chemical¶
Bindings for core::chemical namespace
- class pyrosetta.rosetta.core.chemical.AA¶
Bases:
pybind11_object
enumeration for amino acids and nucleotides types with the total number as num_aa_types
Members:
aa_none
aa_ala
first_l_aa
aa_cys
aa_asp
aa_glu
aa_phe
aa_gly
aa_his
aa_ile
aa_lys
aa_leu
aa_met
aa_asn
aa_pro
aa_gln
aa_arg
aa_ser
aa_thr
aa_val
aa_trp
aa_tyr
num_canonical_aas
na_ade
first_DNA_aa
na_cyt
na_gua
na_thy
last_DNA_aa
na_rgu
na_rad
na_rcy
na_ura
aa_dal
first_D_aa
aa_dcs
aa_das
aa_dgu
aa_dph
aa_dhi
aa_dil
aa_dly
aa_dle
aa_dme
aa_dan
aa_dpr
aa_dgn
aa_dar
aa_dse
aa_dth
aa_dva
aa_dtr
aa_dty
last_D_aa
aa_b3a
first_beta3_aa
aa_b3c
aa_b3d
aa_b3e
aa_b3f
aa_b3g
aa_b3h
aa_b3i
aa_b3k
aa_b3l
aa_b3m
aa_b3n
aa_b3p
aa_b3q
aa_b3r
aa_b3s
aa_b3t
aa_b3v
aa_b3w
aa_b3y
aa_b3cisACPC
aa_b3transACPC
aa_b3cisACHC
last_beta3_aa
aa_b2a
first_beta2_aa
last_beta2_aa
na_lra
na_lrc
na_lrg
na_lur
ou3_ala
first_oligourea
ou3_cys
ou3_asp
ou3_glu
ou3_phe
ou3_gly
ou3_his
ou3_ile
ou3_lys
ou3_leu
ou3_met
ou3_asn
ou3_pro
ou3_gln
ou3_arg
ou3_ser
ou3_thr
ou3_val
ou3_trp
ou3_tyr
ou3_aib
last_oligourea
aa_h2o
aa_vrt
aa_unp
aa_unk
num_aa_types
- aa_ala = <AA.aa_ala: 1>¶
- aa_arg = <AA.aa_arg: 15>¶
- aa_asn = <AA.aa_asn: 12>¶
- aa_asp = <AA.aa_asp: 3>¶
- aa_b2a = <AA.aa_b2a: 71>¶
- aa_b3a = <AA.aa_b3a: 48>¶
- aa_b3c = <AA.aa_b3c: 49>¶
- aa_b3cisACHC = <AA.aa_b3cisACHC: 70>¶
- aa_b3cisACPC = <AA.aa_b3cisACPC: 68>¶
- aa_b3d = <AA.aa_b3d: 50>¶
- aa_b3e = <AA.aa_b3e: 51>¶
- aa_b3f = <AA.aa_b3f: 52>¶
- aa_b3g = <AA.aa_b3g: 53>¶
- aa_b3h = <AA.aa_b3h: 54>¶
- aa_b3i = <AA.aa_b3i: 55>¶
- aa_b3k = <AA.aa_b3k: 56>¶
- aa_b3l = <AA.aa_b3l: 57>¶
- aa_b3m = <AA.aa_b3m: 58>¶
- aa_b3n = <AA.aa_b3n: 59>¶
- aa_b3p = <AA.aa_b3p: 60>¶
- aa_b3q = <AA.aa_b3q: 61>¶
- aa_b3r = <AA.aa_b3r: 62>¶
- aa_b3s = <AA.aa_b3s: 63>¶
- aa_b3t = <AA.aa_b3t: 64>¶
- aa_b3transACPC = <AA.aa_b3transACPC: 69>¶
- aa_b3v = <AA.aa_b3v: 65>¶
- aa_b3w = <AA.aa_b3w: 66>¶
- aa_b3y = <AA.aa_b3y: 67>¶
- aa_cys = <AA.aa_cys: 2>¶
- aa_dal = <AA.aa_dal: 29>¶
- aa_dan = <AA.aa_dan: 39>¶
- aa_dar = <AA.aa_dar: 42>¶
- aa_das = <AA.aa_das: 31>¶
- aa_dcs = <AA.aa_dcs: 30>¶
- aa_dgn = <AA.aa_dgn: 41>¶
- aa_dgu = <AA.aa_dgu: 32>¶
- aa_dhi = <AA.aa_dhi: 34>¶
- aa_dil = <AA.aa_dil: 35>¶
- aa_dle = <AA.aa_dle: 37>¶
- aa_dly = <AA.aa_dly: 36>¶
- aa_dme = <AA.aa_dme: 38>¶
- aa_dph = <AA.aa_dph: 33>¶
- aa_dpr = <AA.aa_dpr: 40>¶
- aa_dse = <AA.aa_dse: 43>¶
- aa_dth = <AA.aa_dth: 44>¶
- aa_dtr = <AA.aa_dtr: 46>¶
- aa_dty = <AA.aa_dty: 47>¶
- aa_dva = <AA.aa_dva: 45>¶
- aa_gln = <AA.aa_gln: 14>¶
- aa_glu = <AA.aa_glu: 4>¶
