResidueType, which doesn’t permit modification, and is the main class used by most Rosetta simulations. It’s created from a MutableResidueType, and for efficiency represents the data as a “struct of vectors” representation.

Correspondingly, the main representation of atoms is different between the classes. Whereas the MutableResidueType uses an opaque “vertex descriptor” to identify atoms, the plain ResidueType class uses an integer index. The order of atoms is well-defined, with heavy atoms coming before hydrogens, and backbone atoms coming before sidechain atoms. (and hydrogens in the same order as the heavyatoms they’re connected to).

Properties: Properties of a residue include things like DNA, PROTEIN, CHARGED, etc. These properties indicate the type of residue it is and what properties are associated with the residue. They are set when read in. To add new ResidueProperties, add them to core/chemical/residue_properties/general_properties.list.

Orbitals: Orbitals are indexed separately from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. (I haven’t figured out how to get the reverse to work because of the separate indices.) Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals.

Haro_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

return indices of aromatic Hydrogens

C++: core::chemical::ResidueType::Haro_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpol_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

return indices of polar Hydrogens

C++: core::chemical::ResidueType::Hpol_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_apolar(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of non-polar hydrogens as potential carbon Hbond donors

C++: core::chemical::ResidueType::Hpos_apolar() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_polar(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of polar hydrogens as Hbond donors

C++: core::chemical::ResidueType::Hpos_polar() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

Hpos_polar_sc(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::chemical::ResidueType::Hpos_polar_sc() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

RNA_info(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::rna::RNA_Info

C++: core::chemical::ResidueType::RNA_info() const –> const class core::chemical::rna::RNA_Info &

aa(*args, **kwargs)

Overloaded function.

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const enum core::chemical::AA &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const std::string &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be “aa_unk”.

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

C++: core::chemical::ResidueTypeBase::aa() const –> const enum core::chemical::AA &

abase2(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

get index of an atom’s second base atom

C++: core::chemical::ResidueType::abase2(const unsigned long) const –> unsigned long

accpt_pos(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of atoms as Hbond acceptors

C++: core::chemical::ResidueType::accpt_pos() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

accpt_pos_sc(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of atoms as Hbond acceptors

C++: core::chemical::ResidueType::accpt_pos_sc() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

actcoord_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

get indices for atoms used to define actcoord

C++: core::chemical::ResidueType::actcoord_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

add_adduct(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: pyrosetta.rosetta.core.chemical.Adduct) → None

C++: core::chemical::ResidueTypeBase::add_adduct(class core::chemical::Adduct &) –> void

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: float) → None

Add a numeric property.

C++: core::chemical::ResidueTypeBase::add_numeric_property(const std::string &, double) –> void

add_property(*args, **kwargs)

Overloaded function.

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Add a property to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_property(const std::string &) –> void

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Add a property to this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::add_property(const enum core::chemical::ResidueProperty) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: str) → None

Add a string property.

C++: core::chemical::ResidueTypeBase::add_string_property(const std::string &, std::string) –> void

add_variant_type(*args, **kwargs)

Overloaded function.

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Add a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_variant_type(const enum core::chemical::VariantType) –> void

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Add a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::add_variant_type(const std::string &) –> void

all_bb_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

Indices of all backbone atoms, hydrogens and heavyatoms

C++: core::chemical::ResidueType::all_bb_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

all_sc_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

Indices of all sidechain atoms, hydrogens and heavyatoms

C++: core::chemical::ResidueType::all_sc_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::atom_alias(const std::string &) const –> const std::string &

atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

atom_base(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

get index of an atom’s base atom

C++: core::chemical::ResidueType::atom_base(const unsigned long) const –> unsigned long

atom_being_shadowed(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_shadowing: int) → int
Return the index of the atom that the “atom_shadowing”

atom is shadowing; returns zero if the “atom_shadowing” atom is not shadowing anyone.

C++: core::chemical::ResidueType::atom_being_shadowed(unsigned long) const –> unsigned long

atom_charge(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → float

C++: core::chemical::ResidueType::atom_charge(const unsigned long) const –> double

atom_depends_on_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int, connection_id: int) → bool

Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_connection(const unsigned long, const unsigned long) const –> bool

atom_depends_on_lower_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool

Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(const unsigned long) const –> bool

atom_depends_on_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_polymeric_connection(const unsigned long) const –> bool

atom_depends_on_upper_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(const unsigned long) const –> bool

atom_forms_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → bool

Does an atom form any inter-residue chemical bonds?

C++: core::chemical::ResidueType::atom_forms_residue_connection(const unsigned long) const –> bool

atom_has_property(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int, property: pyrosetta.rosetta.core.chemical.AtomProperty) → bool

C++: core::chemical::ResidueType::atom_has_property(const unsigned long, const enum core::chemical::AtomProperty) const –> bool

atom_index(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → int

get atom index by name

C++: core::chemical::ResidueType::atom_index(const std::string &) const –> unsigned long

atom_is_aro_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

C++: core::chemical::ResidueType::atom_is_aro_hydrogen(unsigned long) const –> bool

atom_is_backbone(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

is a backbone atom (heavy or hydrogen)?

C++: core::chemical::ResidueType::atom_is_backbone(const unsigned long) const –> bool

atom_is_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool
quick lookup: is the atom with the given index a hydrogen or not?

Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.

C++: core::chemical::ResidueType::atom_is_hydrogen(const unsigned long) const –> bool

atom_is_polar_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

C++: core::chemical::ResidueType::atom_is_polar_hydrogen(unsigned long) const –> bool

atom_is_sidechain(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

C++: core::chemical::ResidueType::atom_is_sidechain(const unsigned long) const –> bool

atom_name(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → str

get atom name by index

C++: core::chemical::ResidueType::atom_name(const unsigned long) const –> const std::string &

atom_properties(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.core.chemical.AtomProperties
Get the AtomicProperities object for the atom.

(Note this is only the manually set properties, not all the properties of the atom.)

C++: core::chemical::ResidueType::atom_properties(const unsigned long) const –> const class core::chemical::AtomProperties &

atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.core.chemical.AtomType

Get the chemical atom_type for this atom by it index number in this residue

If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below

C++: core::chemical::ResidueType::atom_type(const unsigned long) const –> const class core::chemical::AtomType &

atom_type_index(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

C++: core::chemical::ResidueType::atom_type_index(unsigned long) const –> unsigned long

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by reference the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set() const –> const class core::chemical::AtomTypeSet &

atom_type_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by const pointer the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set_ptr() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

atoms_are_bonded(self: pyrosetta.rosetta.core.chemical.ResidueType, atomindex1: int, atomindex2: int) → bool

Indicates whether or not two atom indices have a chemical bond linking them.

Note that this assumes that the Rosetta machinery is set up so that if atom 1 is bonded to atom 2, atom 2 is bonded to atom 1. This function breaks if that assumption breaks.

Vikram K. Mulligan

C++: core::chemical::ResidueType::atoms_are_bonded(const unsigned long, const unsigned long) const –> bool

atoms_last_controlled_by_chi(*args, **kwargs)

Overloaded function.

  1. atoms_last_controlled_by_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Read access to the atoms_last_controlled_by_chi_ array

C++: core::chemical::ResidueType::atoms_last_controlled_by_chi() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

  1. atoms_last_controlled_by_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chi: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Read access to the Atoms last controlled by a particular chi

C++: core::chemical::ResidueType::atoms_last_controlled_by_chi(unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

atoms_with_orb_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::chemical::ResidueType::atoms_with_orb_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

atoms_within_one_bond_of_a_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn: int) → pyrosetta.rosetta.utility.vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t
Returns a list of those atoms within one bond of a residue connection. For residue connection i,

its position in this array is a list of pairs of atom-id’s, the first of which is always the id for the atom forming residue connection i.

C++: core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(unsigned long) const –> const class utility::vector1<class utility::keys::Key2Tuple<unsigned long, unsigned long>, class std::allocator<class utility::keys::Key2Tuple<unsigned long, unsigned long> > > &

atoms_within_two_bonds_of_a_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn: int) → pyrosetta.rosetta.utility.vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t
Returns the list of those atoms within two bonds of

residue connection # resconn. Each entry in this list is a triple of atom-id’s, the first of which is always the id for the atom forming residue connection resconn.

C++: core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection(unsigned long) const –> const class utility::vector1<class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long>, class std::allocator<class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long> > > &

attached_H_begin(*args, **kwargs)

Overloaded function.

  1. attached_H_begin(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

for all heavy atoms, index numbers of their first attached Hydrogen

C++: core::chemical::ResidueType::attached_H_begin() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. attached_H_begin(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

index number of the first attached Hydrogen on an atom

C++: core::chemical::ResidueType::attached_H_begin(const unsigned long) const –> unsigned long

attached_H_end(*args, **kwargs)

Overloaded function.

  1. attached_H_end(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

for all heavy atoms, index numbers of their last attached Hydrogen

C++: core::chemical::ResidueType::attached_H_end() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. attached_H_end(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

index number of the last attached Hydrogen on an atom

C++: core::chemical::ResidueType::attached_H_end(const unsigned long) const –> unsigned long

backbone_aa(*args, **kwargs)

Overloaded function.

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

AA to use for backbone scoring

C++: core::chemical::ResidueTypeBase::backbone_aa(const std::string &) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

Set AA to use for backbone scoring directly (without string conversion).

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::backbone_aa(const enum core::chemical::AA) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

C++: core::chemical::ResidueTypeBase::backbone_aa() const –> const enum core::chemical::AA &

base_analogue(*args, **kwargs)

Overloaded function.

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for base-specific generalization (can be more

forgiving than na_analogue for new NA backbones)

C++: core::chemical::ResidueTypeBase::base_analogue(const std::string &) –> void

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for base features

C++: core::chemical::ResidueTypeBase::base_analogue() const –> const enum core::chemical::AA &

base_name(*args, **kwargs)

Overloaded function.

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

Get this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name() const –> const std::string &

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, base_name_in: str) -> None

Set this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name(const std::string &) –> void

bond_ringness(self: pyrosetta.rosetta.core.chemical.ResidueType, atomindex1: int, atomindex2: int) → pyrosetta.rosetta.core.chemical.BondRingness
Returns whether the bond between the atoms is in a ring.

Will return UnknownRingness for something which isn’t bonded.

C++: core::chemical::ResidueType::bond_ringness(const unsigned long, const unsigned long) const –> enum core::chemical::BondRingness

bond_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomindex1: int, atomindex2: int) → pyrosetta.rosetta.core.chemical.BondName
Returns the type of bond between the atoms

Will return UnknownBond for something which isn’t bonded.

C++: core::chemical::ResidueType::bond_type(const unsigned long, const unsigned long) const –> enum core::chemical::BondName

bondangle(self: pyrosetta.rosetta.core.chemical.ResidueType, bondang: int) → pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t
Return the indices for the set of atoms that define a particular

intraresidue angle

C++: core::chemical::ResidueType::bondangle(const unsigned long) const –> const class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long> &

bondangles_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long
Returns the list of all of the indices of all the intraresidue

bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::bondangles_for_atom(unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

bonded_neighbor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::chemical::ResidueType::bonded_neighbor(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

bonded_neighbor_types(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_core_chemical_BondName

C++: core::chemical::ResidueType::bonded_neighbor_types(const unsigned long) const –> const class utility::vector1<enum core::chemical::BondName, class std::allocator<enum core::chemical::BondName> > &

bonded_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of the orbitals bonded to an atom

C++: core::chemical::ResidueType::bonded_orbitals(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

bonds(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
Returns a list of all pairs of atoms which are bonded.

This returned list should only have only one entry per bond (So [1,2] and [2,1] will not both be present.)

C++: core::chemical::ResidueType::bonds() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

branch_connect_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

Return a list of names of atoms at non-polymer connections.

C++: core::chemical::ResidueType::branch_connect_atom_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

branch_connect_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

Return a list of indices of atoms at non-polymer connections.

C++: core::chemical::ResidueType::branch_connect_atoms() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

canonical_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::canonical_atom_alias(const std::string &) const –> const std::string &

canonical_atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::canonical_atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

carbohydrate_info(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::carbohydrates::CarbohydrateInfo

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

C++: core::chemical::ResidueType::carbohydrate_info() const –> class std::shared_ptr<const class core::chemical::carbohydrates::CarbohydrateInfo>

chi_2_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chi_index: int) → int

C++: core::chemical::ResidueType::chi_2_proton_chi(unsigned long) const –> unsigned long

chi_atoms(*args, **kwargs)

Overloaded function.

  1. chi_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

indices of the atoms which are used to define a given chi angle (chino)

C++: core::chemical::ResidueType::chi_atoms(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. chi_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

indices of the atoms which are used to define all the chi angles

C++: core::chemical::ResidueType::chi_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

chi_rotamers(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_std_pair_double_double_t

all rotamers bins (mean, std) for a given chi angle

C++: core::chemical::ResidueType::chi_rotamers(const unsigned long) const –> const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &

custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

Get a list of custom VariantType strings for this ResidueTypeBase (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::custom_variant_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

cut_bond_neighbor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of the bonded neighbors for an atom

C++: core::chemical::ResidueType::cut_bond_neighbor(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

debug_dump_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType) → None

Dump out atomnames and icoor values

C++: core::chemical::ResidueType::debug_dump_icoor() const –> void

defined_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_Adduct

get the adducts defined for this residue

C++: core::chemical::ResidueTypeBase::defined_adducts() const –> const class utility::vector1<class core::chemical::Adduct, class std::allocator<class core::chemical::Adduct> > &

defines_custom_rama_prepro_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → bool
Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_

defined for this ResidueTypeBase (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

C++: core::chemical::ResidueTypeBase::defines_custom_rama_prepro_map(const bool) const –> bool

delete_property(*args, **kwargs)

Overloaded function.

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Delete a property of this ResidueType.

C++: core::chemical::ResidueTypeBase::delete_property(const std::string &) –> void

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Delete a property of this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::delete_property(const enum core::chemical::ResidueProperty) –> void

dihedral(self: pyrosetta.rosetta.core.chemical.ResidueType, dihe: int) → pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t
Return the indices for the set of atoms that define a particular

intraresidue dihedral

C++: core::chemical::ResidueType::dihedral(const unsigned long) const –> const class utility::keys::Key4Tuple<unsigned long, unsigned long, unsigned long, unsigned long> &

dihedrals_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long
Returns the list of all of the indices of all the intraresidue

dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::dihedrals_for_atom(unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

element(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.core.chemical.element.Elements

Convenience function to go directly to the element enum

C++: core::chemical::ResidueType::element(unsigned long) const –> enum core::chemical::element::Elements

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by reference the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set() const –> const class core::chemical::ElementSet &

element_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by const pointer the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set_ptr() const –> class std::shared_ptr<const class core::chemical::ElementSet>

element_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → core::chemical::Element

C++: core::chemical::ResidueType::element_type(unsigned long) const –> class std::shared_ptr<const class core::chemical::Element>

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Turn on the ability to create VariantTypes “on-the-fly”.

C++: core::chemical::ResidueTypeBase::enable_custom_variant_types() –> void

first_sidechain_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

index of the first sidechain atom (heavy or hydrogen)

C++: core::chemical::ResidueType::first_sidechain_atom() const –> unsigned long

first_sidechain_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

index of the first sidehchain hydrogen

C++: core::chemical::ResidueType::first_sidechain_hydrogen() const –> unsigned long

force_nbr_atom_orient(*args, **kwargs)

Overloaded function.

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient() const –> bool

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, force_orient: bool) -> None

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient(bool) –> void

formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

C++: core::chemical::ResidueType::formal_charge(const unsigned long) const –> int

gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → core::chemical::gasteiger::GasteigerAtomTypeData
Get the Gasteiger atom type for this atom

Can be null if the atom type isn’t set.

C++: core::chemical::ResidueType::gasteiger_atom_type(unsigned long) const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>

gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::gasteiger::GasteigerAtomTypeSet

C++: core::chemical::ResidueTypeBase::gasteiger_atom_typeset() const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

get_base_type_cop(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

Get a pointer to this ResidueTypeBase’s base ResidueTypeBase.

Returns the base_type_cop_ pointer if not null, self pointer if null.

C++: core::chemical::ResidueType::get_base_type_cop() const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → str

Gets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::get_disulfide_atom_name() const –> const std::string &

get_metal_binding_atoms(*args, **kwargs)

Overloaded function.

  1. get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_string

  2. get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, metal_binding_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Gets indices of all atoms that can form bonds to metals

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::get_metal_binding_atoms(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

get_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → float

Get a numeric property, if it exists.

C++: core::chemical::ResidueTypeBase::get_numeric_property(const std::string &) const –> double

get_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(const bool) const –> const std::string &

get_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(const bool) const –> const std::string &

get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueType::get_self_ptr() –> class std::shared_ptr<class core::chemical::ResidueType>

get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.std.weak_ptr_core_chemical_ResidueType_t

C++: core::chemical::ResidueType::get_self_weak_ptr() –> class std::weak_ptr<class core::chemical::ResidueType>

get_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → str

Get a string property, if it exists.

C++: core::chemical::ResidueTypeBase::get_string_property(const std::string &) const –> std::string

has(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → bool

is this atom present in this residue?

C++: core::chemical::ResidueType::has(const std::string &) const –> bool

has_orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) → bool

is this orbital present in this residue?

C++: core::chemical::ResidueTypeBase::has_orbital(const std::string &) const –> bool

has_orbital_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this residue type define orbital types?

C++: core::chemical::ResidueTypeBase::has_orbital_types() const –> bool

has_polymer_dependent_groups(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Does this type have groups (not just single atoms) that are polymer-bond dependent?

Always returns false for non-polymeric residue types.

C++: core::chemical::ResidueType::has_polymer_dependent_groups() const –> bool

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> bool

Generic property access.

C++: core::chemical::ResidueTypeBase::has_property(const std::string &) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Generic property access, by ResidueProperty.

C++: core::chemical::ResidueTypeBase::has_property(const enum core::chemical::ResidueProperty) const –> bool

has_sc_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

does this residue have sidechain orbitals?

C++: core::chemical::ResidueType::has_sc_orbitals() const –> bool

has_shadow_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Returns true if this residue has shadow atoms, false otherwise.

C++: core::chemical::ResidueType::has_shadow_atoms() const –> bool

has_variant_type(*args, **kwargs)

Overloaded function.

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Generic variant access.

C++: core::chemical::ResidueTypeBase::has_variant_type(const enum core::chemical::VariantType) const –> bool

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> bool

Generic variant access by string.

C++: core::chemical::ResidueTypeBase::has_variant_type(const std::string &) const –> bool

heavyatom_has_polar_hydrogens(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

C++: core::chemical::ResidueType::heavyatom_has_polar_hydrogens(unsigned long) const –> bool

heavyatom_is_an_acceptor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

C++: core::chemical::ResidueType::heavyatom_is_an_acceptor(unsigned long) const –> bool

icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: int) → pyrosetta.rosetta.core.chemical.AtomICoor

AtomICoord of an atom

C++: core::chemical::ResidueType::icoor(const unsigned long) const –> const class core::chemical::AtomICoor &

ideal_xyz(*args, **kwargs)

Overloaded function.

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::ResidueType::ideal_xyz(const unsigned long) const –> class numeric::xyzVector<double>

  1. ideal_xyz(self: pyrosetta.rosetta.core.chemical.ResidueType, atomname: str) -> pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::ResidueType::ideal_xyz(const std::string &) const –> class numeric::xyzVector<double>

interchangeability_group(*args, **kwargs)

Overloaded function.

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our interchangeability-group id. Used to

determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag.

C++: core::chemical::ResidueTypeBase::interchangeability_group() const –> std::string

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: str) -> None

set our interchangeability-group id

C++: core::chemical::ResidueTypeBase::interchangeability_group(const std::string &) –> void

is_DNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is DNA?

C++: core::chemical::ResidueTypeBase::is_DNA() const –> bool

is_NA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is Nucleic Acid?

C++: core::chemical::ResidueType::is_NA() const –> bool

is_N_substituted(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is N-substituted? Returns true if this aa is aa_pro or aa_dpr, N-methyl amino acid, peptoid, or proline-like oligourea, false otherwise

C++: core::chemical::ResidueType::is_N_substituted() const –> bool

is_PNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is PNA?

C++: core::chemical::ResidueType::is_PNA() const –> bool

is_RNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is RNA?

C++: core::chemical::ResidueTypeBase::is_RNA() const –> bool

is_TNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is TNA?

C++: core::chemical::ResidueType::is_TNA() const –> bool

is_TP3(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Check if residue is a TP3 water.

C++: core::chemical::ResidueType::is_TP3() const –> bool

is_VRT1(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Check if residue is ‘VRT1’

C++: core::chemical::ResidueType::is_VRT1() const –> bool

is_acetylated_nterminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is acetylated n terminus

C++: core::chemical::ResidueType::is_acetylated_nterminus() const –> bool

is_achiral_backbone(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an achiral backbone?

C++: core::chemical::ResidueTypeBase::is_achiral_backbone() const –> bool

is_achiral_sidechain(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this have an achiral sidechain?

Includes gly and aib, and most (but not all) peptoids.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_achiral_sidechain() const –> bool

is_adduct(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is an adduct-modified residue?

C++: core::chemical::ResidueType::is_adduct() const –> bool

is_alpha_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an alpha-amino acid?

C++: core::chemical::ResidueType::is_alpha_aa() const –> bool

is_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an aramid?

C++: core::chemical::ResidueType::is_aramid() const –> bool

is_aromatic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is aromatic?

C++: core::chemical::ResidueType::is_aromatic() const –> bool

is_base_type(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this ResidueTypeBase a base type?

C++: core::chemical::ResidueType::is_base_type() const –> bool

is_beta_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a beta-amino acid?

