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

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_atom(self: pyrosetta.rosetta.core.chemical.AddAtom) → str¶: C++: core::chemical::AddAtom::adds_atom() –> std::string

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

add an atom

C++: core::chemical::AddAtom::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.AddAtomAlias) → str¶: C++: core::chemical::AddAtomAlias::adds_atom() –> std::string

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::AddAtomAlias::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

add a bond

C++: core::chemical::AddBond::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::AddBondType::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Add a chi angle.

C++: core::chemical::AddChi::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Add a rotamer sample.

C++: core::chemical::AddChiRotamer::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

add a property

C++: core::chemical::AddConnect::apply(class core::chemical::ResidueType &) 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: core::chemical::ResidueType, atom: str) → bool¶: C++: core::chemical::AddConnect::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::AddConnectAndTrackingVirt::apply(class core::chemical::ResidueType &) 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: core::chemical::ResidueType, atom: str) → bool¶: C++: core::chemical::AddConnectAndTrackingVirt::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::AddConnectDeleteChildProton::apply(class core::chemical::ResidueType &) 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: core::chemical::ResidueType, atom: str) → bool¶: C++: core::chemical::AddConnectDeleteChildProton::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

add a property

C++: core::chemical::AddProperty::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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.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

class pyrosetta.rosetta.core.chemical.AppendMainchainAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

add a mainchain atom after the last mainchain atom

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

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

set an atom to be the last mainchain atom

C++: core::chemical::AppendMainchainAtom::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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. This does not contain the actual xyz coordinates of the atom, (which are found in core/conformation/Atom.hh). The atom_type properties are assigned by the class AtomSet, which is initiated from the ChemicalManager. AtomType properties are currently read in from the file chemical/atom_type_sets/fa_standard/atom_properties.txt. These properties contain the the properties of LJ_RADIUS, LJ_WDEPTH, LK_DGRFREE, LK_LAMBDA, and LK_VOLUME and are used in the scoring methods fa_atr, fa_rep, and fa_sol, which are located in the Etable (core/scoring/etable/Etable.hh). Additional parameters are acceptor/donor, hybridization, and orbital paramaters. This class should not have information associated with the Conformation or ResidueType; it represents an atom divorced from a particular conformation or residue but not from things that affect it chemically. It is distinct from an Element, in that it can have a particular hybridization state, charge, etc. It is distinct from conformation::Atom in that it does not have coordinates. Everything stored here should be concerning the atom. Conformation information goes in core::conformation, while data for ResidueType is cached there.

chemical::Atoms are stored in chemical::ResidueType (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

assign(self: pyrosetta.rosetta.core.chemical.Atom, 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(*args, **kwargs)¶

Overloaded function.

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

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

atom_type_index(self: pyrosetta.rosetta.core.chemical.Atom, atom_type_index: int) -> None

You probably don’t want to use this directly.: Use ResidueType::set_atom_type() which correctly updates the internal state of the residuetype/atom

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

bonded_orbitals(self: pyrosetta.rosetta.core.chemical.Atom) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::chemical::Atom::bonded_orbitals() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

charge(*args, **kwargs)¶

Overloaded function.

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

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

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.

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

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

element_type(self: pyrosetta.rosetta.core.chemical.Atom, element: pyrosetta.rosetta.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.

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

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

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.

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>

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.

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

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_orbitals(*args, **kwargs)¶

Overloaded function.

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

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

has_orbitals(self: pyrosetta.rosetta.core.chemical.Atom, orbitals: bool) -> None

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

has_property(*args, **kwargs)¶

Overloaded function.

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

Generic property access.

C++: core::chemical::Atom::has_property(const class std::basic_string<char> &) const –> bool

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

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

heavyatom_has_polar_hydrogens(*args, **kwargs)¶

Overloaded function.

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

Get whether or not this heavy atom is a hydrogen-bond donor.

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

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

Set whether or not this heavy atom is a hydrogen-bond donor.

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

ideal_xyz(*args, **kwargs)¶

Overloaded function.

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> &

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_acceptor(*args, **kwargs)¶

Overloaded function.

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

Get whether or not this heavy atom is a hydrogen-bond acceptor.

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

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

Set whether or not this heavy atom is a hydrogen-bond acceptor.

C++: core::chemical::Atom::is_acceptor(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_haro(*args, **kwargs)¶

Overloaded function.

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

Get whether or not this hydrogen atom is bonded to an aromatic ring.

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

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

Set whether or not this hydrogen atom is bonded to an aromatic ring.

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

is_hydrogen(*args, **kwargs)¶

Overloaded function.

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

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

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

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

is_polar_hydrogen(*args, **kwargs)¶

Overloaded function.

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

Get whether or not this hydrogen atom is polar.

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

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

Set whether or not this hydrogen atom is polar.

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

is_virtual(*args, **kwargs)¶

Overloaded function.

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

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

mm_atom_type_index(*args, **kwargs)¶

Overloaded function.

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

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

mm_atom_type_index(self: pyrosetta.rosetta.core.chemical.Atom, mm_atom_type_index: int) -> None

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

mm_name(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: core::chemical::Atom::mm_name(const class std::basic_string<char> &) –> void

name(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: core::chemical::Atom::name(const class std::basic_string<char> &) –> void

properties(self: pyrosetta.rosetta.core.chemical.Atom) → pyrosetta.rosetta.core.chemical.AtomProperties¶

Access the collection of properties for this Atom.

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

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_property(*args, **kwargs)¶

Overloaded function.

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

Generic property setting.

C++: core::chemical::Atom::set_property(const class std::basic_string<char> &, const bool) –> void

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.

show(self: pyrosetta.rosetta.core.chemical.Atom) -> None
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(class std::basic_ostream<char> &) 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.

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>

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>

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_vertex(*args, **kwargs)¶

Overloaded function.

built_atom_vertex(self: pyrosetta.rosetta.core.chemical.AtomICoor, vd: capsule) -> None

C++: core::chemical::AtomICoor::built_atom_vertex(void *) –> void

built_atom_vertex(self: pyrosetta.rosetta.core.chemical.AtomICoor) -> capsule

The vertex descriptor of the atom being built by this icoor: Can be null_vertex if this AtomICoor doesn’t build a physical atom. (e.g. CONNECT, UPPER, LOWER)

C++: core::chemical::AtomICoor::built_atom_vertex() const –> void *

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.

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

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

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.AtomICoor, old_to_new: pyrosetta.rosetta.std.map_void_*_void_*) → None¶

Update the internal VDs based on the provide mapping

C++: core::chemical::AtomICoor::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> 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.

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

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 class std::basic_string<char> &) const –> bool

set_property(*args, **kwargs)¶

Overloaded function.

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

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 class std::basic_string<char> &, const bool) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.core.chemical.AtomProperties) -> None
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(class std::basic_ostream<char> &) 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.

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

property_from_string(property: str) → pyrosetta.rosetta.core.chemical.AtomProperty¶: C++: core::chemical::AtomPropertiesManager::property_from_string(const class std::basic_string<char> &) –> const enum core::chemical::AtomProperty &

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

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 class std::basic_string<char> &) –> 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¶: 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.

name(self: pyrosetta.rosetta.core.chemical.AtomType, setting: str) -> None

C++: core::chemical::AtomType::name(const class std::basic_string<char> &) –> void

name(self: pyrosetta.rosetta.core.chemical.AtomType) -> str

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(class std::basic_ostream<char> &) 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 class std::basic_string<char> &, 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 class std::basic_string<char> &, const bool) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) const –> bool

has_extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, name: str) → bool¶: C++: core::chemical::AtomTypeSet::has_extra_parameter(const class std::basic_string<char> &) 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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.

aromaticity(self: pyrosetta.rosetta.core.chemical.Bond, aroma: pyrosetta.rosetta.core.chemical.BondAromaticity) -> None

C++: core::chemical::Bond::aromaticity(enum core::chemical::BondAromaticity) –> void

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.

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

bond_name(self: pyrosetta.rosetta.core.chemical.Bond) -> pyrosetta.rosetta.core.chemical.BondName

C++: core::chemical::Bond::bond_name() const –> enum core::chemical::BondName

conjugability(*args, **kwargs)¶

Overloaded function.

conjugability(self: pyrosetta.rosetta.core.chemical.Bond, conjug: pyrosetta.rosetta.core.chemical.BondConjugability) -> None

C++: core::chemical::Bond::conjugability(enum core::chemical::BondConjugability) –> void

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.

cut_bond(self: pyrosetta.rosetta.core.chemical.Bond, cut_bond: bool) -> None

C++: core::chemical::Bond::cut_bond(bool) –> void

cut_bond(self: pyrosetta.rosetta.core.chemical.Bond) -> bool

C++: core::chemical::Bond::cut_bond() const –> bool

distance(*args, **kwargs)¶

Overloaded function.

distance(self: pyrosetta.rosetta.core.chemical.Bond, distance: float) -> None

C++: core::chemical::Bond::distance(double) –> void

distance(self: pyrosetta.rosetta.core.chemical.Bond) -> float

C++: core::chemical::Bond::distance() const –> double

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.

isometry(self: pyrosetta.rosetta.core.chemical.Bond, isom: pyrosetta.rosetta.core.chemical.BondIsometry) -> None

C++: core::chemical::Bond::isometry(enum core::chemical::BondIsometry) –> void

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.

order(self: pyrosetta.rosetta.core.chemical.Bond, order: pyrosetta.rosetta.core.chemical.BondOrder) -> None

C++: core::chemical::Bond::order(enum core::chemical::BondOrder) –> void

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(class std::basic_ostream<char> &) const –> void

ringness(*args, **kwargs)¶

Overloaded function.

ringness(self: pyrosetta.rosetta.core.chemical.Bond, ring: pyrosetta.rosetta.core.chemical.BondRingness) -> None

C++: core::chemical::Bond::ringness(enum core::chemical::BondRingness) –> void

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

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

class pyrosetta.rosetta.core.chemical.BondIsometry¶

Bases: pybind11_builtins.pybind11_object

Members:

UnknownIsometry

NoBondIsometry

EIsometry

ZIsometry

class pyrosetta.rosetta.core.chemical.BondName¶

Bases: pybind11_builtins.pybind11_object

Members:

UnknownBond

SingleBond

DoubleBond

TripleBond

AromaticBond

OrbitalBond

class pyrosetta.rosetta.core.chemical.BondOrder¶

Bases: pybind11_builtins.pybind11_object

Members:

UnknownBondOrder

SingleBondOrder

DoubleBondOrder

TripleBondOrder

OrbitalBondOrder

PseudoBondOrder

class pyrosetta.rosetta.core.chemical.BondRingness¶

Bases: pybind11_builtins.pybind11_object

Members:

UnknownRingness

BondNotInRing

BondInRing

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.

get_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) -> core::chemical::PoseResidueTypeSet
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,: If one doesn’t already exist, return a null pointer.

C++: core::chemical::CacheableResidueTypeSets::get_res_type_set(enum core::chemical::TypeSetMode) const –> class std::shared_ptr<const 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.

set_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, rts: core::chemical::PoseResidueTypeSet) -> None
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.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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::ChangeBondType::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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(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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> class std::shared_ptr<const class core::chemical::ElementSet>

gasteiger_atom_type_set(*args, **kwargs)¶

Overloaded function.

gasteiger_atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager) -> core::chemical::gasteiger::GasteigerAtomTypeSet
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 class std::basic_string<char> &) –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &) –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

residue_type_set(*args, **kwargs)¶

Overloaded function.

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>

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 class std::basic_string<char> &) –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

set the NCAA rotamer library path in the residue type

C++: core::chemical::ChiralFlipAtoms::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

set the NCAA rotamer library path in the residue type

C++: core::chemical::ChiralFlipNaming::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::ClearChiRotamers::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::ConnectSulfurAndMakeVirtualProton::apply(class core::chemical::ResidueType &) 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: core::chemical::ResidueType, atom: str) → bool¶: C++: core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::DeleteActCoordAtom::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

delete an atom from ResidueType rsd

C++: core::chemical::DeleteAtom::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::DeleteChildProton::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶: C++: core::chemical::DeleteMetalbindingAtom::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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)

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

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

delete a property

C++: core::chemical::DeleteProperty::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

redefine a chi angle

C++: core::chemical::DeleteTerminalChi::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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>

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

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

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

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

Which property, if any, is added.

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

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: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::DeleteVariantType::apply(class core::chemical::ResidueType &) 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, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> 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

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 > > &

class PrincipalQuantumNumber¶

Bases: pybind11_builtins.pybind11_object

Members:

e_1

e_2

e_3

e_4

e_5

e_6

e_7

MaxPrincipleQuantumNumber

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 &

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 class std::basic_string<char> &) –> enum core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber

get_descriptor(*args, **kwargs)¶

Overloaded function.

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 &

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 &

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 class std::basic_string<char> &) –> 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(class std::basic_istream<char> &) –> class std::basic_istream<char> &

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(class std::basic_ostream<char> &) 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>

class Properties¶

Bases: pybind11_builtins.pybind11_object

enum properties for element types

Members:

Mass

CovalentRadius

VDWaalsRadius

NumberOfProperties

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_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

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(class std::basic_istream<char> &) –> class std::basic_istream<char> &

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(class std::basic_ostream<char> &) 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 class std::basic_string<char> &) const –> bool

element(*args, **kwargs)¶

Overloaded function.

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>

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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::Element>

element_index(*args, **kwargs)¶

Overloaded function.

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

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 class std::basic_string<char> &) 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 class std::basic_string<char> &) –> 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 class std::basic_string<char> &, const class std::basic_string<char> &) 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 class std::basic_string<char> &, const class std::basic_string<char> &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)¶

Overloaded function.

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<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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_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<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<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_d_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, l_rsd: core::chemical::ResidueType) → 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.

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: core::chemical::ResidueType) → 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.

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: core::chemical::ResidueType) → 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.

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> 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) → 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)¶

Overloaded function.

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> 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.

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) const –> bool

merge_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::MergeBehaviorManager¶

accessor for merge behavior manager

C++: core::chemical::ResidueTypeSet::merge_behavior_manager() const –> const class core::chemical::MergeBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → core::chemical::Metapatch¶: C++: core::chemical::ResidueTypeSet::metapatch(const class std::basic_string<char> &) 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) → 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 class std::basic_string<char> &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → 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 class std::basic_string<char> &) 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

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

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

class Type¶

Bases: pybind11_builtins.pybind11_object

ICoordAtomID type

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

Members:

INTERNAL

POLYMER_LOWER

POLYMER_UPPER

CONNECT

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.

atomno(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) -> int

get ICoorAtomID atomno

C++: core::chemical::ICoorAtomID::atomno() const –> unsigned long

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.

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

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

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, old_to_new: pyrosetta.rosetta.std.map_void_*_void_*) → None¶

Update the internal VDs based on the provide mapping

C++: core::chemical::ICoorAtomID::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> void

type(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) → pyrosetta.rosetta.core.chemical.ICoorAtomID.Type¶

get ICoordAtomID type

C++: core::chemical::ICoorAtomID::type() const –> const enum core::chemical::ICoorAtomID::Type &

vertex(*args, **kwargs)¶

Overloaded function.

vertex(self: pyrosetta.rosetta.core.chemical.ICoorAtomID) -> capsule

C++: core::chemical::ICoorAtomID::vertex() const –> void *

vertex(self: pyrosetta.rosetta.core.chemical.ICoorAtomID, vertex: capsule) -> None

C++: core::chemical::ICoorAtomID::vertex(void *) –> void

xyz(*args, **kwargs)¶

Overloaded function.

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> &

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>

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.IdealBondLengthSet¶

Bases: pybind11_builtins.pybind11_object

A set of Elements

This class contains a vector of pointers each of which points to an Element and the vector index is looked up by an element_name string in a map.

assign(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, : pyrosetta.rosetta.core.chemical.IdealBondLengthSet) → pyrosetta.rosetta.core.chemical.IdealBondLengthSet¶: C++: core::chemical::IdealBondLengthSet::operator=(const class core::chemical::IdealBondLengthSet &) –> class core::chemical::IdealBondLengthSet &

contains_bond_length(*args, **kwargs)¶

Overloaded function.

contains_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_name1: str, atom_type_name2: str) -> bool

Check if an ideal bond length is known for this pair of atom types…

C++: core::chemical::IdealBondLengthSet::contains_bond_length(const class std::basic_string<char> &, const class std::basic_string<char> &) const –> bool

contains_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_index1: int, atom_type_index2: int) -> bool

C++: core::chemical::IdealBondLengthSet::contains_bond_length(int, int) const –> bool

get_bond_length(*args, **kwargs)¶

Overloaded function.

get_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_name1: str, atom_type_name2: str) -> float

Lookup the element index by the element_symbol string

C++: core::chemical::IdealBondLengthSet::get_bond_length(const class std::basic_string<char> &, const class std::basic_string<char> &) const –> double

get_bond_length(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, atom_type_index1: int, atom_type_index2: int) -> float

C++: core::chemical::IdealBondLengthSet::get_bond_length(const int, const int) const –> double

print_all_bond_lengths(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet) → None¶

Print all of the symbols of all of the Elements in the set. Usefull for debuging.

C++: core::chemical::IdealBondLengthSet::print_all_bond_lengths() –> void

read_file(self: pyrosetta.rosetta.core.chemical.IdealBondLengthSet, filename: str) → None¶

Load the IdealBondLengthSet from a file

C++: core::chemical::IdealBondLengthSet::read_file(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.chemical.MMAtomType¶

Bases: pybind11_builtins.pybind11_object

Basic MM atom type

Simple class for holding the name and the LJ properties of a Charmm molecular mechanics atom type. Borrows heavily and functions similarly to the rosetta atom type class, AtomType

lj_radius(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the LJ radius of the atom type

C++: core::chemical::MMAtomType::lj_radius() const –> double

lj_radius_sq(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the squared LJ radius of the atom type

C++: core::chemical::MMAtomType::lj_radius_sq() const –> double

lj_three_bond_radius(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the LJ radius for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_radius() const –> double

lj_three_bond_radius_sq(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the squaredLJ radius for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_radius_sq() const –> double

lj_three_bond_wdepth(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the LJ well depth for use when atoms types are seperated by 3 bonds

C++: core::chemical::MMAtomType::lj_three_bond_wdepth() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.chemical.MMAtomType) → float¶

Return the LJ well depth of the atom type

C++: core::chemical::MMAtomType::lj_wdepth() const –> double

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

Return the name of the MMAtomType

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

set_parameter(self: pyrosetta.rosetta.core.chemical.MMAtomType, param: str, setting: float) → None¶

set LJ and LK solvation parameter for this atom type

C++: core::chemical::MMAtomType::set_parameter(const class std::basic_string<char> &, const double) –> void

class pyrosetta.rosetta.core.chemical.MMAtomTypeSet¶

Bases: pybind11_builtins.pybind11_object

A set of MMAtomTypes

This class contains a vector of pointers each of which points to an MMAtomType and the vector index is looked up by an atom_name string in a map.

assign(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, : pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → pyrosetta.rosetta.core.chemical.MMAtomTypeSet¶: C++: core::chemical::MMAtomTypeSet::operator=(const class core::chemical::MMAtomTypeSet &) –> class core::chemical::MMAtomTypeSet &

atom_type_index(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, atom_type_name: str) → int¶

Lookup the atom_type by the atom_type_name string

C++: core::chemical::MMAtomTypeSet::atom_type_index(const class std::basic_string<char> &) const –> int

contains_atom_type(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, atom_type_name: str) → bool¶

Check if there is an atom_type associated with an atom_type_name string

C++: core::chemical::MMAtomTypeSet::contains_atom_type(const class std::basic_string<char> &) const –> bool

n_atomtypes(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → int¶

Number of MM atom types in the set

C++: core::chemical::MMAtomTypeSet::n_atomtypes() const –> unsigned long

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

What the ChemicalManager knows this as, if relevant

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

print_all_types(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) → None¶

Print all of the names of all of the MMAtomTypes in the set. Usefull for debuging.

C++: core::chemical::MMAtomTypeSet::print_all_types() –> void

read_file(self: pyrosetta.rosetta.core.chemical.MMAtomTypeSet, filename: str) → None¶

Load the MMAtomTypeSet from a file

C++: core::chemical::MMAtomTypeSet::read_file(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.core.chemical.Metapatch¶

Bases: pybind11_builtins.pybind11_object

A class patching basic ResidueType to create variant types, containing multiple PatchCase

applies_to(self: pyrosetta.rosetta.core.chemical.Metapatch, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

can I operate on this residue type?

C++: core::chemical::Metapatch::applies_to(const class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.Metapatch, : pyrosetta.rosetta.core.chemical.Metapatch) → pyrosetta.rosetta.core.chemical.Metapatch¶: C++: core::chemical::Metapatch::operator=(const class core::chemical::Metapatch &) –> class core::chemical::Metapatch &

atoms(self: pyrosetta.rosetta.core.chemical.Metapatch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::chemical::Metapatch::atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

get_one_patch(self: pyrosetta.rosetta.core.chemical.Metapatch, atom_name: str) → pyrosetta.rosetta.core.chemical.Patch¶: C++: core::chemical::Metapatch::get_one_patch(const class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::Patch>

meets_requirements(self: pyrosetta.rosetta.core.chemical.Metapatch, r: pyrosetta.rosetta.core.chemical.ResidueType, i: int) → bool¶: C++: core::chemical::Metapatch::meets_requirements(const class core::chemical::ResidueType &, unsigned long) const –> bool

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

unique name of this patch, eg Nter-simple, Cter-full, Phospho, … ?

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

read_file(self: pyrosetta.rosetta.core.chemical.Metapatch, filename: str) → None¶

constructor from file

C++: core::chemical::Metapatch::read_file(const class std::basic_string<char> &) –> void

types(self: pyrosetta.rosetta.core.chemical.Metapatch) → pyrosetta.rosetta.utility.vector1_std_string¶

the variant types created by applying this patch

C++: core::chemical::Metapatch::types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

class pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Set the mainchain torsion indices that a noncanonical rotamer library depends upon.

Vikram K. Mulligan (vmullig.edu).

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions, rsd: core::chemical::ResidueType) → bool¶

Set the mainchain torsion indices that a noncanonical rotamer library depends upon.

C++: core::chemical::NCAARotLibBBTorsions::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions, : pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions) → pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions¶: C++: core::chemical::NCAARotLibBBTorsions::operator=(const class core::chemical::NCAARotLibBBTorsions &) –> class core::chemical::NCAARotLibBBTorsions &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Set the number of rotamer bins per chi for an NCAA that is not in dunbrack.

Vikram K. Mulligan (vmullig.edu).