- aa_gly = <AA.aa_gly: 6>¶
- aa_h2o = <AA.aa_h2o: 97>¶
- aa_his = <AA.aa_his: 7>¶
- aa_ile = <AA.aa_ile: 8>¶
- aa_leu = <AA.aa_leu: 10>¶
- aa_lys = <AA.aa_lys: 9>¶
- aa_met = <AA.aa_met: 11>¶
- aa_none = <AA.aa_none: 0>¶
- aa_phe = <AA.aa_phe: 5>¶
- aa_pro = <AA.aa_pro: 13>¶
- aa_ser = <AA.aa_ser: 16>¶
- aa_thr = <AA.aa_thr: 17>¶
- aa_trp = <AA.aa_trp: 19>¶
- aa_tyr = <AA.aa_tyr: 20>¶
- aa_unk = <AA.aa_unk: 100>¶
- aa_unp = <AA.aa_unp: 99>¶
- aa_val = <AA.aa_val: 18>¶
- aa_vrt = <AA.aa_vrt: 98>¶
- first_DNA_aa = <AA.na_ade: 21>¶
- first_D_aa = <AA.aa_dal: 29>¶
- first_beta2_aa = <AA.aa_b2a: 71>¶
- first_beta3_aa = <AA.aa_b3a: 48>¶
- first_l_aa = <AA.aa_ala: 1>¶
- first_oligourea = <AA.ou3_ala: 76>¶
- last_DNA_aa = <AA.na_thy: 24>¶
- last_D_aa = <AA.aa_dty: 47>¶
- last_beta2_aa = <AA.aa_b2a: 71>¶
- last_beta3_aa = <AA.aa_b3cisACHC: 70>¶
- last_oligourea = <AA.ou3_aib: 96>¶
- na_ade = <AA.na_ade: 21>¶
- na_cyt = <AA.na_cyt: 22>¶
- na_gua = <AA.na_gua: 23>¶
- na_lra = <AA.na_lra: 72>¶
- na_lrc = <AA.na_lrc: 73>¶
- na_lrg = <AA.na_lrg: 74>¶
- na_lur = <AA.na_lur: 75>¶
- na_rad = <AA.na_rad: 26>¶
- na_rcy = <AA.na_rcy: 27>¶
- na_rgu = <AA.na_rgu: 25>¶
- na_thy = <AA.na_thy: 24>¶
- na_ura = <AA.na_ura: 28>¶
- property name¶
- num_aa_types = <AA.aa_unk: 100>¶
- num_canonical_aas = <AA.aa_tyr: 20>¶
- ou3_aib = <AA.ou3_aib: 96>¶
- ou3_ala = <AA.ou3_ala: 76>¶
- ou3_arg = <AA.ou3_arg: 90>¶
- ou3_asn = <AA.ou3_asn: 87>¶
- ou3_asp = <AA.ou3_asp: 78>¶
- ou3_cys = <AA.ou3_cys: 77>¶
- ou3_gln = <AA.ou3_gln: 89>¶
- ou3_glu = <AA.ou3_glu: 79>¶
- ou3_gly = <AA.ou3_gly: 81>¶
- ou3_his = <AA.ou3_his: 82>¶
- ou3_ile = <AA.ou3_ile: 83>¶
- ou3_leu = <AA.ou3_leu: 85>¶
- ou3_lys = <AA.ou3_lys: 84>¶
- ou3_met = <AA.ou3_met: 86>¶
- ou3_phe = <AA.ou3_phe: 80>¶
- ou3_pro = <AA.ou3_pro: 88>¶
- ou3_ser = <AA.ou3_ser: 91>¶
- ou3_thr = <AA.ou3_thr: 92>¶
- ou3_trp = <AA.ou3_trp: 94>¶
- ou3_tyr = <AA.ou3_tyr: 95>¶
- ou3_val = <AA.ou3_val: 93>¶
- property value¶
- class pyrosetta.rosetta.core.chemical.APolarHydrogenFilter¶
Bases:
pybind11_object
The filter responsible for all apolar hydrogens.
- assign(self: pyrosetta.rosetta.core.chemical.APolarHydrogenFilter, : pyrosetta.rosetta.core.chemical.APolarHydrogenFilter) pyrosetta.rosetta.core.chemical.APolarHydrogenFilter ¶
C++: core::chemical::APolarHydrogenFilter::operator=(const class core::chemical::APolarHydrogenFilter &) –> class core::chemical::APolarHydrogenFilter &
- class pyrosetta.rosetta.core.chemical.AcceptorAtomFilter¶
Bases:
pybind11_object
The filter responsible for obtaining all acceptor atoms.