C++: core::chemical::ResidueType::is_beta_aa() const –> bool

is_branch_point(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is a branch-point residue?

C++: core::chemical::ResidueType::is_branch_point() const –> bool

is_canonical(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a canonical residue type (nucleic acid or amino acid)?

Calls is_canonical_aa() and is_canonical_nucleic().

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical() const –> bool

is_canonical_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a canonical amino acid (CANONICAL_AA property)?

Only the standard amino acid types (ACDEFGHIKLMNPQRSTVWY) are canonical.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical_aa() const –> bool

is_canonical_nucleic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)?

Only the standard nucliec acid types (dA, dC, dG, dT, A, C, G, U) are canonical.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical_nucleic() const –> bool

is_carbohydrate(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is carbohydrate?

C++: core::chemical::ResidueType::is_carbohydrate() const –> bool

is_charged(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is charged?

C++: core::chemical::ResidueType::is_charged() const –> bool

is_coarse(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is coarse?

C++: core::chemical::ResidueType::is_coarse() const –> bool

is_cyclic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is cyclic?

C++: core::chemical::ResidueType::is_cyclic() const –> bool

is_d_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-amino acid?

C++: core::chemical::ResidueTypeBase::is_d_aa() const –> bool

is_d_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-RNA?

C++: core::chemical::ResidueTypeBase::is_d_rna() const –> bool

is_disulfide_bonded(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is disulfide?

C++: core::chemical::ResidueType::is_disulfide_bonded() const –> bool

is_gamma_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a gamma-amino acid?

C++: core::chemical::ResidueType::is_gamma_aa() const –> bool

is_inverted_virtual_residue(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Check if atom is an inverted virtual

C++: core::chemical::ResidueType::is_inverted_virtual_residue() const –> bool

is_l_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-amino acid?

C++: core::chemical::ResidueTypeBase::is_l_aa() const –> bool

is_l_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-RNA?

C++: core::chemical::ResidueTypeBase::is_l_rna() const –> bool

is_ligand(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is ligand?

C++: core::chemical::ResidueType::is_ligand() const –> bool

is_lipid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is lipid?

C++: core::chemical::ResidueType::is_lipid() const –> bool

is_lower_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is lower terminus?

C++: core::chemical::ResidueType::is_lower_terminus() const –> bool

is_membrane(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is membrane?

C++: core::chemical::ResidueType::is_membrane() const –> bool

is_meta_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a meta-aramid?

C++: core::chemical::ResidueType::is_meta_aramid() const –> bool

is_metal(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Return true if this residue type is a metal ion, false otherwise.

C++: core::chemical::ResidueType::is_metal() const –> bool

is_metalbinding(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool
Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.),

false otherwise.

C++: core::chemical::ResidueType::is_metalbinding() const –> bool

is_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Get whether this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_metapatched() const –> bool

is_methylated_cterminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is methylated c terminus

C++: core::chemical::ResidueType::is_methylated_cterminus() const –> bool

is_mirrored_type(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a D_AA, R_PEPTOID, or L_RNA?

Convenience function to avoid quering is_d_aa(), is_r_peptoid(), and is_l_rna() repeatedly.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_mirrored_type() const –> bool

is_n_methylated(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this residue N-methylated?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_n_methylated() const –> bool

is_oligourea(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an oligourea?

C++: core::chemical::ResidueType::is_oligourea() const –> bool

is_ortho_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an ortho-aramid?

C++: core::chemical::ResidueType::is_ortho_aramid() const –> bool

is_para_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a para-aramid?

C++: core::chemical::ResidueType::is_para_aramid() const –> bool

is_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is peptoid?

C++: core::chemical::ResidueTypeBase::is_peptoid() const –> bool

is_polar(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is polar?

C++: core::chemical::ResidueType::is_polar() const –> bool

is_polymer(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is polymer?

C++: core::chemical::ResidueTypeBase::is_polymer() const –> bool

is_post_methylene_meta_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a meta-aramid?

C++: core::chemical::ResidueType::is_post_methylene_meta_aramid() const –> bool

is_post_methylene_ortho_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an ortho-aramid?

C++: core::chemical::ResidueType::is_post_methylene_ortho_aramid() const –> bool

is_post_methylene_para_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a para-aramid?

C++: core::chemical::ResidueType::is_post_methylene_para_aramid() const –> bool

is_pre_methylene_meta_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a meta-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_meta_aramid() const –> bool

is_pre_methylene_ortho_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an ortho-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_ortho_aramid() const –> bool

is_pre_methylene_para_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a para-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_para_aramid() const –> bool

is_pre_methylene_post_methylene_meta_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a meta-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid() const –> bool

is_pre_methylene_post_methylene_ortho_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this an ortho-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid() const –> bool

is_pre_methylene_post_methylene_para_aramid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a para-aramid?

C++: core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid() const –> bool

is_protein(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is protein?

C++: core::chemical::ResidueTypeBase::is_protein() const –> bool

is_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) → bool

number of proton chis

C++: core::chemical::ResidueType::is_proton_chi(const unsigned long) const –> bool

is_purine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is purine?

C++: core::chemical::ResidueType::is_purine() const –> bool

is_pyrimidine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is pyrimidine?

C++: core::chemical::ResidueType::is_pyrimidine() const –> bool

is_r_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “R” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_r_peptoid() const –> bool

is_repulsive(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

Check if atom is repulsive.

C++: core::chemical::ResidueType::is_repulsive(const unsigned long) const –> bool

is_ring_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int, atom_id: int) → bool

Return whether this atom is in a particular ring

C++: core::chemical::ResidueType::is_ring_atom(const unsigned long, const unsigned long) const –> bool

is_s_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “S” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_s_peptoid() const –> bool

is_sidechain_amine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is sidechain amine?

C++: core::chemical::ResidueType::is_sidechain_amine() const –> bool

is_sidechain_thiol(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is thiol?

C++: core::chemical::ResidueType::is_sidechain_thiol() const –> bool

is_solvent(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a solvent molecule (SOLVENT property)?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_solvent() const –> bool

is_sri(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this one of SRI’s special heteropolymer building blocks?

C++: core::chemical::ResidueType::is_sri() const –> bool

is_surface(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is surface? (e.g. enamel)

C++: core::chemical::ResidueType::is_surface() const –> bool

is_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is terminus?

C++: core::chemical::ResidueType::is_terminus() const –> bool

is_triazolemer(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a triazolemer?

C++: core::chemical::ResidueType::is_triazolemer() const –> bool

is_upper_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is upper terminus?

C++: core::chemical::ResidueType::is_upper_terminus() const –> bool

is_virtual(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool

Check if atom is virtual.

C++: core::chemical::ResidueType::is_virtual(const unsigned long) const –> bool

is_virtual_residue(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool
Check if residue is ‘VIRTUAL_RESIDUE’

This ONLY checks the VIRTUAL_RESIDUE PROPERTY!

C++: core::chemical::ResidueType::is_virtual_residue() const –> bool

is_virtualizable_by_packer(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Is this a residue type that can be virtualized or devirtualized by the packer?

C++: core::chemical::ResidueType::is_virtualizable_by_packer() const –> bool

is_water(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

is this a water residue type?

C++: core::chemical::ResidueType::is_water() const –> bool

last_backbone_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

index of the last backbone heavy atom

C++: core::chemical::ResidueType::last_backbone_atom() const –> unsigned long

last_controlling_chi(*args, **kwargs)

Overloaded function.

  1. last_controlling_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Read access to the last_controlling_chi_ array

C++: core::chemical::ResidueType::last_controlling_chi() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. last_controlling_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> int

The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.

C++: core::chemical::ResidueType::last_controlling_chi(unsigned long) const –> unsigned long

low_ring_conformers(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

Low-energy ring conformers for each ring

C++: core::chemical::ResidueType::low_ring_conformers() const –> const class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > > &

lower_connect(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::ResidueConnection

C++: core::chemical::ResidueType::lower_connect() const –> const class core::chemical::ResidueConnection &

lower_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

index number of the atom which connects to the lower connection

C++: core::chemical::ResidueType::lower_connect_atom() const –> unsigned long

lower_connect_id(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

C++: core::chemical::ResidueType::lower_connect_id() const –> unsigned long

lowest_ring_conformers(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

For each ring, what’s the lowest conformer?

C++: core::chemical::ResidueType::lowest_ring_conformers() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

mainchain_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, mainchain_index: int) → int

index of mainchain atom

C++: core::chemical::ResidueType::mainchain_atom(const unsigned long) const –> unsigned long

mainchain_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of all mainchain atoms

C++: core::chemical::ResidueType::mainchain_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

mainchain_potentials_match(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, other: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Do the rama_prepro mainchain torsion potentials of this residue match another?

C++: core::chemical::ResidueTypeBase::mainchain_potentials_match(const class core::chemical::ResidueTypeBase &) const –> bool

static make(residue_type: core::chemical::MutableResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

Make a ResidueType from a Modifiable residue type.

In practice, this is the only way to create (or change) a ResidueType object.

By using a static function and not a constructor, this ensures that all ResidueTypes are on the heap (and can shared_from_this()), and allows us to do OP-requiring subobject updates in self_pointer_updates().

C++: core::chemical::ResidueType::make(const class core::chemical::MutableResidueType &) –> class std::shared_ptr<const class core::chemical::ResidueType>

mass(self: pyrosetta.rosetta.core.chemical.ResidueType) → float

get the molecular weight of this residue

C++: core::chemical::ResidueType::mass() const –> double

mm_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → core::chemical::MMAtomType

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueType::mm_atom_type(const unsigned long) const –> const class core::chemical::MMAtomType &

mm_atom_type_index(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

C++: core::chemical::ResidueType::mm_atom_type_index(unsigned long) const –> unsigned long

mm_atom_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::MMAtomTypeSet

C++: core::chemical::ResidueTypeBase::mm_atom_types_ptr() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mm_name(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → str

C++: core::chemical::ResidueType::mm_name(unsigned long) const –> const std::string &

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.TypeSetMode

C++: core::chemical::ResidueTypeBase::mode() const –> enum core::chemical::TypeSetMode

n_hbond_acceptors(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of hbond_acceptors

C++: core::chemical::ResidueType::n_hbond_acceptors() const –> unsigned long

n_hbond_donors(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of hbond_donors

C++: core::chemical::ResidueType::n_hbond_donors() const –> unsigned long

n_non_polymeric_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

C++: core::chemical::ResidueType::n_non_polymeric_residue_connections() const –> unsigned long

n_nus(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

Return number of nu (internal ring) angles.

C++: core::chemical::ResidueType::n_nus() const –> unsigned long

n_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of orbitals

C++: core::chemical::ResidueTypeBase::n_orbitals() const –> unsigned long

n_polymeric_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

C++: core::chemical::ResidueType::n_polymeric_residue_connections() const –> unsigned long

n_possible_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of ResidueConnections, counting polymeric residue connections

C++: core::chemical::ResidueType::n_possible_residue_connections() const –> unsigned long

n_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of proton chis

C++: core::chemical::ResidueType::n_proton_chi() const –> unsigned long

n_residue_connections_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → int

How many inter-residue chemical bonds does a particular atom form?

C++: core::chemical::ResidueType::n_residue_connections_for_atom(const unsigned long) const –> unsigned long

n_ring_conformer_sets(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

C++: core::chemical::ResidueType::n_ring_conformer_sets() const –> unsigned long

n_rings(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

Return the number of rings in this residue.

C++: core::chemical::ResidueType::n_rings() const –> unsigned long

n_virtual_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and

can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueType::n_virtual_atoms() const –> unsigned long

na_analogue(*args, **kwargs)

Overloaded function.

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for fragment sampling and some scoring purposes

C++: core::chemical::ResidueTypeBase::na_analogue(const std::string &) –> void

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for fragment sampling/scoring.

C++: core::chemical::ResidueTypeBase::na_analogue() const –> const enum core::chemical::AA &

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our (unique) residue name

C++: core::chemical::ResidueTypeBase::name() const –> const std::string &

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our (unique) residue name

C++: core::chemical::ResidueTypeBase::name(const std::string &) –> void

name1(*args, **kwargs)

Overloaded function.

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 1letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name3 string.

C++: core::chemical::ResidueTypeBase::name1() const –> char

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, code: str) -> None

set our 1letter code

C++: core::chemical::ResidueTypeBase::name1(const char) –> void

name3(*args, **kwargs)

Overloaded function.

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 3letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The “name3” is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

C++: core::chemical::ResidueTypeBase::name3() const –> const std::string &

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our 3letter code

C++: core::chemical::ResidueTypeBase::name3(const std::string &) –> void

natoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of atoms

C++: core::chemical::ResidueType::natoms() const –> unsigned long

nbonds(*args, **kwargs)

Overloaded function.

  1. nbonds(self: pyrosetta.rosetta.core.chemical.ResidueType) -> int

number of bonds

C++: core::chemical::ResidueType::nbonds() const –> unsigned long

  1. nbonds(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

number of bonds for given atom

C++: core::chemical::ResidueType::nbonds(unsigned long) const –> unsigned long

nbr_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

get nbr_atom used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_atom() const –> unsigned long

nbr_radius(self: pyrosetta.rosetta.core.chemical.ResidueType) → float

get nbr_radius_ used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_radius() const –> double

nbrs(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)

C++: core::chemical::ResidueType::nbrs(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

nchi(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of chi angles

C++: core::chemical::ResidueType::nchi() const –> unsigned long

ndihe(self: pyrosetta.rosetta.core.chemical.ResidueType) → int
Return the number of intraresidue dihedrals. This covers all pairs

of atoms that are separated by four bonds, and all pairs of intervening atoms.

C++: core::chemical::ResidueType::ndihe() const –> unsigned long

net_formal_charge(*args, **kwargs)

Overloaded function.

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> int

Get the nominal net formal charge on this residue type.

This may not match the sum of the formal charges on the atoms

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge() const –> long

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, charge_in: int) -> None

Set the nominal net formal charge on this residue type.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge(long) –> void

new_orbital_icoor_data(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) → core::chemical::orbitals::ICoorOrbitalData

C++: core::chemical::ResidueType::new_orbital_icoor_data(const unsigned long) const –> const class core::chemical::orbitals::ICoorOrbitalData &

nheavyatoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

number of heavy atoms

C++: core::chemical::ResidueType::nheavyatoms() const –> unsigned long

nu_atoms(*args, **kwargs)

Overloaded function.

  1. nu_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, nu_index: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return indices of the atoms used to define a given nu (internal ring) angle.

C++: core::chemical::ResidueType::nu_atoms(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. nu_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Return list of indices of the atoms used to define all the nu (internal ring) angles.

C++: core::chemical::ResidueType::nu_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

num_bondangles(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

get number of intraresidue bond angles

C++: core::chemical::ResidueType::num_bondangles() const –> unsigned long

number_bonded_heavyatoms(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

indicates how many heavyatom bonded neighbors an atom has

C++: core::chemical::ResidueType::number_bonded_heavyatoms(const unsigned long) const –> unsigned long

number_bonded_hydrogens(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int

indicates how many proton bonded neighbors an atom has

C++: core::chemical::ResidueType::number_bonded_hydrogens(const unsigned long) const –> unsigned long

orbital(*args, **kwargs)

Overloaded function.

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const unsigned long) const –> const class core::chemical::Orbital &

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const std::string &) const –> const class core::chemical::Orbital &

orbital_icoor_data(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) → core::chemical::orbitals::ICoorOrbitalData

C++: core::chemical::ResidueType::orbital_icoor_data(const unsigned long) const –> const class core::chemical::orbitals::ICoorOrbitalData &

orbital_index(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → int

get orbital index by name

C++: core::chemical::ResidueTypeBase::orbital_index(const std::string &) const –> unsigned long

orbital_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) → core::chemical::orbitals::OrbitalType

C++: core::chemical::ResidueTypeBase::orbital_type(const unsigned long) const –> const class core::chemical::orbitals::OrbitalType &

orbital_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::orbitals::OrbitalTypeSet

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueTypeBase::orbital_types_ptr() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

path_distance(*args, **kwargs)

Overloaded function.

  1. path_distance(self: pyrosetta.rosetta.core.chemical.ResidueType, at1: int, at2: int) -> int

path distance (number of bonds separated) between a pair of atoms

C++: core::chemical::ResidueType::path_distance(unsigned long, unsigned long) const –> int

  1. path_distance(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> pyrosetta.rosetta.utility.vector1_int

shortest path distance for an atom to all other residue atoms

C++: core::chemical::ResidueType::path_distance(unsigned long) const –> const class utility::vector1<int, class std::allocator<int> > &

path_distances(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t

accessor of path_distance_ data for this residue, which is a 2D array

C++: core::chemical::ResidueType::path_distances() const –> const class utility::vector1<class utility::vector1<int, class std::allocator<int> >, class std::allocator<class utility::vector1<int, class std::allocator<int> > > > &

print_bondangles(self: pyrosetta.rosetta.core.chemical.ResidueType) → None

print intraresidue bond angles to standard out

C++: core::chemical::ResidueType::print_bondangles() const –> void

print_pretty_path_distances(self: pyrosetta.rosetta.core.chemical.ResidueType) → None

print chemical-bond path distances to standard out

C++: core::chemical::ResidueType::print_pretty_path_distances() const –> void

properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.ResidueProperties

Access the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::properties() const –> const class core::chemical::ResidueProperties &

proton_chi_2_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi_id: int) → int

translate proton_chi to global chi

C++: core::chemical::ResidueType::proton_chi_2_chi(unsigned long) const –> unsigned long

proton_chi_extra_samples(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi: int) → pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::ResidueType::proton_chi_extra_samples(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

proton_chi_samples(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi: int) → pyrosetta.rosetta.utility.vector1_double

C++: core::chemical::ResidueType::proton_chi_samples(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

remap_pdb_atom_names(*args, **kwargs)

Overloaded function.

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, rename: bool) -> None

Turn on geometry-based atom renaming when loading this residue type from PDB files

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names(bool) –> void

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Are we using geometry-based atom renaming when loading this residue type from PDB

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names() const –> bool

remove_variant_type(*args, **kwargs)

Overloaded function.

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Remove a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const enum core::chemical::VariantType) –> void

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Remove a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const std::string &) –> void

report_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

C++: core::chemical::ResidueTypeBase::report_adducts() const –> void

requires_actcoord(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool

require actcoord?

C++: core::chemical::ResidueType::requires_actcoord() const –> bool

reset_mainchain_torsion_potential_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set the names of the mainchain torsion potential maps to use to “”.

Also resets the mainchain torsion potential filename strings.

C++: core::chemical::ResidueTypeBase::reset_mainchain_torsion_potential_names() –> void

residue_connect_atom_index(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn_id: int) → int

C++: core::chemical::ResidueType::residue_connect_atom_index(const unsigned long) const –> unsigned long

residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, i: int) → core::chemical::ResidueConnection

Get a ResidueConection.

C++: core::chemical::ResidueType::residue_connection(const unsigned long) const –> const class core::chemical::ResidueConnection &

residue_connection_id_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → int
Convenience access function for the residue connection

at a particular atom; requires that there is exactly one residue connection at this atom.

C++: core::chemical::ResidueType::residue_connection_id_for_atom(const unsigned long) const –> unsigned long

residue_connection_is_polymeric(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn_id: int) → bool

C++: core::chemical::ResidueType::residue_connection_is_polymeric(const unsigned long) const –> bool

residue_connections_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_unsigned_long
/

Accessor for the full complement of residue connections for a single atom.

C++: core::chemical::ResidueType::residue_connections_for_atom(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

ring_atoms(*args, **kwargs)

Overloaded function.

  1. ring_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return list of indices of the atoms within this residue’s nth cycle, not counting virtual atoms.

C++: core::chemical::ResidueType::ring_atoms(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

  1. ring_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Return list of indices of the atoms within this residue’s cycles, not counting virtual atoms.

C++: core::chemical::ResidueType::ring_atoms() const –> const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &

ring_conformer_set(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int) → core::chemical::rings::RingConformerSet
Return a pointer to the object containing the set of ring

conformers possible for this residue’s nth cycle.

C++: core::chemical::ResidueType::ring_conformer_set(unsigned long) const –> class std::shared_ptr<const class core::chemical::rings::RingConformerSet>

ring_saturation_type(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int) → pyrosetta.rosetta.core.chemical.rings.RingSaturationType

Return the saturation level of this residue’s nth cycle.

C++: core::chemical::ResidueType::ring_saturation_type(const unsigned long) const –> enum core::chemical::rings::RingSaturationType

ring_saturation_types(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType

Return the saturation level for all of this residue’s cycles.

C++: core::chemical::ResidueType::ring_saturation_types() const –> const class utility::vector1<enum core::chemical::rings::RingSaturationType, class std::allocator<enum core::chemical::rings::RingSaturationType> > &

root_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

get root_atom used as the base of the icoor tree.

C++: core::chemical::ResidueType::root_atom() const –> unsigned long

rotamer_library_specification(*args, **kwargs)

Overloaded function.

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, : core::chemical::rotamers::RotamerLibrarySpecification) -> None

C++: core::chemical::ResidueTypeBase::rotamer_library_specification(class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>) –> void

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> core::chemical::rotamers::RotamerLibrarySpecification

C++: core::chemical::ResidueTypeBase::rotamer_library_specification() const –> class std::shared_ptr<const class core::chemical::rotamers::RotamerLibrarySpecification>

rotamer_library_specification_nonconst(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::rotamers::RotamerLibrarySpecification

Nonconst access to the RotamerLibrarySpecification.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst() –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

select_orient_atoms(*args, **kwargs)

Overloaded function.