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins, rsd: core::chemical::ResidueType) → bool¶

Set the number of rotamer bins per chi for an NCAA.

C++: core::chemical::NCAARotLibNumRotamerBins::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins, : pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins) → pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins¶: C++: core::chemical::NCAARotLibNumRotamerBins::operator=(const class core::chemical::NCAARotLibNumRotamerBins &) –> class core::chemical::NCAARotLibNumRotamerBins &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.NCAARotLibPath¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set the path to a rotamer library for an NCAA that is not in dunbrack

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.NCAARotLibPath, rsd: core::chemical::ResidueType) → bool¶

set the NCAA rotamer library path in the residue type

C++: core::chemical::NCAARotLibPath::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.NCAARotLibPath, : pyrosetta.rosetta.core.chemical.NCAARotLibPath) → pyrosetta.rosetta.core.chemical.NCAARotLibPath¶: C++: core::chemical::NCAARotLibPath::operator=(const class core::chemical::NCAARotLibPath &) –> class core::chemical::NCAARotLibPath &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.Orbital¶

Bases: pybind11_builtins.pybind11_object

basic chemical atom

name, element, certain properties and parameters from .params file

assign(self: pyrosetta.rosetta.core.chemical.Orbital, : pyrosetta.rosetta.core.chemical.Orbital) → pyrosetta.rosetta.core.chemical.Orbital¶: C++: core::chemical::Orbital::operator=(const class core::chemical::Orbital &) –> class core::chemical::Orbital &

icoor(*args, **kwargs)¶

Overloaded function.

icoor(self: pyrosetta.rosetta.core.chemical.Orbital) -> pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

C++: core::chemical::Orbital::icoor() –> class core::chemical::orbitals::ICoorOrbitalData &

icoor(self: pyrosetta.rosetta.core.chemical.Orbital, icoor: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) -> None

C++: core::chemical::Orbital::icoor(const class core::chemical::orbitals::ICoorOrbitalData &) –> void

ideal_xyz(*args, **kwargs)¶

Overloaded function.

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

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

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

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

name(*args, **kwargs)¶

Overloaded function.

name(self: pyrosetta.rosetta.core.chemical.Orbital) -> str

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

name(self: pyrosetta.rosetta.core.chemical.Orbital, name: str) -> None

C++: core::chemical::Orbital::name(const class std::basic_string<char> &) –> void

new_icoor(*args, **kwargs)¶

Overloaded function.

new_icoor(self: pyrosetta.rosetta.core.chemical.Orbital) -> pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

C++: core::chemical::Orbital::new_icoor() –> class core::chemical::orbitals::ICoorOrbitalData &

new_icoor(self: pyrosetta.rosetta.core.chemical.Orbital, new_icoor: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) -> None

C++: core::chemical::Orbital::new_icoor(const class core::chemical::orbitals::ICoorOrbitalData &) –> void

orbital_type_index(*args, **kwargs)¶

Overloaded function.

orbital_type_index(self: pyrosetta.rosetta.core.chemical.Orbital) -> int

C++: core::chemical::Orbital::orbital_type_index() const –> const unsigned long &

orbital_type_index(self: pyrosetta.rosetta.core.chemical.Orbital, atom_type_index: int) -> None

C++: core::chemical::Orbital::orbital_type_index(const unsigned long &) –> void

print(self: pyrosetta.rosetta.core.chemical.Orbital, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::Orbital::print(class std::basic_ostream<char> &) const –> void

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.Orbital, old_to_new: pyrosetta.rosetta.std.map_void_*_void_*) → None¶

Update the internal VDs based on the provide mapping

C++: core::chemical::Orbital::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> void

class pyrosetta.rosetta.core.chemical.Patch¶

Bases: pybind11_builtins.pybind11_object

A class patching basic ResidueType to create variant types, containing multiple PatchCase

add_case(self: pyrosetta.rosetta.core.chemical.Patch, pcase: pyrosetta.rosetta.core.chemical.PatchCase) → None¶: C++: core::chemical::Patch::add_case(class std::shared_ptr<class core::chemical::PatchCase>) –> void

adds_atoms(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of added atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::adds_atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

adds_properties(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of added property names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::adds_properties(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

applies_to(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

can I operate on this residue type?

C++: core::chemical::Patch::applies_to(const class core::chemical::ResidueType &) const –> bool

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.ResidueType
apply(self: pyrosetta.rosetta.core.chemical.Patch, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.ResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::Patch::apply(const class core::chemical::ResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::ResidueType>

assign(self: pyrosetta.rosetta.core.chemical.Patch, : pyrosetta.rosetta.core.chemical.Patch) → pyrosetta.rosetta.core.chemical.Patch¶: C++: core::chemical::Patch::operator=(const class core::chemical::Patch &) –> class core::chemical::Patch &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool¶

Does the patch potentially change the connections for the given atom on the ResidueType

C++: core::chemical::Patch::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) const –> bool

deletes_atoms(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted atom names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_atoms(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_properties(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted property names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_properties(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

deletes_variants(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted variant names, useful for identifying patches that go with PDB residues

C++: core::chemical::Patch::deletes_variants(const class core::chemical::ResidueType &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

generates_aa(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.AA¶

returns new AA, if changed.

C++: core::chemical::Patch::generates_aa(const class core::chemical::ResidueType &) const –> enum core::chemical::AA

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

returns new interchangeability_group, if changed. Only one new interchangeability_group allowed.

C++: core::chemical::Patch::generates_interchangeability_group(const class core::chemical::ResidueType &) const –> std::string

generates_new_name3(self: pyrosetta.rosetta.core.chemical.Patch, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

returns new name3, if changed. Only one new name3 allowed.

C++: core::chemical::Patch::generates_new_name3(const class core::chemical::ResidueType &) const –> std::string

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

unique name of this patch, eg Nter-simple, Cter-full, Phospho, … ?

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

patched_name(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

Returns the name of the residueType after applying the patch: (Theoretical - doesn’t actually check if the patch would be applied.)

C++: core::chemical::Patch::patched_name(const class core::chemical::ResidueType &) const –> std::string

read_file(self: pyrosetta.rosetta.core.chemical.Patch, filename: str) → None¶

constructor from file

C++: core::chemical::Patch::read_file(const class std::basic_string<char> &) –> void

replaces(self: pyrosetta.rosetta.core.chemical.Patch, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

do I replace this residue type?

C++: core::chemical::Patch::replaces(const class core::chemical::ResidueType &) const –> bool

replaces_residue_type(self: pyrosetta.rosetta.core.chemical.Patch, replaces: bool) → None¶: C++: core::chemical::Patch::replaces_residue_type(bool) –> void

set_name(self: pyrosetta.rosetta.core.chemical.Patch, name: str) → None¶: C++: core::chemical::Patch::set_name(class std::basic_string<char>) –> void

set_selector(self: pyrosetta.rosetta.core.chemical.Patch, selector: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → None¶: C++: core::chemical::Patch::set_selector(const class core::chemical::ResidueTypeSelector &) –> void

types(*args, **kwargs)¶

Overloaded function.

types(self: pyrosetta.rosetta.core.chemical.Patch) -> pyrosetta.rosetta.utility.vector1_std_string

the variant types created by applying this patch

C++: core::chemical::Patch::types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

types(self: pyrosetta.rosetta.core.chemical.Patch, types: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: core::chemical::Patch::types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

class pyrosetta.rosetta.core.chemical.PatchCase¶

Bases: pybind11_builtins.pybind11_object

A single case of a patch, eg proline Nterminus is a case of NtermProteinFull

add_operation(self: pyrosetta.rosetta.core.chemical.PatchCase, operation: pyrosetta.rosetta.core.chemical.PatchOperation) → None¶

add one more operation in this PatchCase

C++: core::chemical::PatchCase::add_operation(class std::shared_ptr<class core::chemical::PatchOperation>) –> void

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

returns list of added atom names, useful for identifying patches that go with PDB residues

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

adds_properties(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of added property names, useful for identifying patches that go with PDB residues

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

applies_to(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

whether the PatchCase is applicable to this ResidueType?

C++: core::chemical::PatchCase::applies_to(const class core::chemical::ResidueType &) const –> bool

apply(*args, **kwargs)¶

Overloaded function.

apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.ResidueType
apply(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, instantiate: bool) -> pyrosetta.rosetta.core.chemical.ResidueType

returns patched residue, 0 if patch failed

C++: core::chemical::PatchCase::apply(const class core::chemical::ResidueType &, const bool) const –> class std::shared_ptr<class core::chemical::ResidueType>

assign(self: pyrosetta.rosetta.core.chemical.PatchCase, : pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.core.chemical.PatchCase¶: C++: core::chemical::PatchCase::operator=(const class core::chemical::PatchCase &) –> class core::chemical::PatchCase &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchCase, rsd_in: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → bool¶

Can the patch case change the connections for atom on the ResidueType?

C++: core::chemical::PatchCase::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) const –> bool

deletes_atoms(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted atom names, useful for identifying patches that go with PDB residues

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

deletes_properties(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted property names, useful for identifying patches that go with PDB residues

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

deletes_variants(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.utility.vector1_std_string¶

returns list of deleted variant names, useful for identifying patches that go with PDB residues

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

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

returns interchangeability group, if set.

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

generates_new_name3(self: pyrosetta.rosetta.core.chemical.PatchCase) → str¶

returns new name3, if changed

C++: core::chemical::PatchCase::generates_new_name3() const –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchCase) → bool¶: C++: core::chemical::PatchCase::may_change_aa() const –> bool

selector(self: pyrosetta.rosetta.core.chemical.PatchCase) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶

to which ResidueTypes this PatchCase applies to?

C++: core::chemical::PatchCase::selector() –> class core::chemical::ResidueTypeSelector &

set_selector(self: pyrosetta.rosetta.core.chemical.PatchCase, selector: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → None¶: C++: core::chemical::PatchCase::set_selector(const class core::chemical::ResidueTypeSelector &) –> void

class pyrosetta.rosetta.core.chemical.PatchOperation¶

Bases: pybind11_builtins.pybind11_object

A single operation that needs to be applied in a residue patch

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.PatchOperation, rsd: core::chemical::ResidueType) → bool¶

Returns true to signal failure, false to indicate success.

C++: core::chemical::PatchOperation::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.PatchOperation) → pyrosetta.rosetta.core.chemical.PatchOperation¶: C++: core::chemical::PatchOperation::operator=(const class core::chemical::PatchOperation &) –> class core::chemical::PatchOperation &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

Returns the name of the patch operation. Useful for debugging.

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.PolarHydrogenFilter¶

Bases: pybind11_builtins.pybind11_object

The filter responsible for all polar hydrogens.

assign(self: pyrosetta.rosetta.core.chemical.PolarHydrogenFilter, : pyrosetta.rosetta.core.chemical.PolarHydrogenFilter) → pyrosetta.rosetta.core.chemical.PolarHydrogenFilter¶: C++: core::chemical::PolarHydrogenFilter::operator=(const class core::chemical::PolarHydrogenFilter &) –> class core::chemical::PolarHydrogenFilter &

class pyrosetta.rosetta.core.chemical.PoseResidueTypeSet¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSet

A ResidueTypeSet which can be cached in the Pose

add_base_residue_type(*args, **kwargs)¶

Overloaded function.

add_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, new_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None

C++: core::chemical::PoseResidueTypeSet::add_base_residue_type(class std::shared_ptr<class core::chemical::ResidueType>) –> void

add_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filename: str) -> None

C++: core::chemical::PoseResidueTypeSet::add_base_residue_type(const class std::basic_string<char> &) –> void

add_patches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, patch_filenames: pyrosetta.rosetta.utility.vector1_std_string, metapatch_filenames: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::chemical::PoseResidueTypeSet::add_patches(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

add_unpatchable_residue_type(*args, **kwargs)¶

Overloaded function.

add_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, new_type: pyrosetta.rosetta.core.chemical.ResidueType) -> None

C++: core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type(class std::shared_ptr<class core::chemical::ResidueType>) –> void

add_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filename: str) -> None

C++: core::chemical::PoseResidueTypeSet::add_unpatchable_residue_type(const class std::basic_string<char> &) –> void

atom_type_set(*args, **kwargs)¶

Overloaded function.

atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.AtomTypeSet

C++: core::chemical::PoseResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, atom_types: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::atom_type_set(class std::shared_ptr<const class core::chemical::AtomTypeSet>) –> void

base_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶

the residues with no patches applied

C++: core::chemical::PoseResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

clone(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.core.chemical.PoseResidueTypeSet¶: C++: core::chemical::PoseResidueTypeSet::clone() const –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>

default_rts(*args, **kwargs)¶

Overloaded function.

default_rts(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, setting: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> None

Set the default fall-back ResidueTypeSet

C++: core::chemical::PoseResidueTypeSet::default_rts(class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> void

default_rts(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ResidueTypeSet

What is the default fall-back ResidueTypesSet

C++: core::chemical::PoseResidueTypeSet::default_rts() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>

element_set(*args, **kwargs)¶

Overloaded function.

element_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ElementSet

C++: core::chemical::PoseResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>

element_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, elements: pyrosetta.rosetta.core.chemical.ElementSet) -> None

C++: core::chemical::PoseResidueTypeSet::element_set(class std::shared_ptr<const class core::chemical::ElementSet>) –> void

generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, base_residue_name: str, interchangeability_group: str) → bool¶

Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated))

C++: core::chemical::PoseResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const class std::basic_string<char> &, const class std::basic_string<char> &) const –> bool

generates_patched_residue_type_with_name3(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, base_residue_name: str, name3: str) → bool¶

Check if a base type (like “SER”) generates any types with another name3 (like “SEP”)

C++: core::chemical::PoseResidueTypeSet::generates_patched_residue_type_with_name3(const class std::basic_string<char> &, const class std::basic_string<char> &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)¶

Overloaded function.

get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, 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::PoseResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<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_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, 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::PoseResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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_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<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<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_d_equivalent(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, l_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: core::chemical::PoseResidueTypeSet::get_d_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_l_equivalent(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, d_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: core::chemical::PoseResidueTypeSet::get_l_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_mirrored_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, original_rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: core::chemical::PoseResidueTypeSet::get_mirrored_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_aa(*args, **kwargs)¶

Overloaded function.

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> 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) → 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)¶

Overloaded function.

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> 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.

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 class std::basic_string<char> &) const –> bool

has_metapatch(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → bool¶

Do we have this metapatch?

C++: core::chemical::PoseResidueTypeSet::has_metapatch(const class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) const –> bool

merge_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::MergeBehaviorManager¶

accessor for merge behavior manager

C++: core::chemical::ResidueTypeSet::merge_behavior_manager() const –> const class core::chemical::MergeBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → pyrosetta.rosetta.core.chemical.Metapatch¶: C++: core::chemical::PoseResidueTypeSet::metapatch(const class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::Metapatch>

metapatch_map(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t¶

the metapatches, index by name.

C++: core::chemical::PoseResidueTypeSet::metapatch_map() const –> const class std::map<std::string, class std::shared_ptr<const class core::chemical::Metapatch>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class core::chemical::Metapatch> > > > &

metapatches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Metapatch_t¶

the metapatches

C++: core::chemical::PoseResidueTypeSet::metapatches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Metapatch>, class std::allocator<class std::shared_ptr<const class core::chemical::Metapatch> > >

mm_atom_type_set(*args, **kwargs)¶

Overloaded function.

mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> pyrosetta.rosetta.core.chemical.MMAtomTypeSet

C++: core::chemical::PoseResidueTypeSet::mm_atom_type_set() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mm_atom_types: pyrosetta.rosetta.core.chemical.MMAtomTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::mm_atom_type_set(class std::shared_ptr<const class core::chemical::MMAtomTypeSet>) –> void

mode(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.TypeSetMode¶

The type of the ResidueTypeSet

The difference between a ResidueTypeSet name and a ResidueTypeSet mode is that a a ResidueTypeSet name should uniquely identify a ResidueTypeSet (at lease those within the ChemicalManger) but more than one ResidueTypeSet may have the same mode. The mode specifies what compatibility class (full atom, centroid) the ResidueTypeSet has.

C++: core::chemical::ResidueTypeSet::mode() const –> enum core::chemical::TypeSetMode

name_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → 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 class std::basic_string<char> &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

orbital_type_set(*args, **kwargs)¶

Overloaded function.

orbital_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) -> core::chemical::orbitals::OrbitalTypeSet

C++: core::chemical::PoseResidueTypeSet::orbital_type_set() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

orbital_type_set(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, orbital_types: core::chemical::orbitals::OrbitalTypeSet) -> None

C++: core::chemical::PoseResidueTypeSet::orbital_type_set(class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>) –> void

patch_map(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.std.map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t¶

the patches, index by name.

C++: core::chemical::PoseResidueTypeSet::patch_map() const –> const class std::map<std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > > > > > &

patches(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t¶

the patches

C++: core::chemical::PoseResidueTypeSet::patches() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >

read_files_for_base_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::chemical::PoseResidueTypeSet::read_files_for_base_residue_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

read_files_for_unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, filenames: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: core::chemical::PoseResidueTypeSet::read_files_for_unpatchable_residue_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

remove_base_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → None¶: C++: core::chemical::PoseResidueTypeSet::remove_base_residue_type(const class std::basic_string<char> &) –> void

remove_unpatchable_residue_type(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, name: str) → None¶: C++: core::chemical::PoseResidueTypeSet::remove_unpatchable_residue_type(const class std::basic_string<char> &) –> void

set_merge_behavior_manager(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet, mbm: pyrosetta.rosetta.core.chemical.MergeBehaviorManager) → None¶: C++: core::chemical::PoseResidueTypeSet::set_merge_behavior_manager(class std::shared_ptr<const class core::chemical::MergeBehaviorManager>) –> void

unpatchable_residue_types(self: pyrosetta.rosetta.core.chemical.PoseResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶

the residues with no patches applied

C++: core::chemical::PoseResidueTypeSet::unpatchable_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

class pyrosetta.rosetta.core.chemical.PrependMainchainAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

add a mainchain atom before the first mainchain atom

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.PrependMainchainAtom, rsd: core::chemical::ResidueType) → bool¶

set an atom to be the first mainchain atom

C++: core::chemical::PrependMainchainAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.PrependMainchainAtom, : pyrosetta.rosetta.core.chemical.PrependMainchainAtom) → pyrosetta.rosetta.core.chemical.PrependMainchainAtom¶: C++: core::chemical::PrependMainchainAtom::operator=(const class core::chemical::PrependMainchainAtom &) –> class core::chemical::PrependMainchainAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.RamaPreproFilename¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Set the filenames for RamaPrePro scoring tables.

Vikram K. Mulligan (vmullig.edu)

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.RamaPreproFilename, rsd: core::chemical::ResidueType) → bool¶

Set the RamaPrepro library paths in the residue type.

C++: core::chemical::RamaPreproFilename::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RamaPreproFilename, : pyrosetta.rosetta.core.chemical.RamaPreproFilename) → pyrosetta.rosetta.core.chemical.RamaPreproFilename¶: C++: core::chemical::RamaPreproFilename::operator=(const class core::chemical::RamaPreproFilename &) –> class core::chemical::RamaPreproFilename &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.RamaPreproResname¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Set the residue name for RamaPrePro scoring tables.

This is the name in the scoring table AND the reference string used to look up the table. Should be unique.

Vikram K. Mulligan (vmullig.edu)

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.RamaPreproResname, rsd: core::chemical::ResidueType) → bool¶

Set the RamaPrepro reference string in the residue type.

C++: core::chemical::RamaPreproResname::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RamaPreproResname, : pyrosetta.rosetta.core.chemical.RamaPreproResname) → pyrosetta.rosetta.core.chemical.RamaPreproResname¶: C++: core::chemical::RamaPreproResname::operator=(const class core::chemical::RamaPreproResname &) –> class core::chemical::RamaPreproResname &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.RealFilter¶

Bases: pybind11_builtins.pybind11_object

A filtered graph that doesn’t contain fake/virtual atoms and fake/virtual bonds.

assign(self: pyrosetta.rosetta.core.chemical.RealFilter, : pyrosetta.rosetta.core.chemical.RealFilter) → pyrosetta.rosetta.core.chemical.RealFilter¶: C++: core::chemical::RealFilter::operator=(const class core::chemical::RealFilter &) –> class core::chemical::RealFilter &

class pyrosetta.rosetta.core.chemical.RedefineChi¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Redefine a chi angle: Added by Andy M. Chen in June 2009 This is needed for certain PTMs

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.RedefineChi, rsd: core::chemical::ResidueType) → bool¶

redefine a chi angle

C++: core::chemical::RedefineChi::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RedefineChi, : pyrosetta.rosetta.core.chemical.RedefineChi) → pyrosetta.rosetta.core.chemical.RedefineChi¶: C++: core::chemical::RedefineChi::operator=(const class core::chemical::RedefineChi &) –> class core::chemical::RedefineChi &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Remove existing rotamer specifications (of any type).

Vikram K. Mulligan (vmullig.edu)

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications, rsd: core::chemical::ResidueType) → bool¶

Strip all RotamerSpecifications from the ResidueType.