- assign(self: pyrosetta.rosetta.core.chemical.AcceptorAtomFilter, : pyrosetta.rosetta.core.chemical.AcceptorAtomFilter) pyrosetta.rosetta.core.chemical.AcceptorAtomFilter ¶
C++: core::chemical::AcceptorAtomFilter::operator=(const class core::chemical::AcceptorAtomFilter &) –> class core::chemical::AcceptorAtomFilter &
- class pyrosetta.rosetta.core.chemical.AddAtom¶
Bases:
PatchOperation
add an atom to ResidueType
- adds_atoms(self: pyrosetta.rosetta.core.chemical.AddAtom) pyrosetta.rosetta.utility.vector1_std_string ¶
C++: core::chemical::AddAtom::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
add an atom
C++: core::chemical::AddAtom::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddAtom, : pyrosetta.rosetta.core.chemical.AddAtom) pyrosetta.rosetta.core.chemical.AddAtom ¶
C++: core::chemical::AddAtom::operator=(const class core::chemical::AddAtom &) –> class core::chemical::AddAtom &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddAtom) str ¶
Return the name of this PatchOperation (“AddAtom”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddAtom::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddAtomAlias¶
Bases:
PatchOperation
A patch operation for adding an atom alias to a ResidueType.
See residue_io.cc for a description of atom aliases.
Atom aliases were graciously added to Rosetta by Rocco Moretti.
Labonte <JWLabonte.edu>
- adds_atoms(self: pyrosetta.rosetta.core.chemical.AddAtomAlias) pyrosetta.rosetta.utility.vector1_std_string ¶
Return a list of all atom names that this operation adds (as aliases).
All of the aliases for an atom must be offered as options to the ResidueTypeFinder.
C++: core::chemical::AddAtomAlias::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddAtomAlias, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Apply this patch to the given ResidueType.
C++: core::chemical::AddAtomAlias::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddAtomAlias, : pyrosetta.rosetta.core.chemical.AddAtomAlias) pyrosetta.rosetta.core.chemical.AddAtomAlias ¶
C++: core::chemical::AddAtomAlias::operator=(const class core::chemical::AddAtomAlias &) –> class core::chemical::AddAtomAlias &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddAtomAlias) str ¶
Return the name of this PatchOperation (“AddAtomAlias”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddAtomAlias::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddBond¶
Bases:
PatchOperation
add a bond to ResidueType
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddBond, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
add a bond
C++: core::chemical::AddBond::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddBond, : pyrosetta.rosetta.core.chemical.AddBond) pyrosetta.rosetta.core.chemical.AddBond ¶
C++: core::chemical::AddBond::operator=(const class core::chemical::AddBond &) –> class core::chemical::AddBond &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddBond) str ¶
Return the name of this PatchOperation (“AddBond”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddBond::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddBondType¶
Bases:
PatchOperation
A patch operation for adding a specific type of bond to a ResidueType.
See residue_io.cc for a description of bond types.
Labonte <JWLabonte.edu>
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddBondType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Apply this patch to the given ResidueType.
C++: core::chemical::AddBondType::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddBondType, : pyrosetta.rosetta.core.chemical.AddBondType) pyrosetta.rosetta.core.chemical.AddBondType ¶
C++: core::chemical::AddBondType::operator=(const class core::chemical::AddBondType &) –> class core::chemical::AddBondType &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddBondType) str ¶
Return the name of this PatchOperation (“AddBondType”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddBondType::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddChi¶
Bases:
PatchOperation
Add a chi angle to ResidueType.
Added by Andy M. Chen in June 2009
This is needed for PTMs, which often result in one or more extra chi angles.
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Add a chi angle.
C++: core::chemical::AddChi::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddChi, : pyrosetta.rosetta.core.chemical.AddChi) pyrosetta.rosetta.core.chemical.AddChi ¶
C++: core::chemical::AddChi::operator=(const class core::chemical::AddChi &) –> class core::chemical::AddChi &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddChi) str ¶
Return the name of this PatchOperation (“AddChi”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddChi::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddChiRotamer¶
Bases:
PatchOperation
Add a rotamer sample to a chi angle of the ResidueType.
Added by Andy M. Chen in June 2009
This is needed for PTMs.
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddChiRotamer, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Add a rotamer sample.