  1. select_orient_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, center: int, nbr1: int, nbr2: int) -> None

Selects three atoms for orienting this residue type

C++: core::chemical::ResidueType::select_orient_atoms(unsigned long &, unsigned long &, unsigned long &) const –> void

  1. select_orient_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> Tuple[int, int, int]

Selects three atoms for orienting this residue type

Returns tuple of form [center, nbr1, nbr2]

C++: core::chemical::ResidueType::select_orient_atoms() const –> class std::tuple<unsigned long, unsigned long, unsigned long>

select_orient_atoms_standard_logic(self: pyrosetta.rosetta.core.chemical.ResidueType, center: int, nbr1: int, nbr2: int, ignore_virtuals: bool) → None

Pick atoms to use for orienting one Residue onto another, using standard logic.

Standard logic applies to case in which (a) the residue has backbone atoms, and (b) the residue has sidechain atoms, and (c) the orient mode has not been set explicitly to force_nbr_atom_orient. We loop through all backbone atoms and find the first atom that is bonded to a sidechain atom AND two other backbone atoms. The first such atom becomes “center”, and its two backbone neighbors become “nbr1” and “nbr2”.

If ignore_virtuals is true, none of the atoms involved can be virtuals. If false, they can be.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueType::select_orient_atoms_standard_logic(unsigned long &, unsigned long &, unsigned long &, const bool) const –> void

set_adduct_flag(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: bool) → None

C++: core::chemical::ResidueTypeBase::set_adduct_flag(bool) –> void

set_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, n: str) → None

Sets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::set_disulfide_atom_name(const std::string &) –> void

set_gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::gasteiger::GasteigerAtomTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>) –> void

set_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set that this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::set_metapatched() –> void

set_orbital_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::orbitals::OrbitalTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_orbital_typeset(class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>) –> void

set_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, properties: pyrosetta.rosetta.core.chemical.ResidueProperties) → None

Set the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::set_properties(class std::shared_ptr<class core::chemical::ResidueProperties>) –> void

set_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str, pre_proline_position: bool) → None

Set the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_mainchain_torsion_potential_name(const std::string &, const bool) –> void

set_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, filename_in: str, pre_proline_position: bool) → None

Set the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_map_file_name(const std::string &, const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.ResidueType) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.ResidueType, output: pyrosetta.rosetta.std.ostream) -> None

  3. show(self: pyrosetta.rosetta.core.chemical.ResidueType, output: pyrosetta.rosetta.std.ostream, output_atomic_details: bool) -> None

Generate string representation of ResidueType for debugging purposes.

C++: core::chemical::ResidueType::show(std::ostream &, bool) const –> void

show_all_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::ResidueType::show_all_atom_names(std::ostream &) const –> void

strip_rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Remove any rotamer library specifications attached to this ResidueTypeBase.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::strip_rotamer_library_specification() –> void

upper_connect(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::ResidueConnection

C++: core::chemical::ResidueType::upper_connect() const –> const class core::chemical::ResidueConnection &

upper_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

index number of the atom which connects to the upper connection

C++: core::chemical::ResidueType::upper_connect_atom() const –> unsigned long

upper_connect_id(self: pyrosetta.rosetta.core.chemical.ResidueType) → int

C++: core::chemical::ResidueType::upper_connect_id() const –> unsigned long

variant_type_enums(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Get a vector of VariantType enums for this ResidueTypeBase.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::variant_type_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

get all the variant types for this ResidueTypeBase

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants.

– rhiju (merging roccomoretti/restypeset_fiddle)

C++: core::chemical::ResidueTypeBase::variant_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

within1bonds_sets_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
Returns a list of pairs for atom# atomid where

first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::within1bonds_sets_for_atom(unsigned long) const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

within2bonds_sets_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
Returns a list of pairs for atom # atomid where

first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::within2bonds_sets_for_atom(unsigned long) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

class pyrosetta.rosetta.core.chemical.ResidueTypeBase

Bases: pybind11_object

A base class for definiting types of residues

This class is a base class for the “chemical” information for residues in Rosetta. It’s a base class for two different classes. ResidueType, which is the main class used by Rosetta, but which is a fixed-content type, and MutableResidueType, which is a modifiable class. The two type also differ also in how Atoms information is represented. The atom information in MutableResidueType is represented in a molecular graph, which is more convenient for modification, with atoms referenced primarily by “vertex descriptor” in the graph. The atom information in ResidueType is in a struct-of-arrays format, which allows better optimization, with atoms in a defined order. There are also differences in guarantees for each class. ResidueType has certain atom ordering guarantees which MutableResidueType lacks.

To accomodate the two different classes, this base class only stores the common, (non-atom dependent) information, along with some convenient accessors.

See the documentation of each class for more information.

A note on things which belong in this class: Only include things which are atom-independent, and are “primary” information. (Things which can/should be derived from atoms or other info should be placed in the plain ResidueType class, and updated on MutableResidueType -> ResidueType conversion. You can also include (as a virtual method) functions needed for PatchSelector function, but any atom indexing/references should be name-based.

aa(*args, **kwargs)

Overloaded function.

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const enum core::chemical::AA &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueTypeBase::aa(const std::string &) –> void

  1. aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be “aa_unk”.

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

C++: core::chemical::ResidueTypeBase::aa() const –> const enum core::chemical::AA &

add_adduct(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: pyrosetta.rosetta.core.chemical.Adduct) → None

C++: core::chemical::ResidueTypeBase::add_adduct(class core::chemical::Adduct &) –> void

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: float) → None

Add a numeric property.

C++: core::chemical::ResidueTypeBase::add_numeric_property(const std::string &, double) –> void

add_property(*args, **kwargs)

Overloaded function.

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Add a property to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_property(const std::string &) –> void

  1. add_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Add a property to this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::add_property(const enum core::chemical::ResidueProperty) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str, value: str) → None

Add a string property.

C++: core::chemical::ResidueTypeBase::add_string_property(const std::string &, std::string) –> void

add_variant_type(*args, **kwargs)

Overloaded function.

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Add a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::add_variant_type(const enum core::chemical::VariantType) –> void

  1. add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Add a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::add_variant_type(const std::string &) –> void

atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::atom_alias(const std::string &) const –> const std::string &

atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by reference the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set() const –> const class core::chemical::AtomTypeSet &

atom_type_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::AtomTypeSet

access by const pointer the atomset for which this residue is constructed

C++: core::chemical::ResidueTypeBase::atom_type_set_ptr() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

backbone_aa(*args, **kwargs)

Overloaded function.

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

AA to use for backbone scoring

C++: core::chemical::ResidueTypeBase::backbone_aa(const std::string &) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: pyrosetta.rosetta.core.chemical.AA) -> None

Set AA to use for backbone scoring directly (without string conversion).

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::backbone_aa(const enum core::chemical::AA) –> void

  1. backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

C++: core::chemical::ResidueTypeBase::backbone_aa() const –> const enum core::chemical::AA &

base_analogue(*args, **kwargs)

Overloaded function.

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for base-specific generalization (can be more

forgiving than na_analogue for new NA backbones)

C++: core::chemical::ResidueTypeBase::base_analogue(const std::string &) –> void

  1. base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for base features

C++: core::chemical::ResidueTypeBase::base_analogue() const –> const enum core::chemical::AA &

base_name(*args, **kwargs)

Overloaded function.

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

Get this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name() const –> const std::string &

  1. base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, base_name_in: str) -> None

Set this ResidueTypeBase’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueTypeBase::base_name(const std::string &) –> void

canonical_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → str

returns atom alias

C++: core::chemical::ResidueTypeBase::canonical_atom_alias(const std::string &) const –> const std::string &

canonical_atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.std.map_std_string_std_string

returns atom aliases

C++: core::chemical::ResidueTypeBase::canonical_atom_aliases() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

Get a list of custom VariantType strings for this ResidueTypeBase (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::custom_variant_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

defined_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_Adduct

get the adducts defined for this residue

C++: core::chemical::ResidueTypeBase::defined_adducts() const –> const class utility::vector1<class core::chemical::Adduct, class std::allocator<class core::chemical::Adduct> > &

defines_custom_rama_prepro_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → bool
Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_

defined for this ResidueTypeBase (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

C++: core::chemical::ResidueTypeBase::defines_custom_rama_prepro_map(const bool) const –> bool

delete_property(*args, **kwargs)

Overloaded function.

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> None

Delete a property of this ResidueType.

C++: core::chemical::ResidueTypeBase::delete_property(const std::string &) –> void

  1. delete_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> None

Delete a property of this ResidueType, by properties enum.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeBase::delete_property(const enum core::chemical::ResidueProperty) –> void

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by reference the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set() const –> const class core::chemical::ElementSet &

element_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ElementSet

access by const pointer the element set for which this residue is constructed

C++: core::chemical::ResidueTypeBase::element_set_ptr() const –> class std::shared_ptr<const class core::chemical::ElementSet>

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Turn on the ability to create VariantTypes “on-the-fly”.

C++: core::chemical::ResidueTypeBase::enable_custom_variant_types() –> void

force_nbr_atom_orient(*args, **kwargs)

Overloaded function.

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient() const –> bool

  1. force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, force_orient: bool) -> None

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueTypeBase::force_nbr_atom_orient(bool) –> void

gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::gasteiger::GasteigerAtomTypeSet

C++: core::chemical::ResidueTypeBase::gasteiger_atom_typeset() const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

get_base_type_cop(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::ResidueType

Get a pointer to this ResidueTypeBase’s base ResidueTypeBase.

NOTE: Behavior when is_base_type() == true varies by subclass!

C++: core::chemical::ResidueTypeBase::get_base_type_cop() const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → str

Gets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::get_disulfide_atom_name() const –> const std::string &

get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::ResidueTypeBase::get_metal_binding_atoms() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

get_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → float

Get a numeric property, if it exists.

C++: core::chemical::ResidueTypeBase::get_numeric_property(const std::string &) const –> double

get_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(const bool) const –> const std::string &

get_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, pre_proline_position: bool) → str

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(const bool) const –> const std::string &

get_string_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, tag: str) → str

Get a string property, if it exists.

C++: core::chemical::ResidueTypeBase::get_string_property(const std::string &) const –> std::string

has(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, atom_name: str) → bool

is this atom present in this residue?

C++: core::chemical::ResidueTypeBase::has(const std::string &) const –> bool

has_orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) → bool

is this orbital present in this residue?

C++: core::chemical::ResidueTypeBase::has_orbital(const std::string &) const –> bool

has_orbital_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this residue type define orbital types?

C++: core::chemical::ResidueTypeBase::has_orbital_types() const –> bool

has_property(*args, **kwargs)

Overloaded function.

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: str) -> bool

Generic property access.

C++: core::chemical::ResidueTypeBase::has_property(const std::string &) const –> bool

  1. has_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Generic property access, by ResidueProperty.

C++: core::chemical::ResidueTypeBase::has_property(const enum core::chemical::ResidueProperty) const –> bool

has_variant_type(*args, **kwargs)

Overloaded function.

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Generic variant access.

C++: core::chemical::ResidueTypeBase::has_variant_type(const enum core::chemical::VariantType) const –> bool

  1. has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> bool

Generic variant access by string.

C++: core::chemical::ResidueTypeBase::has_variant_type(const std::string &) const –> bool

interchangeability_group(*args, **kwargs)

Overloaded function.

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our interchangeability-group id. Used to

determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag.

C++: core::chemical::ResidueTypeBase::interchangeability_group() const –> std::string

  1. interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: str) -> None

set our interchangeability-group id

C++: core::chemical::ResidueTypeBase::interchangeability_group(const std::string &) –> void

is_DNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is DNA?

C++: core::chemical::ResidueTypeBase::is_DNA() const –> bool

is_RNA(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is RNA?

C++: core::chemical::ResidueTypeBase::is_RNA() const –> bool

is_achiral_backbone(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an achiral backbone?

C++: core::chemical::ResidueTypeBase::is_achiral_backbone() const –> bool

is_achiral_sidechain(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Does this have an achiral sidechain?

Includes gly and aib, and most (but not all) peptoids.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_achiral_sidechain() const –> bool

is_base_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this ResidueTypeBase a base type?

C++: core::chemical::ResidueTypeBase::is_base_type() const –> bool

is_d_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-amino acid?

C++: core::chemical::ResidueTypeBase::is_d_aa() const –> bool

is_d_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this a d-RNA?

C++: core::chemical::ResidueTypeBase::is_d_rna() const –> bool

is_l_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-amino acid?

C++: core::chemical::ResidueTypeBase::is_l_aa() const –> bool

is_l_rna(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is this an l-RNA?

C++: core::chemical::ResidueTypeBase::is_l_rna() const –> bool

is_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Get whether this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_metapatched() const –> bool

is_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is peptoid?

C++: core::chemical::ResidueTypeBase::is_peptoid() const –> bool

is_polymer(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is polymer?

C++: core::chemical::ResidueTypeBase::is_polymer() const –> bool

is_protein(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

is protein?

C++: core::chemical::ResidueTypeBase::is_protein() const –> bool

is_r_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “R” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_r_peptoid() const –> bool

is_s_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Is this a peptoid with a chiral side-chain with “S” chirality?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::is_s_peptoid() const –> bool

mainchain_potentials_match(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, other: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Do the rama_prepro mainchain torsion potentials of this residue match another?

C++: core::chemical::ResidueTypeBase::mainchain_potentials_match(const class core::chemical::ResidueTypeBase &) const –> bool

mm_atom_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::MMAtomTypeSet

C++: core::chemical::ResidueTypeBase::mm_atom_types_ptr() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.TypeSetMode

C++: core::chemical::ResidueTypeBase::mode() const –> enum core::chemical::TypeSetMode

n_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of orbitals

C++: core::chemical::ResidueTypeBase::n_orbitals() const –> unsigned long

n_virtual_atoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and

can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::n_virtual_atoms() const –> unsigned long

na_analogue(*args, **kwargs)

Overloaded function.

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, type: str) -> None

NA to use for fragment sampling and some scoring purposes

C++: core::chemical::ResidueTypeBase::na_analogue(const std::string &) –> void

  1. na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for fragment sampling/scoring.

C++: core::chemical::ResidueTypeBase::na_analogue() const –> const enum core::chemical::AA &

name(*args, **kwargs)

Overloaded function.

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our (unique) residue name

C++: core::chemical::ResidueTypeBase::name() const –> const std::string &

  1. name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our (unique) residue name

C++: core::chemical::ResidueTypeBase::name(const std::string &) –> void

name1(*args, **kwargs)

Overloaded function.

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 1letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name3 string.

C++: core::chemical::ResidueTypeBase::name1() const –> char

  1. name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, code: str) -> None

set our 1letter code

C++: core::chemical::ResidueTypeBase::name1(const char) –> void

name3(*args, **kwargs)

Overloaded function.

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> str

get our 3letter code. This is set in the

ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The “name3” is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

C++: core::chemical::ResidueTypeBase::name3() const –> const std::string &

  1. name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str) -> None

set our 3letter code

C++: core::chemical::ResidueTypeBase::name3(const std::string &) –> void

natoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of atoms

C++: core::chemical::ResidueTypeBase::natoms() const –> unsigned long

nbonds(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of bonds

C++: core::chemical::ResidueTypeBase::nbonds() const –> unsigned long

net_formal_charge(*args, **kwargs)

Overloaded function.

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> int

Get the nominal net formal charge on this residue type.

This may not match the sum of the formal charges on the atoms

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge() const –> long

  1. net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, charge_in: int) -> None

Set the nominal net formal charge on this residue type.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::net_formal_charge(long) –> void

nheavyatoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → int

number of heavy atoms

C++: core::chemical::ResidueTypeBase::nheavyatoms() const –> unsigned long

orbital(*args, **kwargs)

Overloaded function.

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const unsigned long) const –> const class core::chemical::Orbital &

  1. orbital(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_name: str) -> core::chemical::Orbital

C++: core::chemical::ResidueTypeBase::orbital(const std::string &) const –> const class core::chemical::Orbital &

orbital_index(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name: str) → int

get orbital index by name

C++: core::chemical::ResidueTypeBase::orbital_index(const std::string &) const –> unsigned long

orbital_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, orbital_index: int) → core::chemical::orbitals::OrbitalType

C++: core::chemical::ResidueTypeBase::orbital_type(const unsigned long) const –> const class core::chemical::orbitals::OrbitalType &

orbital_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::orbitals::OrbitalTypeSet

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueTypeBase::orbital_types_ptr() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.ResidueProperties

Access the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::properties() const –> const class core::chemical::ResidueProperties &

remap_pdb_atom_names(*args, **kwargs)

Overloaded function.

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, rename: bool) -> None

Turn on geometry-based atom renaming when loading this residue type from PDB files

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names(bool) –> void

  1. remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> bool

Are we using geometry-based atom renaming when loading this residue type from PDB

C++: core::chemical::ResidueTypeBase::remap_pdb_atom_names() const –> bool

remove_variant_type(*args, **kwargs)

Overloaded function.

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Remove a variant type to this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const enum core::chemical::VariantType) –> void

  1. remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, variant_type: str) -> None

Remove a variant type to this ResidueTypeBase by string.

C++: core::chemical::ResidueTypeBase::remove_variant_type(const std::string &) –> void

report_adducts(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

C++: core::chemical::ResidueTypeBase::report_adducts() const –> void

reset_mainchain_torsion_potential_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set the names of the mainchain torsion potential maps to use to “”.

Also resets the mainchain torsion potential filename strings.

C++: core::chemical::ResidueTypeBase::reset_mainchain_torsion_potential_names() –> void

rotamer_library_specification(*args, **kwargs)

Overloaded function.

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, : core::chemical::rotamers::RotamerLibrarySpecification) -> None

C++: core::chemical::ResidueTypeBase::rotamer_library_specification(class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>) –> void

  1. rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> core::chemical::rotamers::RotamerLibrarySpecification

C++: core::chemical::ResidueTypeBase::rotamer_library_specification() const –> class std::shared_ptr<const class core::chemical::rotamers::RotamerLibrarySpecification>

rotamer_library_specification_nonconst(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → core::chemical::rotamers::RotamerLibrarySpecification

Nonconst access to the RotamerLibrarySpecification.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst() –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

set_adduct_flag(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, adduct_in: bool) → None

C++: core::chemical::ResidueTypeBase::set_adduct_flag(bool) –> void

set_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, n: str) → None

Sets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueTypeBase::set_disulfide_atom_name(const std::string &) –> void

set_gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::gasteiger::GasteigerAtomTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>) –> void

set_metapatched(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Set that this is a metapatched ResidueType.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::set_metapatched() –> void

set_orbital_typeset(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, setting: core::chemical::orbitals::OrbitalTypeSet) → None

C++: core::chemical::ResidueTypeBase::set_orbital_typeset(class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>) –> void

set_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, properties: pyrosetta.rosetta.core.chemical.ResidueProperties) → None

Set the collection of properties for this ResidueTypeBase.

C++: core::chemical::ResidueTypeBase::set_properties(class std::shared_ptr<class core::chemical::ResidueProperties>) –> void

set_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, name_in: str, pre_proline_position: bool) → None

Set the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_mainchain_torsion_potential_name(const std::string &, const bool) –> void

set_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, filename_in: str, pre_proline_position: bool) → None

Set the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueTypeBase::set_rama_prepro_map_file_name(const std::string &, const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) -> None

  2. show(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, output: pyrosetta.rosetta.std.ostream) -> None

  3. show(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, output: pyrosetta.rosetta.std.ostream, output_atomic_details: bool) -> None

Generate string representation of ResidueTypeBase for debugging purposes.

C++: core::chemical::ResidueTypeBase::show(std::ostream &, bool) const –> void

show_all_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase, out: pyrosetta.rosetta.std.ostream) → None

C++: core::chemical::ResidueTypeBase::show_all_atom_names(std::ostream &) const –> void

strip_rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None

Remove any rotamer library specifications attached to this ResidueTypeBase.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeBase::strip_rotamer_library_specification() –> void

variant_type_enums(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Get a vector of VariantType enums for this ResidueTypeBase.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueTypeBase::variant_type_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

variant_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.utility.vector1_std_string

get all the variant types for this ResidueTypeBase

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants.

– rhiju (merging roccomoretti/restypeset_fiddle)

C++: core::chemical::ResidueTypeBase::variant_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

class pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Bases: pybind11_object

aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::aa(const enum core::chemical::AA &) –> class core::chemical::ResidueTypeFinder &

atom_names_soft(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::atom_names_soft(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class core::chemical::ResidueTypeFinder &

base_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.core.chemical.ResidueProperty) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::base_property(const enum core::chemical::ResidueProperty) –> class core::chemical::ResidueTypeFinder &

base_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, basetype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder
Allow a base type to be specified rigidly. Since any ResidueType’s base type COP can now be accessed easily,

this is a far more efficient way to prune the set of possible ResidueTypes.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeFinder::base_type(const class std::shared_ptr<const class core::chemical::ResidueType> &) –> class core::chemical::ResidueTypeFinder &

check_nucleic_acid_virtual_phosphates(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: bool) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::check_nucleic_acid_virtual_phosphates(const bool) –> class core::chemical::ResidueTypeFinder &

connect_atoms(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Attempt to find ResidueTypes with connection points on the given atoms

C++: core::chemical::ResidueTypeFinder::connect_atoms(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class core::chemical::ResidueTypeFinder &

disable_metapatches(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Disable metapatches and do not consider them while patching.

By default, metapatched ResidueTypes will be considered. This disables that.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeFinder::disable_metapatches() –> class core::chemical::ResidueTypeFinder &

disallow_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::disallow_properties(const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &) –> class core::chemical::ResidueTypeFinder &

disallow_variants(*args, **kwargs)

Overloaded function.

  1. disallow_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

  2. disallow_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, clear_existing: bool) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Provide a list of VariantTypes that a matched ResidueType must NOT have.