C++: core::chemical::RemoveRotamerSpecifications::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications, : pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications) → pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications¶: C++: core::chemical::RemoveRotamerSpecifications::operator=(const class core::chemical::RemoveRotamerSpecifications &) –> class core::chemical::RemoveRotamerSpecifications &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.RenameAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

rename atom

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.RenameAtom, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::RenameAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.RenameAtom, : pyrosetta.rosetta.core.chemical.RenameAtom) → pyrosetta.rosetta.core.chemical.RenameAtom¶: C++: core::chemical::RenameAtom::operator=(const class core::chemical::RenameAtom &) –> class core::chemical::RenameAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

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

class pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace a mainchain atom

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom, rsd: core::chemical::ResidueType) → bool¶

set an atom to be the last mainchain atom

C++: core::chemical::ReplaceMainchainAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom, : pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom) → pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom¶: C++: core::chemical::ReplaceMainchainAtom::operator=(const class core::chemical::ReplaceMainchainAtom &) –> class core::chemical::ReplaceMainchainAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with bromine

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithBromine::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine¶: C++: core::chemical::ReplaceProtonWithBromine::operator=(const class core::chemical::ReplaceProtonWithBromine &) –> class core::chemical::ReplaceProtonWithBromine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with chlorine

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithChlorine::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine¶: C++: core::chemical::ReplaceProtonWithChlorine::operator=(const class core::chemical::ReplaceProtonWithChlorine &) –> class core::chemical::ReplaceProtonWithChlorine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with ethyl

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithEthyl::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl¶: C++: core::chemical::ReplaceProtonWithEthyl::operator=(const class core::chemical::ReplaceProtonWithEthyl &) –> class core::chemical::ReplaceProtonWithEthyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with fluorine

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithFluorine::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine¶: C++: core::chemical::ReplaceProtonWithFluorine::operator=(const class core::chemical::ReplaceProtonWithFluorine &) –> class core::chemical::ReplaceProtonWithFluorine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with hydroxyl

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithHydroxyl::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl¶: C++: core::chemical::ReplaceProtonWithHydroxyl::operator=(const class core::chemical::ReplaceProtonWithHydroxyl &) –> class core::chemical::ReplaceProtonWithHydroxyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with iodine

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithIodine::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine¶: C++: core::chemical::ReplaceProtonWithIodine::operator=(const class core::chemical::ReplaceProtonWithIodine &) –> class core::chemical::ReplaceProtonWithIodine &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with methoxy

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithMethoxy::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy¶: C++: core::chemical::ReplaceProtonWithMethoxy::operator=(const class core::chemical::ReplaceProtonWithMethoxy &) –> class core::chemical::ReplaceProtonWithMethoxy &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with methyl

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithMethyl::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl¶: C++: core::chemical::ReplaceProtonWithMethyl::operator=(const class core::chemical::ReplaceProtonWithMethyl &) –> class core::chemical::ReplaceProtonWithMethyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

replace proton with trifluoromethyl

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::ReplaceProtonWithTrifluoromethyl::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl, : pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl) → pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl¶: C++: core::chemical::ReplaceProtonWithTrifluoromethyl::operator=(const class core::chemical::ReplaceProtonWithTrifluoromethyl &) –> class core::chemical::ReplaceProtonWithTrifluoromethyl &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ResConnID¶

Bases: pybind11_builtins.pybind11_object

The ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue’s index and the ResidueConnection index.

assign(self: pyrosetta.rosetta.core.chemical.ResConnID, : pyrosetta.rosetta.core.chemical.ResConnID) → pyrosetta.rosetta.core.chemical.ResConnID¶: C++: core::chemical::ResConnID::operator=(const class core::chemical::ResConnID &) –> class core::chemical::ResConnID &

connid(*args, **kwargs)¶

Overloaded function.

connid(self: pyrosetta.rosetta.core.chemical.ResConnID) -> int

C++: core::chemical::ResConnID::connid() const –> unsigned long

connid(self: pyrosetta.rosetta.core.chemical.ResConnID, : int) -> None

C++: core::chemical::ResConnID::connid(unsigned long) –> void

incomplete(self: pyrosetta.rosetta.core.chemical.ResConnID) → bool¶: C++: core::chemical::ResConnID::incomplete() const –> bool

mark_incomplete(self: pyrosetta.rosetta.core.chemical.ResConnID) → None¶: C++: core::chemical::ResConnID::mark_incomplete() –> void

resid(*args, **kwargs)¶

Overloaded function.

resid(self: pyrosetta.rosetta.core.chemical.ResConnID) -> int

C++: core::chemical::ResConnID::resid() const –> unsigned long

resid(self: pyrosetta.rosetta.core.chemical.ResConnID, : int) -> None

C++: core::chemical::ResConnID::resid(unsigned long) –> void

class pyrosetta.rosetta.core.chemical.ResetBondLength¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

A patch operation for resetting the length of a bond within a ResidueType.

This is useful for when an atom is rehybridized within a patch file.

Labonte <JWLabonte.edu>

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.ResetBondLength, rsd: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::ResetBondLength::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.ResetBondLength, : pyrosetta.rosetta.core.chemical.ResetBondLength) → pyrosetta.rosetta.core.chemical.ResetBondLength¶: C++: core::chemical::ResetBondLength::operator=(const class core::chemical::ResetBondLength &) –> class core::chemical::ResetBondLength &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.ResidueConnection¶

Bases: pybind11_builtins.pybind11_object

A simple class marking atoms at inter-residue connections.

Each residue type specifies some number of positions at which it is expecting to form a chemical bond with another residue. Think of them as ports: they are parts of the residue where there are chemical bonds beyond the intra-residue chemical bonds are expected – places where they can be chemically linked to the outside world. A conformation::Residue will require that its ResidueConnections be fulfilled by other Residues – the ResConnID class describes how two residues are connected: e.g., the third ResConnID for residue 10 would say “I connect to residue 58 at residue 58’s third residue connection” if residue 10 and residue 58 were disulfide bonded as the disulfide connection id is “3” for two mid-protein cystine residues. The advantages of separating ResidueConnections from atoms themselves are that 1) it allows multiple residue connections to stem from the same atom – useful for single-atom residues, such as coordinated metals (Zn, Mg), and 2) it allows one residue to change its set of atoms without invalidating the bond information (e.g. the atom index) on its partner. For example, if a chain-break were placed between residues 57 and 58, then residue 58 will get an extra C-prev virtual atom, and the index of SG will change. Residue 10, if it had recorded the SG index would have to find SG’s new index. If instead, the connection point is represented simply as connection point 3, and if the new residue type (the chainbreak disulfide residue) has the same number of residue connections as the original residue type (it will!) then nothing about residue 10 needs to be updated.

atomno(*args, **kwargs)¶

Overloaded function.

atomno(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> int

get atom index number

C++: core::chemical::ResidueConnection::atomno() const –> int

atomno(self: pyrosetta.rosetta.core.chemical.ResidueConnection, atomno_in: int) -> None

set atom index number

C++: core::chemical::ResidueConnection::atomno(const unsigned long) –> void

icoor(*args, **kwargs)¶

Overloaded function.

icoor(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> pyrosetta.rosetta.core.chemical.AtomICoor

get atom’s AtomICoor

C++: core::chemical::ResidueConnection::icoor() const –> const class core::chemical::AtomICoor &

icoor(self: pyrosetta.rosetta.core.chemical.ResidueConnection, ic: pyrosetta.rosetta.core.chemical.AtomICoor) -> None

set atom’s AtomICoor

C++: core::chemical::ResidueConnection::icoor(const class core::chemical::AtomICoor &) –> void

index(*args, **kwargs)¶

Overloaded function.

index(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> int

C++: core::chemical::ResidueConnection::index() const –> int

index(self: pyrosetta.rosetta.core.chemical.ResidueConnection, index_in: int) -> None

C++: core::chemical::ResidueConnection::index(int) –> void

remap_atom_vds(self: pyrosetta.rosetta.core.chemical.ResidueConnection, old_to_new: pyrosetta.rosetta.std.map_void_*_void_*) → None¶

Update the internal VDs based on the provide mapping

C++: core::chemical::ResidueConnection::remap_atom_vds(const class std::map<void *, void *, struct std::less<void *>, class std::allocator<struct std::pair<void *const, void *> > > &) –> void

vertex(*args, **kwargs)¶

Overloaded function.

vertex(self: pyrosetta.rosetta.core.chemical.ResidueConnection) -> capsule

get the vetex associated with this residue connection

C++: core::chemical::ResidueConnection::vertex() const –> void *

vertex(self: pyrosetta.rosetta.core.chemical.ResidueConnection, vertex: capsule) -> None

set the vertex of this residue connection

C++: core::chemical::ResidueConnection::vertex(void *const) –> void

class pyrosetta.rosetta.core.chemical.ResidueProperties¶

Bases: pybind11_builtins.pybind11_object

This is a container class for the large assortment of properties associated with ResidueTypes. It prevents ResidueType from becoming cluttered with an over-abundance of properties and related methods.

This is the first step in a major refactor of how properties are handled in Rosetta. For now, I have just gathered all the properties related code into one place, so that changes to the system can be more readily made. Previous behavior has been maintained. In the future, I have several ideas for further improvements. ~Labonte

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, tag: str, value: float) → None¶

Add a numeric property.

C++: core::chemical::ResidueProperties::add_numeric_property(const class std::basic_string<char> &, const double) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, tag: str, value: str) → None¶

Add a string property.

C++: core::chemical::ResidueProperties::add_string_property(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → None¶

Turn on the ability to create VariantTypes “on-the-fly”.

Custom” VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

C++: core::chemical::ResidueProperties::enable_custom_variant_types() –> void

generate_property_to_string_vector() → pyrosetta.rosetta.utility.vector1_std_string¶

Generate the map of (ResidueProperty->string). (This is actually a vector since we’re going from an enum – which can be

a vector index – to a string).

Used to initialize the const static vector. Since c++11 initialization of const static singletons is inherently threadsafe, we don’t subsequently have to worry about mutexes for access to this.

This is implemented in core/chemical/ResidueProperty_mappings.cc, an automatically-generated file. DO NOT EDIT THAT FILE DIRECTLY. Intead, edit the generating script.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueProperties::generate_property_to_string_vector() –> const class utility::vector1<std::string, class std::allocator<std::string > > *

generate_variant_to_string_vector() → pyrosetta.rosetta.utility.vector1_std_string¶

Generate the map of (VariantType->string). (This is actually a vector since we’re going from an enum – which can be

a vector index – to a string).

Used to initialize the const static vector. Since c++11 initialization of const static singletons is inherently threadsafe, we don’t subsequently have to worry about mutexes for access to this.

This is implemented in core/chemical/VariantType_mappings.cc, an automatically-generated file. DO NOT EDIT THAT FILE DIRECTLY. Intead, edit the generating script.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueProperties::generate_variant_to_string_vector() –> const class utility::vector1<std::string, class std::allocator<std::string > > *

get_list_of_custom_variants(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string¶

Return a list of custom VariantTypes only for this ResidueType.

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

get_list_of_custom_variants_by_reference(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string¶

Get a const-access reference to the list of custom VariantType strings for this ResidueType.

This will not include enum-based standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueProperties::get_list_of_custom_variants_by_reference() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

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

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

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

get_list_of_variant_enums(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType¶

Return a list of VariantType enums for this ResidueType.

This will not include custom, string-based variant types generated on the fly.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueProperties::get_list_of_variant_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

get_list_of_variants(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.utility.vector1_std_string¶

Generate and return a list of strings representing the VariantTypes of this ResidueType.

This will include both custom, string-based variants made on-the-fly AND the standard variants that are enumerated.

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

get_property_from_string(property: str) → pyrosetta.rosetta.core.chemical.ResidueProperty¶

Static constant data access

Get the ResidueProperty enum value from the corresponding string. This private static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it’s a handy function for other code to use (VKM, 22 July 2015).

C++: core::chemical::ResidueProperties::get_property_from_string(const class std::basic_string<char> &) –> const enum core::chemical::ResidueProperty &

get_string_from_property(property: pyrosetta.rosetta.core.chemical.ResidueProperty) → str¶

Get a string from the corresponding ResidueProperty enum value.

This private static class method is defined in ResidueProperty_mappings.cc, which is auto-generated by the add_ResidueType_enum_files.py script. Note – made public because it’s a handy function for other code to use (VKM, 22 July 2015).

C++: core::chemical::ResidueProperties::get_string_from_property(const enum core::chemical::ResidueProperty) –> const std::string &

get_string_from_variant(variant: pyrosetta.rosetta.core.chemical.VariantType) → str¶: C++: core::chemical::ResidueProperties::get_string_from_variant(const enum core::chemical::VariantType) –> const std::string &

get_variant_from_string(variant: str) → pyrosetta.rosetta.core.chemical.VariantType¶: C++: core::chemical::ResidueProperties::get_variant_from_string(const class std::basic_string<char> &) –> const enum core::chemical::VariantType &

has_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → bool¶

Does this ResidueType contain additional VariantTypes than the standard list?

C++: core::chemical::ResidueProperties::has_custom_variant_types() const –> bool

has_property(*args, **kwargs)¶

Overloaded function.

has_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Get whether or not this ResidueType has the requested property.

C++: core::chemical::ResidueProperties::has_property(const enum core::chemical::ResidueProperty) const –> bool

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

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

C++: core::chemical::ResidueProperties::has_property(const class std::basic_string<char> &) const –> bool

is_variant_type(*args, **kwargs)¶

Overloaded function.

is_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Get whether or not this ResidueType is of the requested VariantType.

C++: core::chemical::ResidueProperties::is_variant_type(const enum core::chemical::VariantType) const –> bool

is_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: str) -> bool

Get whether or not this ResidueType is of the requested VariantType by string.

C++: core::chemical::ResidueProperties::is_variant_type(const class std::basic_string<char> &) const –> bool

numeric_properties(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.std.map_std_string_double¶: C++: core::chemical::ResidueProperties::numeric_properties() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

set_property(*args, **kwargs)¶

Overloaded function.

set_property(self: pyrosetta.rosetta.core.chemical.ResidueProperties, property: pyrosetta.rosetta.core.chemical.ResidueProperty, setting: bool) -> None

Set the status of the given property for this ResidueType.

C++: core::chemical::ResidueProperties::set_property(const enum core::chemical::ResidueProperty, const bool) –> void

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

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

C++: core::chemical::ResidueProperties::set_property(const class std::basic_string<char> &, const bool) –> void

set_variant_type(*args, **kwargs)¶

Overloaded function.

set_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: pyrosetta.rosetta.core.chemical.VariantType, setting: bool) -> None

Set the status of a given VariantType for this ResidueType.

C++: core::chemical::ResidueProperties::set_variant_type(const enum core::chemical::VariantType, const bool) –> void

set_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueProperties, variant_type: str, setting: bool) -> None

Set the status of a given VariantType for this ResidueType by string.

C++: core::chemical::ResidueProperties::set_variant_type(const class std::basic_string<char> &, const bool) –> void

show(*args, **kwargs)¶

Overloaded function.

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

Generate string representation of ResidueProperties for debugging purposes.

C++: core::chemical::ResidueProperties::show(class std::basic_ostream<char> &) const –> void

string_properties(self: pyrosetta.rosetta.core.chemical.ResidueProperties) → pyrosetta.rosetta.std.map_std_string_std_string¶: C++: core::chemical::ResidueProperties::string_properties() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

class pyrosetta.rosetta.core.chemical.ResidueProperty¶

Bases: pybind11_builtins.pybind11_object

Enumerators for all the properties that can be assigned to a ResidueType.

Members:

NO_PROPERTY

FIRST_PROPERTY

POLYMER

LIGAND

PROTEIN

CANONICAL_AA

CANONICAL_NUCLEIC

DNA

RNA

TNA

PNA

PEPTOID

OLIGOUREA

CARBOHYDRATE

LIPID

TERPENE

NUCLEOTIDE_DIPHOSPHATE

SRI

TRIAZOLE_LINKER

METAL

SURFACE

WATER

SOLVENT

VIRTUAL_RESIDUE

INVERTED_VIRTUAL_RESIDUE

LOWER_TERMINUS

UPPER_TERMINUS

BRANCH_POINT

TERMINUS

LOWERTERM_TRUNC

UPPERTERM_TRUNC

COARSE

ADDUCT

SC_ORBITALS

FRAGMENT

UPPERTERM_CAP

LOWERTERM_CAP

POLAR

HYDROPHOBIC

CHARGED

NEGATIVE_CHARGE

POSITIVE_CHARGE

AROMATIC

ALIPHATIC

CYCLIC

METALBINDING

SIDECHAIN_THIOL

DISULFIDE_BONDED

ELECTROPHILE

SIDECHAIN_AMINE

MEMBRANE

PHOSPHONATE

PHOSPHONATE_UPPER

ACETYLATED_NTERMINUS

METHYLATED_CTERMINUS

ALPHA_AA

BETA_AA

GAMMA_AA

L_AA

D_AA

ACHIRAL_BACKBONE

TAUTOMER

PURINE

PYRIMIDINE

L_RNA

D_RNA

TRIOSE

TETROSE

PENTOSE

HEXOSE

HEPTOSE

OCTOSE

NONOSE

ALDOSE

KETOSE

L_SUGAR

D_SUGAR

OXIROSE

OXETOSE

FURANOSE

PYRANOSE

SEPTANOSE

ALPHA_SUGAR

BETA_SUGAR

SIALIC_ACID

C1_MODIFIED

C2_MODIFIED

C3_MODIFIED

C4_MODIFIED

C5_MODIFIED

C6_MODIFIED

C7_MODIFIED

C8_MODIFIED

C9_MODIFIED

GLYCOSIDE

ALDONIC_ACID

URONIC_ACID

DEOXY_SUGAR

AMINO_SUGAR

ACETYLAMINO_SUGAR

ACETYL_SUGAR

R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

SULFATED_SUGAR

SULFOAMINO_SUGAR

C_METHYLATED_SUGAR

PHOSPHATE

N_PROPERTIES

class pyrosetta.rosetta.core.chemical.ResidueType¶

Bases: pybind11_builtins.pybind11_object

A class for defining a type of residue

This class contains the “chemical” information for residues as well as the ideal xyz and internal coordinates for a residue (generated xyz coordinates are found in core/conformation/Residue.hh). A ResidueType in Rosetta can be a ligand, DNA, amino acid, or basically anything. ResidueTypes are generated through .params files, which are read from the database chemical/residue_types. For ligands, a parameter has to be provided to rosetta through the -extra_res_fa flag. Primary data are set through the residue_io.cc class. The primary data that are set are: atoms, mmatoms, orbitals, and properties of the particular ResidueType. These properties can be modified through patches, which create new ResidueTypes, and are controlled through PatchOperations.cc.

The data structure of a ResidueType is based on a boost::graph implementation. Vertex descriptors (VD, yeah, I know, the name is kind of bad) are the atoms, while the edge descriptors (ED, yet another bad name) are the bonds. Initially, when a ResidueType is constructed, the following primary data are set:

atom_base_; chi_atoms_; nu_atoms_; ring_atoms_; mainchain_atoms_; nbr_atom_; actcoord_atoms_; cut_bond_neighbor_; atom_shadowed_;

When this data is set, it is set based on vertex descriptors. Because vertex descriptors never change, like atom indices, there is no need to reorder this primary data; however, because Rosetta relies heavily on atom indices to access data, atom indices for the above data have to be generated. To do this, when finalized is called, a function specifically designed to generate the atom indices for the primary data is called: generate_atom_indices. This function iterates over the vertex descriptors assigned in the primary data and creates private data based on atom indices. For example, atom_base_ has atom_base_indices_. When the function atom_base(atomno) is called, the private datum atom_base_indices_ is called. This allows for the external interface of ResidueType to be accessed by atom indices while the internal functions in ResidueType work off of vertex descriptors. This also removes the need to have the former old2new reordering scheme.

Atoms: Setting of atoms includes indexing the atoms into vectors, saving their names into vectors/maps, saving the associated mm_atom_type into a vector, saving bond connections into vectors, etc, etc. On any given residue, the heavy atoms are put into the vector first, (their indices are first,) and hydrogens are put in last.

Properties: Properties of a residue include things like DNA, PROTEIN, CHARGED, etc. These properties indicate the type of residue it is and what properties are associated with the residue. They are set when read in. To add new ResidueProperties, add them to core/chemical/residue_properties/general_properties.list.

Orbitals: Orbitals are indexed separately from atoms. They function much the same way as atoms, except for some key differences. To find atoms bonded to orbitals, you must provide the atom index, not the orbital index. (I haven’t figured out how to get the reverse to work because of the separate indices.) Orbital xyz coordinates are not updated when atom coordinates are. This is to keep speed consistent with just having atoms. To output the orbitals, use the flag -output_orbitals.

Haro_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

return indices of aromatic Hydrogens

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

Hpol_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

return indices of polar Hydrogens

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

Hpos_apolar(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of non-polar hydrogens as potential carbon Hbond donors

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

Hpos_polar(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of polar hydrogens as Hbond donors

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

Hpos_polar_sc(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::chemical::ResidueType::Hpos_polar_sc() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

RNA_info(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::rna::RNA_Info¶: C++: core::chemical::ResidueType::RNA_info() const –> const class core::chemical::rna::RNA_Info &

aa(*args, **kwargs)¶

Overloaded function.

aa(self: pyrosetta.rosetta.core.chemical.ResidueType, type: pyrosetta.rosetta.core.chemical.AA) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueType::aa(const enum core::chemical::AA &) –> void

aa(self: pyrosetta.rosetta.core.chemical.ResidueType, type: str) -> None

set our aa-type (could be “UNK”)

C++: core::chemical::ResidueType::aa(const class std::basic_string<char> &) –> void

aa(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.AA

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be “aa_unk”.

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

C++: core::chemical::ResidueType::aa() const –> const enum core::chemical::AA &

abase2(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int¶

get index of an atom’s second base atom

C++: core::chemical::ResidueType::abase2(const unsigned long) const –> unsigned long

accpt_pos(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of atoms as Hbond acceptors

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

accpt_pos_sc(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of atoms as Hbond acceptors

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

actcoord_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

get indices for atoms used to define actcoord

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

add_actcoord_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → None¶

add an atom to the list for calculating actcoord center

C++: core::chemical::ResidueType::add_actcoord_atom(const class std::basic_string<char> &) –> void

add_adduct(self: pyrosetta.rosetta.core.chemical.ResidueType, adduct_in: pyrosetta.rosetta.core.chemical.Adduct) → None¶: C++: core::chemical::ResidueType::add_adduct(class core::chemical::Adduct &) –> void

add_atom(*args, **kwargs)¶

Overloaded function.

add_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str, atom_type_name: str, mm_atom_type_name: str, charge: float) -> capsule

add an atom into this residue: Will return the vertex descriptor of the added atom.

C++: core::chemical::ResidueType::add_atom(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const double) –> void *

add_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) -> capsule
add_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) -> capsule

add an atom into this residue, with just the name.: Will return the vertex descriptor of the added atom.

C++: core::chemical::ResidueType::add_atom(const class std::basic_string<char> &) –> void *

add_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: pyrosetta.rosetta.core.chemical.Atom, icoor: pyrosetta.rosetta.core.chemical.AtomICoor) -> capsule

C++: core::chemical::ResidueType::add_atom(const class core::chemical::Atom &, const class core::chemical::AtomICoor &) –> void *

add_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueType, rosetta_atom: str, alias: str) → None¶

Add an alias name for an atom.