C++: core::chemical::AddChiRotamer::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddChiRotamer, : pyrosetta.rosetta.core.chemical.AddChiRotamer) pyrosetta.rosetta.core.chemical.AddChiRotamer ¶
C++: core::chemical::AddChiRotamer::operator=(const class core::chemical::AddChiRotamer &) –> class core::chemical::AddChiRotamer &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddChiRotamer) str ¶
Return the name of this PatchOperation (“AddChiRotamer”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddChiRotamer::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddConnect¶
Bases:
PatchOperation
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddConnect, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
add a property
C++: core::chemical::AddConnect::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddConnect, : pyrosetta.rosetta.core.chemical.AddConnect) pyrosetta.rosetta.core.chemical.AddConnect ¶
C++: core::chemical::AddConnect::operator=(const class core::chemical::AddConnect &) –> class core::chemical::AddConnect &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnect, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) bool ¶
C++: core::chemical::AddConnect::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddConnect) str ¶
Return the name of this PatchOperation (“AddConnect”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddConnect::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt¶
Bases:
PatchOperation
add a connect and tracking virt to the atom
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::AddConnectAndTrackingVirt::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, : pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt) pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt ¶
C++: core::chemical::AddConnectAndTrackingVirt::operator=(const class core::chemical::AddConnectAndTrackingVirt &) –> class core::chemical::AddConnectAndTrackingVirt &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) bool ¶
C++: core::chemical::AddConnectAndTrackingVirt::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt) str ¶
Return the name of this PatchOperation (“AddConnectAndTrackingVirt”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddConnectAndTrackingVirt::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton¶
Bases:
PatchOperation
add a connect to the atom, delete child proton
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::AddConnectDeleteChildProton::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, : pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton) pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton ¶
C++: core::chemical::AddConnectDeleteChildProton::operator=(const class core::chemical::AddConnectDeleteChildProton &) –> class core::chemical::AddConnectDeleteChildProton &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) bool ¶
C++: core::chemical::AddConnectDeleteChildProton::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton) str ¶
Return the name of this PatchOperation (“AddConnectDeleteChildProton”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddConnectDeleteChildProton::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddProperty¶
Bases:
PatchOperation
add a property to ResidueType
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.AddProperty) str ¶
Which property, if any, is added.
C++: core::chemical::AddProperty::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.AddProperty) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::AddProperty::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddProperty, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
add a property
C++: core::chemical::AddProperty::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddProperty, : pyrosetta.rosetta.core.chemical.AddProperty) pyrosetta.rosetta.core.chemical.AddProperty ¶
C++: core::chemical::AddProperty::operator=(const class core::chemical::AddProperty &) –> class core::chemical::AddProperty &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddProperty) str ¶
Return the name of this PatchOperation (“AddProperty”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddProperty::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AddProtonChi¶
Bases:
PatchOperation
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AddProtonChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
add a proton chi angle
C++: core::chemical::AddProtonChi::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AddProtonChi, : pyrosetta.rosetta.core.chemical.AddProtonChi) pyrosetta.rosetta.core.chemical.AddProtonChi ¶
C++: core::chemical::AddProtonChi::operator=(const class core::chemical::AddProtonChi &) –> class core::chemical::AddProtonChi &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AddProtonChi) str ¶
Return the name of this PatchOperation (“AddProtonChi”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AddProtonChi::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.Adduct¶
Bases:
pybind11_object
Description of optional single-atom residue adducts
- adduct_name(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to adduct_name string
C++: core::chemical::Adduct::adduct_name() const –> const std::string &
- assign(self: pyrosetta.rosetta.core.chemical.Adduct, : pyrosetta.rosetta.core.chemical.Adduct) pyrosetta.rosetta.core.chemical.Adduct ¶
C++: core::chemical::Adduct::operator=(const class core::chemical::Adduct &) –> class core::chemical::Adduct &
- atom_charge(self: pyrosetta.rosetta.core.chemical.Adduct) float ¶
C++: core::chemical::Adduct::atom_charge() const –> double
- atom_name(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to atom_name string
C++: core::chemical::Adduct::atom_name() const –> const std::string &
- atom_type_name(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to atom type string
C++: core::chemical::Adduct::atom_type_name() const –> const std::string &
- d(self: pyrosetta.rosetta.core.chemical.Adduct) float ¶
C++: core::chemical::Adduct::d() const –> double
- mm_atom_type_name(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to mm type string
C++: core::chemical::Adduct::mm_atom_type_name() const –> const std::string &
- phi(self: pyrosetta.rosetta.core.chemical.Adduct) float ¶
accessor for Adduct geometric info
C++: core::chemical::Adduct::phi() const –> double
- stub_atom(self: pyrosetta.rosetta.core.chemical.Adduct, atm: int) str ¶
const accessor to stub_atom strings by index
C++: core::chemical::Adduct::stub_atom(const int) const –> const std::string &
- stub_atom1(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to stub_atom1 name string
C++: core::chemical::Adduct::stub_atom1() const –> const std::string &
- stub_atom2(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to stub_atom2 name string
C++: core::chemical::Adduct::stub_atom2() const –> const std::string &
- stub_atom3(self: pyrosetta.rosetta.core.chemical.Adduct) str ¶
accessor to stub_atom3 name string
C++: core::chemical::Adduct::stub_atom3() const –> const std::string &
- theta(self: pyrosetta.rosetta.core.chemical.Adduct) float ¶
C++: core::chemical::Adduct::theta() const –> double
- class pyrosetta.rosetta.core.chemical.Ancestor¶
Bases:
pybind11_object
Change the parent, grandparent, or great-grandparent of an atom
Members:
anc_parent
anc_grandparent
anc_greatgrandparent
- anc_grandparent = <Ancestor.anc_grandparent: 1>¶
- anc_greatgrandparent = <Ancestor.anc_greatgrandparent: 2>¶
- anc_parent = <Ancestor.anc_parent: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.AppendMainchainAtom¶
Bases:
PatchOperation
add a mainchain atom after the last mainchain atom
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
set an atom to be the last mainchain atom
C++: core::chemical::AppendMainchainAtom::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom, : pyrosetta.rosetta.core.chemical.AppendMainchainAtom) pyrosetta.rosetta.core.chemical.AppendMainchainAtom ¶
C++: core::chemical::AppendMainchainAtom::operator=(const class core::chemical::AppendMainchainAtom &) –> class core::chemical::AppendMainchainAtom &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.AppendMainchainAtom) str ¶
Return the name of this PatchOperation (“AppendMainchainAtom”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AppendMainchainAtom::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.AromaticAtomFilter¶
Bases:
pybind11_object
The filter responsible for all aromatic atoms.