By default, this overwrites the existing list. To append to the existing list, set clear_existing to false.

C++: core::chemical::ResidueTypeFinder::disallow_variants(const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) –> class core::chemical::ResidueTypeFinder &

discouraged_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::discouraged_properties(const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &) –> class core::chemical::ResidueTypeFinder &

get_all_possible_residue_types(*args, **kwargs)

Overloaded function.

  1. get_all_possible_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

  2. get_all_possible_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, allow_extra_variants: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Find all residues which match the requirement criteria

Will apply preferences/discouragements.

C++: core::chemical::ResidueTypeFinder::get_all_possible_residue_types(const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_best_match_residue_type_for_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, atom_names: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class std::shared_ptr<const class core::chemical::ResidueType>

get_possible_base_residue_types(*args, **kwargs)

Overloaded function.

  1. get_possible_base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

  2. get_possible_base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, include_unpatchable: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

  3. get_possible_base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, include_unpatchable: bool, apply_all_filters: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Find all base residue types which match the relevant requirement criteria

C++: core::chemical::ResidueTypeFinder::get_possible_base_residue_types(const bool, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_possible_base_unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get the unpatchable residue types where the any ResidueType with a

non-self “base residue type” (as annotated in the ResidueType itself) filtered out.

C++: core::chemical::ResidueTypeFinder::get_possible_base_unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_possible_unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Find all unpatchable residue types which match the relevant requirement criteria

C++: core::chemical::ResidueTypeFinder::get_possible_unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_representative_type(*args, **kwargs)

Overloaded function.

  1. get_representative_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) -> pyrosetta.rosetta.core.chemical.ResidueType

  2. get_representative_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, metapatches: bool) -> pyrosetta.rosetta.core.chemical.ResidueType

Find a residue which matches all the requirement criteria.

Typically this will be the “simplest” type that does so, though that’s not guaranteed. Will ignore preferences/discouragements.

C++: core::chemical::ResidueTypeFinder::get_representative_type(const bool) const –> class std::shared_ptr<const class core::chemical::ResidueType>

ignore_atom_named_H(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: bool) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::ignore_atom_named_H(const bool) –> class core::chemical::ResidueTypeFinder &

interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: str) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::interchangeability_group(const std::string &) –> class core::chemical::ResidueTypeFinder &

name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: str) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::name1(const char &) –> class core::chemical::ResidueTypeFinder &

name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: str) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::name3(const std::string &) –> class core::chemical::ResidueTypeFinder &

no_metapatches(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder) → bool

Have metapatched ResidueTypes been disabled (true)? Or are they to be considered (false)?

Vikram K. Mulligan (vmullig.uw.edu).

C++: core::chemical::ResidueTypeFinder::no_metapatches() const –> bool

patch_names(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::patch_names(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class core::chemical::ResidueTypeFinder &

preferred_properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::preferred_properties(const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &) –> class core::chemical::ResidueTypeFinder &

properties(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::properties(const class utility::vector1<enum core::chemical::ResidueProperty, class std::allocator<enum core::chemical::ResidueProperty> > &) –> class core::chemical::ResidueTypeFinder &

residue_base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: str) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::residue_base_name(const std::string &) –> class core::chemical::ResidueTypeFinder &

set_no_CCD_on_name3_match(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: bool) → None
Don’t consider CCD components if we already have a Rosetta type with the same three letter code,

even if the two residue types have completely different chemical structure. Note we already have a mechanism (the exclude_pdb_component_list.txt file in the database) to exclude CCD components which chemically match the Rosetta type (and this exclusion is always on).

C++: core::chemical::ResidueTypeFinder::set_no_CCD_on_name3_match(bool) –> void

variant_exceptions(*args, **kwargs)

Overloaded function.

  1. variant_exceptions(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

  2. variant_exceptions(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string, clear_existing: bool) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Variant exceptions are variants which are excluded from consideration

during the allow_extra_variants = false filtering

C++: core::chemical::ResidueTypeFinder::variant_exceptions(const class utility::vector1<std::string, class std::allocator<std::string > > &, const bool) –> class core::chemical::ResidueTypeFinder &

  1. variant_exceptions(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

  2. variant_exceptions(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, clear_existing: bool) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Provide a list of VariantTypes that will be ignored when matching.

By default, this overwritest the existing list. To append to the existing list, set clear_existing=false.

Variant exceptions are variants which are excluded from consideration during the allow_extra_variants = false filtering

C++: core::chemical::ResidueTypeFinder::variant_exceptions(const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) –> class core::chemical::ResidueTypeFinder &

variants(*args, **kwargs)

Overloaded function.

  1. variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

  2. variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, clear_existing: bool) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Add a set of VariantTypes, all of which matching ResidueTypes MUST have.

By default, clears old required VariantType list. To append to list, set clear_existing=false.

C++: core::chemical::ResidueTypeFinder::variants(const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) –> class core::chemical::ResidueTypeFinder &

  1. variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::variants(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class core::chemical::ResidueTypeFinder &

  1. variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, std_variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, custom_variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

  2. variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, std_variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, custom_variants: pyrosetta.rosetta.utility.vector1_std_string, clear_existing: bool) -> pyrosetta.rosetta.core.chemical.ResidueTypeFinder

Specify a list of standard variant types (by enum) and custom variant types (by string).

This is the most efficient way to handle variants, since it minimizes the string handling. Everything that can be handled by enum is handled by enum.

A vector of enums of standard variants that the ResidueTypeFinder should match.

A vector of strings of custom variant types that the ResidueTypeFinder should match. Note that standard types should NOT be included in this list. There is no check for this!

If true (default), the existing VariantType lists are cleared. If false, this just appends to those lists.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeFinder::variants(const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const bool) –> class core::chemical::ResidueTypeFinder &

variants_in_sets(self: pyrosetta.rosetta.core.chemical.ResidueTypeFinder, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_core_chemical_VariantType_std_allocator_core_chemical_VariantType_t) → pyrosetta.rosetta.core.chemical.ResidueTypeFinder

C++: core::chemical::ResidueTypeFinder::variants_in_sets(const class utility::vector1<class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >, class std::allocator<class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > > > &) –> class core::chemical::ResidueTypeFinder &

class pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter, : pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter) → pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter

C++: core::chemical::ResidueTypeKinWriter::operator=(const class core::chemical::ResidueTypeKinWriter &) –> class core::chemical::ResidueTypeKinWriter &

write_kin_header(*args, **kwargs)

Overloaded function.

  1. write_kin_header(self: pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter, ostr: pyrosetta.rosetta.std.ostream, restype: pyrosetta.rosetta.core.chemical.ResidueType) -> None

  2. write_kin_header(self: pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter, ostr: pyrosetta.rosetta.std.ostream, restype: pyrosetta.rosetta.core.chemical.ResidueType, which_kin: int) -> None

write the header for the kinemage to center on this residue

C++: core::chemical::ResidueTypeKinWriter::write_kin_header(std::ostream &, const class core::chemical::ResidueType &, unsigned long) const –> void

write_restype(*args, **kwargs)

Overloaded function.

  1. write_restype(self: pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter, ostr: pyrosetta.rosetta.std.ostream, restype: pyrosetta.rosetta.core.chemical.ResidueType) -> None

  2. write_restype(self: pyrosetta.rosetta.core.chemical.ResidueTypeKinWriter, ostr: pyrosetta.rosetta.std.ostream, restype: pyrosetta.rosetta.core.chemical.ResidueType, which_kin: int) -> None

Write out settings for a particular ResidueType

This should be similar to the kinemage files that molfile_to_params.py writes

C++: core::chemical::ResidueTypeKinWriter::write_restype(std::ostream &, const class core::chemical::ResidueType &, unsigned long) const –> void

class pyrosetta.rosetta.core.chemical.ResidueTypeSelector

Bases: pybind11_object

A class picking out a subset of ResidueType by multiple criteria

add_line(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, line: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::add_line(const std::string &) –> class core::chemical::ResidueTypeSelector &

assign(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, : pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::operator=(const class core::chemical::ResidueTypeSelector &) –> class core::chemical::ResidueTypeSelector &

clear(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::clear() –> class core::chemical::ResidueTypeSelector &

exclude_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::exclude_variants() –> class core::chemical::ResidueTypeSelector &

match_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, rsd_type_to_match: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::match_variants(const class core::chemical::ResidueTypeBase &) –> class core::chemical::ResidueTypeSelector &

set_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::set_aa(const enum core::chemical::AA) –> class core::chemical::ResidueTypeSelector &

set_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, n: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::set_name1(const char) –> class core::chemical::ResidueTypeSelector &

set_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, property: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector

C++: core::chemical::ResidueTypeSelector::set_property(const std::string) –> class core::chemical::ResidueTypeSelector &

class pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Bases: pybind11_object

A base class for defining a ResidueTypeSelector by a single criterion

assign(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle, : pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

C++: core::chemical::ResidueTypeSelectorSingle::operator=(const class core::chemical::ResidueTypeSelectorSingle &) –> class core::chemical::ResidueTypeSelectorSingle &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.ResidueTypeSet

Bases: pybind11_object

An abstract interface to a set of ResidueTypes

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.AtomTypeSet

C++: core::chemical::ResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

The list of ResidueTypes that don’t have any patches, but can be patched.

C++: core::chemical::ResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ElementSet

C++: core::chemical::ResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>

generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, interchangeability_group: str) → bool
Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated))

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const std::string &, const std::string &) const –> bool

generates_patched_residue_type_with_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, name3: str) → bool
Check if a base type (like “SER”) generates any types with another name3 (like “SEP”)

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3(const std::string &, const std::string &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)

Overloaded function.

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

  1. get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants, making exceptions for some variants.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants, but exceptions must be standard types, listed in VariantType.hh. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_by_basetype(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Given a base residue type, desired variants, and undesired variants, retrieve a list

of cached ResidueTypeCOPs. If not cached, generate the data and cache them.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

A list of ResidueTypeCOPs matching the desired variants, with the desired base type.

This function is threadsafe. Caching and retrieveal are handled with a ReadWriteMutex.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_all_types_with_variants_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Gets all non-patched types with the given aa type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_aa(enum core::chemical::AA) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name1

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name1(char) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_base_types_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Get all non-patched ResidueTypes with the given name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_base_types_name3(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

get_d_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, l_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType

Given a D-residue, get its L-equivalent.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not a D-residue. Preserves variant types. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Works for L-amino acids and L-peptoids (peptoids with chiral “L” sidechains”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeSet::get_d_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_l_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, d_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType
Given an L-residue, get its D-equivalent.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not an L-residue. Preserves variant types.

Works for D-amino acids and D-peptoids (peptoids with chiral “D” sidechains”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueTypeSet::get_l_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_mirrored_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, original_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType
Given a residue, get its mirror-image type.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

Returns the same residue if this is an ACHIRAL type (e.g. gly), the D-equivalent for an L-residue, the L-equivalent of a D-residue, or NULL if this is an L-residue with no D-equivalent (or a D- with no L-equivalent). Preserves variant types.

C++: core::chemical::ResidueTypeSet::get_mirrored_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t
Get the patches corresponding to a patch name.

Will get both regular an metapatches

C++: core::chemical::ResidueTypeSet::get_patches(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

get_representative_type_aa(*args, **kwargs)

Overloaded function.

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given aa type and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_base_name(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name1 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(*args, **kwargs)

Overloaded function.

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

Get the base ResidueType with the given name3 and variants

Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

  1. get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> pyrosetta.rosetta.core.chemical.ResidueType

Note for derived classes: this method will obtain a read lock, and possibly

a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_custom_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_added(*args, **kwargs)

Overloaded function.

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) -> pyrosetta.rosetta.core.chemical.ResidueType

Query a variant ResidueType by its base ResidueType and VariantType

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

  1. get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) -> pyrosetta.rosetta.core.chemical.ResidueType

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → pyrosetta.rosetta.core.chemical.ResidueType
return the residuetype we get from variant rsd type after removing the desired variant type

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &

get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ResidueTypeSet

C++: core::chemical::ResidueTypeSet::get_self_ptr() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t

C++: core::chemical::ResidueTypeSet::get_self_weak_ptr() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>

has_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
Does this ResidueTypeSet have ResidueTypes with the given interchangeability group?

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_interchangeability_group(const std::string &) const –> bool

has_metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool

Do we have this metapatch?

C++: core::chemical::ResidueTypeSet::has_metapatch(const std::string &) const –> bool

has_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → bool
query if a ResidueType of the unique residue id (name) is present.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name(const std::string &) const –> bool

has_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) → bool
query if any ResidueTypes in the set have a “name3” that matches the input name3

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::has_name3(const std::string &) const –> bool

merge_split_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::io::MergeAndSplitBehaviorManager

accessor for merge/split behavior manager

C++: core::chemical::ResidueTypeSet::merge_split_behavior_manager() const –> const class core::chemical::io::MergeAndSplitBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → core::chemical::Metapatch

C++: core::chemical::ResidueTypeSet::metapatch(const std::string &) const –> class std::shared_ptr<const class core::chemical::Metapatch>

metapatch_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches, index by name.

C++: core::chemical::ResidueTypeSet::metapatch_map() const –> const class std::map<std::string, class std::shared_ptr<const class core::chemical::Metapatch>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class core::chemical::Metapatch> > > > &

metapatches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Metapatch_t

the metapatches

C++: core::chemical::ResidueTypeSet::metapatches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Metapatch>, class std::allocator<class std::shared_ptr<const class core::chemical::Metapatch> > >

mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::MMAtomTypeSet

C++: core::chemical::ResidueTypeSet::mm_atom_type_set() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.TypeSetMode

The type of the ResidueTypeSet

The difference between a ResidueTypeSet name and a ResidueTypeSet mode is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same mode. The mode specifies what compatibility class (full atom, centroid) the ResidueTypeSet has.

C++: core::chemical::ResidueTypeSet::mode() const –> enum core::chemical::TypeSetMode

name_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
query ResidueType by its unique residue id. Note for derived classes: this

method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

since within a ResidueTypeSet, each residue id must be unique, this method only returns one residue type or it exits (the program!) without a match.

C++: core::chemical::ResidueTypeSet::name_map(const std::string &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.ResidueType
Get ResidueType by exact name, returning COP. Will return null pointer

for no matches. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::name_mapOP(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

orbital_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::orbitals::OrbitalTypeSet

C++: core::chemical::ResidueTypeSet::orbital_type_set() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

patch_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t

the patches, index by name.

C++: core::chemical::ResidueTypeSet::patch_map() const –> const class std::map<std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > > > > > &

patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t

the patches

C++: core::chemical::ResidueTypeSet::patches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

The list of ResidueTypes which shouldn’t get patches applied to them

C++: core::chemical::ResidueTypeSet::unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

class pyrosetta.rosetta.core.chemical.ResidueTypeSetCache

Bases: pybind11_object

add_pass_through(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, residue_type: pyrosetta.rosetta.core.chemical.ResidueType) → None
Add a ResidueType to the cache which isn’t strictly in the associated ResidueTypeSet,

but is included here for efficiency/convenience

C++: core::chemical::ResidueTypeSetCache::add_pass_through(class std::shared_ptr<const class core::chemical::ResidueType>) –> void

add_prohibited(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, rsd_name: str) → None

C++: core::chemical::ResidueTypeSetCache::add_prohibited(const std::string &) –> void

add_residue_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, residue_type: pyrosetta.rosetta.core.chemical.ResidueType) → None

C++: core::chemical::ResidueTypeSetCache::add_residue_type(class std::shared_ptr<const class core::chemical::ResidueType>) –> void

all_types_with_variants_aa_already_cached(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) → bool
Returns whether or not the all_types_with_variants_aa map already

has an entry for the given combination of aa, variants, and exceptions. If so, then the cached data may be directly retrieved.

C++: core::chemical::ResidueTypeSetCache::all_types_with_variants_aa_already_cached(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> bool

all_types_with_variants_residuetypecops_already_cached(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) → bool

Have we already cached this combination of base type, variants, and exceptions?

This function is not threadsafe. It is assumed that thread locking will be handled by whatever is calling this.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

TRUE if we have cached this combination, FALSE otherwise.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSetCache::all_types_with_variants_residuetypecops_already_cached(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> bool

cache_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, cached_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) → None

C++: core::chemical::ResidueTypeSetCache::cache_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >) –> void

cache_all_types_with_variants_residuetypecops(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool, types_to_cache: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) → None

Cache this combination of base type, variants, and exceptions.

This function is not threadsafe. It is assumed that thread locking will be handled by whatever is calling this.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

A vector of ResidueTypeCOPs to associate with the key defined by the five variables above.

Nothing.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSetCache::cache_all_types_with_variants_residuetypecops(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &) –> void

clear_cached_maps(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache) → None

C++: core::chemical::ResidueTypeSetCache::clear_cached_maps() –> void

clone(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ResidueTypeSetCache

C++: core::chemical::ResidueTypeSetCache::clone(const class core::chemical::ResidueTypeSet &) const –> class std::shared_ptr<class core::chemical::ResidueTypeSetCache>

has_generated_residue_type(*args, **kwargs)

Overloaded function.

  1. has_generated_residue_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) -> bool

C++: core::chemical::ResidueTypeSetCache::has_generated_residue_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> bool

  1. has_generated_residue_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, rsd_name: str) -> bool

C++: core::chemical::ResidueTypeSetCache::has_generated_residue_type(const std::string &) const –> bool

has_restype_with_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, name3: str) → bool
Does this cache already have a residue with the given name3

This is likely to be slow, as it looks at all the generated residue types.

C++: core::chemical::ResidueTypeSetCache::has_restype_with_name3(const std::string &) const –> bool

interchangeability_group_generated_by_base_residue_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache) → pyrosetta.rosetta.std.map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t

interchangeability groups that appear upon patch application.

To call this function, the ResidueTypeSet will need to obtain a write lock if the maps_up_to_date function returns false. Otherwise, a read lock will suffice.

C++: core::chemical::ResidueTypeSetCache::interchangeability_group_generated_by_base_residue_name() –> const class std::map<std::string, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > > &

is_pass_through(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, name_in: str) → bool

Is the ResidueType one of the pass-through convenience types?

C++: core::chemical::ResidueTypeSetCache::is_pass_through(const std::string &) –> bool

is_prohibited(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, rsd_name: str) → bool

C++: core::chemical::ResidueTypeSetCache::is_prohibited(const std::string &) const –> bool

maps_up_to_date(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache) → bool
The RTSC performs just-in-time updates on data members that are accessed

through two of its methods – before calling these methods, the ResidueTypeSet may need to obtain a write lock on the RTSC. Thse are: - name3_generated_by_base_residue_name, and - interchangeability_group_generated_by_base_residue_name

C++: core::chemical::ResidueTypeSetCache::maps_up_to_date() const –> bool

name3_generated_by_base_residue_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache) → pyrosetta.rosetta.std.map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t

information on residue types whose name3’s can be changed by patches.

To call this function, the ResidueTypeSet will need to obtain a write lock if the maps_up_to_date function returns false. Otherwise, a read lock will suffice.

C++: core::chemical::ResidueTypeSetCache::name3_generated_by_base_residue_name() –> const class std::map<std::string, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > > > > &

name_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, name_in: str) → pyrosetta.rosetta.core.chemical.ResidueType

Main accessor function into ResidueTypeSetCache

C++: core::chemical::ResidueTypeSetCache::name_map(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

name_map_or_null(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, name_in: str) → pyrosetta.rosetta.core.chemical.ResidueType

Like name_map, but returns a nullptr rather than raising an error if the entry can’t be found

C++: core::chemical::ResidueTypeSetCache::name_map_or_null(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

remove_residue_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, name: str) → None

C++: core::chemical::ResidueTypeSetCache::remove_residue_type(const std::string &) –> void

retrieve_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

C++: core::chemical::ResidueTypeSetCache::retrieve_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

retrieve_all_types_with_variants_residuetypecops(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Retrieve this combination of base type, variants, and exceptions. NOTE THAT THIS ASSUMES THIS INFORMATION WAS

ALREADY CACHED!

This function is not threadsafe. It is assumed that thread locking will be handled by whatever is calling this.

A ResidueTypeCOP to a base residue type, used for looking up the variant.

A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.

A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.

A list of VariantTypes that are ignored in matching.

If true, metapatches are ignored.

A vector of ResidueTypeCOPs with the given base type and the associated variant types.

Vikram K. Mulligan (vmulligan.org).

