chemical

Bindings for core::chemical namespace

class pyrosetta.rosetta.core.chemical.AA

Bases: pybind11_builtins.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

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_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: 96>
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: 99>
aa_unp = <AA.aa_unp: 98>
aa_val = <AA.aa_val: 18>
aa_vrt = <AA.aa_vrt: 97>
first_DNA_aa = <AA.na_ade: 21>
first_D_aa = <AA.aa_dal: 29>
first_beta3_aa = <AA.aa_b3a: 48>
first_l_aa = <AA.aa_ala: 1>
first_oligourea = <AA.ou3_ala: 75>
last_DNA_aa = <AA.na_thy: 24>
last_D_aa = <AA.aa_dty: 47>
last_beta3_aa = <AA.aa_b3cisACHC: 70>
last_oligourea = <AA.ou3_aib: 95>
na_ade = <AA.na_ade: 21>
na_cyt = <AA.na_cyt: 22>
na_gua = <AA.na_gua: 23>
na_lra = <AA.na_lra: 71>
na_lrc = <AA.na_lrc: 72>
na_lrg = <AA.na_lrg: 73>
na_lur = <AA.na_lur: 74>
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: 99>
num_canonical_aas = <AA.aa_tyr: 20>
ou3_aib = <AA.ou3_aib: 95>
ou3_ala = <AA.ou3_ala: 75>
ou3_arg = <AA.ou3_arg: 89>
ou3_asn = <AA.ou3_asn: 86>
ou3_asp = <AA.ou3_asp: 77>
ou3_cys = <AA.ou3_cys: 76>
ou3_gln = <AA.ou3_gln: 88>
ou3_glu = <AA.ou3_glu: 78>
ou3_gly = <AA.ou3_gly: 80>
ou3_his = <AA.ou3_his: 81>
ou3_ile = <AA.ou3_ile: 82>
ou3_leu = <AA.ou3_leu: 84>
ou3_lys = <AA.ou3_lys: 83>
ou3_met = <AA.ou3_met: 85>
ou3_phe = <AA.ou3_phe: 79>
ou3_pro = <AA.ou3_pro: 87>
ou3_ser = <AA.ou3_ser: 90>
ou3_thr = <AA.ou3_thr: 91>
ou3_trp = <AA.ou3_trp: 93>
ou3_tyr = <AA.ou3_tyr: 94>
ou3_val = <AA.ou3_val: 92>
class pyrosetta.rosetta.core.chemical.APolarHydrogenFilter

Bases: pybind11_builtins.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_builtins.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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_builtins.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_builtins.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
class pyrosetta.rosetta.core.chemical.AppendMainchainAtom

Bases: pyrosetta.rosetta.core.chemical.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_builtins.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_builtins.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_builtins.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_builtins.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: pyrosetta.rosetta.utility.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_builtins.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
class pyrosetta.rosetta.core.chemical.AtomType

Bases: pybind11_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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_builtins.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
class pyrosetta.rosetta.core.chemical.BondConjugability

Bases: pybind11_builtins.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
class pyrosetta.rosetta.core.chemical.BondIsometry

Bases: pybind11_builtins.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
class pyrosetta.rosetta.core.chemical.BondName

Bases: pybind11_builtins.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
class pyrosetta.rosetta.core.chemical.BondOrder

Bases: pybind11_builtins.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
class pyrosetta.rosetta.core.chemical.BondRingness

Bases: pybind11_builtins.pybind11_object

Members:

UnknownRingness

BondNotInRing

BondInRing

BondInRing = <BondRingness.BondInRing: 2>
BondNotInRing = <BondRingness.BondNotInRing: 1>
UnknownRingness = <BondRingness.UnknownRingness: 0>
property name
class pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets

Bases: pyrosetta.rosetta.basic.datacache.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.utility.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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: pyrosetta.rosetta.core.chemical.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_builtins.pybind11_object

describes the electron configuration of atoms

Describes the electron configuration of an atom on quantum chemistry level.

class AngularMomentumQuantumNumber

Bases: pybind11_builtins.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
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_builtins.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
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_builtins.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_builtins.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
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_builtins.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: pyrosetta.rosetta.core.chemical.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_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

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

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_builtins.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
class pyrosetta.rosetta.core.chemical.HeavyAtomFilter

Bases: pybind11_builtins.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_builtins.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_builtins.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_builtins.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
class pyrosetta.rosetta.core.chemical.HydrogenAtomFilter

Bases: pybind11_builtins.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_builtins.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_builtins.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