C++: core::chemical::ResidueType::add_atom_alias(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_bond(*args, **kwargs)¶

Overloaded function.

add_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str) -> None
add_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str, bondLabel: pyrosetta.rosetta.core.chemical.BondName) -> None

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

C++: core::chemical::ResidueType::add_bond(const class std::basic_string<char> &, const class std::basic_string<char> &, enum core::chemical::BondName) –> void

add_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom1: capsule, atom2: capsule) -> None
add_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom1: capsule, atom2: capsule, bondLabel: pyrosetta.rosetta.core.chemical.BondName) -> None

add a bond between atom1 and atom2, specifying a bond type (SingleBond, DoubleBond, TripleBond, AromaticBond)

C++: core::chemical::ResidueType::add_bond(void *, void *, enum core::chemical::BondName) –> void

add_canonical_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueType, rosetta_atom: str, alias: str) → None¶

store canonical to alias mapping

C++: core::chemical::ResidueType::add_canonical_atom_alias(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_chi(*args, **kwargs)¶

Overloaded function.

add_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int, atom1: capsule, atom2: capsule, atom3: capsule, atom4: capsule) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::ResidueType::add_chi(const unsigned long, void *, void *, void *, void *) –> void

add_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, atom1: capsule, atom2: capsule, atom3: capsule, atom4: capsule) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::ResidueType::add_chi(void *, void *, void *, void *) –> void

add_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) -> None

Add a chi (side-chain) angle defined by four atoms.

C++: core::chemical::ResidueType::add_chi(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) -> None

Add a chi (side-chain) angle defined by four atoms to the end of the list of chis.

C++: core::chemical::ResidueType::add_chi(const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_chi_rotamer(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int, mean: float, sdev: float) → None¶

Add a rotamer bin for a given chi.

C++: core::chemical::ResidueType::add_chi_rotamer(const unsigned long, const double, const double) –> void

add_chi_rotamer_to_last_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, mean: float, sdev: float) → None¶

Adds a chi rotamer bin to the highest-indexed chi in the list of chis for this ResidueType.

C++: core::chemical::ResidueType::add_chi_rotamer_to_last_chi(const double, const double) –> void

add_cut_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str) → None¶

add a bond between atom1 and atom2, if bond type is not specified, default to a SingleBond

C++: core::chemical::ResidueType::add_cut_bond(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_metalbinding_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → None¶

Add an atom to the list of atoms that can potentially form a bond to a metal ion.

Note that the atom must exist in the residue type (the function checks for this at runtime).

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueType::add_metalbinding_atom(const class std::basic_string<char> &) –> void

add_metapatch_connect(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → None¶: C++: core::chemical::ResidueType::add_metapatch_connect(const class std::basic_string<char> &) –> void

add_nu(self: pyrosetta.rosetta.core.chemical.ResidueType, nu_index: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) → None¶

Add a nu (internal cyclic) angle defined by four atoms.

C++: core::chemical::ResidueType::add_nu(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

add_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueType, tag: str, value: float) → None¶

Add a numeric property.

C++: core::chemical::ResidueType::add_numeric_property(const class std::basic_string<char> &, double) –> void

add_orbital(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_name: str, orbital_type_name: str) → None¶

add an orbital onto a residue based upon atom

C++: core::chemical::ResidueType::add_orbital(class std::basic_string<char> &, class std::basic_string<char> &) –> void

add_orbital_bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, orbital_name: str) → None¶

add an orbital bond between an atom and an orbital.

NOTE!!!!! This is indexed based upon atoms, not orbitals. That means that in your params file you must have the atom as the first and orbital as the second.

C++: core::chemical::ResidueType::add_orbital_bond(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

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

Add a property to this ResidueType.

C++: core::chemical::ResidueType::add_property(const class std::basic_string<char> &) –> void

add_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → int¶

add a non-polymeric ResidueConnection

For polymeric connections, see set_lower_connect() and set_upper_connect() Doesn’t set the ideal geometry – maybe it should?

C++: core::chemical::ResidueType::add_residue_connection(const class std::basic_string<char> &) –> unsigned long

add_ring(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int, ring_atoms: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Add a ring definition.

C++: core::chemical::ResidueType::add_ring(const unsigned long, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

add_string_property(self: pyrosetta.rosetta.core.chemical.ResidueType, tag: str, value: str) → None¶

Add a string property.

C++: core::chemical::ResidueType::add_string_property(const class std::basic_string<char> &, class std::basic_string<char>) –> void

add_variant_type(*args, **kwargs)¶

Overloaded function.

add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Add a variant type to this ResidueType.

C++: core::chemical::ResidueType::add_variant_type(const enum core::chemical::VariantType) –> void

add_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: str) -> None

Add a variant type to this ResidueType by string.

C++: core::chemical::ResidueType::add_variant_type(const class std::basic_string<char> &) –> void

all_bb_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Indices of all backbone atoms, hydrogens and heavyatoms

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

all_sc_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Indices of all sidechain atoms, hydrogens and heavyatoms

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

assign(self: pyrosetta.rosetta.core.chemical.ResidueType, src: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶

Copies <src> into the ResidueType

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

assign_internal_coordinates(*args, **kwargs)¶

Overloaded function.

assign_internal_coordinates(self: pyrosetta.rosetta.core.chemical.ResidueType) -> None

Assign internal coordinates from the set ideal xyz coordinates.: Note that it currently does not obey mainchain designations or cut bonds.

C++: core::chemical::ResidueType::assign_internal_coordinates() –> void

assign_internal_coordinates(self: pyrosetta.rosetta.core.chemical.ResidueType, new_root: capsule) -> None

@ recursive function to assign internal coordinates: Note that it currently does not work well with polymers.

C++: core::chemical::ResidueType::assign_internal_coordinates(void *) –> void

assign_neighbor_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::ResidueType::assign_neighbor_atom() –> void

atom(*args, **kwargs)¶

Overloaded function.

atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) -> pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::ResidueType::atom(const unsigned long) –> class core::chemical::Atom &

atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) -> pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::ResidueType::atom(const class std::basic_string<char> &) –> class core::chemical::Atom &

atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_vd: capsule) -> pyrosetta.rosetta.core.chemical.Atom

C++: core::chemical::ResidueType::atom(void *const) –> class core::chemical::Atom &

atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.std.map_std_string_std_string¶

returns atom aliases

C++: core::chemical::ResidueType::atom_aliases() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

atom_base(*args, **kwargs)¶

Overloaded function.

atom_base(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> int

get index of an atom’s base atom

C++: core::chemical::ResidueType::atom_base(const unsigned long) const –> unsigned long

atom_base(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: capsule) -> capsule

get vd of an atom’s base atom

C++: core::chemical::ResidueType::atom_base(void *const) const –> void *

atom_being_shadowed(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_shadowing: int) → int¶

Return the index of the atom that the “atom_shadowing”: atom is shadowing; returns zero if the “atom_shadowing” atom is not shadowing anyone.

C++: core::chemical::ResidueType::atom_being_shadowed(unsigned long) const –> unsigned long

atom_depends_on_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int, connection_id: int) → bool¶

Does an atom with a given index have an icoor that depends, directly or indirectly, on a particular connection ID?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_connection(const unsigned long, const unsigned long) const –> bool

atom_depends_on_lower_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool¶

Does an atom with a given index have an icoor that depends, directly or indirectly, on the lower polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(const unsigned long) const –> bool

atom_depends_on_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool¶

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper or lower polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_polymeric_connection(const unsigned long) const –> bool

atom_depends_on_upper_polymeric_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_index: int) → bool¶

Does an atom with a given index have an icoor that depends, directly or indirectly, on the upper polymeric connection?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(const unsigned long) const –> bool

atom_forms_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → bool¶

Does an atom form any inter-residue chemical bonds?

C++: core::chemical::ResidueType::atom_forms_residue_connection(const unsigned long) const –> bool

atom_index(*args, **kwargs)¶

Overloaded function.

atom_index(self: pyrosetta.rosetta.core.chemical.ResidueType, name: str) -> int

get atom index by name

C++: core::chemical::ResidueType::atom_index(const class std::basic_string<char> &) const –> unsigned long

atom_index(self: pyrosetta.rosetta.core.chemical.ResidueType, vd: capsule) -> int

get atom index by vertex descriptor

C++: core::chemical::ResidueType::atom_index(void *const &) const –> unsigned long

atom_is_backbone(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶

is a backbone atom (heavy or hydrogen)?

C++: core::chemical::ResidueType::atom_is_backbone(const unsigned long) const –> bool

atom_is_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶

quick lookup: is the atom with the given index a hydrogen or not?: Atoms are sorted so that heavy atoms come first and hydrogen atoms come last.

C++: core::chemical::ResidueType::atom_is_hydrogen(const unsigned long) const –> bool

atom_is_polar_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶: C++: core::chemical::ResidueType::atom_is_polar_hydrogen(unsigned long) const –> bool

atom_is_sidechain(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶: C++: core::chemical::ResidueType::atom_is_sidechain(const unsigned long) const –> bool

atom_iterators(self: pyrosetta.rosetta.core.chemical.ResidueType) → Tuple[std::_List_iterator<void*>, std::_List_iterator<void*>]¶: C++: core::chemical::ResidueType::atom_iterators() const –> struct std::pair<struct std::_List_iterator<void *>, struct std::_List_iterator<void *> >

atom_name(*args, **kwargs)¶

Overloaded function.

atom_name(self: pyrosetta.rosetta.core.chemical.ResidueType, index: int) -> str

get atom name by index

C++: core::chemical::ResidueType::atom_name(const unsigned long) const –> const std::string &

atom_name(self: pyrosetta.rosetta.core.chemical.ResidueType, vd: capsule) -> str

get atom name by vertex descriptor

C++: core::chemical::ResidueType::atom_name(void *const) const –> const std::string &

atom_type(*args, **kwargs)¶

Overloaded function.

atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> pyrosetta.rosetta.core.chemical.AtomType

Get the chemical atom_type for this atom by it index number in this residue

If we want the atom_type index (integer), we get this from the conformation::Atom itself, as seen in the code below

C++: core::chemical::ResidueType::atom_type(const unsigned long) const –> const class core::chemical::AtomType &

atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, vd: capsule) -> pyrosetta.rosetta.core.chemical.AtomType

Get the chemical atom_type for this atom by it index number in this residue

C++: core::chemical::ResidueType::atom_type(void *const) const –> const class core::chemical::AtomType &

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.AtomTypeSet¶

access by reference the atomset for which this residue is constructed

C++: core::chemical::ResidueType::atom_type_set() const –> const class core::chemical::AtomTypeSet &

atom_type_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.AtomTypeSet¶

access by const pointer the atomset for which this residue is constructed

C++: core::chemical::ResidueType::atom_type_set_ptr() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

atom_vertex(*args, **kwargs)¶

Overloaded function.

atom_vertex(self: pyrosetta.rosetta.core.chemical.ResidueType, name: str) -> capsule

get the vertex descriptor from the name of the atom.

C++: core::chemical::ResidueType::atom_vertex(const class std::basic_string<char> &) const –> void *

atom_vertex(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> capsule

Get the vertex descriptor from the atom index.

C++: core::chemical::ResidueType::atom_vertex(const unsigned long &) const –> void *

atoms_are_bonded(self: pyrosetta.rosetta.core.chemical.ResidueType, atomindex1: int, atomindex2: int) → bool¶

Indicates whether or not two atom indices have a chemical bond linking them.

Note that this assumes that the Rosetta machinery is set up so that if atom 1 is bonded to atom 2, atom 2 is bonded to atom 1. This function breaks if that assumption breaks.

Vikram K. Mulligan

C++: core::chemical::ResidueType::atoms_are_bonded(const unsigned long, const unsigned long) const –> bool

atoms_last_controlled_by_chi(*args, **kwargs)¶

Overloaded function.

atoms_last_controlled_by_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Read access to the atoms_last_controlled_by_chi_ array

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

atoms_last_controlled_by_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chi: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Read access to the Atoms last controlled by a particular chi

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

atoms_with_orb_index(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::chemical::ResidueType::atoms_with_orb_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

atoms_within_one_bond_of_a_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn: int) → pyrosetta.rosetta.utility.vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t¶

Returns a list of those atoms within one bond of a residue connection. For residue connection i,: its position in this array is a list of pairs of atom-id’s, the first of which is always the id for the atom forming residue connection i.

C++: core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(unsigned long) const –> const class utility::vector1<class utility::keys::Key2Tuple<unsigned long, unsigned long>, class std::allocator<class utility::keys::Key2Tuple<unsigned long, unsigned long> > > &

atoms_within_two_bonds_of_a_residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn: int) → pyrosetta.rosetta.utility.vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t¶

Returns the list of those atoms within two bonds of: residue connection # resconn. Each entry in this list is a triple of atom-id’s, the first of which is always the id for the atom forming residue connection resconn.

C++: core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection(unsigned long) const –> const class utility::vector1<class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long>, class std::allocator<class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long> > > &

attached_H_begin(*args, **kwargs)¶

Overloaded function.

attached_H_begin(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

index number of the first attached Hydrogen on an atom

C++: core::chemical::ResidueType::attached_H_begin(const unsigned long) const –> unsigned long

attached_H_begin(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

for all heavy atoms, index numbers of their first attached Hydrogen

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

attached_H_end(*args, **kwargs)¶

Overloaded function.

attached_H_end(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

index number of the last attached Hydrogen on an atom

C++: core::chemical::ResidueType::attached_H_end(const unsigned long) const –> unsigned long

attached_H_end(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

for all heavy atoms, index numbers of their last attached Hydrogen

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

autodetermine_chi_bonds(*args, **kwargs)¶

Overloaded function.

autodetermine_chi_bonds(self: pyrosetta.rosetta.core.chemical.ResidueType) -> None
autodetermine_chi_bonds(self: pyrosetta.rosetta.core.chemical.ResidueType, max_proton_chi_samples: int) -> None

Regenerate the rotatable chi bonds from the internal graph structure.

If the number of proton chi samples would exceed max_proton_chi_samples, don’t add extra sampling to proton chis. As a special case, if this is zero don’t add any proton chi sampling at all.

Requires that Icoor and atom base records are up-to-date, and that ring bonds have been annotated.

C++: core::chemical::ResidueType::autodetermine_chi_bonds(unsigned long) –> void

backbone_aa(*args, **kwargs)¶

Overloaded function.

backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueType, type: str) -> None

AA to use for backbone scoring

C++: core::chemical::ResidueType::backbone_aa(const class std::basic_string<char> &) –> void

backbone_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.AA

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

C++: core::chemical::ResidueType::backbone_aa() const –> const enum core::chemical::AA &

base_analogue(*args, **kwargs)¶

Overloaded function.

base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueType, type: str) -> None

NA to use for base-specific generalization (can be more: forgiving than na_analogue for new NA backbones)

C++: core::chemical::ResidueType::base_analogue(const class std::basic_string<char> &) –> void

base_analogue(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for base features

C++: core::chemical::ResidueType::base_analogue() const –> const enum core::chemical::AA &

base_name(*args, **kwargs)¶

Overloaded function.

base_name(self: pyrosetta.rosetta.core.chemical.ResidueType) -> str

Get this ResidueType’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueType::base_name() const –> const std::string &

base_name(self: pyrosetta.rosetta.core.chemical.ResidueType, base_name_in: str) -> None

Set this ResidueType’s base name (shared with other residue types with the same base type).

C++: core::chemical::ResidueType::base_name(const class std::basic_string<char> &) –> void

bond(*args, **kwargs)¶

Overloaded function.

bond(self: pyrosetta.rosetta.core.chemical.ResidueType, vd1: capsule, vd2: capsule) -> pyrosetta.rosetta.core.chemical.Bond

C++: core::chemical::ResidueType::bond(void *, void *) –> class core::chemical::Bond &

bond(self: pyrosetta.rosetta.core.chemical.ResidueType, atom1: str, atom2: str) -> pyrosetta.rosetta.core.chemical.Bond

C++: core::chemical::ResidueType::bond(const class std::basic_string<char> &, const class std::basic_string<char> &) –> class core::chemical::Bond &

bondangle(self: pyrosetta.rosetta.core.chemical.ResidueType, bondang: int) → pyrosetta.rosetta.utility.keys.Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t¶

Return the indices for the set of atoms that define a particular: intraresidue angle

C++: core::chemical::ResidueType::bondangle(const unsigned long) const –> const class utility::keys::Key3Tuple<unsigned long, unsigned long, unsigned long> &

bondangles_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the list of all of the indices of all the intraresidue: bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.

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

bonded_neighbor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: core::chemical::ResidueType::bonded_neighbor(const unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

bonded_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of the orbitals bonded to an atom

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

branch_connect_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

Return a list of names of atoms at non-polymer connections.

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

branch_connect_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Return a list of indices of atoms at non-polymer connections.

C++: core::chemical::ResidueType::branch_connect_atoms() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

canonical_atom_aliases(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.std.map_std_string_std_string¶

returns atom aliases

C++: core::chemical::ResidueType::canonical_atom_aliases() const –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > >

carbohydrate_info(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::carbohydrates::CarbohydrateInfo¶

Return the CarbohydrateInfo object containing sugar-specific properties for this residue.

C++: core::chemical::ResidueType::carbohydrate_info() const –> class std::shared_ptr<const class core::chemical::carbohydrates::CarbohydrateInfo>

change_bond_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str, old_bond_label: pyrosetta.rosetta.core.chemical.BondName, new_bond_label: pyrosetta.rosetta.core.chemical.BondName) → None¶

Change the bond type of the given bond from one type to another.

C++: core::chemical::ResidueType::change_bond_type(const class std::basic_string<char> &, const class std::basic_string<char> &, const enum core::chemical::BondName, const enum core::chemical::BondName) –> void

chi_2_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chi_index: int) → int¶: C++: core::chemical::ResidueType::chi_2_proton_chi(unsigned long) const –> unsigned long

chi_atom_vds(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_void_*¶

VDs of the atoms which are used to define a given chi angle (chino)

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

chi_atoms(*args, **kwargs)¶

Overloaded function.

chi_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

indices of the atoms which are used to define a given chi angle (chino)

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

chi_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

indices of the atoms which are used to define all the chi angles

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

chi_rotamers(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) → pyrosetta.rosetta.utility.vector1_std_pair_double_double_t¶

all rotamers bins (mean, std) for a given chi angle

C++: core::chemical::ResidueType::chi_rotamers(const unsigned long) const –> const class utility::vector1<struct std::pair<double, double>, class std::allocator<struct std::pair<double, double> > > &

clear_chi_rotamers(self: pyrosetta.rosetta.core.chemical.ResidueType, chi_no: int) → None¶

Delete all of the chi rotamer bins from the specified chi for this ResidueType.

C++: core::chemical::ResidueType::clear_chi_rotamers(const unsigned long) –> void

clear_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

clear orbitals

C++: core::chemical::ResidueType::clear_orbitals() –> void

clone(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶

make a copy

C++: core::chemical::ResidueType::clone() const –> class std::shared_ptr<class core::chemical::ResidueType>

custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

Get a list of custom VariantType strings for this ResidueType (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueType::custom_variant_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

cut_bond_neighbor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of the bonded neighbors for an atom

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

debug_dump_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Dump out atomnames and icoor values

C++: core::chemical::ResidueType::debug_dump_icoor() const –> void

defined_adducts(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_Adduct¶

get the adducts defined for this residue

C++: core::chemical::ResidueType::defined_adducts() const –> const class utility::vector1<class core::chemical::Adduct, class std::allocator<class core::chemical::Adduct> > &

defines_custom_rama_prepro_map(self: pyrosetta.rosetta.core.chemical.ResidueType, pre_proline_position: bool) → bool¶

Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_

defined for this ResidueType (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

C++: core::chemical::ResidueType::defines_custom_rama_prepro_map(const bool) const –> bool

delete_act_coord_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → None¶

Remove an atom from the list of act coord atoms

(used in patching when it kills the valence that is thus used)

Andrew Watkins (amw579.edu)

C++: core::chemical::ResidueType::delete_act_coord_atom(const class std::basic_string<char> &) –> void

delete_atom(*args, **kwargs)¶

Overloaded function.

delete_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, name: str) -> None

flag an atom for deletion by adding its index to the delete_atom_ list

C++: core::chemical::ResidueType::delete_atom(const class std::basic_string<char> &) –> void

delete_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, index: int) -> None

C++: core::chemical::ResidueType::delete_atom(const unsigned long) –> void

delete_atom_alias(*args, **kwargs)¶

Overloaded function.

delete_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueType, alias: str) -> None
delete_atom_alias(self: pyrosetta.rosetta.core.chemical.ResidueType, alias: str, error: bool) -> None

Remove a given alias name for an atom.

If error is true, raise error if the alias can’t be found

C++: core::chemical::ResidueType::delete_atom_alias(const class std::basic_string<char> &, bool) –> void

delete_child_proton(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) → None¶: C++: core::chemical::ResidueType::delete_child_proton(const class std::basic_string<char> &) –> void

delete_metalbinding_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) → None¶

Remove an atom from the list of atoms that can potentially form a bond to a metal ion

(used in patching when it kills the valence that is thus used)

Andrew Watkins (amw579.edu)

C++: core::chemical::ResidueType::delete_metalbinding_atom(const class std::basic_string<char> &) –> void

delete_property(self: pyrosetta.rosetta.core.chemical.ResidueType, property: str) → None¶

Add a property of this ResidueType.

C++: core::chemical::ResidueType::delete_property(const class std::basic_string<char> &) –> void

delete_terminal_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

delete terminal chi angle

C++: core::chemical::ResidueType::delete_terminal_chi() –> void

dihedral(self: pyrosetta.rosetta.core.chemical.ResidueType, dihe: int) → pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t¶

Return the indices for the set of atoms that define a particular: intraresidue dihedral

C++: core::chemical::ResidueType::dihedral(const unsigned long) const –> const class utility::keys::Key4Tuple<unsigned long, unsigned long, unsigned long, unsigned long> &

dihedrals_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the list of all of the indices of all the intraresidue: dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

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

dump_vd_info(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::ResidueType::dump_vd_info() const –> void

element_set(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ElementSet¶

access by reference the element set for which this residue is constructed

C++: core::chemical::ResidueType::element_set() const –> const class core::chemical::ElementSet &

element_set_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ElementSet¶

access by const pointer the element set for which this residue is constructed

C++: core::chemical::ResidueType::element_set_ptr() const –> class std::shared_ptr<const class core::chemical::ElementSet>

enable_custom_variant_types(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Turn on the ability to create VariantTypes “on-the-fly”.

C++: core::chemical::ResidueType::enable_custom_variant_types() –> void

fill_ideal_xyz_from_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::ResidueType::fill_ideal_xyz_from_icoor() –> void

finalize(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

recalculate derived data, potentially reordering atom-indices

C++: core::chemical::ResidueType::finalize() –> void

finalized(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

finalized? should always be true, except in very special case early in on-the-fly ResidueTypeSet.