- assign(self: pyrosetta.rosetta.core.chemical.AromaticAtomFilter, : pyrosetta.rosetta.core.chemical.AromaticAtomFilter) pyrosetta.rosetta.core.chemical.AromaticAtomFilter ¶
C++: core::chemical::AromaticAtomFilter::operator=(const class core::chemical::AromaticAtomFilter &) –> class core::chemical::AromaticAtomFilter &
- class pyrosetta.rosetta.core.chemical.Atom¶
Bases:
pybind11_object
This class contains the “chemical” information for atoms in a MutableResidueType. This does not contain the actual xyz coordinates of the atom, (which are found in core/conformation/Atom.hh) It is also not used for the plain ResidueType class, which holds the corresponding information intenrally. This class should contain the information that’s associated with the atom, calculated from other info. (Do that in the MutableResidueType -> ResidueType transition. )
chemical::Atoms are stored in chemical::MutableResidueType (within its ResidueGraph);
conformation::Atoms are stored in conformation::Residue
- absolute_stereochemistry(self: pyrosetta.rosetta.core.chemical.Atom) str ¶
Return the absolute stereochemistry (R/S designation) of this stereocenter.
C++: core::chemical::Atom::absolute_stereochemistry() const –> char
- add_bonded_orbital(self: pyrosetta.rosetta.core.chemical.Atom, orbital_index: int) None ¶
C++: core::chemical::Atom::add_bonded_orbital(unsigned long) –> void
- assign(self: pyrosetta.rosetta.core.chemical.Atom, : pyrosetta.rosetta.core.chemical.Atom) pyrosetta.rosetta.core.chemical.Atom ¶
C++: core::chemical::Atom::operator=(const class core::chemical::Atom &) –> class core::chemical::Atom &
- atom_type_index(self: pyrosetta.rosetta.core.chemical.Atom) int ¶
C++: core::chemical::Atom::atom_type_index() const –> const unsigned long &
- bonded_orbitals(self: pyrosetta.rosetta.core.chemical.Atom) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
Which orbital indicies are attached to this atom?
C++: core::chemical::Atom::bonded_orbitals() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &
- charge(*args, **kwargs)¶
Overloaded function.
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) -> 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: 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_property(*args, **kwargs)¶
Overloaded function.
has_property(self: pyrosetta.rosetta.core.chemical.Atom, property: str) -> bool
- Generic property access.
IMPORTANT – This only looks at manually set properties, not any automatically derived ones.
C++: core::chemical::Atom::has_property(const std::string &) const –> bool
has_property(self: pyrosetta.rosetta.core.chemical.Atom, property: pyrosetta.rosetta.core.chemical.AtomProperty) -> bool
- Generic property access.
IMPORTANT – This only looks at manually set properties, not any automatically derived ones.
C++: core::chemical::Atom::has_property(const enum core::chemical::AtomProperty) const –> bool
- icoor(*args, **kwargs)¶
Overloaded function.
icoor(self: pyrosetta.rosetta.core.chemical.Atom) -> core::chemical::MutableICoorRecord
The ICoor record for this residue – may be null.
C++: core::chemical::Atom::icoor() const –> class std::shared_ptr<const class core::chemical::MutableICoorRecord>
icoor(self: pyrosetta.rosetta.core.chemical.Atom, icoor_record: core::chemical::MutableICoorRecord) -> None
C++: core::chemical::Atom::icoor(class std::shared_ptr<const class core::chemical::MutableICoorRecord>) –> void
- ideal_xyz(*args, **kwargs)¶
Overloaded function.
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_actcoord(*args, **kwargs)¶
Overloaded function.
is_actcoord(self: pyrosetta.rosetta.core.chemical.Atom) -> bool
Is this atom part of the action coordinate centers?