C++: core::chemical::ResidueTypeSetCache::retrieve_all_types_with_variants_residuetypecops(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

update_residue_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSetCache, residue_type_original: pyrosetta.rosetta.core.chemical.ResidueType, residue_type_new: pyrosetta.rosetta.core.chemical.ResidueType) → None

C++: core::chemical::ResidueTypeSetCache::update_residue_type(class std::shared_ptr<const class core::chemical::ResidueType>, class std::shared_ptr<const class core::chemical::ResidueType>) –> void

class pyrosetta.rosetta.core.chemical.RestypeDestructionEvent

Bases: pybind11_object

special signal that the ResidueType is getting destroyed

assign(self: pyrosetta.rosetta.core.chemical.RestypeDestructionEvent, : pyrosetta.rosetta.core.chemical.RestypeDestructionEvent) → pyrosetta.rosetta.core.chemical.RestypeDestructionEvent

copy assignment

C++: core::chemical::RestypeDestructionEvent::operator=(const struct core::chemical::RestypeDestructionEvent &) –> struct core::chemical::RestypeDestructionEvent &

class pyrosetta.rosetta.core.chemical.Selector_AA

Bases: ResidueTypeSelectorSingle

Does the residue belong to ANY of these AAs?

assign(self: pyrosetta.rosetta.core.chemical.Selector_AA, : pyrosetta.rosetta.core.chemical.Selector_AA) → pyrosetta.rosetta.core.chemical.Selector_AA

C++: core::chemical::Selector_AA::operator=(const class core::chemical::Selector_AA &) –> class core::chemical::Selector_AA &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_BASENAME

Bases: ResidueTypeSelectorSingle

Does the residue have to ANY of these basenames?

assign(self: pyrosetta.rosetta.core.chemical.Selector_BASENAME, : pyrosetta.rosetta.core.chemical.Selector_BASENAME) → pyrosetta.rosetta.core.chemical.Selector_BASENAME

C++: core::chemical::Selector_BASENAME::operator=(const class core::chemical::Selector_BASENAME &) –> class core::chemical::Selector_BASENAME &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_CMDFLAG

Bases: ResidueTypeSelectorSingle

Is a certain string in the command-line option -chemical:allow_patch present ?

this selector does actually not depend on the residuetype it is queried for

assign(self: pyrosetta.rosetta.core.chemical.Selector_CMDFLAG, : pyrosetta.rosetta.core.chemical.Selector_CMDFLAG) → pyrosetta.rosetta.core.chemical.Selector_CMDFLAG

C++: core::chemical::Selector_CMDFLAG::operator=(const class core::chemical::Selector_CMDFLAG &) –> class core::chemical::Selector_CMDFLAG &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS

Bases: ResidueTypeSelectorSingle

Does the residue have ALL of the listed atoms?:

assign(self: pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS, : pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS) → pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS

C++: core::chemical::Selector_HAS_ATOMS::operator=(const class core::chemical::Selector_HAS_ATOMS &) –> class core::chemical::Selector_HAS_ATOMS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS

Bases: ResidueTypeSelectorSingle

Does the residue have ALL of the variant types and no more

assign(self: pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS, : pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS) → pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS

C++: core::chemical::Selector_MATCH_VARIANTS::operator=(const class core::chemical::Selector_MATCH_VARIANTS &) –> class core::chemical::Selector_MATCH_VARIANTS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NAME1

Bases: ResidueTypeSelectorSingle

Does the residue belong to ANY of these one-letter codes?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NAME1, : pyrosetta.rosetta.core.chemical.Selector_NAME1) → pyrosetta.rosetta.core.chemical.Selector_NAME1

C++: core::chemical::Selector_NAME1::operator=(const class core::chemical::Selector_NAME1 &) –> class core::chemical::Selector_NAME1 &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NAME3

Bases: ResidueTypeSelectorSingle

Does the residue have ANY of these three-letter codes?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NAME3, : pyrosetta.rosetta.core.chemical.Selector_NAME3) → pyrosetta.rosetta.core.chemical.Selector_NAME3

C++: core::chemical::Selector_NAME3::operator=(const class core::chemical::Selector_NAME3 &) –> class core::chemical::Selector_NAME3 &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS

Bases: ResidueTypeSelectorSingle

Does the residue have NO variant types?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS, : pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS) → pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS

C++: core::chemical::Selector_NO_VARIANTS::operator=(const class core::chemical::Selector_NO_VARIANTS &) –> class core::chemical::Selector_NO_VARIANTS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_PROPERTY

Bases: ResidueTypeSelectorSingle

Does the residue have ANY of these properties?

Phil Bradley

Vikram K. Mulligan – Rewrote this on 23 Aug 2016 to use Properties enums, which was needed for speed with the ResidueTypeFinder.

Andy Watkins – Rewrote this on 10 Jan 2019 to use modern loops

assign(self: pyrosetta.rosetta.core.chemical.Selector_PROPERTY, : pyrosetta.rosetta.core.chemical.Selector_PROPERTY) → pyrosetta.rosetta.core.chemical.Selector_PROPERTY

C++: core::chemical::Selector_PROPERTY::operator=(const class core::chemical::Selector_PROPERTY &) –> class core::chemical::Selector_PROPERTY &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_UPPER_ATOM

Bases: ResidueTypeSelectorSingle

Does the main chain of this residue follow from the given position label?

By position, it is meant the atom to which the UPPER connection is attached.

This selector was added primarily for use with carbohydrate residues, which have a wide assortment of main- chain designations. To properly patch upper terminus variants, it is necessary to know which atoms need to be added and, particularly, at which position to add them. However, this selector can be used for any residue subclass that contains variability in the main chain. See patches/carbohydrates/upper_terminus.txt for an example of use.

Labonte

assign(self: pyrosetta.rosetta.core.chemical.Selector_UPPER_ATOM, : pyrosetta.rosetta.core.chemical.Selector_UPPER_ATOM) → pyrosetta.rosetta.core.chemical.Selector_UPPER_ATOM

C++: core::chemical::Selector_UPPER_ATOM::operator=(const class core::chemical::Selector_UPPER_ATOM &) –> class core::chemical::Selector_UPPER_ATOM &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE

Bases: ResidueTypeSelectorSingle

Does the residue have ANY of variant types?

Phil Bradley

Vikram K. Mulligan – Rewrote this on 23 Aug 2016 to use VariantType enums, which was needed for speed with the ResidueTypeFinder.

assign(self: pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE, : pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE) → pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE

C++: core::chemical::Selector_VARIANT_TYPE::operator=(const class core::chemical::Selector_VARIANT_TYPE &) –> class core::chemical::Selector_VARIANT_TYPE &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool

C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive

Bases: PatchOperation

set the residue neighbor radius

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the residue neighbor atom

C++: core::chemical::SetAllAtomsRepulsive::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive, : pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive) → pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive

C++: core::chemical::SetAllAtomsRepulsive::operator=(const class core::chemical::SetAllAtomsRepulsive &) –> class core::chemical::SetAllAtomsRepulsive &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive) → str

Return the name of this PatchOperation (“SetAllAtomsRepulsive”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetAllAtomsRepulsive::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetAtomType

Bases: PatchOperation

set atom’s chemical type

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetAtomType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::SetAtomType::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAtomType, : pyrosetta.rosetta.core.chemical.SetAtomType) → pyrosetta.rosetta.core.chemical.SetAtomType

C++: core::chemical::SetAtomType::operator=(const class core::chemical::SetAtomType &) –> class core::chemical::SetAtomType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetAtomType) → str

Return the name of this PatchOperation (“SetAtomType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetAtomType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetAtomicCharge

Bases: PatchOperation

set an atom’s charge

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetAtomicCharge, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom’s charge

C++: core::chemical::SetAtomicCharge::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAtomicCharge, : pyrosetta.rosetta.core.chemical.SetAtomicCharge) → pyrosetta.rosetta.core.chemical.SetAtomicCharge

C++: core::chemical::SetAtomicCharge::operator=(const class core::chemical::SetAtomicCharge &) –> class core::chemical::SetAtomicCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetAtomicCharge) → str

Return the name of this PatchOperation (“SetAtomicCharge”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetAtomicCharge::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom

Bases: PatchOperation

set an atom as backbone heavy atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom in ResidueType rsd as backbone heavy atom

C++: core::chemical::SetBackboneHeavyatom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom, : pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom) → pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom

C++: core::chemical::SetBackboneHeavyatom::operator=(const class core::chemical::SetBackboneHeavyatom &) –> class core::chemical::SetBackboneHeavyatom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom) → str

Return the name of this PatchOperation (“SetBackboneHeavyatom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetBackboneHeavyatom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetBaseName

Bases: PatchOperation

Alter the base name.

This creates a new base residue type, clearing anything after the colon in the name.

Vikram K. Mulligan (vmulligan.org).

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetBaseName, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to generate a new base residue type.

C++: core::chemical::SetBaseName::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetBaseName, : pyrosetta.rosetta.core.chemical.SetBaseName) → pyrosetta.rosetta.core.chemical.SetBaseName

C++: core::chemical::SetBaseName::operator=(const class core::chemical::SetBaseName &) –> class core::chemical::SetBaseName &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.SetBaseName) → bool

This patch operaton DOES result in a new base residue type.

C++: core::chemical::SetBaseName::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.SetBaseName) → bool

Generates a new aa

C++: core::chemical::SetBaseName::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetBaseName) → str

Return the name of this PatchOperation (“SetBaseName”).

C++: core::chemical::SetBaseName::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetDisulfideAtomName

Bases: PatchOperation

set an atom as this residue’s disulfide forming atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetDisulfideAtomName, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom in ResidueType rsd as backbone heavy atom

C++: core::chemical::SetDisulfideAtomName::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetDisulfideAtomName, : pyrosetta.rosetta.core.chemical.SetDisulfideAtomName) → pyrosetta.rosetta.core.chemical.SetDisulfideAtomName

C++: core::chemical::SetDisulfideAtomName::operator=(const class core::chemical::SetDisulfideAtomName &) –> class core::chemical::SetDisulfideAtomName &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetDisulfideAtomName) → str

Return the name of this PatchOperation (“SetDisulfideAtomName”).

Andy Watkins (amw579.edu)

C++: core::chemical::SetDisulfideAtomName::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetFormalCharge

Bases: PatchOperation

A patch operation for setting the formal charge of a ResidueType’s atom.

Labonte <JWLabonte.edu>

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetFormalCharge, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::SetFormalCharge::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetFormalCharge, : pyrosetta.rosetta.core.chemical.SetFormalCharge) → pyrosetta.rosetta.core.chemical.SetFormalCharge

C++: core::chemical::SetFormalCharge::operator=(const class core::chemical::SetFormalCharge &) –> class core::chemical::SetFormalCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetFormalCharge) → str

Return the name of this PatchOperation (“SetFormalCharge”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetFormalCharge::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetICoor

Bases: PatchOperation

set an atom’s AtomICoord

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetICoor, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom’s AtomICoord

C++: core::chemical::SetICoor::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetICoor, : pyrosetta.rosetta.core.chemical.SetICoor) → pyrosetta.rosetta.core.chemical.SetICoor

C++: core::chemical::SetICoor::operator=(const class core::chemical::SetICoor &) –> class core::chemical::SetICoor &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetICoor) → str

Return the name of this PatchOperation (“SetICoor”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetICoor::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetIO_String

Bases: PatchOperation

set residue’s name1 and name3

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.SetIO_String) → bool

C++: core::chemical::SetIO_String::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetIO_String, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::SetIO_String::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetIO_String, : pyrosetta.rosetta.core.chemical.SetIO_String) → pyrosetta.rosetta.core.chemical.SetIO_String

C++: core::chemical::SetIO_String::operator=(const class core::chemical::SetIO_String &) –> class core::chemical::SetIO_String &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.SetIO_String) → str

Generates name3.

C++: core::chemical::SetIO_String::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetIO_String) → str

Return the name of this PatchOperation (“SetIO_String”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetIO_String::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String

Bases: PatchOperation

set the interchangeability_group string for a ResidueType

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::SetInterchangeabilityGroup_String::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String, : pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String) → pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String

C++: core::chemical::SetInterchangeabilityGroup_String::operator=(const class core::chemical::SetInterchangeabilityGroup_String &) –> class core::chemical::SetInterchangeabilityGroup_String &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String) → str

C++: core::chemical::SetInterchangeabilityGroup_String::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String) → str

Return the name of this PatchOperation (“SetInterchangeabilityGroup_String”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetInterchangeabilityGroup_String::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetMMAtomType

Bases: PatchOperation

set atom’s MM chemical type

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetMMAtomType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::SetMMAtomType::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetMMAtomType, : pyrosetta.rosetta.core.chemical.SetMMAtomType) → pyrosetta.rosetta.core.chemical.SetMMAtomType

C++: core::chemical::SetMMAtomType::operator=(const class core::chemical::SetMMAtomType &) –> class core::chemical::SetMMAtomType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetMMAtomType) → str

Return the name of this PatchOperation (“SetMMAtomType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetMMAtomType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNbrAtom

Bases: PatchOperation

set the residue neighbor atom

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNbrAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the residue neighbor atom

C++: core::chemical::SetNbrAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNbrAtom, : pyrosetta.rosetta.core.chemical.SetNbrAtom) → pyrosetta.rosetta.core.chemical.SetNbrAtom

C++: core::chemical::SetNbrAtom::operator=(const class core::chemical::SetNbrAtom &) –> class core::chemical::SetNbrAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNbrAtom) → str

Return the name of this PatchOperation (“SetNbrAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNbrAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNbrRadius

Bases: PatchOperation

set the residue neighbor radius

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNbrRadius, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set the residue neighbor atom

C++: core::chemical::SetNbrRadius::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNbrRadius, : pyrosetta.rosetta.core.chemical.SetNbrRadius) → pyrosetta.rosetta.core.chemical.SetNbrRadius

C++: core::chemical::SetNbrRadius::operator=(const class core::chemical::SetNbrRadius &) –> class core::chemical::SetNbrRadius &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNbrRadius) → str

Return the name of this PatchOperation (“SetNbrRadius”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNbrRadius::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNetFormalCharge

Bases: PatchOperation

A patch operation for setting the net formal charge of a whole ResidueType.

Vikram K. Mulligan (vmullig.edu)

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Apply this patch to the given ResidueType.

C++: core::chemical::SetNetFormalCharge::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge, : pyrosetta.rosetta.core.chemical.SetNetFormalCharge) → pyrosetta.rosetta.core.chemical.SetNetFormalCharge

C++: core::chemical::SetNetFormalCharge::operator=(const class core::chemical::SetNetFormalCharge &) –> class core::chemical::SetNetFormalCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge) → str

Return the name of this PatchOperation (“SetNetFormalCharge”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNetFormalCharge::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetOrientAtom

Bases: PatchOperation

Set orient atom selection mode.

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetOrientAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::SetOrientAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetOrientAtom, : pyrosetta.rosetta.core.chemical.SetOrientAtom) → pyrosetta.rosetta.core.chemical.SetOrientAtom

C++: core::chemical::SetOrientAtom::operator=(const class core::chemical::SetOrientAtom &) –> class core::chemical::SetOrientAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetOrientAtom) → str

Return the name of this PatchOperation (“SetOrientAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetOrientAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom

Bases: PatchOperation

set an atom as polymer connection

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set an atom in ResidueType rsd as a polymer connection atom

C++: core::chemical::SetPolymerConnectAtom::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, : pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom) → pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom

C++: core::chemical::SetPolymerConnectAtom::operator=(const class core::chemical::SetPolymerConnectAtom &) –> class core::chemical::SetPolymerConnectAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool

C++: core::chemical::SetPolymerConnectAtom::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom) → str

Return the name of this PatchOperation (“SetPolymerConnectAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetPolymerConnectAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetVirtualShadow

Bases: PatchOperation

set virtual shadow atoms

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::SetVirtualShadow::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow, : pyrosetta.rosetta.core.chemical.SetVirtualShadow) → pyrosetta.rosetta.core.chemical.SetVirtualShadow

C++: core::chemical::SetVirtualShadow::operator=(const class core::chemical::SetVirtualShadow &) –> class core::chemical::SetVirtualShadow &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow) → str

Return the name of this PatchOperation (“SetVirtualShadow”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetVirtualShadow::name() const –> std::string

class pyrosetta.rosetta.core.chemical.Set_AA

Bases: PatchOperation

set residue’s aa

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.Set_AA) → bool

C++: core::chemical::Set_AA::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.Set_AA, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

set atom’s chemical type

C++: core::chemical::Set_AA::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.Set_AA, : pyrosetta.rosetta.core.chemical.Set_AA) → pyrosetta.rosetta.core.chemical.Set_AA

C++: core::chemical::Set_AA::operator=(const class core::chemical::Set_AA &) –> class core::chemical::Set_AA &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.Set_AA) → bool

Generates a new aa

C++: core::chemical::Set_AA::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.Set_AA) → str

Return the name of this PatchOperation (“Set_AA”).

C++: core::chemical::Set_AA::name() const –> std::string

class pyrosetta.rosetta.core.chemical.TypeSetMode

Bases: pybind11_object

A type set category is the “compatibility class” of a type set.

That is, all e.g. ResidueTypes of a given TypeSetMode should be “compatible” with the scale of modeling resolution, indepenent of if they’re in the same ResidueTypeSet.

Members:

INVALID_t

FULL_ATOM_t

DEFAULT_t

CENTROID_t

CENTROID_ROT_t

HYBRID_FA_STANDARD_CENTROID_t

COARSE_RNA_t

MIXED_t

TYPE_SET_MODES_LENGTH

CENTROID_ROT_t = <TypeSetMode.CENTROID_ROT_t: 4>
CENTROID_t = <TypeSetMode.CENTROID_t: 3>
COARSE_RNA_t = <TypeSetMode.COARSE_RNA_t: 6>
DEFAULT_t = <TypeSetMode.DEFAULT_t: 2>
FULL_ATOM_t = <TypeSetMode.FULL_ATOM_t: 1>
HYBRID_FA_STANDARD_CENTROID_t = <TypeSetMode.HYBRID_FA_STANDARD_CENTROID_t: 5>
INVALID_t = <TypeSetMode.INVALID_t: 0>
MIXED_t = <TypeSetMode.MIXED_t: 7>
TYPE_SET_MODES_LENGTH = <TypeSetMode.MIXED_t: 7>
property name
property value
class pyrosetta.rosetta.core.chemical.VDDistanceMatrix

Bases: pybind11_object

Utility class for VD-indexed matrix

assign(self: pyrosetta.rosetta.core.chemical.VDDistanceMatrix, : pyrosetta.rosetta.core.chemical.VDDistanceMatrix) → pyrosetta.rosetta.core.chemical.VDDistanceMatrix

C++: core::chemical::VDDistanceMatrix::operator=(const class core::chemical::VDDistanceMatrix &) –> class core::chemical::VDDistanceMatrix &

find_max_over(self: pyrosetta.rosetta.core.chemical.VDDistanceMatrix, a: capsule) → float

C++: core::chemical::VDDistanceMatrix::find_max_over(void *) –> double

floyd_warshall(self: pyrosetta.rosetta.core.chemical.VDDistanceMatrix) → None

C++: core::chemical::VDDistanceMatrix::floyd_warshall() –> void

class pyrosetta.rosetta.core.chemical.VariantType

Bases: pybind11_object

Enumerators for all the ResidueType variants.

VariantTypes are primarily utilized by the patch system. All the type does is add an identifier that can be used later on in different protocols. It also helps the patch system keep track of which residues are patched with which patches.

Members:

NO_VARIANT

FIRST_VARIANT

UPPER_TERMINUS_VARIANT

LOWER_TERMINUS_VARIANT

UPPERTERM_TRUNC_VARIANT

LOWERTERM_TRUNC_VARIANT

PHOSPHONATE_UPPER_VARIANT

CUTPOINT_LOWER

CUTPOINT_UPPER

NTERM_CONNECT

CTERM_CONNECT

DISULFIDE

SC_BRANCH_POINT

C1_BRANCH_POINT

C2_BRANCH_POINT

C3_BRANCH_POINT

C4_BRANCH_POINT

C5_BRANCH_POINT

C6_BRANCH_POINT

C7_BRANCH_POINT

C8_BRANCH_POINT

C9_BRANCH_POINT

SIDECHAIN_CONJUGATION

SG_CONNECT

NE2_CONNECT

ZN_CONNECT

VIRTUAL_METAL_CONJUGATION

METHYLATED_NTERM_VARIANT

ACETYLATED_NTERMINUS_VARIANT

ACETYLATED_NTERMINUS_CONNECTION_VARIANT

METHYLATED_CTERMINUS_VARIANT

DIMETHYLATED_CTERMINUS_VARIANT

OOP_PRE

OOP_POST

HBS_PRE

HBS_POST

A3B_HBS_PRE

A3B_HBS_POST

CA_CONNECT

CA_CONNECT2

CA_CONNECT3

CA_CONNECT4

CA_CONNECT5

CA_CONNECT6

CA_CONNECT7

OE1_CONNECT

OE2_CONNECT

OD1_CONNECT

OD2_CONNECT

O_CONNECT

OG_CONNECT

OG1_CONNECT

PROTONATED

DEPROTONATED

ALTERNATIVE_PROTONATION

METHYLATION

DIMETHYLATION

TRIMETHYLATION

ACETYLATION

PHOSPHORYLATION

SULFATION

HYDROXYLATION

HYDROXYLATION1

HYDROXYLATION2

CARBOXYLATION

DIIODINATION

N_METHYLATION

VIRTUAL_BB

VIRTUAL_SIDE_CHAIN

VIRTUAL_RESIDUE_VARIANT

VIRTUAL_NTERM

VIRTUAL_PHOSPHATE

VIRTUAL_DNA_PHOSPHATE

REPLS_BB

REPLONLY

REPL_PHOSPHATE

VIRTUAL_RIBOSE

VIRTUAL_BACKBONE_EXCEPT_C1PRIME

VIRTUAL_BASE

VIRTUAL_BASE_HEAVY_ATOM

VIRTUAL_RNA_RESIDUE

VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE

BULGE

VIRTUAL_O2PRIME_HYDROGEN

THREE_PRIME_END_OH

THREE_PRIME_PHOSPHATE

THREE_PRIME_AZIDE

THREE_PRIME_DEOXY

FIVE_PRIME_END_OH

FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE

FIVE_PRIME_END_PHOSPHATE

FIVE_PRIME_PHOSPHATE

FIVE_PRIME_RME_PHOSPHATE

FIVEPRIME_CAP

THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE

DEOXY_O2PRIME

UPPER_CONNECTION_RNA

THREE_PRIME_PACKABLE_PHOSPHATE

FIVE_PRIME_PACKABLE_PHOSPHATE

FIVE_PRIME_PACKABLE_TRIPHOSPHATE

PROTONATED_N1

PROTONATED_N3

THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE

BLOCK_STACK_ABOVE

BLOCK_STACK_BELOW

N_ACETYLATION

N_FORMYLATION

C_METHYLAMIDATION

CTERM_AMIDATION

C5_METHYLATED_NA

ALDONIC_ACID_VARIANT

C2_KETOALDONIC_ACID

C3_KETOALDONIC_ACID

C4_KETOALDONIC_ACID

C5_KETOALDONIC_ACID

C6_KETOALDONIC_ACID

C7_KETOALDONIC_ACID

C8_KETOALDONIC_ACID

URONIC_ACID_VARIANT

C1_DEOXY_SUGAR

C2_DEOXY_SUGAR

C3_DEOXY_SUGAR

C4_DEOXY_SUGAR

C5_DEOXY_SUGAR

C6_DEOXY_SUGAR

C7_DEOXY_SUGAR

C8_DEOXY_SUGAR

C9_DEOXY_SUGAR

C1_AMINO_SUGAR

C2_AMINO_SUGAR

C3_AMINO_SUGAR

C4_AMINO_SUGAR

C5_AMINO_SUGAR

C6_AMINO_SUGAR

C7_AMINO_SUGAR

C8_AMINO_SUGAR

C9_AMINO_SUGAR

C1_ACETYLAMINO_SUGAR

C2_ACETYLAMINO_SUGAR

C3_ACETYLAMINO_SUGAR

C4_ACETYLAMINO_SUGAR

C5_ACETYLAMINO_SUGAR

C6_ACETYLAMINO_SUGAR

C7_ACETYLAMINO_SUGAR

C8_ACETYLAMINO_SUGAR

C9_ACETYLAMINO_SUGAR

C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C1_PHOSPHORYLATED_SUGAR

C2_PHOSPHORYLATED_SUGAR

C3_PHOSPHORYLATED_SUGAR

C4_PHOSPHORYLATED_SUGAR

C5_PHOSPHORYLATED_SUGAR

C6_PHOSPHORYLATED_SUGAR

C7_PHOSPHORYLATED_SUGAR

C8_PHOSPHORYLATED_SUGAR

C9_PHOSPHORYLATED_SUGAR

C1_SULFATED_SUGAR

C2_SULFATED_SUGAR

C3_SULFATED_SUGAR

C4_SULFATED_SUGAR

C5_SULFATED_SUGAR

C6_SULFATED_SUGAR

C7_SULFATED_SUGAR

C8_SULFATED_SUGAR

C9_SULFATED_SUGAR

C1_SULFOAMINO_SUGAR

C2_SULFOAMINO_SUGAR

C3_SULFOAMINO_SUGAR

C4_SULFOAMINO_SUGAR

C5_SULFOAMINO_SUGAR

C6_SULFOAMINO_SUGAR

C7_SULFOAMINO_SUGAR

C8_SULFOAMINO_SUGAR

C9_SULFOAMINO_SUGAR

C1_THIO_SUGAR

C2_THIO_SUGAR

C3_THIO_SUGAR

C4_THIO_SUGAR

C5_THIO_SUGAR

C6_THIO_SUGAR

C7_THIO_SUGAR

C8_THIO_SUGAR

C9_THIO_SUGAR

C1_METHYLATED_SUGAR

C2_METHYLATED_SUGAR

C3_METHYLATED_SUGAR

C4_METHYLATED_SUGAR

C5_METHYLATED_SUGAR

C6_METHYLATED_SUGAR

C7_METHYLATED_SUGAR

C8_METHYLATED_SUGAR

C9_METHYLATED_SUGAR

C1_PHOSPHATE

C2_PHOSPHATE

C3_PHOSPHATE

C4_PHOSPHATE

C5_PHOSPHATE

C6_PHOSPHATE

C7_PHOSPHATE

C8_PHOSPHATE

C9_PHOSPHATE

O1_ACETYL_SUGAR

O2_ACETYL_SUGAR

O3_ACETYL_SUGAR

O4_ACETYL_SUGAR

O5_ACETYL_SUGAR

O6_ACETYL_SUGAR

O7_ACETYL_SUGAR

O8_ACETYL_SUGAR

O9_ACETYL_SUGAR

O1_BUTYRYL_SUGAR

O2_BUTYRYL_SUGAR

O3_BUTYRYL_SUGAR

O4_BUTYRYL_SUGAR

O5_BUTYRYL_SUGAR

O6_BUTYRYL_SUGAR

O7_BUTYRYL_SUGAR

O8_BUTYRYL_SUGAR

O9_BUTYRYL_SUGAR

O1_PROPARGYL_SUGAR

O2_PROPARGYL_SUGAR

O3_PROPARGYL_SUGAR

O4_PROPARGYL_SUGAR

O5_PROPARGYL_SUGAR

O6_PROPARGYL_SUGAR

O7_PROPARGYL_SUGAR

O8_PROPARGYL_SUGAR

O9_PROPARGYL_SUGAR

O1_LACTYL_SUGAR

O2_LACTYL_SUGAR

O3_LACTYL_SUGAR

O4_LACTYL_SUGAR

O5_LACTYL_SUGAR

O6_LACTYL_SUGAR

O7_LACTYL_SUGAR

O8_LACTYL_SUGAR

O9_LACTYL_SUGAR

C1_GLYCOLYLAMINO_SUGAR

C2_GLYCOLYLAMINO_SUGAR

C3_GLYCOLYLAMINO_SUGAR

C4_GLYCOLYLAMINO_SUGAR

C5_GLYCOLYLAMINO_SUGAR

C6_GLYCOLYLAMINO_SUGAR

C7_GLYCOLYLAMINO_SUGAR

C8_GLYCOLYLAMINO_SUGAR

C9_GLYCOLYLAMINO_SUGAR

C1_FLUORO_SUGAR

C2_FLUORO_SUGAR

C3_FLUORO_SUGAR

C4_FLUORO_SUGAR

C5_FLUORO_SUGAR

C6_FLUORO_SUGAR

C7_FLUORO_SUGAR

C8_FLUORO_SUGAR

C9_FLUORO_SUGAR

O1_METHYL_SUGAR

O2_METHYL_SUGAR

O3_METHYL_SUGAR

O4_METHYL_SUGAR

O5_METHYL_SUGAR

O6_METHYL_SUGAR

O7_METHYL_SUGAR

O8_METHYL_SUGAR

O9_METHYL_SUGAR

METHYL_GLYCOSIDE

TRIAZOLAMERN

TRIAZOLAMERC

CA2_COORDINATION

MG2_COORDINATION

CU2_COORDINATION

CO2_COORDINATION

FE2_COORDINATION

FE3_COORDINATION

MN2_COORDINATION

LA3_COORDINATION

LU3_COORDINATION

TB3_COORDINATION

TM3_COORDINATION

DY3_COORDINATION

YB3_COORDINATION

ADDUCT_VARIANT

CENTROID_WITH_HA

SPECIAL_ROT

SC_FRAGMENT

SHOVE_BB

N_VARIANTS

A3B_HBS_POST = <VariantType.A3B_HBS_POST: 36>
A3B_HBS_PRE = <VariantType.A3B_HBS_PRE: 35>
ACETYLATED_NTERMINUS_CONNECTION_VARIANT = <VariantType.ACETYLATED_NTERMINUS_CONNECTION_VARIANT: 28>
ACETYLATED_NTERMINUS_VARIANT = <VariantType.ACETYLATED_NTERMINUS_VARIANT: 27>
ACETYLATION = <VariantType.ACETYLATION: 57>
ADDUCT_VARIANT = <VariantType.ADDUCT_VARIANT: 287>
ALDONIC_ACID_VARIANT = <VariantType.ALDONIC_ACID_VARIANT: 109>
ALTERNATIVE_PROTONATION = <VariantType.ALTERNATIVE_PROTONATION: 53>
BLOCK_STACK_ABOVE = <VariantType.BLOCK_STACK_ABOVE: 102>
BLOCK_STACK_BELOW = <VariantType.BLOCK_STACK_BELOW: 103>
BULGE = <VariantType.BULGE: 81>
C1_ACETYLAMINO_SUGAR = <VariantType.C1_ACETYLAMINO_SUGAR: 136>
C1_AMINO_SUGAR = <VariantType.C1_AMINO_SUGAR: 127>
C1_BRANCH_POINT = <VariantType.C1_BRANCH_POINT: 12>
C1_DEOXY_SUGAR = <VariantType.C1_DEOXY_SUGAR: 118>
C1_FLUORO_SUGAR = <VariantType.C1_FLUORO_SUGAR: 253>
C1_GLYCOLYLAMINO_SUGAR = <VariantType.C1_GLYCOLYLAMINO_SUGAR: 244>
C1_METHYLATED_SUGAR = <VariantType.C1_METHYLATED_SUGAR: 190>
C1_PHOSPHATE = <VariantType.C1_PHOSPHATE: 199>
C1_PHOSPHORYLATED_SUGAR = <VariantType.C1_PHOSPHORYLATED_SUGAR: 154>
C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 145>
C1_SULFATED_SUGAR = <VariantType.C1_SULFATED_SUGAR: 163>
C1_SULFOAMINO_SUGAR = <VariantType.C1_SULFOAMINO_SUGAR: 172>
C1_THIO_SUGAR = <VariantType.C1_THIO_SUGAR: 181>
C2_ACETYLAMINO_SUGAR = <VariantType.C2_ACETYLAMINO_SUGAR: 137>
C2_AMINO_SUGAR = <VariantType.C2_AMINO_SUGAR: 128>
C2_BRANCH_POINT = <VariantType.C2_BRANCH_POINT: 13>
C2_DEOXY_SUGAR = <VariantType.C2_DEOXY_SUGAR: 119>
C2_FLUORO_SUGAR = <VariantType.C2_FLUORO_SUGAR: 254>
C2_GLYCOLYLAMINO_SUGAR = <VariantType.C2_GLYCOLYLAMINO_SUGAR: 245>
C2_KETOALDONIC_ACID = <VariantType.C2_KETOALDONIC_ACID: 110>
C2_METHYLATED_SUGAR = <VariantType.C2_METHYLATED_SUGAR: 191>
C2_PHOSPHATE = <VariantType.C2_PHOSPHATE: 200>
C2_PHOSPHORYLATED_SUGAR = <VariantType.C2_PHOSPHORYLATED_SUGAR: 155>
C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 146>
C2_SULFATED_SUGAR = <VariantType.C2_SULFATED_SUGAR: 164>
C2_SULFOAMINO_SUGAR = <VariantType.C2_SULFOAMINO_SUGAR: 173>
C2_THIO_SUGAR = <VariantType.C2_THIO_SUGAR: 182>
C3_ACETYLAMINO_SUGAR = <VariantType.C3_ACETYLAMINO_SUGAR: 138>
C3_AMINO_SUGAR = <VariantType.C3_AMINO_SUGAR: 129>
C3_BRANCH_POINT = <VariantType.C3_BRANCH_POINT: 14>
C3_DEOXY_SUGAR = <VariantType.C3_DEOXY_SUGAR: 120>
C3_FLUORO_SUGAR = <VariantType.C3_FLUORO_SUGAR: 255>
C3_GLYCOLYLAMINO_SUGAR = <VariantType.C3_GLYCOLYLAMINO_SUGAR: 246>
C3_KETOALDONIC_ACID = <VariantType.C3_KETOALDONIC_ACID: 111>
C3_METHYLATED_SUGAR = <VariantType.C3_METHYLATED_SUGAR: 192>
C3_PHOSPHATE = <VariantType.C3_PHOSPHATE: 201>
C3_PHOSPHORYLATED_SUGAR = <VariantType.C3_PHOSPHORYLATED_SUGAR: 156>
C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 147>
C3_SULFATED_SUGAR = <VariantType.C3_SULFATED_SUGAR: 165>
C3_SULFOAMINO_SUGAR = <VariantType.C3_SULFOAMINO_SUGAR: 174>
C3_THIO_SUGAR = <VariantType.C3_THIO_SUGAR: 183>
C4_ACETYLAMINO_SUGAR = <VariantType.C4_ACETYLAMINO_SUGAR: 139>
C4_AMINO_SUGAR = <VariantType.C4_AMINO_SUGAR: 130>
C4_BRANCH_POINT = <VariantType.C4_BRANCH_POINT: 15>
C4_DEOXY_SUGAR = <VariantType.C4_DEOXY_SUGAR: 121>
C4_FLUORO_SUGAR = <VariantType.C4_FLUORO_SUGAR: 256>
C4_GLYCOLYLAMINO_SUGAR = <VariantType.C4_GLYCOLYLAMINO_SUGAR: 247>
C4_KETOALDONIC_ACID = <VariantType.C4_KETOALDONIC_ACID: 112>
C4_METHYLATED_SUGAR = <VariantType.C4_METHYLATED_SUGAR: 193>
C4_PHOSPHATE = <VariantType.C4_PHOSPHATE: 202>
C4_PHOSPHORYLATED_SUGAR = <VariantType.C4_PHOSPHORYLATED_SUGAR: 157>
C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 148>
C4_SULFATED_SUGAR = <VariantType.C4_SULFATED_SUGAR: 166>
C4_SULFOAMINO_SUGAR = <VariantType.C4_SULFOAMINO_SUGAR: 175>
C4_THIO_SUGAR = <VariantType.C4_THIO_SUGAR: 184>
C5_ACETYLAMINO_SUGAR = <VariantType.C5_ACETYLAMINO_SUGAR: 140>
C5_AMINO_SUGAR = <VariantType.C5_AMINO_SUGAR: 131>
C5_BRANCH_POINT = <VariantType.C5_BRANCH_POINT: 16>
C5_DEOXY_SUGAR = <VariantType.C5_DEOXY_SUGAR: 122>
C5_FLUORO_SUGAR = <VariantType.C5_FLUORO_SUGAR: 257>
C5_GLYCOLYLAMINO_SUGAR = <VariantType.C5_GLYCOLYLAMINO_SUGAR: 248>
C5_KETOALDONIC_ACID = <VariantType.C5_KETOALDONIC_ACID: 113>
C5_METHYLATED_NA = <VariantType.C5_METHYLATED_NA: 108>
C5_METHYLATED_SUGAR = <VariantType.C5_METHYLATED_SUGAR: 194>
C5_PHOSPHATE = <VariantType.C5_PHOSPHATE: 203>
C5_PHOSPHORYLATED_SUGAR = <VariantType.C5_PHOSPHORYLATED_SUGAR: 158>
C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 149>
C5_SULFATED_SUGAR = <VariantType.C5_SULFATED_SUGAR: 167>
C5_SULFOAMINO_SUGAR = <VariantType.C5_SULFOAMINO_SUGAR: 176>
C5_THIO_SUGAR = <VariantType.C5_THIO_SUGAR: 185>
C6_ACETYLAMINO_SUGAR = <VariantType.C6_ACETYLAMINO_SUGAR: 141>
C6_AMINO_SUGAR = <VariantType.C6_AMINO_SUGAR: 132>
C6_BRANCH_POINT = <VariantType.C6_BRANCH_POINT: 17>
C6_DEOXY_SUGAR = <VariantType.C6_DEOXY_SUGAR: 123>
C6_FLUORO_SUGAR = <VariantType.C6_FLUORO_SUGAR: 258>
C6_GLYCOLYLAMINO_SUGAR = <VariantType.C6_GLYCOLYLAMINO_SUGAR: 249>
C6_KETOALDONIC_ACID = <VariantType.C6_KETOALDONIC_ACID: 114>
C6_METHYLATED_SUGAR = <VariantType.C6_METHYLATED_SUGAR: 195>
C6_PHOSPHATE = <VariantType.C6_PHOSPHATE: 204>
C6_PHOSPHORYLATED_SUGAR = <VariantType.C6_PHOSPHORYLATED_SUGAR: 159>
C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 150>
C6_SULFATED_SUGAR = <VariantType.C6_SULFATED_SUGAR: 168>
C6_SULFOAMINO_SUGAR = <VariantType.C6_SULFOAMINO_SUGAR: 177>
C6_THIO_SUGAR = <VariantType.C6_THIO_SUGAR: 186>
C7_ACETYLAMINO_SUGAR = <VariantType.C7_ACETYLAMINO_SUGAR: 142>
C7_AMINO_SUGAR = <VariantType.C7_AMINO_SUGAR: 133>
C7_BRANCH_POINT = <VariantType.C7_BRANCH_POINT: 18>
C7_DEOXY_SUGAR = <VariantType.C7_DEOXY_SUGAR: 124>
C7_FLUORO_SUGAR = <VariantType.C7_FLUORO_SUGAR: 259>
C7_GLYCOLYLAMINO_SUGAR = <VariantType.C7_GLYCOLYLAMINO_SUGAR: 250>
C7_KETOALDONIC_ACID = <VariantType.C7_KETOALDONIC_ACID: 115>
C7_METHYLATED_SUGAR = <VariantType.C7_METHYLATED_SUGAR: 196>
C7_PHOSPHATE = <VariantType.C7_PHOSPHATE: 205>
C7_PHOSPHORYLATED_SUGAR = <VariantType.C7_PHOSPHORYLATED_SUGAR: 160>
C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 151>
C7_SULFATED_SUGAR = <VariantType.C7_SULFATED_SUGAR: 169>
C7_SULFOAMINO_SUGAR = <VariantType.C7_SULFOAMINO_SUGAR: 178>
C7_THIO_SUGAR = <VariantType.C7_THIO_SUGAR: 187>
C8_ACETYLAMINO_SUGAR = <VariantType.C8_ACETYLAMINO_SUGAR: 143>
C8_AMINO_SUGAR = <VariantType.C8_AMINO_SUGAR: 134>
C8_BRANCH_POINT = <VariantType.C8_BRANCH_POINT: 19>
C8_DEOXY_SUGAR = <VariantType.C8_DEOXY_SUGAR: 125>
C8_FLUORO_SUGAR = <VariantType.C8_FLUORO_SUGAR: 260>
C8_GLYCOLYLAMINO_SUGAR = <VariantType.C8_GLYCOLYLAMINO_SUGAR: 251>
C8_KETOALDONIC_ACID = <VariantType.C8_KETOALDONIC_ACID: 116>
C8_METHYLATED_SUGAR = <VariantType.C8_METHYLATED_SUGAR: 197>
C8_PHOSPHATE = <VariantType.C8_PHOSPHATE: 206>
C8_PHOSPHORYLATED_SUGAR = <VariantType.C8_PHOSPHORYLATED_SUGAR: 161>
C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 152>
C8_SULFATED_SUGAR = <VariantType.C8_SULFATED_SUGAR: 170>
C8_SULFOAMINO_SUGAR = <VariantType.C8_SULFOAMINO_SUGAR: 179>
C8_THIO_SUGAR = <VariantType.C8_THIO_SUGAR: 188>
C9_ACETYLAMINO_SUGAR = <VariantType.C9_ACETYLAMINO_SUGAR: 144>
C9_AMINO_SUGAR = <VariantType.C9_AMINO_SUGAR: 135>
C9_BRANCH_POINT = <VariantType.C9_BRANCH_POINT: 20>
C9_DEOXY_SUGAR = <VariantType.C9_DEOXY_SUGAR: 126>
C9_FLUORO_SUGAR = <VariantType.C9_FLUORO_SUGAR: 261>
C9_GLYCOLYLAMINO_SUGAR = <VariantType.C9_GLYCOLYLAMINO_SUGAR: 252>
C9_METHYLATED_SUGAR = <VariantType.C9_METHYLATED_SUGAR: 198>
C9_PHOSPHATE = <VariantType.C9_PHOSPHATE: 207>
C9_PHOSPHORYLATED_SUGAR = <VariantType.C9_PHOSPHORYLATED_SUGAR: 162>
C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR = <VariantType.C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR: 153>
C9_SULFATED_SUGAR = <VariantType.C9_SULFATED_SUGAR: 171>
C9_SULFOAMINO_SUGAR = <VariantType.C9_SULFOAMINO_SUGAR: 180>
C9_THIO_SUGAR = <VariantType.C9_THIO_SUGAR: 189>
CA2_COORDINATION = <VariantType.CA2_COORDINATION: 274>
CARBOXYLATION = <VariantType.CARBOXYLATION: 63>
CA_CONNECT = <VariantType.CA_CONNECT: 37>
CA_CONNECT2 = <VariantType.CA_CONNECT2: 38>
CA_CONNECT3 = <VariantType.CA_CONNECT3: 39>
CA_CONNECT4 = <VariantType.CA_CONNECT4: 40>
CA_CONNECT5 = <VariantType.CA_CONNECT5: 41>
CA_CONNECT6 = <VariantType.CA_CONNECT6: 42>
CA_CONNECT7 = <VariantType.CA_CONNECT7: 43>
CENTROID_WITH_HA = <VariantType.CENTROID_WITH_HA: 288>
CO2_COORDINATION = <VariantType.CO2_COORDINATION: 277>
CTERM_AMIDATION = <VariantType.CTERM_AMIDATION: 107>
CTERM_CONNECT = <VariantType.CTERM_CONNECT: 9>
CU2_COORDINATION = <VariantType.CU2_COORDINATION: 276>
CUTPOINT_LOWER = <VariantType.CUTPOINT_LOWER: 6>
CUTPOINT_UPPER = <VariantType.CUTPOINT_UPPER: 7>
C_METHYLAMIDATION = <VariantType.C_METHYLAMIDATION: 106>
DEOXY_O2PRIME = <VariantType.DEOXY_O2PRIME: 94>
DEPROTONATED = <VariantType.DEPROTONATED: 52>
DIIODINATION = <VariantType.DIIODINATION: 64>
DIMETHYLATED_CTERMINUS_VARIANT = <VariantType.DIMETHYLATED_CTERMINUS_VARIANT: 30>
DIMETHYLATION = <VariantType.DIMETHYLATION: 55>
DISULFIDE = <VariantType.DISULFIDE: 10>
DY3_COORDINATION = <VariantType.DY3_COORDINATION: 285>
FE2_COORDINATION = <VariantType.FE2_COORDINATION: 278>
FE3_COORDINATION = <VariantType.FE3_COORDINATION: 279>
FIRST_VARIANT = <VariantType.FIRST_VARIANT: 1>
FIVEPRIME_CAP = <VariantType.FIVEPRIME_CAP: 92>
FIVE_PRIME_END_OH = <VariantType.FIVE_PRIME_END_OH: 87>
FIVE_PRIME_END_PHOSPHATE = <VariantType.FIVE_PRIME_END_PHOSPHATE: 89>
FIVE_PRIME_PACKABLE_PHOSPHATE = <VariantType.FIVE_PRIME_PACKABLE_PHOSPHATE: 97>
FIVE_PRIME_PACKABLE_TRIPHOSPHATE = <VariantType.FIVE_PRIME_PACKABLE_TRIPHOSPHATE: 98>
FIVE_PRIME_PHOSPHATE = <VariantType.FIVE_PRIME_PHOSPHATE: 90>
FIVE_PRIME_RME_PHOSPHATE = <VariantType.FIVE_PRIME_RME_PHOSPHATE: 91>
FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE = <VariantType.FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE: 88>
HBS_POST = <VariantType.HBS_POST: 34>
HBS_PRE = <VariantType.HBS_PRE: 33>
HYDROXYLATION = <VariantType.HYDROXYLATION: 60>
HYDROXYLATION1 = <VariantType.HYDROXYLATION1: 61>
HYDROXYLATION2 = <VariantType.HYDROXYLATION2: 62>
LA3_COORDINATION = <VariantType.LA3_COORDINATION: 281>
LOWERTERM_TRUNC_VARIANT = <VariantType.LOWERTERM_TRUNC_VARIANT: 4>
LOWER_TERMINUS_VARIANT = <VariantType.LOWER_TERMINUS_VARIANT: 2>
LU3_COORDINATION = <VariantType.LU3_COORDINATION: 282>
METHYLATED_CTERMINUS_VARIANT = <VariantType.METHYLATED_CTERMINUS_VARIANT: 29>
METHYLATED_NTERM_VARIANT = <VariantType.METHYLATED_NTERM_VARIANT: 26>
METHYLATION = <VariantType.METHYLATION: 54>
METHYL_GLYCOSIDE = <VariantType.METHYL_GLYCOSIDE: 271>
MG2_COORDINATION = <VariantType.MG2_COORDINATION: 275>
MN2_COORDINATION = <VariantType.MN2_COORDINATION: 280>
NE2_CONNECT = <VariantType.NE2_CONNECT: 23>
NO_VARIANT = <VariantType.NO_VARIANT: 0>
NTERM_CONNECT = <VariantType.NTERM_CONNECT: 8>
N_ACETYLATION = <VariantType.N_ACETYLATION: 104>
N_FORMYLATION = <VariantType.N_FORMYLATION: 105>
N_METHYLATION = <VariantType.N_METHYLATION: 65>
N_VARIANTS = <VariantType.SHOVE_BB: 291>
O1_ACETYL_SUGAR = <VariantType.O1_ACETYL_SUGAR: 208>
O1_BUTYRYL_SUGAR = <VariantType.O1_BUTYRYL_SUGAR: 217>
O1_LACTYL_SUGAR = <VariantType.O1_LACTYL_SUGAR: 235>
O1_METHYL_SUGAR = <VariantType.O1_METHYL_SUGAR: 262>
O1_PROPARGYL_SUGAR = <VariantType.O1_PROPARGYL_SUGAR: 226>
O2_ACETYL_SUGAR = <VariantType.O2_ACETYL_SUGAR: 209>
O2_BUTYRYL_SUGAR = <VariantType.O2_BUTYRYL_SUGAR: 218>
O2_LACTYL_SUGAR = <VariantType.O2_LACTYL_SUGAR: 236>
O2_METHYL_SUGAR = <VariantType.O2_METHYL_SUGAR: 263>
O2_PROPARGYL_SUGAR = <VariantType.O2_PROPARGYL_SUGAR: 227>
O3_ACETYL_SUGAR = <VariantType.O3_ACETYL_SUGAR: 210>
O3_BUTYRYL_SUGAR = <VariantType.O3_BUTYRYL_SUGAR: 219>
O3_LACTYL_SUGAR = <VariantType.O3_LACTYL_SUGAR: 237>
O3_METHYL_SUGAR = <VariantType.O3_METHYL_SUGAR: 264>
O3_PROPARGYL_SUGAR = <VariantType.O3_PROPARGYL_SUGAR: 228>
O4_ACETYL_SUGAR = <VariantType.O4_ACETYL_SUGAR: 211>
O4_BUTYRYL_SUGAR = <VariantType.O4_BUTYRYL_SUGAR: 220>
O4_LACTYL_SUGAR = <VariantType.O4_LACTYL_SUGAR: 238>
O4_METHYL_SUGAR = <VariantType.O4_METHYL_SUGAR: 265>
O4_PROPARGYL_SUGAR = <VariantType.O4_PROPARGYL_SUGAR: 229>
O5_ACETYL_SUGAR = <VariantType.O5_ACETYL_SUGAR: 212>
O5_BUTYRYL_SUGAR = <VariantType.O5_BUTYRYL_SUGAR: 221>
O5_LACTYL_SUGAR = <VariantType.O5_LACTYL_SUGAR: 239>
O5_METHYL_SUGAR = <VariantType.O5_METHYL_SUGAR: 266>
O5_PROPARGYL_SUGAR = <VariantType.O5_PROPARGYL_SUGAR: 230>
O6_ACETYL_SUGAR = <VariantType.O6_ACETYL_SUGAR: 213>
O6_BUTYRYL_SUGAR = <VariantType.O6_BUTYRYL_SUGAR: 222>
O6_LACTYL_SUGAR = <VariantType.O6_LACTYL_SUGAR: 240>
O6_METHYL_SUGAR = <VariantType.O6_METHYL_SUGAR: 267>
O6_PROPARGYL_SUGAR = <VariantType.O6_PROPARGYL_SUGAR: 231>
O7_ACETYL_SUGAR = <VariantType.O7_ACETYL_SUGAR: 214>
O7_BUTYRYL_SUGAR = <VariantType.O7_BUTYRYL_SUGAR: 223>
O7_LACTYL_SUGAR = <VariantType.O7_LACTYL_SUGAR: 241>
O7_METHYL_SUGAR = <VariantType.O7_METHYL_SUGAR: 268>
O7_PROPARGYL_SUGAR = <VariantType.O7_PROPARGYL_SUGAR: 232>
O8_ACETYL_SUGAR = <VariantType.O8_ACETYL_SUGAR: 215>
O8_BUTYRYL_SUGAR = <VariantType.O8_BUTYRYL_SUGAR: 224>
O8_LACTYL_SUGAR = <VariantType.O8_LACTYL_SUGAR: 242>
O8_METHYL_SUGAR = <VariantType.O8_METHYL_SUGAR: 269>
O8_PROPARGYL_SUGAR = <VariantType.O8_PROPARGYL_SUGAR: 233>
O9_ACETYL_SUGAR = <VariantType.O9_ACETYL_SUGAR: 216>
O9_BUTYRYL_SUGAR = <VariantType.O9_BUTYRYL_SUGAR: 225>
O9_LACTYL_SUGAR = <VariantType.O9_LACTYL_SUGAR: 243>
O9_METHYL_SUGAR = <VariantType.O9_METHYL_SUGAR: 270>
O9_PROPARGYL_SUGAR = <VariantType.O9_PROPARGYL_SUGAR: 234>
OD1_CONNECT = <VariantType.OD1_CONNECT: 46>
OD2_CONNECT = <VariantType.OD2_CONNECT: 47>
OE1_CONNECT = <VariantType.OE1_CONNECT: 44>
OE2_CONNECT = <VariantType.OE2_CONNECT: 45>
OG1_CONNECT = <VariantType.OG1_CONNECT: 50>
OG_CONNECT = <VariantType.OG_CONNECT: 49>
OOP_POST = <VariantType.OOP_POST: 32>
OOP_PRE = <VariantType.OOP_PRE: 31>
O_CONNECT = <VariantType.O_CONNECT: 48>
PHOSPHONATE_UPPER_VARIANT = <VariantType.PHOSPHONATE_UPPER_VARIANT: 5>
PHOSPHORYLATION = <VariantType.PHOSPHORYLATION: 58>
PROTONATED = <VariantType.PROTONATED: 51>
PROTONATED_N1 = <VariantType.PROTONATED_N1: 99>
PROTONATED_N3 = <VariantType.PROTONATED_N3: 100>
REPLONLY = <VariantType.REPLONLY: 73>
REPLS_BB = <VariantType.REPLS_BB: 72>
REPL_PHOSPHATE = <VariantType.REPL_PHOSPHATE: 74>
SC_BRANCH_POINT = <VariantType.SC_BRANCH_POINT: 11>
SC_FRAGMENT = <VariantType.SC_FRAGMENT: 290>
SG_CONNECT = <VariantType.SG_CONNECT: 22>
SHOVE_BB = <VariantType.SHOVE_BB: 291>
SIDECHAIN_CONJUGATION = <VariantType.SIDECHAIN_CONJUGATION: 21>
SPECIAL_ROT = <VariantType.SPECIAL_ROT: 289>
SULFATION = <VariantType.SULFATION: 59>
TB3_COORDINATION = <VariantType.TB3_COORDINATION: 283>
THREE_PRIME_AZIDE = <VariantType.THREE_PRIME_AZIDE: 85>
THREE_PRIME_DEOXY = <VariantType.THREE_PRIME_DEOXY: 86>
THREE_PRIME_END_OH = <VariantType.THREE_PRIME_END_OH: 83>
THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE = <VariantType.THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE: 101>
THREE_PRIME_PACKABLE_PHOSPHATE = <VariantType.THREE_PRIME_PACKABLE_PHOSPHATE: 96>
THREE_PRIME_PHOSPHATE = <VariantType.THREE_PRIME_PHOSPHATE: 84>
THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE = <VariantType.THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE: 93>
TM3_COORDINATION = <VariantType.TM3_COORDINATION: 284>
TRIAZOLAMERC = <VariantType.TRIAZOLAMERC: 273>
TRIAZOLAMERN = <VariantType.TRIAZOLAMERN: 272>
TRIMETHYLATION = <VariantType.TRIMETHYLATION: 56>
UPPERTERM_TRUNC_VARIANT = <VariantType.UPPERTERM_TRUNC_VARIANT: 3>
UPPER_CONNECTION_RNA = <VariantType.UPPER_CONNECTION_RNA: 95>
UPPER_TERMINUS_VARIANT = <VariantType.FIRST_VARIANT: 1>
URONIC_ACID_VARIANT = <VariantType.URONIC_ACID_VARIANT: 117>
VIRTUAL_BACKBONE_EXCEPT_C1PRIME = <VariantType.VIRTUAL_BACKBONE_EXCEPT_C1PRIME: 76>
VIRTUAL_BASE = <VariantType.VIRTUAL_BASE: 77>
VIRTUAL_BASE_HEAVY_ATOM = <VariantType.VIRTUAL_BASE_HEAVY_ATOM: 78>
VIRTUAL_BB = <VariantType.VIRTUAL_BB: 66>
VIRTUAL_DNA_PHOSPHATE = <VariantType.VIRTUAL_DNA_PHOSPHATE: 71>
VIRTUAL_METAL_CONJUGATION = <VariantType.VIRTUAL_METAL_CONJUGATION: 25>
VIRTUAL_NTERM = <VariantType.VIRTUAL_NTERM: 69>
VIRTUAL_O2PRIME_HYDROGEN = <VariantType.VIRTUAL_O2PRIME_HYDROGEN: 82>
VIRTUAL_PHOSPHATE = <VariantType.VIRTUAL_PHOSPHATE: 70>
VIRTUAL_RESIDUE_VARIANT = <VariantType.VIRTUAL_RESIDUE_VARIANT: 68>
VIRTUAL_RIBOSE = <VariantType.VIRTUAL_RIBOSE: 75>
VIRTUAL_RNA_RESIDUE = <VariantType.VIRTUAL_RNA_RESIDUE: 79>
VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE = <VariantType.VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE: 80>
VIRTUAL_SIDE_CHAIN = <VariantType.VIRTUAL_SIDE_CHAIN: 67>
YB3_COORDINATION = <VariantType.YB3_COORDINATION: 286>
ZN_CONNECT = <VariantType.ZN_CONNECT: 24>
property name
property value
class pyrosetta.rosetta.core.chemical.VirtualizeAll