C++: core::chemical::ResidueType::finalized() const –> bool

first_sidechain_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

index of the first sidechain atom (heavy or hydrogen)

C++: core::chemical::ResidueType::first_sidechain_atom() const –> unsigned long

first_sidechain_hydrogen(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

index of the first sidehchain hydrogen

C++: core::chemical::ResidueType::first_sidechain_hydrogen() const –> unsigned long

force_nbr_atom_orient(*args, **kwargs)¶

Overloaded function.

force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueType, force_orient: bool) -> None

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueType::force_nbr_atom_orient(bool) –> void

force_nbr_atom_orient(self: pyrosetta.rosetta.core.chemical.ResidueType) -> bool

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

C++: core::chemical::ResidueType::force_nbr_atom_orient() const –> bool

gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → core::chemical::gasteiger::GasteigerAtomTypeData¶

Get the MM atom_type for this atom by its index number in this residue

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

gasteiger_atom_typeset(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::gasteiger::GasteigerAtomTypeSet¶: C++: core::chemical::ResidueType::gasteiger_atom_typeset() const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>

get_base_type_cop(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶

Get a pointer to this ResidueType’s base ResidueType.

Returns the base_type_cop_ pointer if not null, self pointer if null.

C++: core::chemical::ResidueType::get_base_type_cop() const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

Gets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueType::get_disulfide_atom_name() const –> std::string

get_metal_binding_atoms(*args, **kwargs)¶

Overloaded function.

get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, metal_binding_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Gets indices of all atoms that can form bonds to metals

Vikram K. Mulligan (vmullig.edu).

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

get_metal_binding_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_string

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

get_numeric_property(self: pyrosetta.rosetta.core.chemical.ResidueType, tag: str) → float¶

Get a numeric property, if it exists.

C++: core::chemical::ResidueType::get_numeric_property(const class std::basic_string<char> &) const –> double

get_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueType, pre_proline_position: bool) → str¶

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueType::get_rama_prepro_mainchain_torsion_potential_name(const bool) const –> const std::string &

get_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueType, pre_proline_position: bool) → str¶

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueType), though this can be overridden.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueType::get_rama_prepro_map_file_name(const bool) const –> const std::string &

get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶: C++: core::chemical::ResidueType::get_self_ptr() –> class std::shared_ptr<class core::chemical::ResidueType>

get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.std.weak_ptr_core_chemical_ResidueType_t¶: C++: core::chemical::ResidueType::get_self_weak_ptr() –> class std::weak_ptr<class core::chemical::ResidueType>

get_string_property(self: pyrosetta.rosetta.core.chemical.ResidueType, tag: str) → str¶

Get a string property, if it exists.

C++: core::chemical::ResidueType::get_string_property(const class std::basic_string<char> &) const –> std::string

has(*args, **kwargs)¶

Overloaded function.

has(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) -> bool

is this atom present in this residue?

C++: core::chemical::ResidueType::has(const class std::basic_string<char> &) const –> bool

has(self: pyrosetta.rosetta.core.chemical.ResidueType, vd: capsule) -> bool

is this vertex descriptor present in this residue?

C++: core::chemical::ResidueType::has(void *const) const –> bool

has_orbital(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_name: str) → bool¶

is this orbital present in this residue?

C++: core::chemical::ResidueType::has_orbital(const class std::basic_string<char> &) const –> bool

has_polymer_dependent_groups(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Does this type have groups (not just single atoms) that are polymer-bond dependent?

C++: core::chemical::ResidueType::has_polymer_dependent_groups() const –> bool

has_property(*args, **kwargs)¶

Overloaded function.

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

Generic property access.

C++: core::chemical::ResidueType::has_property(const class std::basic_string<char> &) const –> bool

has_property(self: pyrosetta.rosetta.core.chemical.ResidueType, property: pyrosetta.rosetta.core.chemical.ResidueProperty) -> bool

Generic property access, by ResidueProperty.

C++: core::chemical::ResidueType::has_property(const enum core::chemical::ResidueProperty) const –> bool

has_sc_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

does this residue have sidechain orbitals?

C++: core::chemical::ResidueType::has_sc_orbitals() const –> bool

has_shadow_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Returns true if this residue has shadow atoms, false otherwise.

C++: core::chemical::ResidueType::has_shadow_atoms() const –> bool

has_variant_type(*args, **kwargs)¶

Overloaded function.

has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> bool

Generic variant access.

C++: core::chemical::ResidueType::has_variant_type(const enum core::chemical::VariantType) const –> bool

has_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: str) -> bool

Generic variant access by string.

C++: core::chemical::ResidueType::has_variant_type(const class std::basic_string<char> &) const –> bool

heavyatom_has_polar_hydrogens(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶: C++: core::chemical::ResidueType::heavyatom_has_polar_hydrogens(unsigned long) const –> bool

heavyatom_is_an_acceptor(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶: C++: core::chemical::ResidueType::heavyatom_is_an_acceptor(unsigned long) const –> bool

icoor(*args, **kwargs)¶

Overloaded function.

icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: int) -> pyrosetta.rosetta.core.chemical.AtomICoor

AtomICoord of an atom

C++: core::chemical::ResidueType::icoor(const unsigned long) const –> const class core::chemical::AtomICoor &

icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: capsule) -> pyrosetta.rosetta.core.chemical.AtomICoor

AtomICoord of an atom

C++: core::chemical::ResidueType::icoor(void *const) const –> const class core::chemical::AtomICoor &

improper_dihedral(self: pyrosetta.rosetta.core.chemical.ResidueType, dihe: int) → pyrosetta.rosetta.utility.keys.Key4Tuple_unsigned_long_unsigned_long_unsigned_long_unsigned_long_t¶

Return the indices for the set of atoms that define a particular: intraresidue improper dihedral

C++: core::chemical::ResidueType::improper_dihedral(const unsigned long) const –> const class utility::keys::Key4Tuple<unsigned long, unsigned long, unsigned long, unsigned long> &

improper_dihedrals_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Returns the list of all of the indices of all the intraresidue: dihedrals a particular atom is involved in. Useful for calculating the derivatives for an atom.

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

interchangeability_group(*args, **kwargs)¶

Overloaded function.

interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueType) -> str

get our interchangeability-group id. Used to: determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypes ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypes .params file with the INTERCHANGEABILITY_GROUP tag.

C++: core::chemical::ResidueType::interchangeability_group() const –> std::string

interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueType, setting: str) -> None

set our interchangeability-group id

C++: core::chemical::ResidueType::interchangeability_group(class std::basic_string<char>) –> void

is_DNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is DNA?

C++: core::chemical::ResidueType::is_DNA() const –> bool

is_NA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is Nucleic Acid?

C++: core::chemical::ResidueType::is_NA() const –> bool

is_PNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is PNA?

C++: core::chemical::ResidueType::is_PNA() const –> bool

is_RNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is RNA?

C++: core::chemical::ResidueType::is_RNA() const –> bool

is_TNA(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is TNA?

C++: core::chemical::ResidueType::is_TNA() const –> bool

is_acetylated_nterminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is acetylated n terminus

C++: core::chemical::ResidueType::is_acetylated_nterminus() const –> bool

is_achiral_backbone(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this an achiral backbone?

C++: core::chemical::ResidueType::is_achiral_backbone() const –> bool

is_adduct(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is an adduct-modified residue?

C++: core::chemical::ResidueType::is_adduct() const –> bool

is_alpha_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this an alpha-amino acid?

C++: core::chemical::ResidueType::is_alpha_aa() const –> bool

is_aromatic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is aromatic?

C++: core::chemical::ResidueType::is_aromatic() const –> bool

is_base_type(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this ResidueType a base type?

C++: core::chemical::ResidueType::is_base_type() const –> bool

is_beta_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a beta-amino acid?

C++: core::chemical::ResidueType::is_beta_aa() const –> bool

is_branch_point(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is a branch-point residue?

C++: core::chemical::ResidueType::is_branch_point() const –> bool

is_canonical(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a canonical residue type (nucleic acid or amino acid)?

Calls is_canonical_aa() and is_canonical_nucleic().

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical() const –> bool

is_canonical_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a canonical amino acid (CANONICAL_AA property)?

Only the standard amino acid types (ACDEFGHIKLMNPQRSTVWY) are canonical.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical_aa() const –> bool

is_canonical_nucleic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a canonical nucleic acid (CANONICAL_NUCLEIC property)?

Only the standard nucliec acid types (dA, dC, dG, dT, A, C, G, U) are canonical.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_canonical_nucleic() const –> bool

is_carbohydrate(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is carbohydrate?

C++: core::chemical::ResidueType::is_carbohydrate() const –> bool

is_charged(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is charged?

C++: core::chemical::ResidueType::is_charged() const –> bool

is_coarse(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is coarse?

C++: core::chemical::ResidueType::is_coarse() const –> bool

is_cyclic(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is cyclic?

C++: core::chemical::ResidueType::is_cyclic() const –> bool

is_d_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this a d-amino acid?

C++: core::chemical::ResidueType::is_d_aa() const –> bool

is_d_rna(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this a d-RNA?

C++: core::chemical::ResidueType::is_d_rna() const –> bool

is_disulfide_bonded(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is disulfide?

C++: core::chemical::ResidueType::is_disulfide_bonded() const –> bool

is_gamma_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a gamma-amino acid?

C++: core::chemical::ResidueType::is_gamma_aa() const –> bool

is_inverted_virtual_residue(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Check if atom is an inverted virtual

C++: core::chemical::ResidueType::is_inverted_virtual_residue() const –> bool

is_l_aa(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this an l-amino acid?

C++: core::chemical::ResidueType::is_l_aa() const –> bool

is_l_rna(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this an l-RNA?

C++: core::chemical::ResidueType::is_l_rna() const –> bool

is_ligand(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is ligand?

C++: core::chemical::ResidueType::is_ligand() const –> bool

is_lipid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is lipid?

C++: core::chemical::ResidueType::is_lipid() const –> bool

is_lower_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is lower terminus?

C++: core::chemical::ResidueType::is_lower_terminus() const –> bool

is_membrane(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is membrane?

C++: core::chemical::ResidueType::is_membrane() const –> bool

is_metal(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Return true if this residue type is a metal ion, false otherwise.

C++: core::chemical::ResidueType::is_metal() const –> bool

is_metalbinding(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Return true if this residue type is a type that can bind to a metal ion (e.g. His, Asp, Cys, etc.),: false otherwise.

C++: core::chemical::ResidueType::is_metalbinding() const –> bool

is_methylated_cterminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is methylated c terminus

C++: core::chemical::ResidueType::is_methylated_cterminus() const –> bool

is_oligourea(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this an oligourea?

C++: core::chemical::ResidueType::is_oligourea() const –> bool

is_peptoid(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is peptoid?

C++: core::chemical::ResidueType::is_peptoid() const –> bool

is_polar(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is polar?

C++: core::chemical::ResidueType::is_polar() const –> bool

is_polymer(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is polymer?

C++: core::chemical::ResidueType::is_polymer() const –> bool

is_protein(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is protein?

C++: core::chemical::ResidueType::is_protein() const –> bool

is_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int) → bool¶

number of proton chis

C++: core::chemical::ResidueType::is_proton_chi(const unsigned long) const –> bool

is_purine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is purine?

C++: core::chemical::ResidueType::is_purine() const –> bool

is_pyrimidine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is pyrimidine?

C++: core::chemical::ResidueType::is_pyrimidine() const –> bool

is_repulsive(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶

Check if atom is repulsive.

C++: core::chemical::ResidueType::is_repulsive(const unsigned long) const –> bool

is_ring_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int, atom_id: int) → bool¶

Return whether this atom is in a particular ring

C++: core::chemical::ResidueType::is_ring_atom(const unsigned long, const unsigned long) const –> bool

is_sidechain_amine(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is sidechain amine?

C++: core::chemical::ResidueType::is_sidechain_amine() const –> bool

is_sidechain_thiol(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is thiol?

C++: core::chemical::ResidueType::is_sidechain_thiol() const –> bool

is_solvent(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a solvent molecule (SOLVENT property)?

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::is_solvent() const –> bool

is_sri(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this one of SRI’s special heteropolymer building blocks?

C++: core::chemical::ResidueType::is_sri() const –> bool

is_surface(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is surface? (e.g. enamel)

C++: core::chemical::ResidueType::is_surface() const –> bool

is_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is terminus?

C++: core::chemical::ResidueType::is_terminus() const –> bool

is_triazolemer(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is this a triazolemer?

C++: core::chemical::ResidueType::is_triazolemer() const –> bool

is_upper_terminus(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is upper terminus?

C++: core::chemical::ResidueType::is_upper_terminus() const –> bool

is_virtual(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → bool¶

Check if atom is virtual.

C++: core::chemical::ResidueType::is_virtual(const unsigned long) const –> bool

is_virtual_residue(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Check if residue is ‘VIRTUAL_RESIDUE’: This ONLY checks the VIRTUAL_RESIDUE PROPERTY!

C++: core::chemical::ResidueType::is_virtual_residue() const –> bool

is_water(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

is this a water residue type?

C++: core::chemical::ResidueType::is_water() const –> bool

last_backbone_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

index of the last backbone heavy atom

C++: core::chemical::ResidueType::last_backbone_atom() const –> unsigned long

last_controlling_chi(*args, **kwargs)¶

Overloaded function.

last_controlling_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Read access to the last_controlling_chi_ array

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

last_controlling_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) -> int

The last_controlling_chi for an atom. 0 if an atom is controlled by no chi.

C++: core::chemical::ResidueType::last_controlling_chi(unsigned long) const –> unsigned long

lower_connect(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::ResidueConnection¶: C++: core::chemical::ResidueType::lower_connect() const –> const class core::chemical::ResidueConnection &

lower_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

index number of the atom which connects to the lower connection

C++: core::chemical::ResidueType::lower_connect_atom() const –> unsigned long

lower_connect_id(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::ResidueType::lower_connect_id() const –> unsigned long

mainchain_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: int) → int¶

index of mainchain atom

C++: core::chemical::ResidueType::mainchain_atom(const unsigned long) const –> unsigned long

mainchain_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of all mainchain atoms

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

mainchain_potentials_match(self: pyrosetta.rosetta.core.chemical.ResidueType, other: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Do the rama_prepro mainchain torsion potentials of this residue match another?

C++: core::chemical::ResidueType::mainchain_potentials_match(const class core::chemical::ResidueType &) const –> bool

mass(self: pyrosetta.rosetta.core.chemical.ResidueType) → float¶

get the molecular weight of this residue

C++: core::chemical::ResidueType::mass() const –> const double &

mm_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.core.chemical.MMAtomType¶

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueType::mm_atom_type(const unsigned long) const –> const class core::chemical::MMAtomType &

mm_atom_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.MMAtomTypeSet¶

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueType::mm_atom_types_ptr() const –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>

mode(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.TypeSetMode¶: C++: core::chemical::ResidueType::mode() const –> enum core::chemical::TypeSetMode

n_hbond_acceptors(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of hbond_acceptors

C++: core::chemical::ResidueType::n_hbond_acceptors() const –> unsigned long

n_hbond_donors(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of hbond_donors

C++: core::chemical::ResidueType::n_hbond_donors() const –> unsigned long

n_non_polymeric_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::ResidueType::n_non_polymeric_residue_connections() const –> unsigned long

n_nus(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

Return number of nu (internal ring) angles.

C++: core::chemical::ResidueType::n_nus() const –> unsigned long

n_orbitals(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of orbitals

C++: core::chemical::ResidueType::n_orbitals() const –> unsigned long

n_polymeric_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::ResidueType::n_polymeric_residue_connections() const –> unsigned long

n_possible_residue_connections(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of ResidueConnections, counting polymeric residue connections

C++: core::chemical::ResidueType::n_possible_residue_connections() const –> unsigned long

n_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of proton chis

C++: core::chemical::ResidueType::n_proton_chi() const –> unsigned long

n_residue_connections_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → int¶

How many inter-residue chemical bonds does a particular atom form?

C++: core::chemical::ResidueType::n_residue_connections_for_atom(const unsigned long) const –> unsigned long

n_ring_conformer_sets(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::ResidueType::n_ring_conformer_sets() const –> unsigned long

n_rings(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

Return the number of rings in this residue.

C++: core::chemical::ResidueType::n_rings() const –> unsigned long

n_virtual_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and

can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueType::n_virtual_atoms() const –> unsigned long

na_analogue(*args, **kwargs)¶

Overloaded function.

na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueType, type: str) -> None

NA to use for fragment sampling and some scoring purposes

C++: core::chemical::ResidueType::na_analogue(const class std::basic_string<char> &) –> void

na_analogue(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.chemical.AA

Returns the nucleic acid type to be used for fragment sampling/scoring.

C++: core::chemical::ResidueType::na_analogue() const –> const enum core::chemical::AA &

name(*args, **kwargs)¶

Overloaded function.

name(self: pyrosetta.rosetta.core.chemical.ResidueType) -> str

get our (unique) residue name

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

name(self: pyrosetta.rosetta.core.chemical.ResidueType, name_in: str) -> None

set our (unique) residue name

C++: core::chemical::ResidueType::name(const class std::basic_string<char> &) –> void

name1(*args, **kwargs)¶

Overloaded function.

name1(self: pyrosetta.rosetta.core.chemical.ResidueType) -> str

get our 1letter code. This is set in the: ResidueType .params file through the IO_STRING tag along with the name3 string.

C++: core::chemical::ResidueType::name1() const –> char

name1(self: pyrosetta.rosetta.core.chemical.ResidueType, code: str) -> None

set our 1letter code

C++: core::chemical::ResidueType::name1(const char) –> void

name3(*args, **kwargs)¶

Overloaded function.

name3(self: pyrosetta.rosetta.core.chemical.ResidueType) -> str

get our 3letter code. This is set in the

ResidueType .params file through the IO_STRING tag along with the name1 string NOTE: The “name3” is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

C++: core::chemical::ResidueType::name3() const –> const std::string &

name3(self: pyrosetta.rosetta.core.chemical.ResidueType, name_in: str) -> None

set our 3letter code

C++: core::chemical::ResidueType::name3(const class std::basic_string<char> &) –> void

natoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of atoms

C++: core::chemical::ResidueType::natoms() const –> unsigned long

nbonds(*args, **kwargs)¶

Overloaded function.

nbonds(self: pyrosetta.rosetta.core.chemical.ResidueType) -> int

number of bonds

C++: core::chemical::ResidueType::nbonds() const –> unsigned long

nbonds(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> int

number of bonds for given atom

C++: core::chemical::ResidueType::nbonds(unsigned long) const –> unsigned long

nbonds(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: capsule) -> int

number of bonds for given atom

C++: core::chemical::ResidueType::nbonds(void *) const –> unsigned long

nbr_atom(*args, **kwargs)¶

Overloaded function.

nbr_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str) -> None

set nbr_atom used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_atom(const class std::basic_string<char> &) –> void

nbr_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, vertex: capsule) -> None

set nbr_atom used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_atom(void *) –> void

nbr_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) -> int

get nbr_atom used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_atom() const –> unsigned long

nbr_radius(*args, **kwargs)¶

Overloaded function.

nbr_radius(self: pyrosetta.rosetta.core.chemical.ResidueType, radius: float) -> None

set nbr_radius_ used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_radius(const double) –> void

nbr_radius(self: pyrosetta.rosetta.core.chemical.ResidueType) -> float

get nbr_radius_ used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_radius() const –> double

nbr_vertex(self: pyrosetta.rosetta.core.chemical.ResidueType) → capsule¶

get VD used to define residue-level neighbors

C++: core::chemical::ResidueType::nbr_vertex() const –> void *

nbrs(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

indices of the bonded neighbors for an atom, shortcut for bonded_neighbor(atomno)

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

nchi(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of chi angles

C++: core::chemical::ResidueType::nchi() const –> unsigned long

ndihe(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

Return the number of intraresidue dihedrals. This covers all pairs: of atoms that are separated by four bonds, and all pairs of intervening atoms.

C++: core::chemical::ResidueType::ndihe() const –> unsigned long

net_formal_charge(*args, **kwargs)¶

Overloaded function.

net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueType) -> int

Get the net formal charge on this residue type.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::net_formal_charge() const –> long

net_formal_charge(self: pyrosetta.rosetta.core.chemical.ResidueType, charge_in: int) -> None

Set the net formal charge on this residue type.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::net_formal_charge(long) –> void

new_orbital_icoor_data(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) → core::chemical::orbitals::ICoorOrbitalData¶: C++: core::chemical::ResidueType::new_orbital_icoor_data(const unsigned long) const –> const class core::chemical::orbitals::ICoorOrbitalData &

nheavyatoms(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

number of heavy atoms

C++: core::chemical::ResidueType::nheavyatoms() const –> unsigned long

nondefault(self: pyrosetta.rosetta.core.chemical.ResidueType, in: bool) → None¶: C++: core::chemical::ResidueType::nondefault(const bool) –> void

nu_atoms(*args, **kwargs)¶

Overloaded function.

nu_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, nu_index: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return indices of the atoms used to define a given nu (internal ring) angle.

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

nu_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Return list of indices of the atoms used to define all the nu (internal ring) angles.

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

num_bondangles(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

get number of intraresidue bond angles

C++: core::chemical::ResidueType::num_bondangles() const –> unsigned long

number_bonded_heavyatoms(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int¶

indicates how many heavyatom bonded neighbors an atom has

C++: core::chemical::ResidueType::number_bonded_heavyatoms(const unsigned long) const –> unsigned long

number_bonded_hydrogens(self: pyrosetta.rosetta.core.chemical.ResidueType, atomno: int) → int¶

indicates how many proton bonded neighbors an atom has

C++: core::chemical::ResidueType::number_bonded_hydrogens(const unsigned long) const –> unsigned long

orbital(*args, **kwargs)¶

Overloaded function.

orbital(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) -> core::chemical::Orbital

C++: core::chemical::ResidueType::orbital(const unsigned long) const –> const class core::chemical::Orbital &

orbital(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_name: str) -> core::chemical::Orbital

C++: core::chemical::ResidueType::orbital(const class std::basic_string<char> &) const –> const class core::chemical::Orbital &

orbital_icoor_data(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) → core::chemical::orbitals::ICoorOrbitalData¶: C++: core::chemical::ResidueType::orbital_icoor_data(const unsigned long) const –> const class core::chemical::orbitals::ICoorOrbitalData &

orbital_index(self: pyrosetta.rosetta.core.chemical.ResidueType, name: str) → int¶

get orbital index by name

C++: core::chemical::ResidueType::orbital_index(const class std::basic_string<char> &) const –> unsigned long

orbital_type(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital_index: int) → core::chemical::orbitals::OrbitalType¶: C++: core::chemical::ResidueType::orbital_type(const int) const –> const class core::chemical::orbitals::OrbitalType &

orbital_types_ptr(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::orbitals::OrbitalTypeSet¶

Get the MM atom_type for this atom by its index number in this residue

C++: core::chemical::ResidueType::orbital_types_ptr() const –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>

path_distance(*args, **kwargs)¶

Overloaded function.

path_distance(self: pyrosetta.rosetta.core.chemical.ResidueType, at1: int, at2: int) -> int

path distance (number of bonds separated) between a pair of atoms

C++: core::chemical::ResidueType::path_distance(unsigned long, unsigned long) const –> int

path_distance(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: int) -> pyrosetta.rosetta.utility.vector1_int

shortest path distance for an atom to all other residue atoms

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

path_distances(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t¶

accessor of path_distance_ data for this residue, which is a 2D array

C++: core::chemical::ResidueType::path_distances() const –> const class utility::vector1<class utility::vector1<int, class std::allocator<int> >, class std::allocator<class utility::vector1<int, class std::allocator<int> > > > &

placeholder_clone(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶

make a copy

C++: core::chemical::ResidueType::placeholder_clone() const –> class std::shared_ptr<class core::chemical::ResidueType>

print_bondangles(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

print intraresidue bond angles to standard out

C++: core::chemical::ResidueType::print_bondangles() const –> void

print_dihedrals(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::ResidueType::print_dihedrals() const –> void

print_pretty_path_distances(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

print chemical-bond path distances to standard out

C++: core::chemical::ResidueType::print_pretty_path_distances() const –> void

properties(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::ResidueProperties¶

Access the collection of properties for this ResidueType.