The geometric center of all atoms listed as actcoords are the residue’s “action coordinate” (for pair energy)
C++: core::chemical::Atom::is_actcoord() const –> const bool &
is_actcoord(self: pyrosetta.rosetta.core.chemical.Atom, setting: bool) -> None
C++: core::chemical::Atom::is_actcoord(bool) –> void
- is_backbone(*args, **kwargs)¶
Overloaded function.
is_backbone(self: pyrosetta.rosetta.core.chemical.Atom) -> bool
C++: core::chemical::Atom::is_backbone() const –> const bool &
is_backbone(self: pyrosetta.rosetta.core.chemical.Atom, setting: bool) -> None
C++: core::chemical::Atom::is_backbone(bool) –> void
- is_fake(self: pyrosetta.rosetta.core.chemical.Atom) bool ¶
Return true if this represents a fake/mock atom.
C++: core::chemical::Atom::is_fake() const –> bool
- is_hydrogen(self: pyrosetta.rosetta.core.chemical.Atom) bool ¶
C++: core::chemical::Atom::is_hydrogen() const –> bool
- is_virtual(*args, **kwargs)¶
Overloaded function.
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
is_virtual(self: pyrosetta.rosetta.core.chemical.Atom) -> bool
Get whether or not this atom is virtual.
C++: core::chemical::Atom::is_virtual() const –> bool
- mm_name(*args, **kwargs)¶
Overloaded function.
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 std::string &) –> void
- name(self: pyrosetta.rosetta.core.chemical.Atom) str ¶
C++: core::chemical::Atom::name() const –> const std::string &
- properties(self: pyrosetta.rosetta.core.chemical.Atom) core::chemical::AtomProperties ¶
- Access the collection of properties for this Atom.
IMPORTANT – This only looks at manually set properties, not any automatically derived ones.
C++: core::chemical::Atom::properties() const –> const class core::chemical::AtomProperties &
- reset_all_properies(self: pyrosetta.rosetta.core.chemical.Atom, setting: core::chemical::AtomProperties) None ¶
Discard all the current properties, and set the the passed values.
C++: core::chemical::Atom::reset_all_properies(const class core::chemical::AtomProperties &) –> void
- set_absolute_stereochemistry(self: pyrosetta.rosetta.core.chemical.Atom, setting: str) None ¶
Set the absolute stereochemistry (R/S designation) of this stereocenter.
C++: core::chemical::Atom::set_absolute_stereochemistry(const char) –> void
- set_bonded_orbitals(self: pyrosetta.rosetta.core.chemical.Atom, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
C++: core::chemical::Atom::set_bonded_orbitals(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void
- set_property(*args, **kwargs)¶
Overloaded function.
set_property(self: pyrosetta.rosetta.core.chemical.Atom, property: str, setting: bool) -> None
C++: core::chemical::Atom::set_property(const std::string &, const bool) –> void
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, out: pyrosetta.rosetta.std.ostream) -> None
Generate string representation of chemical::Atom for debugging purposes.
C++: core::chemical::Atom::show(std::ostream &) const –> void
show(self: pyrosetta.rosetta.core.chemical.Atom) -> None
Generate string representation of chemical::Atom to std::cout for debugging purposes.
C++: core::chemical::Atom::show() const –> void
- class pyrosetta.rosetta.core.chemical.AtomICoor¶
Bases:
pybind11_object
A basic class containing info of internal coordinates needed for building an atom within a ResidueType
In atom tree, each atom is defined by its internal coordinates, which include a bond distance, a bond angle and a torsion angle. Of course, all these internal coordinates are only meaningful in the context of three reference (stub) atoms. AtomICoor information is stored in the residue param files and some terms are defined as following: - bond distance d_ is that between the atom to be built (child) and stub_atom1 (parent) - bond angle theta_ is that defined by child-parent-stub2(angle) - torsion angle phi_ is that defined by child-parent-stub2-stub3(torsion)
- assign(self: pyrosetta.rosetta.core.chemical.AtomICoor, : pyrosetta.rosetta.core.chemical.AtomICoor) pyrosetta.rosetta.core.chemical.AtomICoor ¶
C++: core::chemical::AtomICoor::operator=(const class core::chemical::AtomICoor &) –> class core::chemical::AtomICoor &
- build(*args, **kwargs)¶
Overloaded function.
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(self: pyrosetta.rosetta.core.chemical.AtomICoor) str ¶
The name of the atom being built by this icoor
C++: core::chemical::AtomICoor::built_atom() const –> const std::string &
- d(self: pyrosetta.rosetta.core.chemical.AtomICoor) float ¶
C++: core::chemical::AtomICoor::d() const –> double
- depends_on_a_true_index(self: pyrosetta.rosetta.core.chemical.AtomICoor, atomvect: pyrosetta.rosetta.utility.vector1_bool) bool ¶
- Given a Boolean vector corresponding to atom indices, determine whether any of the stub
indices depends on one of the atoms that are “true”.