Bases: PatchOperation

virtualize all

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.VirtualizeAll, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::VirtualizeAll::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.VirtualizeAll, : pyrosetta.rosetta.core.chemical.VirtualizeAll) → pyrosetta.rosetta.core.chemical.VirtualizeAll

C++: core::chemical::VirtualizeAll::operator=(const class core::chemical::VirtualizeAll &) –> class core::chemical::VirtualizeAll &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.VirtualizeAll) → str

Return the name of this PatchOperation (“VirtualizeAll”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::VirtualizeAll::name() const –> std::string

class pyrosetta.rosetta.core.chemical.VirtualizeSidechain

Bases: PatchOperation

virtualize sidechain

adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.utility.vector1_std_string

Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.

This includes both atoms and all possible aliases for those atoms.

C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() const –> std::string

adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is added.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

C++: core::chemical::VirtualizeSidechain::apply(class core::chemical::MutableResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain, : pyrosetta.rosetta.core.chemical.VirtualizeSidechain) → pyrosetta.rosetta.core.chemical.VirtualizeSidechain

C++: core::chemical::VirtualizeSidechain::operator=(const class core::chemical::VirtualizeSidechain &) –> class core::chemical::VirtualizeSidechain &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) → bool

Can this case change connections for the atom on the residue?

  • Be a little careful, as the passed atom name string may not have the same

whitespace padding as any internal atom name.

C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool

deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::deletes_atom() –> std::string

deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which property, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_property() const –> std::string

deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.ResidueProperty

Which property, if any, is deleted.

This returns an enum value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() const –> std::string

deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.VariantType

Which variant, if any, is deleted, by enum.

C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType

generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates base residue – legacy for D_AA – do not use otherwise.

C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain) → str

Return the name of this PatchOperation (“VirtualizeSidechain”).

Andrew M. Watkins (amw579.edu).

C++: core::chemical::VirtualizeSidechain::name() const –> std::string

pyrosetta.rosetta.core.chemical.aa_from_name(name: str) → pyrosetta.rosetta.core.chemical.AA

Give an AA string 3-letter code, return its enum type.

C++: core::chemical::aa_from_name(const std::string &) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.aa_from_one_or_three(name: str) → pyrosetta.rosetta.core.chemical.AA

C++: core::chemical::aa_from_one_or_three(const std::string &) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.aa_from_oneletter_code(onelettercode: str) → pyrosetta.rosetta.core.chemical.AA

give a 1 letter code and return the string name

C++: core::chemical::aa_from_oneletter_code(char) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.add_atom_type_set_parameters_from_command_line(atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None

Add additional parameter files not present in <atom-set-name>/extras.txt.

C++: core::chemical::add_atom_type_set_parameters_from_command_line(const std::string &, class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.add_atom_types_from_command_line(atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None

Add additional atomy types not present in <atom-set-name>/atom_properties.txt.

C++: core::chemical::add_atom_types_from_command_line(const std::string &, class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.add_mm_atom_type_set_parameters_from_command_line(mm_atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → None

Add additional mm atom parameters not present in <mm-atom-type-set-name>/mm_atom_properties.txt

C++: core::chemical::add_mm_atom_type_set_parameters_from_command_line(const std::string &, class core::chemical::MMAtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.annotate_backbone(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → None
Annotate “backbone” atoms.

For the purpose of this function, backbone atoms are any atoms which are connected to another backbone atom by a non-rotatable, non-cut bond. Atoms connected to the upper and/or lower connect points are always backbone. Important - if Chis/cuts aren’t properly annotated, all atoms will be backbone.

C++: core::chemical::annotate_backbone(class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.apply_adducts_to_residue(rsd: pyrosetta.rosetta.core.chemical.ResidueType, add_mask: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.core.chemical.MutableResidueType

Apply adducts to residue using a boolean mask

C++: core::chemical::apply_adducts_to_residue(const class core::chemical::ResidueType &, class utility::vector1<bool, class std::allocator<bool> > &) –> class std::shared_ptr<class core::chemical::MutableResidueType>

pyrosetta.rosetta.core.chemical.apply_symm_b3g_corrections(child_atom: str, phi: float, theta: float, d: float, parent_atom: str, angle_atom: str, torsion_atom: str) → None

Symmetrize the b3g params file (if the user has used the -symmetric_gly_tables option).

Ugh. Special-case logic.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

C++: core::chemical::apply_symm_b3g_corrections(const std::string &, double &, double &, double &, std::string &, std::string &, std::string &) –> void

pyrosetta.rosetta.core.chemical.apply_symm_gly_corrections(child_atom: str, phi: float, theta: float, d: float, parent_atom: str, angle_atom: str, torsion_atom: str) → None

Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option).

Ugh. Special-case logic.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

C++: core::chemical::apply_symm_gly_corrections(const std::string &, double &, double &, double &, std::string &, std::string &, std::string &) –> void

pyrosetta.rosetta.core.chemical.calculate_rigid_matrix(res: pyrosetta.rosetta.core.chemical.MutableResidueType, distances: pyrosetta.rosetta.core.chemical.VDDistanceMatrix) → None
Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square

Helper for find_nbr_dist

C++: core::chemical::calculate_rigid_matrix(const class core::chemical::MutableResidueType &, class core::chemical::VDDistanceMatrix &) –> void

pyrosetta.rosetta.core.chemical.case_from_lines(*args, **kwargs)

Overloaded function.

  1. case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.PatchCase

  2. case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string, res_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.PatchCase

  3. case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string, res_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, patch_name: str) -> pyrosetta.rosetta.core.chemical.PatchCase

create a PatchCase from input lines

add selector_ from lines enclosed by “BEGIN_SELECTOR” and “END_SELECTOR”. add operations_ from each input line containing a single operation

C++: core::chemical::case_from_lines(const class utility::vector1<std::string, class std::allocator<std::string > > &, enum core::chemical::TypeSetMode, const std::string &) –> class std::shared_ptr<class core::chemical::PatchCase>

pyrosetta.rosetta.core.chemical.clean_up_dangling_connect(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, remove_type: pyrosetta.rosetta.core.chemical.ICoordAtomIDType) → None
Attempt to find new ICOOR definitions for entries in the ResidueType which rely on a now-deleted upper/lower connection

(Connection type is specified by the passed type.)

C++: core::chemical::clean_up_dangling_connect(class core::chemical::MutableResidueType &, enum core::chemical::ICoordAtomIDType) –> void

pyrosetta.rosetta.core.chemical.compare_atom_icoor(*args, **kwargs)

Overloaded function.

  1. compare_atom_icoor(aic1: pyrosetta.rosetta.core.chemical.AtomICoor, aic2: pyrosetta.rosetta.core.chemical.AtomICoor) -> bool

  2. compare_atom_icoor(aic1: pyrosetta.rosetta.core.chemical.AtomICoor, aic2: pyrosetta.rosetta.core.chemical.AtomICoor, fuzzy: bool) -> bool

Are the two ResidueConnection objects equivalent

Here instead of in operator== because of the fuzzy-real issue.

C++: core::chemical::compare_atom_icoor(const class core::chemical::AtomICoor &, const class core::chemical::AtomICoor &, bool) –> bool

pyrosetta.rosetta.core.chemical.compare_residue_connection(*args, **kwargs)

Overloaded function.

  1. compare_residue_connection(rc1: pyrosetta.rosetta.core.chemical.ResidueConnection, rc2: pyrosetta.rosetta.core.chemical.ResidueConnection) -> bool

  2. compare_residue_connection(rc1: pyrosetta.rosetta.core.chemical.ResidueConnection, rc2: pyrosetta.rosetta.core.chemical.ResidueConnection, fuzzy: bool) -> bool

Are the two ResidueConnection objects equivalent

Here instead of in operator== because of the fuzzy-real issue.

C++: core::chemical::compare_residue_connection(const class core::chemical::ResidueConnection &, const class core::chemical::ResidueConnection &, bool) –> bool

pyrosetta.rosetta.core.chemical.complex_ring_detection(res: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

C++: core::chemical::complex_ring_detection(class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.convert_to_BondName(id: str) → pyrosetta.rosetta.core.chemical.BondName

C++: core::chemical::convert_to_BondName(const std::string &) –> enum core::chemical::BondName

pyrosetta.rosetta.core.chemical.create_bond_length(atom1: core::chemical::gasteiger::GasteigerAtomTypeData, atom2: core::chemical::gasteiger::GasteigerAtomTypeData, bond_type: pyrosetta.rosetta.core.chemical.BondName) → float

this will create a bond length based on gasteiger atom type definitions of bonds

C++: core::chemical::create_bond_length(const class core::chemical::gasteiger::GasteigerAtomTypeData &, const class core::chemical::gasteiger::GasteigerAtomTypeData &, enum core::chemical::BondName) –> double

pyrosetta.rosetta.core.chemical.deep_copy(*args, **kwargs)

Overloaded function.