C++: core::chemical::ResidueType::properties() const –> const class core::chemical::ResidueProperties &

proton_chi_2_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi_id: int) → int¶

translate proton_chi to global chi

C++: core::chemical::ResidueType::proton_chi_2_chi(unsigned long) const –> unsigned long

proton_chi_extra_samples(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi: int) → pyrosetta.rosetta.utility.vector1_double¶: C++: core::chemical::ResidueType::proton_chi_extra_samples(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

proton_chi_samples(self: pyrosetta.rosetta.core.chemical.ResidueType, proton_chi: int) → pyrosetta.rosetta.utility.vector1_double¶: C++: core::chemical::ResidueType::proton_chi_samples(unsigned long) const –> const class utility::vector1<double, class std::allocator<double> > &

real_to_virtual(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

make all atoms virtual, set variant of this residue type as VIRTUAL: Virtual residues are exactly the same, but they are not not scored! Please use Pose.freal_to_virtual, unless you know what you are doing!

C++: core::chemical::ResidueType::real_to_virtual() –> void

redefine_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int, atom_name1: str, atom_name2: str, atom_name3: str, atom_name4: str) → None¶

redefine a chi angle based on four atoms

C++: core::chemical::ResidueType::redefine_chi(const unsigned long, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

remap_pdb_atom_names(*args, **kwargs)¶

Overloaded function.

remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType, rename: bool) -> None

Turn on geometry-based atom renaming when loading this residue type from PDB files

C++: core::chemical::ResidueType::remap_pdb_atom_names(bool) –> void

remap_pdb_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType) -> bool

Are we using geometry-based atom renaming when loading this residue type from PDB

C++: core::chemical::ResidueType::remap_pdb_atom_names() const –> bool

remove_variant_type(*args, **kwargs)¶

Overloaded function.

remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: pyrosetta.rosetta.core.chemical.VariantType) -> None

Remove a variant type to this ResidueType.

C++: core::chemical::ResidueType::remove_variant_type(const enum core::chemical::VariantType) –> void

remove_variant_type(self: pyrosetta.rosetta.core.chemical.ResidueType, variant_type: str) -> None

Remove a variant type to this ResidueType by string.

C++: core::chemical::ResidueType::remove_variant_type(const class std::basic_string<char> &) –> void

report_adducts(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::ResidueType::report_adducts() –> void

require_final(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

an assertion function to ensure an ResidueType has been finalized

C++: core::chemical::ResidueType::require_final() const –> void

requires_actcoord(self: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

require actcoord?

C++: core::chemical::ResidueType::requires_actcoord() const –> bool

reset_base_type_cop(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Reset the base type COP to be null. This implies that this ResidueType is a base type.

C++: core::chemical::ResidueType::reset_base_type_cop() –> void

reset_bond_distance_to_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, d: float) → None¶

Reset the bond distance to an atom whose internal coordinates have already been set.

C++: core::chemical::ResidueType::reset_bond_distance_to_atom(const class std::basic_string<char> &, const double) –> void

reset_mainchain_torsion_potential_names(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Set the names of the mainchain torsion potential maps to use to “”.

Also resets the mainchain torsion potential filename strings.

C++: core::chemical::ResidueType::reset_mainchain_torsion_potential_names() –> void

residue_connect_atom_index(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn_id: int) → int¶: C++: core::chemical::ResidueType::residue_connect_atom_index(const unsigned long) const –> unsigned long

residue_connection(self: pyrosetta.rosetta.core.chemical.ResidueType, i: int) → core::chemical::ResidueConnection¶

Get a ResidueConection.

C++: core::chemical::ResidueType::residue_connection(const unsigned long) –> class core::chemical::ResidueConnection &

residue_connection_id_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → int¶

Convenience access function for the residue connection: at a particular atom; requires that there is exactly one residue connection at this atom.

C++: core::chemical::ResidueType::residue_connection_id_for_atom(const unsigned long) const –> unsigned long

residue_connection_is_polymeric(self: pyrosetta.rosetta.core.chemical.ResidueType, resconn_id: int) → bool¶: C++: core::chemical::ResidueType::residue_connection_is_polymeric(const unsigned long) const –> bool

residue_connections_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

/: Accessor for the full complement of residue connections for a single atom.

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

ring_atoms(*args, **kwargs)¶

Overloaded function.

ring_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Return list of indices of the atoms within this residue’s nth cycle, not counting virtual atoms.

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

ring_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

Return list of indices of the atoms within this residue’s cycles, not counting virtual atoms.

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

ring_conformer_set(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int) → core::chemical::rings::RingConformerSet¶

Return a pointer to the object containing the set of ring: conformers possible for this residue’s nth cycle.

C++: core::chemical::ResidueType::ring_conformer_set(unsigned long) const –> class std::shared_ptr<const class core::chemical::rings::RingConformerSet>

root_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → capsule¶

get root_atom used as the base of the icoor tree.

C++: core::chemical::ResidueType::root_atom() const –> void *

rotamer_aa(self: pyrosetta.rosetta.core.chemical.ResidueType, type: str) → None¶

AA to use for rotamer scoring

C++: core::chemical::ResidueType::rotamer_aa(const class std::basic_string<char> &) –> void

rotamer_library_specification(*args, **kwargs)¶

Overloaded function.

rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueType, : core::chemical::rotamers::RotamerLibrarySpecification) -> None

C++: core::chemical::ResidueType::rotamer_library_specification(class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>) –> void

rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueType) -> core::chemical::rotamers::RotamerLibrarySpecification

C++: core::chemical::ResidueType::rotamer_library_specification() const –> class std::shared_ptr<const class core::chemical::rotamers::RotamerLibrarySpecification>

rotamer_library_specification_nonconst(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::rotamers::RotamerLibrarySpecification¶

Nonconst access to the RotamerLibrarySpecification.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::rotamer_library_specification_nonconst() –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

select_orient_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, center: int, nbr1: int, nbr2: int) → None¶

Selects three atoms for orienting this residue type

C++: core::chemical::ResidueType::select_orient_atoms(unsigned long &, unsigned long &, unsigned long &) const –> void

set_adduct_flag(self: pyrosetta.rosetta.core.chemical.ResidueType, adduct_in: bool) → None¶: C++: core::chemical::ResidueType::set_adduct_flag(bool) –> void

set_atom_base(*args, **kwargs)¶

Overloaded function.

set_atom_base(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name1: str, atom_name2: str) -> None

sets atom_base[ atom1 ] = atom2

C++: core::chemical::ResidueType::set_atom_base(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_atom_base(self: pyrosetta.rosetta.core.chemical.ResidueType, atom1: capsule, atom2: capsule) -> None

sets atom_base[ atom1 ] = atom2, vertex descriptor version

C++: core::chemical::ResidueType::set_atom_base(void *const &, void *const &) –> void

set_atom_type(*args, **kwargs)¶

Overloaded function.

set_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str, atom_type_name: str) -> None

set atom type

C++: core::chemical::ResidueType::set_atom_type(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: capsule, atom_type_name: str) -> None

set atom type

C++: core::chemical::ResidueType::set_atom_type(void *, const class std::basic_string<char> &) –> void

set_atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueType, setting: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None¶

Change which atom type set this ResidueType points to: WARNING - While this tries to switch over the atom types, it will null out any that don’t have exact name correspondences. You NEED to go through and manually reset the types on all atoms. Exposed for black-magic use only.

C++: core::chemical::ResidueType::set_atom_type_set(class std::shared_ptr<const class core::chemical::AtomTypeSet>) –> void

set_backbone_heavyatom(self: pyrosetta.rosetta.core.chemical.ResidueType, name: str) → None¶

set an atom as backbone heavy atom

backbone stuff is a little tricky if we want to allow newly added atoms, eg in patching, to be backbone atoms. We move any exsiting backbone heavy atoms back into force_bb_ list and add the new one. Afterwards, the new backbone heavy atom list will be generated in finalize() using info from force_bb_.

C++: core::chemical::ResidueType::set_backbone_heavyatom(const class std::basic_string<char> &) –> void

set_base_type_cop(self: pyrosetta.rosetta.core.chemical.ResidueType, new_base_type: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Set the base type COP. This implies that this ResidueType is NOT a base type.

C++: core::chemical::ResidueType::set_base_type_cop(class std::shared_ptr<const class core::chemical::ResidueType>) –> void

set_disulfide_atom_name(self: pyrosetta.rosetta.core.chemical.ResidueType, n: str) → None¶

Sets disulfide atom name

Andrew M. Watkins (amw579.edu).

C++: core::chemical::ResidueType::set_disulfide_atom_name(class std::basic_string<char>) –> void

set_gasteiger_atom_type(*args, **kwargs)¶

Overloaded function.

set_gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str, gasteiger_atom_type_name: str) -> None

set gasteiger atom type

C++: core::chemical::ResidueType::set_gasteiger_atom_type(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: capsule, gasteiger_atom_type_name: str) -> None

set gasteiger atom type

C++: core::chemical::ResidueType::set_gasteiger_atom_type(void *, const class std::basic_string<char> &) –> void

set_gasteiger_typeset(self: pyrosetta.rosetta.core.chemical.ResidueType, gasteiger_atom_types: core::chemical::gasteiger::GasteigerAtomTypeSet) → None¶

Manually set the gasteiger typeset - will use the default set otherwise

C++: core::chemical::ResidueType::set_gasteiger_typeset(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>) –> void

set_icoor(*args, **kwargs)¶

Overloaded function.

set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str) -> None
set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str, update_xyz: bool) -> None

set AtomICoor for an atom

phi and theta are in radians

C++: core::chemical::ResidueType::set_icoor(const class std::basic_string<char> &, const double, const double, const double, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &, const bool) –> void

set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: capsule, stub_atom2: capsule, stub_atom3: capsule) -> None
set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: capsule, phi: float, theta: float, d: float, stub_atom1: capsule, stub_atom2: capsule, stub_atom3: capsule, update_xyz: bool) -> None

set AtomICoor for an atom, vertex descriptor version

phi and theta are in radians

C++: core::chemical::ResidueType::set_icoor(void *const &, const double, const double, const double, void *const &, void *const &, void *const &, const bool) –> void

set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: pyrosetta.rosetta.core.chemical.ICoorAtomID, stub_atom2: pyrosetta.rosetta.core.chemical.ICoorAtomID, stub_atom3: pyrosetta.rosetta.core.chemical.ICoorAtomID) -> None
set_icoor(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, phi: float, theta: float, d: float, stub_atom1: pyrosetta.rosetta.core.chemical.ICoorAtomID, stub_atom2: pyrosetta.rosetta.core.chemical.ICoorAtomID, stub_atom3: pyrosetta.rosetta.core.chemical.ICoorAtomID, update_xyz: bool) -> None

set AtomICoor for an atom

phi and theta are in radians

C++: core::chemical::ResidueType::set_icoor(const class std::basic_string<char> &, const double, const double, const double, const class core::chemical::ICoorAtomID &, const class core::chemical::ICoorAtomID &, const class core::chemical::ICoorAtomID &, const bool) –> void

set_ideal_xyz(*args, **kwargs)¶

Overloaded function.

set_ideal_xyz(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: str, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::ResidueType::set_ideal_xyz(const class std::basic_string<char> &, const class numeric::xyzVector<double> &) –> void

set_ideal_xyz(self: pyrosetta.rosetta.core.chemical.ResidueType, index: int, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::ResidueType::set_ideal_xyz(unsigned long, const class numeric::xyzVector<double> &) –> void

set_ideal_xyz(self: pyrosetta.rosetta.core.chemical.ResidueType, atm: capsule, xyz_in: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::chemical::ResidueType::set_ideal_xyz(void *, const class numeric::xyzVector<double> &) –> void

set_low_energy_ring_conformers(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int, conformers: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Set this cyclic residue’s low-energy ring conformers for the nth ring by IUPAC name.

C++: core::chemical::ResidueType::set_low_energy_ring_conformers(const unsigned long, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

set_lower_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atm_name: str) → None¶

set the atom which connects to the lower connection

C++: core::chemical::ResidueType::set_lower_connect_atom(const class std::basic_string<char> &) –> void

set_lowest_energy_ring_conformer(self: pyrosetta.rosetta.core.chemical.ResidueType, ring_num: int, conformer: str) → None¶

Set this cyclic residue’s lowest-energy ring conformer for the nth ring by IUPAC name.

C++: core::chemical::ResidueType::set_lowest_energy_ring_conformer(const unsigned long, const class std::basic_string<char> &) –> void

set_mainchain_atoms(self: pyrosetta.rosetta.core.chemical.ResidueType, mainchain: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

set indices of all mainchain atoms

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

set_mm_atom_type(self: pyrosetta.rosetta.core.chemical.ResidueType, atom_name: str, mm_atom_type_name: str) → None¶

set mm atom type

C++: core::chemical::ResidueType::set_mm_atom_type(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_orbital_icoor_id(self: pyrosetta.rosetta.core.chemical.ResidueType, orbital: str, phi: float, theta: float, d: float, stub_atom1: str, stub_atom2: str, stub_atom3: str) → None¶

set OrbitalICoor for an orbital

C++: core::chemical::ResidueType::set_orbital_icoor_id(const class std::basic_string<char> &, const double, const double, const double, const class std::basic_string<char> &, const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_properties(self: pyrosetta.rosetta.core.chemical.ResidueType, properties: core::chemical::ResidueProperties) → None¶

Set the collection of properties for this ResidueType.

C++: core::chemical::ResidueType::set_properties(class std::shared_ptr<class core::chemical::ResidueProperties>) –> void

set_proton_chi(self: pyrosetta.rosetta.core.chemical.ResidueType, chino: int, dihedral_samples: pyrosetta.rosetta.utility.vector1_double, extra_samples: pyrosetta.rosetta.utility.vector1_double) → None¶

Annotate a given chi as a proton chi, and set the sampling behavior: If the chi is already listed as a proton chi, change the sampling behavior

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

set_rama_prepro_mainchain_torsion_potential_name(self: pyrosetta.rosetta.core.chemical.ResidueType, name_in: str, pre_proline_position: bool) → None¶

Set the key name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueType::set_rama_prepro_mainchain_torsion_potential_name(const class std::basic_string<char> &, const bool) –> void

set_rama_prepro_map_file_name(self: pyrosetta.rosetta.core.chemical.ResidueType, filename_in: str, pre_proline_position: bool) → None¶

Set the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we’re interested in.

C++: core::chemical::ResidueType::set_rama_prepro_map_file_name(const class std::basic_string<char> &, const bool) –> void

set_shadowing_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: str, atom_being_shadowed: str) → None¶: C++: core::chemical::ResidueType::set_shadowing_atom(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

set_upper_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atm_name: str) → None¶

set the atom which connects to the upper connection

C++: core::chemical::ResidueType::set_upper_connect_atom(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.core.chemical.ResidueType) -> None
show(self: pyrosetta.rosetta.core.chemical.ResidueType, output: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.core.chemical.ResidueType, output: pyrosetta.rosetta.std.ostream, output_atomic_details: bool) -> None

Generate string representation of ResidueType for debugging purposes.

C++: core::chemical::ResidueType::show(class std::basic_ostream<char> &, bool) const –> void

show_all_atom_names(self: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::ResidueType::show_all_atom_names(class std::basic_ostream<char> &) const –> void

smallest_ring_size(*args, **kwargs)¶

Overloaded function.

smallest_ring_size(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: capsule) -> int
smallest_ring_size(self: pyrosetta.rosetta.core.chemical.ResidueType, atom: capsule, max_size: int) -> int

A graph-based function to determine the size of the smallest ring that involves a given atom.

C++: core::chemical::ResidueType::smallest_ring_size(void *const &, const unsigned long &) const –> unsigned long

strip_rotamer_library_specification(self: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Remove any rotamer library specifications attached to this ResidueType.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::ResidueType::strip_rotamer_library_specification() –> void

update_actcoord(self: pyrosetta.rosetta.core.chemical.ResidueType, rot: core::conformation::Residue) → None¶

update actcoord

C++: core::chemical::ResidueType::update_actcoord(class core::conformation::Residue &) const –> void

upper_connect(self: pyrosetta.rosetta.core.chemical.ResidueType) → core::chemical::ResidueConnection¶: C++: core::chemical::ResidueType::upper_connect() const –> const class core::chemical::ResidueConnection &

upper_connect_atom(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶

index number of the atom which connects to the upper connection

C++: core::chemical::ResidueType::upper_connect_atom() const –> unsigned long

upper_connect_id(self: pyrosetta.rosetta.core.chemical.ResidueType) → int¶: C++: core::chemical::ResidueType::upper_connect_id() const –> unsigned long

variant_type_enums(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType¶

Get a vector of VariantType enums for this ResidueType.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::ResidueType::variant_type_enums() const –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

variant_types(self: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶

get all the variant types for this ResidueType

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants.

– rhiju (merging roccomoretti/restypeset_fiddle)

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

within1bonds_sets_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶

Returns a list of pairs for atom# atomid where: first == the residue_connection id that lists atomid as being within one bond of a residue connection, and second == the index of the entry containing this atom in the atoms_within_one_bond_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::within1bonds_sets_for_atom(unsigned long) const –> const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &

within2bonds_sets_for_atom(self: pyrosetta.rosetta.core.chemical.ResidueType, atomid: int) → pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t¶

Returns a list of pairs for atom # atomid where: first == the residue_connection id that lists this atom as being within two bonds of a residue connection, and second == the index of the entry containing this atom in the atoms_within_two_bonds_of_a_residue_connection_[ first ] array. Useful for calculating the derivatives for an atom.

C++: core::chemical::ResidueType::within2bonds_sets_for_atom(unsigned long) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

class pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶

Bases: pybind11_builtins.pybind11_object

A class picking out a subset of ResidueType by multiple criteria

add_line(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, line: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::add_line(const class std::basic_string<char> &) –> class core::chemical::ResidueTypeSelector &

assign(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, : pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::operator=(const class core::chemical::ResidueTypeSelector &) –> class core::chemical::ResidueTypeSelector &

clear(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::clear() –> class core::chemical::ResidueTypeSelector &

exclude_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::exclude_variants() –> class core::chemical::ResidueTypeSelector &

match_variants(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, rsd_type_to_match: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::match_variants(const class core::chemical::ResidueType &) –> class core::chemical::ResidueTypeSelector &

set_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::set_aa(const enum core::chemical::AA) –> class core::chemical::ResidueTypeSelector &

set_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, n: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::set_name1(const char) –> class core::chemical::ResidueTypeSelector &

set_property(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelector, property: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelector¶: C++: core::chemical::ResidueTypeSelector::set_property(const class std::basic_string<char>) –> class core::chemical::ResidueTypeSelector &

class pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle¶

Bases: pybind11_builtins.pybind11_object

A base class for defining a ResidueTypeSelector by a single criterion

assign(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle, : pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle¶: C++: core::chemical::ResidueTypeSelectorSingle::operator=(const class core::chemical::ResidueTypeSelectorSingle &) –> class core::chemical::ResidueTypeSelectorSingle &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.ResidueTypeSet¶

Bases: pybind11_builtins.pybind11_object

An abstract interface to a set of ResidueTypes

atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.AtomTypeSet¶: C++: core::chemical::ResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>

base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t¶

The list of ResidueTypes that don’t have any patches, but can be patched.

C++: core::chemical::ResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >

element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.chemical.ElementSet¶: C++: core::chemical::ResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>

generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, interchangeability_group: str) → bool¶

Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated)): Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const class std::basic_string<char> &, const class std::basic_string<char> &) 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 class std::basic_string<char> &, const class std::basic_string<char> &) const –> bool

get_all_types_with_variants_aa(*args, **kwargs)¶

Overloaded function.

get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<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_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t

Gets all types with the given aa type and variants, making exceptions for some variants.

Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.

The number of variants must match exactly. Variants can be custom variants, but exceptions must be standard types, listed in VariantType.hh. (It’s assumed that the passed VariantTypeList contains no duplicates.)

C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, 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_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<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<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_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 class std::basic_string<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_d_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, l_rsd: core::chemical::ResidueType) → 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.

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: core::chemical::ResidueType) → 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.

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: core::chemical::ResidueType) → 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.

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> 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) → 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(*args, **kwargs)¶

Overloaded function.

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> 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.