Called by ResidueType::update_polymer_dependent_groups() when figuring out which atoms depend on atoms that depend on a connection.
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::AtomICoor::depends_on_a_true_index(const class utility::vector1<bool, class std::allocator<bool> > &) const –> bool
- depends_on_polymer_lower(self: pyrosetta.rosetta.core.chemical.AtomICoor) bool ¶
Is this icoor immediately dependent on LOWER?
Returns true if stub atom 1, 2, or 3 is LOWER.
C++: core::chemical::AtomICoor::depends_on_polymer_lower() const –> bool
- depends_on_polymer_upper(self: pyrosetta.rosetta.core.chemical.AtomICoor) bool ¶
Is this icoor immediately dependent on UPPER?
Returns true if stub atom 1, 2, or 3 is UPPER.
C++: core::chemical::AtomICoor::depends_on_polymer_upper() const –> bool
- depends_on_residue_connection(*args, **kwargs)¶
Overloaded function.
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
- show(self: pyrosetta.rosetta.core.chemical.AtomICoor, : pyrosetta.rosetta.std.ostream) None ¶
C++: core::chemical::AtomICoor::show(std::ostream &) const –> void
- stub_atom(self: pyrosetta.rosetta.core.chemical.AtomICoor, atm: int) pyrosetta.rosetta.core.chemical.ICoorAtomID ¶
accessor to stub_atom ICoorAtomID
C++: core::chemical::AtomICoor::stub_atom(const int) –> class core::chemical::ICoorAtomID &
- stub_atom1(self: pyrosetta.rosetta.core.chemical.AtomICoor) pyrosetta.rosetta.core.chemical.ICoorAtomID ¶
C++: core::chemical::AtomICoor::stub_atom1() const –> const class core::chemical::ICoorAtomID &
- stub_atom2(self: pyrosetta.rosetta.core.chemical.AtomICoor) pyrosetta.rosetta.core.chemical.ICoorAtomID ¶
accessor to stub_atom2 ICoorAtomID
C++: core::chemical::AtomICoor::stub_atom2() const –> const class core::chemical::ICoorAtomID &
- stub_atom3(self: pyrosetta.rosetta.core.chemical.AtomICoor) pyrosetta.rosetta.core.chemical.ICoorAtomID ¶
accessor to stub_atom3 ICoorAtomID
C++: core::chemical::AtomICoor::stub_atom3() const –> const class core::chemical::ICoorAtomID &
- theta(self: pyrosetta.rosetta.core.chemical.AtomICoor) float ¶
C++: core::chemical::AtomICoor::theta() const –> double
- class pyrosetta.rosetta.core.chemical.AtomProperties¶
Bases:
pybind11_object
This is a container class for storing properties specific to a ResidueType’s atoms. These properties belong to a particular ResidueType’s Atoms; they do not belong to an AtomType. chemical::Atoms store both AtomTypes and AtomProperties.
- assign(self: pyrosetta.rosetta.core.chemical.AtomProperties, object_to_copy: pyrosetta.rosetta.core.chemical.AtomProperties) pyrosetta.rosetta.core.chemical.AtomProperties ¶
C++: core::chemical::AtomProperties::operator=(const class core::chemical::AtomProperties &) –> class core::chemical::AtomProperties &
- get_list_of_properties(self: pyrosetta.rosetta.core.chemical.AtomProperties) pyrosetta.rosetta.utility.vector1_std_string ¶
Generate and return a list of strings representing the properties of this Atom.
C++: core::chemical::AtomProperties::get_list_of_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- has_property(*args, **kwargs)¶
Overloaded function.
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 std::string &) 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 std::string &, 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(std::ostream &) const –> void
- class pyrosetta.rosetta.core.chemical.AtomPropertiesManager¶
Bases:
SingletonBase_core_chemical_AtomPropertiesManager_t
This class is a singleton and manages AtomProperties enum mappings.
- static get_instance() core::chemical::AtomPropertiesManager ¶
C++: utility::SingletonBase<core::chemical::AtomPropertiesManager>::get_instance() –> class core::chemical::AtomPropertiesManager *
- static property_from_string(property: str) pyrosetta.rosetta.core.chemical.AtomProperty ¶
C++: core::chemical::AtomPropertiesManager::property_from_string(const std::string &) –> const enum core::chemical::AtomProperty &
- static string_from_property(property: pyrosetta.rosetta.core.chemical.AtomProperty) str ¶
C++: core::chemical::AtomPropertiesManager::string_from_property(const enum core::chemical::AtomProperty) –> const std::string &
- class pyrosetta.rosetta.core.chemical.AtomProperty¶
Bases:
pybind11_object
Enumerators for all the properties that can be assigned to a chemical::Atom.