  1. deep_copy(source: core::chemical::AtomProperties) -> core::chemical::AtomProperties

C++: core::chemical::deep_copy(const class core::chemical::AtomProperties &) –> class std::shared_ptr<class core::chemical::AtomProperties>

  1. deep_copy(source: core::chemical::ResidueProperties) -> core::chemical::ResidueProperties

C++: core::chemical::deep_copy(const class core::chemical::ResidueProperties &) –> class std::shared_ptr<class core::chemical::ResidueProperties>

  1. deep_copy(source: core::chemical::Orbital) -> core::chemical::Orbital

C++: core::chemical::deep_copy(const class core::chemical::Orbital &) –> class std::shared_ptr<class core::chemical::Orbital>

pyrosetta.rosetta.core.chemical.detect_ld_chirality_from_polymer_residue(*args, **kwargs)

Overloaded function.

  1. detect_ld_chirality_from_polymer_residue(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, is_d_aa: bool, is_l_aa: bool) -> None

C++: core::chemical::detect_ld_chirality_from_polymer_residue(const class core::chemical::MutableResidueType &, bool &, bool &) –> void

  1. detect_ld_chirality_from_polymer_residue(xyz: pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t, name3: str, is_d_aa: bool, is_l_aa: bool) -> None

C++: core::chemical::detect_ld_chirality_from_polymer_residue(const class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > &, const std::string &, bool &, bool &) –> void

pyrosetta.rosetta.core.chemical.enlarge_h_lj_wdepth(*args, **kwargs)

Overloaded function.

  1. enlarge_h_lj_wdepth(lj_wdepth: pyrosetta.rosetta.utility.vector1_double, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA

C++: core::chemical::enlarge_h_lj_wdepth(class utility::vector1<double, class std::allocator<double> > &, const class core::chemical::AtomTypeSet &) –> void

  1. enlarge_h_lj_wdepth(atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA

C++: core::chemical::enlarge_h_lj_wdepth(class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.error_check_requested_adducts(add_map: pyrosetta.rosetta.std.map_std_string_int, rsd_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) → None

Make sure requested adducts exist in some residue

C++: core::chemical::error_check_requested_adducts(const class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > > &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &) –> void

pyrosetta.rosetta.core.chemical.find_best_match(*args, **kwargs)

Overloaded function.

  1. find_best_match(rsd_type_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, atom_names: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType

  2. find_best_match(rsd_type_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, atom_names: pyrosetta.rosetta.utility.vector1_std_string, ignore_atom_named_H: bool) -> pyrosetta.rosetta.core.chemical.ResidueType

look for best match to atom_names

C++: core::chemical::find_best_match(const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const bool) –> class std::shared_ptr<const class core::chemical::ResidueType>

pyrosetta.rosetta.core.chemical.find_bonds_in_rings(*args, **kwargs)

Overloaded function.

  1. find_bonds_in_rings(res: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. find_bonds_in_rings(res: pyrosetta.rosetta.core.chemical.MutableResidueType, complex_ring_detection: bool) -> None

Determine which bonds are in rings, and set the BondRingness property of each

C++: core::chemical::find_bonds_in_rings(class core::chemical::MutableResidueType &, const bool) –> void

pyrosetta.rosetta.core.chemical.find_chi_bonds(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t
Find which bonds are rotatatable (chi) bonds

Returns a list of four vds representing the chi

C++: core::chemical::find_chi_bonds(const class core::chemical::MutableResidueType &) –> class utility::vector1<class utility::vector1<void *, class std::allocator<void *> >, class std::allocator<class utility::vector1<void *, class std::allocator<void *> > > >

pyrosetta.rosetta.core.chemical.find_nbr_dist(res: pyrosetta.rosetta.core.chemical.MutableResidueType, nbr_atom: capsule) → float
Find the neighbor distance to the given neighbor atom.

If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance.

The neighbor distance here is adjusted for rotatable bonds - It should be at least as large as the maximum neighbor distance in any torsional rotamer If the neighbor atom is not provided, the atom chosen will be a multiply-bonded heavy atom.

Assumes:

  • All atoms and bond are present

  • All ideal_xyz coordinates have been set

  • All elements have been set

  • All ring bonds have been annotated

C++: core::chemical::find_nbr_dist(const class core::chemical::MutableResidueType &, void *&) –> double

pyrosetta.rosetta.core.chemical.fixup_patches(string_in: str) → str

Replaces the deprecated “_p:” linker connecting ResidueType base names with their patch names with “:”.

C++: core::chemical::fixup_patches(const std::string &) –> std::string

pyrosetta.rosetta.core.chemical.formatted_icoord_tree(*args, **kwargs)

Overloaded function.

  1. formatted_icoord_tree(restype: pyrosetta.rosetta.core.chemical.ResidueType) -> str

Return a string representing the internal coordinates tree of this ResidueType.

C++: core::chemical::formatted_icoord_tree(const class core::chemical::ResidueType &) –> std::string

  1. formatted_icoord_tree(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) -> str

Return a string representing the internal coordinates tree of this MutableResidueType (if any)

C++: core::chemical::formatted_icoord_tree(const class core::chemical::MutableResidueType &) –> std::string

pyrosetta.rosetta.core.chemical.full_name_from_aa(aa: pyrosetta.rosetta.core.chemical.AA) → str

give the canonical “full” ResidueType name for given AA

C++: core::chemical::full_name_from_aa(enum core::chemical::AA) –> std::string

pyrosetta.rosetta.core.chemical.get_D_equivalent(aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.AA

Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined).

C++: core::chemical::get_D_equivalent(const enum core::chemical::AA) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.get_L_equivalent(aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.AA

Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined).

C++: core::chemical::get_L_equivalent(const enum core::chemical::AA) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.get_connection_number(: str) → int

Get the connection number from a string representing an CONNECT type (e.g. 4 from CONN4)

C++: core::chemical::get_connection_number(const std::string &) –> unsigned long

pyrosetta.rosetta.core.chemical.get_patch_names(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string

C++: core::chemical::get_patch_names(const class core::chemical::ResidueType &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.chemical.get_residue_path_distances(res: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t

relies on class Graph to find all pairs shortest path information

C++: core::chemical::get_residue_path_distances(const class core::chemical::ResidueType &) –> class ObjexxFCL::FArray2D<int>

pyrosetta.rosetta.core.chemical.get_terminal_varianttypes() → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

Get a list of those VariantTypes that affect termini.

Vikram K. Mulligan.

C++: core::chemical::get_terminal_varianttypes() –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

pyrosetta.rosetta.core.chemical.heavy_atom_names_match(first: pyrosetta.rosetta.core.chemical.ResidueType, second: pyrosetta.rosetta.core.chemical.ResidueType) → bool

Return true if the two residues have the same number and name of heavy atoms.

C++: core::chemical::heavy_atom_names_match(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.is_aa_name_unknown(name: str) → bool

Given aa three letter string, return true if it is an unknown aa.

Steven Cobms (steven.combs1.com)

C++: core::chemical::is_aa_name_unknown(const std::string &) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_D_aa(aa: pyrosetta.rosetta.core.chemical.AA) → bool

Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::is_canonical_D_aa(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_L_aa_excluding_gly(aa: pyrosetta.rosetta.core.chemical.AA) → bool

Give an enum type, return true if and only if it is an L-amino acid of a canonical type.

Returns FALSE for glycine.

Vikram K. Mulligan (vmulligan.org)

C++: core::chemical::is_canonical_L_aa_excluding_gly(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_L_aa_or_gly(aa: pyrosetta.rosetta.core.chemical.AA) → bool

Given an enum type, return true if and only if it is a canonical L-amino acid.

Also returns true if this is a glycine.

Steven Cobms (steven.combs1.com)

C++: core::chemical::is_canonical_L_aa_or_gly(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_beta3_aa(aa: pyrosetta.rosetta.core.chemical.AA) → bool

Given an enum type, return true if and only if it is a canonical beta-amino acid.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::is_canonical_beta3_aa(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_mainchain_torsion_also_ring_torsion(res_type: pyrosetta.rosetta.core.chemical.ResidueType, torsion_index: int) → bool

Are these main-chain torsions also ring torsions?

C++: core::chemical::is_mainchain_torsion_also_ring_torsion(const class core::chemical::ResidueType &, unsigned long) –> bool

pyrosetta.rosetta.core.chemical.is_sp2_proton_chi(chi: int, restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → bool

Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom?

The use case is to see if the proton chi should flat or staggered with rotamers

C++: core::chemical::is_sp2_proton_chi(unsigned long, const class core::chemical::MutableResidueType &) –> bool

pyrosetta.rosetta.core.chemical.mainchain_path(res: pyrosetta.rosetta.core.chemical.MutableResidueType) → pyrosetta.rosetta.utility.vector1_void_*
Figure out the shortest path between the upper and lower connect atoms (inclusive)

Will return an empty vector if one does not exist.

C++: core::chemical::mainchain_path(const class core::chemical::MutableResidueType &) –> class utility::vector1<void *, class std::allocator<void *> >

pyrosetta.rosetta.core.chemical.make_centroid(*args, **kwargs)

Overloaded function.

  1. make_centroid(res: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

Make a centroid version of the fullatom ResidueType passed in.

May return a nullptr if the conversion is not possible

This uses the same crude heuristics as in molfile_to_params That is, all heavy atoms and polar hydrogens are transfered over 1:1, and non-polar hydrogens are deleted.

Of particular note is that it makes no attempt to transfer things over into “Superatoms”

Current limitation: it cannot convert a ResidueType which has connections, if any of the ICOORs depend on deleted hydrogens.

Assumes:

  • Input ResidueType is complete and finalized

C++: core::chemical::make_centroid(const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. make_centroid(res: pyrosetta.rosetta.core.chemical.MutableResidueType) -> pyrosetta.rosetta.core.chemical.MutableResidueType

C++: core::chemical::make_centroid(const class core::chemical::MutableResidueType &) –> class std::shared_ptr<class core::chemical::MutableResidueType>

pyrosetta.rosetta.core.chemical.modify_atom_properties_from_command_line(atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None

Modify atom_type properties from the command line.

C++: core::chemical::modify_atom_properties_from_command_line(const std::string &, class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.name_from_aa(aa: pyrosetta.rosetta.core.chemical.AA) → str

give a enum type and return the string name

C++: core::chemical::name_from_aa(enum core::chemical::AA) –> std::string

pyrosetta.rosetta.core.chemical.nonadduct_variants_match(res1: pyrosetta.rosetta.core.chemical.ResidueTypeBase, res2: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Similar to variants_match(), but allows different adduct-modified states.

C++: core::chemical::nonadduct_variants_match(const class core::chemical::ResidueTypeBase &, const class core::chemical::ResidueTypeBase &) –> bool

pyrosetta.rosetta.core.chemical.one_indexed_chr_chains() → str

pad chr_chains with a dummy char in the first element so that it can be indexed starting at 1

C++: core::chemical::one_indexed_chr_chains() –> std::string

pyrosetta.rosetta.core.chemical.oneletter_code_from_aa(aa: pyrosetta.rosetta.core.chemical.AA) → str

give a enum type and return the string name

C++: core::chemical::oneletter_code_from_aa(enum core::chemical::AA) –> char

pyrosetta.rosetta.core.chemical.oneletter_code_specifies_aa(onelettercode: str) → bool

C++: core::chemical::oneletter_code_specifies_aa(char) –> bool

pyrosetta.rosetta.core.chemical.pH_mode_exceptions() → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType

C++: core::chemical::pH_mode_exceptions() –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

pyrosetta.rosetta.core.chemical.parse_adduct_string(add_vec: pyrosetta.rosetta.utility.options.StringVectorOption) → pyrosetta.rosetta.std.map_std_string_int

Convert input string to map of adducts->max usage

C++: core::chemical::parse_adduct_string(class utility::options::StringVectorOption &) –> class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > >

pyrosetta.rosetta.core.chemical.pretty_print_atomicoor(*args, **kwargs)

Overloaded function.

  1. pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, rsd_type: core::chemical::ResidueType) -> None

print the icoord table starting at the root.

C++: core::chemical::pretty_print_atomicoor(std::ostream &, const class core::chemical::ResidueType &) –> void

  1. pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, start: pyrosetta.rosetta.core.chemical.AtomICoor, rsd_type: core::chemical::ResidueType) -> None

  2. pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, start: pyrosetta.rosetta.core.chemical.AtomICoor, rsd_type: core::chemical::ResidueType, indent: int) -> None

print the icoord table starting with the given icoord record

C++: core::chemical::pretty_print_atomicoor(std::ostream &, const class core::chemical::AtomICoor &, const class core::chemical::ResidueType &, unsigned long) –> void

pyrosetta.rosetta.core.chemical.print_chis(*args, **kwargs)

Overloaded function.

  1. print_chis(out: pyrosetta.rosetta.std.ostream, res: pyrosetta.rosetta.core.chemical.ResidueType) -> None

Utility to examine chi output.

C++: core::chemical::print_chis(std::ostream &, const class core::chemical::ResidueType &) –> void

  1. print_chis(out: pyrosetta.rosetta.std.ostream, res: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

Utility to examine chi output.

C++: core::chemical::print_chis(std::ostream &, const class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.quick_ring_detection(res: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

C++: core::chemical::quick_ring_detection(class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.read_topology_file(*args, **kwargs)

Overloaded function.

  1. read_topology_file(filename: str, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(const std::string &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. read_topology_file(istream: pyrosetta.rosetta.utility.io.izstream, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(class utility::io::izstream &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

  1. read_topology_file(istream: pyrosetta.rosetta.std.istream, filename: str, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.MutableResidueType

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(std::istream &, const std::string &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::MutableResidueType>

pyrosetta.rosetta.core.chemical.real_to_virtual(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) → None
Virtualize convert the MutableResidueType to a virtual type

NOTE: This function does not rename the residue type

C++: core::chemical::real_to_virtual(class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.rename_atoms(*args, **kwargs)

Overloaded function.

  1. rename_atoms(res: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. rename_atoms(res: pyrosetta.rosetta.core.chemical.MutableResidueType, preserve: bool) -> None

Rename atoms in the residue type such that their names are unique.

If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.)

C++: core::chemical::rename_atoms(class core::chemical::MutableResidueType &, bool) –> void

pyrosetta.rosetta.core.chemical.residue_selector_single_from_line(line: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

create a singe ResidueTypeSelector from an input line.

C++: core::chemical::residue_selector_single_from_line(const std::string &) –> class std::shared_ptr<class core::chemical::ResidueTypeSelectorSingle>

pyrosetta.rosetta.core.chemical.residue_type_all_patches_name(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → str

helper function, returns the name of all added patches

C++: core::chemical::residue_type_all_patches_name(const class core::chemical::ResidueType &) –> std::string

pyrosetta.rosetta.core.chemical.residue_type_base_name(rsd_type: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → str

helper function, returns the base residue name prior to any patching

C++: core::chemical::residue_type_base_name(const class core::chemical::ResidueTypeBase &) –> std::string

pyrosetta.rosetta.core.chemical.residue_types_identical(res1: pyrosetta.rosetta.core.chemical.ResidueType, res2: pyrosetta.rosetta.core.chemical.ResidueType) → bool
Are two ResidueTypes equivalent?

This is here rather than as an operator on ResidueType because it’s not the sort of thing one should be doing normally. This looks for exact equivalence, including atom order.

C++: core::chemical::residue_types_identical(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.rosetta_recharge_fullatom(res: pyrosetta.rosetta.core.chemical.MutableResidueType) → None

Apply molfile_to_params style partial charges to the ResidueType.

These partial charges are based off of the Rosetta atom type, adjusted such that the net partial charge is equal to the net formal charge.

These charges are almost certainly dodgy. If you have any other source of partial charges that are at all reasonable, you probably want to consider those instead.

Assumes:

  • All atoms and bond are present.

  • All atom types have been set.

  • Formal charges (if any) have been set.

C++: core::chemical::rosetta_recharge_fullatom(class core::chemical::MutableResidueType &) –> void

pyrosetta.rosetta.core.chemical.rosetta_retype_fullatom(*args, **kwargs)

Overloaded function.

  1. rosetta_retype_fullatom(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. rosetta_retype_fullatom(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, preserve: bool) -> None

Reassign Rosetta atom types based on the current fullatom heuristics.

If preserve is true, only retype those atoms which have an atom_type_index of zero.

C++: core::chemical::rosetta_retype_fullatom(class core::chemical::MutableResidueType &, bool) –> void

pyrosetta.rosetta.core.chemical.rsd_set_from_cmd_line() → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t

Return a constant access pointer to the ResidueTypeSet specified by the command-line options.

C++: core::chemical::rsd_set_from_cmd_line() –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>

pyrosetta.rosetta.core.chemical.set_up_mapfile_reassignments_from_commandline(rsd: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → None
Certain commandline flags override the default RamaPrePro maps used by the 20

canonical amino acids. This function applies those overrides.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::set_up_mapfile_reassignments_from_commandline(class std::shared_ptr<class core::chemical::ResidueTypeBase>) –> void

pyrosetta.rosetta.core.chemical.setup_atom_type_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, atom_type_reassignments: pyrosetta.rosetta.std.map_std_string_std_string) → None

C++: core::chemical::setup_atom_type_reassignments_from_commandline(const std::string &, enum core::chemical::TypeSetMode, class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &) –> void

pyrosetta.rosetta.core.chemical.setup_atomic_charge_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, atomic_charge_reassignments: pyrosetta.rosetta.std.map_std_string_double) → None

C++: core::chemical::setup_atomic_charge_reassignments_from_commandline(const std::string &, enum core::chemical::TypeSetMode, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

pyrosetta.rosetta.core.chemical.setup_icoor_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, icoor_reassignments: pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t) → None

C++: core::chemical::setup_icoor_reassignments_from_commandline(const std::string &, enum core::chemical::TypeSetMode, class std::map<std::string, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<std::string, class std::allocator<std::string > > > > > &) –> void

pyrosetta.rosetta.core.chemical.shortest_path(res: pyrosetta.rosetta.core.chemical.MutableResidueType, start: capsule, end: capsule) → pyrosetta.rosetta.utility.vector1_void_*
Figure out the shortest path between two atoms (inclusive)

Will return an empty vector if one does not exist.

C++: core::chemical::shortest_path(const class core::chemical::MutableResidueType &, void *, void *) –> class utility::vector1<void *, class std::allocator<void *> >

pyrosetta.rosetta.core.chemical.string_from_type_set_mode(mode: pyrosetta.rosetta.core.chemical.TypeSetMode) → str

C++: core::chemical::string_from_type_set_mode(enum core::chemical::TypeSetMode) –> std::string

pyrosetta.rosetta.core.chemical.string_to_icoord_type(: str) → pyrosetta.rosetta.core.chemical.ICoordAtomIDType

Convert a string designation into the corresponding ICoordAtomIDType enum.

C++: core::chemical::string_to_icoord_type(const std::string &) –> enum core::chemical::ICoordAtomIDType

pyrosetta.rosetta.core.chemical.tag_from_line(line: str) → str

handy function, return the first word from a line

C++: core::chemical::tag_from_line(const std::string &) –> std::string

pyrosetta.rosetta.core.chemical.type_set_mode_from_string(*args, **kwargs)

Overloaded function.

  1. type_set_mode_from_string(mode: str) -> pyrosetta.rosetta.core.chemical.TypeSetMode

  2. type_set_mode_from_string(mode: str, fail: bool) -> pyrosetta.rosetta.core.chemical.TypeSetMode

If fail is true, utility_exit if the mode cannot be converted,

if not, return the invalid type.

C++: core::chemical::type_set_mode_from_string(const std::string &, bool) –> enum core::chemical::TypeSetMode

pyrosetta.rosetta.core.chemical.unset_acceptor_ether_oxygens(atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None

Rhiju. O3’, O4’, O5’ in nucleic acids are ethers – turn them off as acceptors for H-bonds.

C++: core::chemical::unset_acceptor_ether_oxygens(class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.variants_match(res1: pyrosetta.rosetta.core.chemical.ResidueTypeBase, res2: pyrosetta.rosetta.core.chemical.ResidueTypeBase) → bool

Are these two residues patched in exactly the same way?

C++: core::chemical::variants_match(const class core::chemical::ResidueTypeBase &, const class core::chemical::ResidueTypeBase &) –> bool

pyrosetta.rosetta.core.chemical.variants_match_with_exceptions(res1: pyrosetta.rosetta.core.chemical.ResidueTypeBase, res2: pyrosetta.rosetta.core.chemical.ResidueTypeBase, list_of_variants_to_ignore: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) → bool

Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions?

C++: core::chemical::variants_match_with_exceptions(const class core::chemical::ResidueTypeBase &, const class core::chemical::ResidueTypeBase &, class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >) –> bool

pyrosetta.rosetta.core.chemical.write_graphviz(*args, **kwargs)

Overloaded function.

  1. write_graphviz(rsd: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream) -> None

  2. write_graphviz(rsd: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream, header: bool) -> None

Produces a graphviz dot representation of the ResidueType to the given output stream

If header is true (the default) a line with an explanatory message will be printed first.

C++: core::chemical::write_graphviz(const class core::chemical::ResidueType &, std::ostream &, bool) –> void

  1. write_graphviz(rsd: pyrosetta.rosetta.core.chemical.MutableResidueType, out: pyrosetta.rosetta.std.ostream) -> None

  2. write_graphviz(rsd: pyrosetta.rosetta.core.chemical.MutableResidueType, out: pyrosetta.rosetta.std.ostream, header: bool) -> None

C++: core::chemical::write_graphviz(const class core::chemical::MutableResidueType &, std::ostream &, bool) –> void

pyrosetta.rosetta.core.chemical.write_topology_file(*args, **kwargs)

Overloaded function.

  1. write_topology_file(rsd: pyrosetta.rosetta.core.chemical.ResidueType) -> None

  2. write_topology_file(rsd: pyrosetta.rosetta.core.chemical.ResidueType, filename: str) -> None

writes a .params file from a given ResidueType object

C++: core::chemical::write_topology_file(const class core::chemical::ResidueType &, std::string) –> void