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> 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 class std::basic_string<char> &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> 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 class std::basic_string<char> &) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 &

get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: core::chemical::ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) → 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) 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 class std::basic_string<char> &) const –> bool

merge_behavior_manager(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → core::chemical::MergeBehaviorManager¶

accessor for merge behavior manager

C++: core::chemical::ResidueTypeSet::merge_behavior_manager() const –> const class core::chemical::MergeBehaviorManager &

metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → core::chemical::Metapatch¶: C++: core::chemical::ResidueTypeSet::metapatch(const class std::basic_string<char> &) 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_map(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → 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 class std::basic_string<char> &) const –> const class core::chemical::ResidueType &

name_mapOP(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) → 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 class std::basic_string<char> &) 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.RestypeDestructionEvent¶

Bases: pybind11_builtins.pybind11_object

special signal that the ResidueType is getting destroyed

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

copy assignment

C++: core::chemical::RestypeDestructionEvent::operator=(const struct core::chemical::RestypeDestructionEvent &) –> struct core::chemical::RestypeDestructionEvent &

class pyrosetta.rosetta.core.chemical.Selector_AA¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue belong to ANY of these AAs?

assign(self: pyrosetta.rosetta.core.chemical.Selector_AA, : pyrosetta.rosetta.core.chemical.Selector_AA) → pyrosetta.rosetta.core.chemical.Selector_AA¶: C++: core::chemical::Selector_AA::operator=(const class core::chemical::Selector_AA &) –> class core::chemical::Selector_AA &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_CMDFLAG¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Is a certain string in the command-line option -chemical:allow_patch present ?

this selector does actually not depend on the residuetype it is queried for

assign(self: pyrosetta.rosetta.core.chemical.Selector_CMDFLAG, : pyrosetta.rosetta.core.chemical.Selector_CMDFLAG) → pyrosetta.rosetta.core.chemical.Selector_CMDFLAG¶: C++: core::chemical::Selector_CMDFLAG::operator=(const class core::chemical::Selector_CMDFLAG &) –> class core::chemical::Selector_CMDFLAG &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have ALL of the listed atoms?:

assign(self: pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS, : pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS) → pyrosetta.rosetta.core.chemical.Selector_HAS_ATOMS¶: C++: core::chemical::Selector_HAS_ATOMS::operator=(const class core::chemical::Selector_HAS_ATOMS &) –> class core::chemical::Selector_HAS_ATOMS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have ALL of the variant types and no more

assign(self: pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS, : pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS) → pyrosetta.rosetta.core.chemical.Selector_MATCH_VARIANTS¶: C++: core::chemical::Selector_MATCH_VARIANTS::operator=(const class core::chemical::Selector_MATCH_VARIANTS &) –> class core::chemical::Selector_MATCH_VARIANTS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NAME1¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue belong to ANY of these one-letter codes?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NAME1, : pyrosetta.rosetta.core.chemical.Selector_NAME1) → pyrosetta.rosetta.core.chemical.Selector_NAME1¶: C++: core::chemical::Selector_NAME1::operator=(const class core::chemical::Selector_NAME1 &) –> class core::chemical::Selector_NAME1 &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NAME3¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have to ANY of these three-letter codes?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NAME3, : pyrosetta.rosetta.core.chemical.Selector_NAME3) → pyrosetta.rosetta.core.chemical.Selector_NAME3¶: C++: core::chemical::Selector_NAME3::operator=(const class core::chemical::Selector_NAME3 &) –> class core::chemical::Selector_NAME3 &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have NO variant types?

assign(self: pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS, : pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS) → pyrosetta.rosetta.core.chemical.Selector_NO_VARIANTS¶: C++: core::chemical::Selector_NO_VARIANTS::operator=(const class core::chemical::Selector_NO_VARIANTS &) –> class core::chemical::Selector_NO_VARIANTS &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_PROPERTY¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have ANY of these properties?

assign(self: pyrosetta.rosetta.core.chemical.Selector_PROPERTY, : pyrosetta.rosetta.core.chemical.Selector_PROPERTY) → pyrosetta.rosetta.core.chemical.Selector_PROPERTY¶: C++: core::chemical::Selector_PROPERTY::operator=(const class core::chemical::Selector_PROPERTY &) –> class core::chemical::Selector_PROPERTY &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the main chain of this residue follow from the given position label?

By position, it is meant the single digit integer by which atoms are labeled to indicate their position. For example, if an upper connection is from C8 of a generic residue, the position is 8.

This selector was added primarily for use with carbohydrate residues, which have a wide assortment of main- chain designations. To properly patch upper terminus variants, it is necessary to know which atoms need to be added and, particularly, at which position to add them. However, this selector could be adapted for any residue subclass that contains variability in the main chain, provided the nomenclature is consistent and numerical. See patches/carbohydrates/upper_terminus.txt for an example of use.

Labonte

assign(self: pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION, : pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION) → pyrosetta.rosetta.core.chemical.Selector_UPPER_POSITION¶: C++: core::chemical::Selector_UPPER_POSITION::operator=(const class core::chemical::Selector_UPPER_POSITION &) –> class core::chemical::Selector_UPPER_POSITION &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE¶

Bases: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle

Does the residue have ANY of variant types?

assign(self: pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE, : pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE) → pyrosetta.rosetta.core.chemical.Selector_VARIANT_TYPE¶: C++: core::chemical::Selector_VARIANT_TYPE::operator=(const class core::chemical::Selector_VARIANT_TYPE &) –> class core::chemical::Selector_VARIANT_TYPE &

desired_result(self: pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle) → bool¶: C++: core::chemical::ResidueTypeSelectorSingle::desired_result() const –> bool

class pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set the residue neighbor radius

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive, rsd: core::chemical::ResidueType) → bool¶

set the residue neighbor atom

C++: core::chemical::SetAllAtomsRepulsive::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive, : pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive) → pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive¶: C++: core::chemical::SetAllAtomsRepulsive::operator=(const class core::chemical::SetAllAtomsRepulsive &) –> class core::chemical::SetAllAtomsRepulsive &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetAtomType¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set atom’s chemical type

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetAtomType, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::SetAtomType::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAtomType, : pyrosetta.rosetta.core.chemical.SetAtomType) → pyrosetta.rosetta.core.chemical.SetAtomType¶: C++: core::chemical::SetAtomType::operator=(const class core::chemical::SetAtomType &) –> class core::chemical::SetAtomType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetAtomicCharge¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set an atom’s charge

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetAtomicCharge, rsd: core::chemical::ResidueType) → bool¶

set an atom’s charge

C++: core::chemical::SetAtomicCharge::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetAtomicCharge, : pyrosetta.rosetta.core.chemical.SetAtomicCharge) → pyrosetta.rosetta.core.chemical.SetAtomicCharge¶: C++: core::chemical::SetAtomicCharge::operator=(const class core::chemical::SetAtomicCharge &) –> class core::chemical::SetAtomicCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set an atom as backbone heavy atom

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom, rsd: core::chemical::ResidueType) → bool¶

set an atom in ResidueType rsd as backbone heavy atom

C++: core::chemical::SetBackboneHeavyatom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom, : pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom) → pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom¶: C++: core::chemical::SetBackboneHeavyatom::operator=(const class core::chemical::SetBackboneHeavyatom &) –> class core::chemical::SetBackboneHeavyatom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetFormalCharge¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

A patch operation for setting the formal charge of a ResidueType’s atom.

Labonte <JWLabonte.edu>

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetFormalCharge, rsd: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::SetFormalCharge::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetFormalCharge, : pyrosetta.rosetta.core.chemical.SetFormalCharge) → pyrosetta.rosetta.core.chemical.SetFormalCharge¶: C++: core::chemical::SetFormalCharge::operator=(const class core::chemical::SetFormalCharge &) –> class core::chemical::SetFormalCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetICoor¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set an atom’s AtomICoord

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetICoor, rsd: core::chemical::ResidueType) → bool¶

set an atom’s AtomICoord

C++: core::chemical::SetICoor::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetICoor, : pyrosetta.rosetta.core.chemical.SetICoor) → pyrosetta.rosetta.core.chemical.SetICoor¶: C++: core::chemical::SetICoor::operator=(const class core::chemical::SetICoor &) –> class core::chemical::SetICoor &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetIO_String¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set residue’s name1 and name3

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

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

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

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

Which property, if any, is added.

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

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.SetIO_String) → bool¶: C++: core::chemical::SetIO_String::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetIO_String, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::SetIO_String::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetIO_String, : pyrosetta.rosetta.core.chemical.SetIO_String) → pyrosetta.rosetta.core.chemical.SetIO_String¶: C++: core::chemical::SetIO_String::operator=(const class core::chemical::SetIO_String &) –> class core::chemical::SetIO_String &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

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

Generates interchangeability_group.

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

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

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

class pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set the interchangeability_group string for a ResidueType

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

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

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

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

Which property, if any, is added.

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

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

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

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

apply(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::SetInterchangeabilityGroup_String::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String, : pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String) → pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String¶: C++: core::chemical::SetInterchangeabilityGroup_String::operator=(const class core::chemical::SetInterchangeabilityGroup_String &) –> class core::chemical::SetInterchangeabilityGroup_String &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

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

Which variant, if any, is deleted.

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

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String) → str¶: C++: core::chemical::SetInterchangeabilityGroup_String::generates_interchangeability_group() –> std::string

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

Generates name3.

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

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

Generates a new aa

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

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

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

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetInterchangeabilityGroup_String::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetMMAtomType¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set atom’s MM chemical type

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetMMAtomType, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::SetMMAtomType::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetMMAtomType, : pyrosetta.rosetta.core.chemical.SetMMAtomType) → pyrosetta.rosetta.core.chemical.SetMMAtomType¶: C++: core::chemical::SetMMAtomType::operator=(const class core::chemical::SetMMAtomType &) –> class core::chemical::SetMMAtomType &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetMMAtomType) → str¶

Return the name of this PatchOperation (“SetMMAtomType”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetMMAtomType::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNbrAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set the residue neighbor atom

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNbrAtom, rsd: core::chemical::ResidueType) → bool¶

set the residue neighbor atom

C++: core::chemical::SetNbrAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNbrAtom, : pyrosetta.rosetta.core.chemical.SetNbrAtom) → pyrosetta.rosetta.core.chemical.SetNbrAtom¶: C++: core::chemical::SetNbrAtom::operator=(const class core::chemical::SetNbrAtom &) –> class core::chemical::SetNbrAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNbrAtom) → str¶

Return the name of this PatchOperation (“SetNbrAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNbrAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNbrRadius¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set the residue neighbor radius

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNbrRadius, rsd: core::chemical::ResidueType) → bool¶

set the residue neighbor atom

C++: core::chemical::SetNbrRadius::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNbrRadius, : pyrosetta.rosetta.core.chemical.SetNbrRadius) → pyrosetta.rosetta.core.chemical.SetNbrRadius¶: C++: core::chemical::SetNbrRadius::operator=(const class core::chemical::SetNbrRadius &) –> class core::chemical::SetNbrRadius &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNbrRadius) → str¶

Return the name of this PatchOperation (“SetNbrRadius”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNbrRadius::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetNetFormalCharge¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

A patch operation for setting the net formal charge of a whole ResidueType.

Vikram K. Mulligan (vmullig.edu)

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge, rsd: core::chemical::ResidueType) → bool¶

Apply this patch to the given ResidueType.

C++: core::chemical::SetNetFormalCharge::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge, : pyrosetta.rosetta.core.chemical.SetNetFormalCharge) → pyrosetta.rosetta.core.chemical.SetNetFormalCharge¶: C++: core::chemical::SetNetFormalCharge::operator=(const class core::chemical::SetNetFormalCharge &) –> class core::chemical::SetNetFormalCharge &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetNetFormalCharge) → str¶

Return the name of this PatchOperation (“SetNetFormalCharge”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetNetFormalCharge::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetOrientAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

Set orient atom selection mode.

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetOrientAtom, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::SetOrientAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetOrientAtom, : pyrosetta.rosetta.core.chemical.SetOrientAtom) → pyrosetta.rosetta.core.chemical.SetOrientAtom¶: C++: core::chemical::SetOrientAtom::operator=(const class core::chemical::SetOrientAtom &) –> class core::chemical::SetOrientAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetOrientAtom) → str¶

Return the name of this PatchOperation (“SetOrientAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetOrientAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set an atom as polymer connection

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, rsd: core::chemical::ResidueType) → bool¶

set an atom in ResidueType rsd as a polymer connection atom

C++: core::chemical::SetPolymerConnectAtom::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, : pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom) → pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom¶: C++: core::chemical::SetPolymerConnectAtom::operator=(const class core::chemical::SetPolymerConnectAtom &) –> class core::chemical::SetPolymerConnectAtom &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom, rsd_type: core::chemical::ResidueType, atom: str) → bool¶: C++: core::chemical::SetPolymerConnectAtom::changes_connections_on(const class core::chemical::ResidueType &, const class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom) → str¶

Return the name of this PatchOperation (“SetPolymerConnectAtom”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetPolymerConnectAtom::name() const –> std::string

class pyrosetta.rosetta.core.chemical.SetVirtualShadow¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set virtual shadow atoms

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::SetVirtualShadow::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow, : pyrosetta.rosetta.core.chemical.SetVirtualShadow) → pyrosetta.rosetta.core.chemical.SetVirtualShadow¶: C++: core::chemical::SetVirtualShadow::operator=(const class core::chemical::SetVirtualShadow &) –> class core::chemical::SetVirtualShadow &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.SetVirtualShadow) → str¶

Return the name of this PatchOperation (“SetVirtualShadow”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::SetVirtualShadow::name() const –> std::string

class pyrosetta.rosetta.core.chemical.Set_AA¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

set residue’s aa

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.Set_AA) → bool¶: C++: core::chemical::Set_AA::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.Set_AA, rsd: core::chemical::ResidueType) → bool¶

set atom’s chemical type

C++: core::chemical::Set_AA::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.Set_AA, : pyrosetta.rosetta.core.chemical.Set_AA) → pyrosetta.rosetta.core.chemical.Set_AA¶: C++: core::chemical::Set_AA::operator=(const class core::chemical::Set_AA &) –> class core::chemical::Set_AA &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.Set_AA) → bool¶

Generates a new aa

C++: core::chemical::Set_AA::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.Set_AA) → str¶

Return the name of this PatchOperation (“Set_AA”).

C++: core::chemical::Set_AA::name() const –> std::string

class pyrosetta.rosetta.core.chemical.TypeSetMode¶

Bases: pybind11_builtins.pybind11_object

A type set category is the “compatibility class” of a type set.: That is, all e.g. ResidueTypes of a given TypeSetMode should be “compatible” with the scale of modeling resolution, indepenent of if they’re in the same ResidueTypeSet.

Members:

INVALID_t

FULL_ATOM_t

DEFAULT_t

CENTROID_t

CENTROID_ROT_t

HYBRID_FA_STANDARD_CENTROID_t

COARSE_RNA_t

MIXED_t

TYPE_SET_MODES_LENGTH

class pyrosetta.rosetta.core.chemical.VariantType¶

Bases: pybind11_builtins.pybind11_object

Enumerators for all the ResidueType variants.

VariantTypes are primarily utilized by the patch system. All the type does is add an identifier that can be used later on in different protocols. It also helps the patch system keep track of which residues are patched with which patches.

Members:

NO_VARIANT

FIRST_VARIANT

UPPER_TERMINUS_VARIANT

LOWER_TERMINUS_VARIANT

UPPERTERM_TRUNC_VARIANT

LOWERTERM_TRUNC_VARIANT

PHOSPHONATE_UPPER_VARIANT

CUTPOINT_LOWER

CUTPOINT_UPPER

NTERM_CONNECT

CTERM_CONNECT

DISULFIDE

SC_BRANCH_POINT

C1_BRANCH_POINT

C2_BRANCH_POINT

C3_BRANCH_POINT

C4_BRANCH_POINT

C5_BRANCH_POINT

C6_BRANCH_POINT

C7_BRANCH_POINT

C8_BRANCH_POINT

C9_BRANCH_POINT

SIDECHAIN_CONJUGATION

SG_CONNECT

NE2_CONNECT

ZN_CONNECT

METHYLATED_NTERM_VARIANT

ACETYLATED_NTERMINUS_VARIANT

METHYLATED_CTERMINUS_VARIANT

OOP_PRE

OOP_POST

HBS_PRE

HBS_POST

A3B_HBS_PRE

A3B_HBS_POST

PROTONATED

DEPROTONATED

ALTERNATIVE_PROTONATION

METHYLATION

DIMETHYLATION

TRIMETHYLATION

ACETYLATION

PHOSPHORYLATION

SULFATION

HYDROXYLATION

HYDROXYLATION1

HYDROXYLATION2

CARBOXYLATION

DIIODINATION

VIRTUAL_BB

VIRTUAL_SIDE_CHAIN

VIRTUAL_RESIDUE_VARIANT

VIRTUAL_NTERM

VIRTUAL_PHOSPHATE

VIRTUAL_DNA_PHOSPHATE

REPLS_BB

REPLONLY

REPL_PHOSPHATE

VIRTUAL_RIBOSE

VIRTUAL_BACKBONE_EXCEPT_C1PRIME

VIRTUAL_BASE

VIRTUAL_BASE_HEAVY_ATOM

VIRTUAL_RNA_RESIDUE

VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE

BULGE

VIRTUAL_O2PRIME_HYDROGEN

THREE_PRIME_END_OH

THREE_PRIME_PHOSPHATE

FIVE_PRIME_END_OH

FIVE_PRIME_END_PHOSPHATE

FIVE_PRIME_PHOSPHATE

FIVEPRIME_CAP

THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE

DEOXY_O2PRIME

UPPER_CONNECTION_RNA

THREE_PRIME_PACKABLE_PHOSPHATE

FIVE_PRIME_PACKABLE_PHOSPHATE

FIVE_PRIME_PACKABLE_TRIPHOSPHATE

PROTONATED_N1

PROTONATED_N3

THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE

BLOCK_STACK_ABOVE

BLOCK_STACK_BELOW

N_ACETYLATION

N_FORMYLATION

C_METHYLAMIDATION

CTERM_AMIDATION

ALDONIC_ACID_VARIANT

C2_KETOALDONIC_ACID

C3_KETOALDONIC_ACID

C4_KETOALDONIC_ACID

C5_KETOALDONIC_ACID

C6_KETOALDONIC_ACID

C7_KETOALDONIC_ACID

C8_KETOALDONIC_ACID

URONIC_ACID_VARIANT

C1_DEOXY_SUGAR

C2_DEOXY_SUGAR

C3_DEOXY_SUGAR

C4_DEOXY_SUGAR

C5_DEOXY_SUGAR

C6_DEOXY_SUGAR

C7_DEOXY_SUGAR

C8_DEOXY_SUGAR

C9_DEOXY_SUGAR

C1_AMINO_SUGAR

C2_AMINO_SUGAR

C3_AMINO_SUGAR

C4_AMINO_SUGAR

C5_AMINO_SUGAR

C6_AMINO_SUGAR

C7_AMINO_SUGAR

C8_AMINO_SUGAR

C9_AMINO_SUGAR

C1_ACETYLAMINO_SUGAR

C2_ACETYLAMINO_SUGAR

C3_ACETYLAMINO_SUGAR

C4_ACETYLAMINO_SUGAR

C5_ACETYLAMINO_SUGAR

C6_ACETYLAMINO_SUGAR

C7_ACETYLAMINO_SUGAR

C8_ACETYLAMINO_SUGAR

C9_ACETYLAMINO_SUGAR

C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR

C1_SULFATED_SUGAR

C2_SULFATED_SUGAR

C3_SULFATED_SUGAR

C4_SULFATED_SUGAR

C5_SULFATED_SUGAR

C6_SULFATED_SUGAR

C7_SULFATED_SUGAR

C8_SULFATED_SUGAR

C9_SULFATED_SUGAR

C1_SULFOAMINO_SUGAR

C2_SULFOAMINO_SUGAR

C3_SULFOAMINO_SUGAR

C4_SULFOAMINO_SUGAR

C5_SULFOAMINO_SUGAR

C6_SULFOAMINO_SUGAR

C7_SULFOAMINO_SUGAR

C8_SULFOAMINO_SUGAR

C9_SULFOAMINO_SUGAR

C1_METHYLATED_SUGAR

C2_METHYLATED_SUGAR

C3_METHYLATED_SUGAR

C4_METHYLATED_SUGAR

C5_METHYLATED_SUGAR

C6_METHYLATED_SUGAR

C7_METHYLATED_SUGAR

C8_METHYLATED_SUGAR

C9_METHYLATED_SUGAR

C1_PHOSPHATE

C2_PHOSPHATE

C3_PHOSPHATE

C4_PHOSPHATE

C5_PHOSPHATE

C6_PHOSPHATE

C7_PHOSPHATE

C8_PHOSPHATE

C9_PHOSPHATE

METHYL_GLYCOSIDE

TRIAZOLAMERN

TRIAZOLAMERC

ADDUCT_VARIANT

CENTROID_WITH_HA

SPECIAL_ROT

SC_FRAGMENT

SHOVE_BB

N_VARIANTS

class pyrosetta.rosetta.core.chemical.VirtualizeAll¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

virtualize all

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.VirtualizeAll, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::VirtualizeAll::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.VirtualizeAll, : pyrosetta.rosetta.core.chemical.VirtualizeAll) → pyrosetta.rosetta.core.chemical.VirtualizeAll¶: C++: core::chemical::VirtualizeAll::operator=(const class core::chemical::VirtualizeAll &) –> class core::chemical::VirtualizeAll &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.VirtualizeAll) → str¶

Return the name of this PatchOperation (“VirtualizeAll”).

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::VirtualizeAll::name() const –> std::string

class pyrosetta.rosetta.core.chemical.VirtualizeSidechain¶

Bases: pyrosetta.rosetta.core.chemical.PatchOperation

virtualize sidechain

adds_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which atom, if any, is added. Used for fast matching of ResidueType/Patches to PDB residues.

C++: core::chemical::PatchOperation::adds_atom() –> std::string

adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which property, if any, is added.

C++: core::chemical::PatchOperation::adds_property() –> std::string

applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.

C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool

apply(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain, rsd: core::chemical::ResidueType) → bool¶: C++: core::chemical::VirtualizeSidechain::apply(class core::chemical::ResidueType &) const –> bool

assign(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain, : pyrosetta.rosetta.core.chemical.VirtualizeSidechain) → pyrosetta.rosetta.core.chemical.VirtualizeSidechain¶: C++: core::chemical::VirtualizeSidechain::operator=(const class core::chemical::VirtualizeSidechain &) –> class core::chemical::VirtualizeSidechain &

changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : 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 class std::basic_string<char> &) 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() –> std::string

deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Which variant, if any, is deleted.

C++: core::chemical::PatchOperation::deletes_variant() –> std::string

generates_base_residue(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() –> bool

generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates interchangeability_group.

C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string

generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) → str¶

Generates name3.

C++: core::chemical::PatchOperation::generates_name3() –> std::string

may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) → bool¶

Generates a new aa

C++: core::chemical::PatchOperation::may_change_aa() –> bool

name(self: pyrosetta.rosetta.core.chemical.VirtualizeSidechain) → str¶

Return the name of this PatchOperation (“VirtualizeSidechain”).

Andrew M. Watkins (amw579.edu).

C++: core::chemical::VirtualizeSidechain::name() const –> std::string

pyrosetta.rosetta.core.chemical.aa_from_name(name: str) → pyrosetta.rosetta.core.chemical.AA¶: Give an AA string name, return its enum type.

C++: core::chemical::aa_from_name(const class std::basic_string<char> &) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.aa_from_one_or_three(name: str) → pyrosetta.rosetta.core.chemical.AA¶: C++: core::chemical::aa_from_one_or_three(const class std::basic_string<char> &) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.aa_from_oneletter_code(onelettercode: str) → pyrosetta.rosetta.core.chemical.AA¶: give a 1 letter code and return the string name

C++: core::chemical::aa_from_oneletter_code(char) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.add_atom_type_set_parameters_from_command_line(atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None¶

Add additional parameter files not present in <atom-set-name>/extras.txt.

C++: core::chemical::add_atom_type_set_parameters_from_command_line(const class std::basic_string<char> &, class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.apply_adducts_to_residue(rsd: pyrosetta.rosetta.core.chemical.ResidueType, add_mask: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.core.chemical.ResidueType¶

Apply adducts to residue using a boolean mask

C++: core::chemical::apply_adducts_to_residue(const class core::chemical::ResidueType &, class utility::vector1<bool, class std::allocator<bool> > &) –> class std::shared_ptr<class core::chemical::ResidueType>

pyrosetta.rosetta.core.chemical.apply_symm_gly_corrections(child_atom: str, phi: float, theta: float, d: float, parent_atom: str, angle_atom: str, torsion_atom: str) → None¶

Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option).

Ugh. Special-case logic.

Vikram K. Mulligan, Baker laboratory (vmullig.edu)

C++: core::chemical::apply_symm_gly_corrections(const class std::basic_string<char> &, double &, double &, double &, class std::basic_string<char> &, class std::basic_string<char> &, class std::basic_string<char> &) –> void

pyrosetta.rosetta.core.chemical.calculate_rigid_matrix(res: pyrosetta.rosetta.core.chemical.ResidueType, distances: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None¶

Calculate the rigid matrix for neighbor atom finding: Assume that distances has been initialized to some really large value, and is square

C++: core::chemical::calculate_rigid_matrix(const class core::chemical::ResidueType &, class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

pyrosetta.rosetta.core.chemical.case_from_lines(*args, **kwargs)¶

Overloaded function.

case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.PatchCase
case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string, res_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.PatchCase
case_from_lines(lines: pyrosetta.rosetta.utility.vector1_std_string, res_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, patch_name: str) -> pyrosetta.rosetta.core.chemical.PatchCase

create a PatchCase from input lines

add selector_ from lines enclosed by “BEGIN_SELECTOR” and “END_SELECTOR”. add operations_ from each input line containing a single operation

C++: core::chemical::case_from_lines(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, enum core::chemical::TypeSetMode, const class std::basic_string<char> &) –> class std::shared_ptr<class core::chemical::PatchCase>

pyrosetta.rosetta.core.chemical.complex_ring_detection(res: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::complex_ring_detection(class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.core.chemical.convert_to_BondName(id: str) → pyrosetta.rosetta.core.chemical.BondName¶: C++: core::chemical::convert_to_BondName(const class std::basic_string<char> &) –> enum core::chemical::BondName

pyrosetta.rosetta.core.chemical.create_bond_length(atom1: core::chemical::gasteiger::GasteigerAtomTypeData, atom2: core::chemical::gasteiger::GasteigerAtomTypeData, bond_type: pyrosetta.rosetta.core.chemical.BondName) → float¶: C++: core::chemical::create_bond_length(const class core::chemical::gasteiger::GasteigerAtomTypeData &, const class core::chemical::gasteiger::GasteigerAtomTypeData &, enum core::chemical::BondName) –> double

pyrosetta.rosetta.core.chemical.define_mainchain_atoms(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER.

C++: core::chemical::define_mainchain_atoms(class std::shared_ptr<class core::chemical::ResidueType>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.chemical.detect_ld_chirality_from_polymer_residue(xyz: pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t, name3: str, is_d_aa: bool, is_l_aa: bool) → None¶: C++: core::chemical::detect_ld_chirality_from_polymer_residue(const class std::map<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > > &, const class std::basic_string<char> &, bool &, bool &) –> void

pyrosetta.rosetta.core.chemical.enlarge_h_lj_wdepth(*args, **kwargs)¶

Overloaded function.

enlarge_h_lj_wdepth(lj_wdepth: pyrosetta.rosetta.utility.vector1_double, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA

C++: core::chemical::enlarge_h_lj_wdepth(class utility::vector1<double, class std::allocator<double> > &, const class core::chemical::AtomTypeSet &) –> void

enlarge_h_lj_wdepth(atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) -> None

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA

C++: core::chemical::enlarge_h_lj_wdepth(class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.error_check_requested_adducts(add_map: pyrosetta.rosetta.std.map_std_string_int, rsd_types: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t) → None¶

Make sure requested adducts exist in some residue

C++: core::chemical::error_check_requested_adducts(const class std::map<class std::basic_string<char>, int, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, int> > > &, const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &) –> void

pyrosetta.rosetta.core.chemical.find_best_match(*args, **kwargs)¶

Overloaded function.

find_best_match(rsd_type_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, atom_names: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType
find_best_match(rsd_type_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t, atom_names: pyrosetta.rosetta.utility.vector1_std_string, ignore_atom_named_H: bool) -> pyrosetta.rosetta.core.chemical.ResidueType

look for best match to atom_names

C++: core::chemical::find_best_match(const class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > > &, const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &, const bool) –> class std::shared_ptr<const class core::chemical::ResidueType>

pyrosetta.rosetta.core.chemical.find_bonds_in_rings(*args, **kwargs)¶

Overloaded function.

find_bonds_in_rings(res: pyrosetta.rosetta.core.chemical.ResidueType) -> None
find_bonds_in_rings(res: pyrosetta.rosetta.core.chemical.ResidueType, complex_ring_detection: bool) -> None

Determine which bonds are in rings, and set the BondRingness property of each

C++: core::chemical::find_bonds_in_rings(class core::chemical::ResidueType &, const bool) –> void

pyrosetta.rosetta.core.chemical.find_chi_bonds(restype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_utility_vector1_void_*_std_allocator_void_*_t¶

Find which bonds are rotatatable (chi) bonds: Returns a list of four vds representing the chi

C++: core::chemical::find_chi_bonds(const class core::chemical::ResidueType &) –> class utility::vector1<class utility::vector1<void *, class std::allocator<void *> >, class std::allocator<class utility::vector1<void *, class std::allocator<void *> > > >

pyrosetta.rosetta.core.chemical.find_nbr_dist(res: pyrosetta.rosetta.core.chemical.ResidueType, nbr_atom: capsule) → float¶

Find the neighbor distance to the given neighbor atom.

If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance.

The neighbor distance here is adjusted for rotatable bonds - It should be at least as large as the maximum neighbor distance in any torsional rotamer If the neighbor atom is not provided, the atom chosen will be a multiply-bonded heavy atom.

Assumes:

All atoms and bond are present

All ideal_xyz coordinates have been set

All elements have been set

All ring bonds have been annotated

C++: core::chemical::find_nbr_dist(const class core::chemical::ResidueType &, void *&) –> double

pyrosetta.rosetta.core.chemical.fixup_patches(string_in: str) → str¶

Replaces the deprecated “_p:” linker connecting ResidueType base names with their patch names with “:”.

C++: core::chemical::fixup_patches(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.chemical.formatted_icoord_tree(restype: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

Return a string representing the internal coordinates tree of this ResidueType.

C++: core::chemical::formatted_icoord_tree(const class core::chemical::ResidueType &) –> std::string

pyrosetta.rosetta.core.chemical.get_D_equivalent(aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.AA¶: Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined).

C++: core::chemical::get_D_equivalent(const enum core::chemical::AA) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.get_L_equivalent(aa: pyrosetta.rosetta.core.chemical.AA) → pyrosetta.rosetta.core.chemical.AA¶: Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined).

C++: core::chemical::get_L_equivalent(const enum core::chemical::AA) –> enum core::chemical::AA

pyrosetta.rosetta.core.chemical.get_patch_names(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: core::chemical::get_patch_names(const class core::chemical::ResidueType &) –> class utility::vector1<std::string, class std::allocator<std::string > >

pyrosetta.rosetta.core.chemical.get_residue_path_distances(res: pyrosetta.rosetta.core.chemical.ResidueType) → ObjexxFCL::FArray2D<int>¶

relies on class Graph to find all pairs shortest path information

C++: core::chemical::get_residue_path_distances(const class core::chemical::ResidueType &) –> class ObjexxFCL::FArray2D<int>

pyrosetta.rosetta.core.chemical.heavy_atom_names_match(first: pyrosetta.rosetta.core.chemical.ResidueType, second: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Return true if the two residues have the same number and name of heavy atoms.

C++: core::chemical::heavy_atom_names_match(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.is_aa_name_unknown(name: str) → bool¶: Given aa three letter string, return true if it is an unknown aa.

Steven Cobms (steven.combs1.com)

C++: core::chemical::is_aa_name_unknown(const class std::basic_string<char> &) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_D_aa(aa: pyrosetta.rosetta.core.chemical.AA) → bool¶: Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid.

Vikram K. Mulligan (vmullig.edu)

C++: core::chemical::is_canonical_D_aa(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_L_aa_or_gly(aa: pyrosetta.rosetta.core.chemical.AA) → bool¶: Given an enum type, return true if and only if it is a canonical L-amino acid.

Also returns true if this is a glycine.

Steven Cobms (steven.combs1.com)

C++: core::chemical::is_canonical_L_aa_or_gly(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_canonical_beta3_aa(aa: pyrosetta.rosetta.core.chemical.AA) → bool¶: Given an enum type, return true if and only if it is a canonical beta-amino acid.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::is_canonical_beta3_aa(const enum core::chemical::AA) –> bool

pyrosetta.rosetta.core.chemical.is_mainchain_torsion_also_ring_torsion(res_type: pyrosetta.rosetta.core.chemical.ResidueType, torsion_index: int) → bool¶

Are these main-chain torsions also ring torsions?

C++: core::chemical::is_mainchain_torsion_also_ring_torsion(const class core::chemical::ResidueType &, unsigned long) –> bool

pyrosetta.rosetta.core.chemical.is_sp2_proton_chi(chi: int, restype: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom?

The use case is to see if the proton chi should flat or staggered with rotamers

C++: core::chemical::is_sp2_proton_chi(unsigned long, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.make_centroid(res: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.chemical.ResidueType¶

Make a centroid version of the fullatom ResidueType passed in.

May return a nullptr if the conversion is not possible

This uses the same crude heuristics as in molfile_to_params That is, all heavy atoms and polar hydrogens are transfered over 1:1, and non-polar hydrogens are deleted.

Of particular note is that it makes no attempt to transfer things over into “Superatoms”

Current limitation: it cannot convert a ResidueType which has connections, if any of the ICOORs depend on deleted hydrogens.

Assumes:

Input ResidueType is complete and finalized

C++: core::chemical::make_centroid(const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::chemical::ResidueType>

class pyrosetta.rosetta.core.chemical.merge_residue_behavior¶

Bases: pybind11_builtins.pybind11_object

Members:

mrb_do_not_merge

mrb_merge_w_prev

mrb_merge_w_next

pyrosetta.rosetta.core.chemical.modify_atom_properties_from_command_line(atom_type_set_tag: str, atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None¶

Modify atom_type properties from the command line.

C++: core::chemical::modify_atom_properties_from_command_line(const class std::basic_string<char> &, class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.name_from_aa(aa: pyrosetta.rosetta.core.chemical.AA) → str¶: give a enum type and return the string name

C++: core::chemical::name_from_aa(enum core::chemical::AA) –> std::string

pyrosetta.rosetta.core.chemical.nonadduct_variants_match(res1: pyrosetta.rosetta.core.chemical.ResidueType, res2: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Similar to variants_match(), but allows different adduct-modified states.

C++: core::chemical::nonadduct_variants_match(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.oneletter_code_from_aa(aa: pyrosetta.rosetta.core.chemical.AA) → str¶: give a enum type and return the string name

C++: core::chemical::oneletter_code_from_aa(enum core::chemical::AA) –> char

pyrosetta.rosetta.core.chemical.oneletter_code_specifies_aa(onelettercode: str) → bool¶: C++: core::chemical::oneletter_code_specifies_aa(char) –> bool

pyrosetta.rosetta.core.chemical.pH_mode_exceptions() → pyrosetta.rosetta.utility.vector1_core_chemical_VariantType¶: C++: core::chemical::pH_mode_exceptions() –> class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >

pyrosetta.rosetta.core.chemical.parse_adduct_string(add_vec: pyrosetta.rosetta.utility.options.StringVectorOption) → pyrosetta.rosetta.std.map_std_string_int¶

Convert input string to map of adducts->max usage

C++: core::chemical::parse_adduct_string(class utility::options::StringVectorOption &) –> class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > >

pyrosetta.rosetta.core.chemical.patch_operation_from_patch_file_line(line: str, atomic_charge_reassignments: pyrosetta.rosetta.std.map_std_string_double) → pyrosetta.rosetta.core.chemical.PatchOperation¶: Virtual constructor, returns 0 if no match

C++: core::chemical::patch_operation_from_patch_file_line(const class std::basic_string<char> &, const class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &) –> class std::shared_ptr<class core::chemical::PatchOperation>

pyrosetta.rosetta.core.chemical.pretty_print_atomicoor(*args, **kwargs)¶

Overloaded function.

pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, rsd_type: core::chemical::ResidueType) -> None

C++: core::chemical::pretty_print_atomicoor(class std::basic_ostream<char> &, const class core::chemical::ResidueType &) –> void

pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, start: pyrosetta.rosetta.core.chemical.AtomICoor, rsd_type: core::chemical::ResidueType) -> None
pretty_print_atomicoor(out: pyrosetta.rosetta.std.ostream, start: pyrosetta.rosetta.core.chemical.AtomICoor, rsd_type: core::chemical::ResidueType, indent: int) -> None

C++: core::chemical::pretty_print_atomicoor(class std::basic_ostream<char> &, const class core::chemical::AtomICoor &, const class core::chemical::ResidueType &, unsigned long) –> void

pyrosetta.rosetta.core.chemical.print_chis(out: pyrosetta.rosetta.std.ostream, res: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Utility to examine chi output.

C++: core::chemical::print_chis(class std::basic_ostream<char> &, const class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.core.chemical.quick_ring_detection(res: pyrosetta.rosetta.core.chemical.ResidueType) → None¶: C++: core::chemical::quick_ring_detection(class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.core.chemical.read_topology_file(*args, **kwargs)¶

Overloaded function.

read_topology_file(filename: str, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ResidueType

function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(const class std::basic_string<char> &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::ResidueType>

read_topology_file(istream: pyrosetta.rosetta.utility.io.izstream, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ResidueType

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(class utility::io::izstream &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::ResidueType>

read_topology_file(istream: pyrosetta.rosetta.std.istream, filename: str, rsd_type_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) -> pyrosetta.rosetta.core.chemical.ResidueType

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

C++: core::chemical::read_topology_file(class std::basic_istream<char> &, const class std::basic_string<char> &, class std::shared_ptr<const class core::chemical::ResidueTypeSet>) –> class std::shared_ptr<class core::chemical::ResidueType>

pyrosetta.rosetta.core.chemical.rename_atoms(*args, **kwargs)¶

Overloaded function.

rename_atoms(res: pyrosetta.rosetta.core.chemical.ResidueType) -> None
rename_atoms(res: pyrosetta.rosetta.core.chemical.ResidueType, preserve: bool) -> None

Rename atoms in the residue type such that their names are unique.: If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.)

C++: core::chemical::rename_atoms(class core::chemical::ResidueType &, bool) –> void

pyrosetta.rosetta.core.chemical.residue_selector_single_from_line(line: str) → pyrosetta.rosetta.core.chemical.ResidueTypeSelectorSingle¶: create a singe ResidueTypeSelector from an input line.

C++: core::chemical::residue_selector_single_from_line(const class std::basic_string<char> &) –> class std::shared_ptr<class core::chemical::ResidueTypeSelectorSingle>

pyrosetta.rosetta.core.chemical.residue_type_all_patches_name(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

helper function, returns the name of all added patches

C++: core::chemical::residue_type_all_patches_name(const class core::chemical::ResidueType &) –> std::string

pyrosetta.rosetta.core.chemical.residue_type_base_name(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType) → str¶

helper function, returns the base residue name prior to any patching

C++: core::chemical::residue_type_base_name(const class core::chemical::ResidueType &) –> std::string

pyrosetta.rosetta.core.chemical.rosetta_recharge_fullatom(res: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Apply molfile_to_params style partial charges to the ResidueType.

These partial charges are based off of the Rosetta atom type, adjusted such that the net partial charge is equal to the net formal charge.

These charges are almost certainly dodgy. If you have any other source of partial charges that are at all reasonable, you probably want to consider those instead.

Assumes:

All atoms and bond are present.

All atom types have been set.

Formal charges (if any) have been set.

C++: core::chemical::rosetta_recharge_fullatom(class core::chemical::ResidueType &) –> void

pyrosetta.rosetta.core.chemical.rosetta_retype_fullatom(*args, **kwargs)¶

Overloaded function.

rosetta_retype_fullatom(restype: pyrosetta.rosetta.core.chemical.ResidueType) -> None
rosetta_retype_fullatom(restype: pyrosetta.rosetta.core.chemical.ResidueType, preserve: bool) -> None

Reassign Rosetta atom types based on the current fullatom heuristics.

If preserve is true, only retype those atoms which have an atom_type_index of zero.

C++: core::chemical::rosetta_retype_fullatom(class core::chemical::ResidueType &, bool) –> void

pyrosetta.rosetta.core.chemical.rsd_set_from_cmd_line() → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t¶

Return a constant access pointer to the ResidueTypeSet specified by the command-line options.

C++: core::chemical::rsd_set_from_cmd_line() –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>

pyrosetta.rosetta.core.chemical.set_up_mapfile_reassignments_from_commandline(rsd: pyrosetta.rosetta.core.chemical.ResidueType) → None¶

Certain commandline flags override the default RamaPrePro maps used by the 20

canonical amino acids. This function applies those overrides.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::set_up_mapfile_reassignments_from_commandline(class std::shared_ptr<class core::chemical::ResidueType>) –> void

pyrosetta.rosetta.core.chemical.setup_atom_type_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, atom_type_reassignments: pyrosetta.rosetta.std.map_std_string_std_string) → None¶: C++: core::chemical::setup_atom_type_reassignments_from_commandline(const class std::basic_string<char> &, enum core::chemical::TypeSetMode, class std::map<class std::basic_string<char>, class std::basic_string<char>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::basic_string<char> > > > &) –> void

pyrosetta.rosetta.core.chemical.setup_atomic_charge_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, atomic_charge_reassignments: pyrosetta.rosetta.std.map_std_string_double) → None¶: C++: core::chemical::setup_atomic_charge_reassignments_from_commandline(const class std::basic_string<char> &, enum core::chemical::TypeSetMode, class std::map<class std::basic_string<char>, double, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, double> > > &) –> void

pyrosetta.rosetta.core.chemical.setup_icoor_reassignments_from_commandline(rsd_type_name: str, rsd_type_set_mode: pyrosetta.rosetta.core.chemical.TypeSetMode, icoor_reassignments: pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t) → None¶: C++: core::chemical::setup_icoor_reassignments_from_commandline(const class std::basic_string<char> &, enum core::chemical::TypeSetMode, class std::map<class std::basic_string<char>, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > > > > &) –> void

pyrosetta.rosetta.core.chemical.string_from_type_set_mode(mode: pyrosetta.rosetta.core.chemical.TypeSetMode) → str¶: C++: core::chemical::string_from_type_set_mode(enum core::chemical::TypeSetMode) –> std::string

pyrosetta.rosetta.core.chemical.tag_from_line(line: str) → str¶

handy function, return the first word from a line

C++: core::chemical::tag_from_line(const class std::basic_string<char> &) –> std::string

pyrosetta.rosetta.core.chemical.type_set_mode_from_string(*args, **kwargs)¶

Overloaded function.

type_set_mode_from_string(mode: str) -> pyrosetta.rosetta.core.chemical.TypeSetMode
type_set_mode_from_string(mode: str, fail: bool) -> pyrosetta.rosetta.core.chemical.TypeSetMode

If fail is true, utility_exit if the mode cannot be converted,: if not, return the invalid type.

C++: core::chemical::type_set_mode_from_string(const class std::basic_string<char> &, bool) –> enum core::chemical::TypeSetMode

pyrosetta.rosetta.core.chemical.unset_acceptor_ether_oxygens(atom_type_set: pyrosetta.rosetta.core.chemical.AtomTypeSet) → None¶

Rhiju. O3’, O4’, O5’ in nucleic acids are ethers – turn them off as acceptors for H-bonds.

C++: core::chemical::unset_acceptor_ether_oxygens(class core::chemical::AtomTypeSet &) –> void

pyrosetta.rosetta.core.chemical.variants_match(res1: pyrosetta.rosetta.core.chemical.ResidueType, res2: pyrosetta.rosetta.core.chemical.ResidueType) → bool¶

Are these two residues patched in exactly the same way?

C++: core::chemical::variants_match(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.chemical.variants_match_with_exceptions(res1: pyrosetta.rosetta.core.chemical.ResidueType, res2: pyrosetta.rosetta.core.chemical.ResidueType, list_of_variants_to_ignore: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) → bool¶

Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions?

C++: core::chemical::variants_match_with_exceptions(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &, class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> >) –> bool

pyrosetta.rosetta.core.chemical.write_graphviz(*args, **kwargs)¶

Overloaded function.

write_graphviz(rsd: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream) -> None
write_graphviz(rsd: pyrosetta.rosetta.core.chemical.ResidueType, out: pyrosetta.rosetta.std.ostream, header: bool) -> None

Produces a graphviz dot representation of the ResidueType to the given output stream: If header is true (the default) a line with an explanatory message will be printed first.

C++: core::chemical::write_graphviz(const class core::chemical::ResidueType &, class std::basic_ostream<char> &, bool) –> void

pyrosetta.rosetta.core.chemical.write_topology_file(*args, **kwargs)¶

Overloaded function.

write_topology_file(rsd: pyrosetta.rosetta.core.chemical.ResidueType) -> None
write_topology_file(rsd: pyrosetta.rosetta.core.chemical.ResidueType, filename: str) -> None

writes a .params file from a given ResidueType object

C++: core::chemical::write_topology_file(const class core::chemical::ResidueType &, class std::basic_string<char>) –> void