Members:
NO_ATOM_PROPERTY
FIRST_ATOM_PROPERTY
H_DONOR
H_ACCEPTOR
POLAR_HYDROGEN
AROMATIC_HYDROGEN
HAS_ORBITALS
VIRTUAL_ATOM
REPULSIVE
AROMATIC_CARBON_WITH_FREE_VALENCE
N_ATOM_PROPERTIES
- AROMATIC_CARBON_WITH_FREE_VALENCE = <AtomProperty.AROMATIC_CARBON_WITH_FREE_VALENCE: 9>¶
- AROMATIC_HYDROGEN = <AtomProperty.AROMATIC_HYDROGEN: 5>¶
- FIRST_ATOM_PROPERTY = <AtomProperty.FIRST_ATOM_PROPERTY: 1>¶
- HAS_ORBITALS = <AtomProperty.HAS_ORBITALS: 6>¶
- H_ACCEPTOR = <AtomProperty.H_ACCEPTOR: 3>¶
- H_DONOR = <AtomProperty.H_DONOR: 2>¶
- NO_ATOM_PROPERTY = <AtomProperty.NO_ATOM_PROPERTY: 0>¶
- N_ATOM_PROPERTIES = <AtomProperty.AROMATIC_CARBON_WITH_FREE_VALENCE: 9>¶
- POLAR_HYDROGEN = <AtomProperty.POLAR_HYDROGEN: 4>¶
- REPULSIVE = <AtomProperty.REPULSIVE: 8>¶
- VIRTUAL_ATOM = <AtomProperty.VIRTUAL_ATOM: 7>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::operator=(const class core::chemical::AtomRefMapping<unsigned long, void *> &) –> class core::chemical::AtomRefMapping<unsigned long, void *> &
- clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) None ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::clear() –> void
- count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, key: int) bool ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::count(const unsigned long &) const –> bool
- empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) bool ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::empty() const –> bool
- erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, in: int) None ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::erase(const unsigned long &) –> void
- identity(*args, **kwargs)¶
Overloaded function.
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, setting: bool) -> None
C++: core::chemical::AtomRefMapping<unsigned long, void *>::identity(bool) –> void
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) -> bool
C++: core::chemical::AtomRefMapping<unsigned long, void *>::identity() const –> bool
- invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) capsule ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalid_entry() const –> void *const &
- invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) int ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalid_key() const –> const unsigned long &
- invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, in: int) None ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::invalidate(const unsigned long &) –> void
- reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t) pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::reverse() const –> class core::chemical::AtomRefMapping<void *, unsigned long>
- reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, out: capsule) int ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::reverse_lookup(void *const &) const –> const unsigned long &
- show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_unsigned_long_void__star__t, output: pyrosetta.rosetta.std.ostream) None ¶
C++: core::chemical::AtomRefMapping<unsigned long, void *>::show(std::ostream &) const –> void
- class pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::operator=(const class core::chemical::AtomRefMapping<void *, unsigned long> &) –> class core::chemical::AtomRefMapping<void *, unsigned long> &
- clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) None ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::clear() –> void
- count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, key: capsule) bool ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::count(void *const &) const –> bool
- empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) bool ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::empty() const –> bool
- erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, in: capsule) None ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::erase(void *const &) –> void
- identity(*args, **kwargs)¶
Overloaded function.
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, setting: bool) -> None
C++: core::chemical::AtomRefMapping<void *, unsigned long>::identity(bool) –> void
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) -> bool
C++: core::chemical::AtomRefMapping<void *, unsigned long>::identity() const –> bool
- invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) int ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalid_entry() const –> const unsigned long &
- invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) capsule ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalid_key() const –> void *const &
- invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, in: capsule) None ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::invalidate(void *const &) –> void
- reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t) core::chemical::AtomRefMapping<unsigned long, void*> ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::reverse() const –> class core::chemical::AtomRefMapping<unsigned long, void *>
- reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, out: int) capsule ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::reverse_lookup(const unsigned long &) const –> void *const &
- show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__unsigned_long_t, output: pyrosetta.rosetta.std.ostream) None ¶
C++: core::chemical::AtomRefMapping<void *, unsigned long>::show(std::ostream &) const –> void
- class pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, : pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t ¶
C++: core::chemical::AtomRefMapping<void *, void *>::operator=(const class core::chemical::AtomRefMapping<void *, void *> &) –> class core::chemical::AtomRefMapping<void *, void *> &
- clear(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) None ¶
C++: core::chemical::AtomRefMapping<void *, void *>::clear() –> void
- count(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, key: capsule) bool ¶
C++: core::chemical::AtomRefMapping<void *, void *>::count(void *const &) const –> bool
- empty(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) bool ¶
C++: core::chemical::AtomRefMapping<void *, void *>::empty() const –> bool
- erase(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, in: capsule) None ¶
C++: core::chemical::AtomRefMapping<void *, void *>::erase(void *const &) –> void
- identity(*args, **kwargs)¶
Overloaded function.
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, setting: bool) -> None
C++: core::chemical::AtomRefMapping<void *, void *>::identity(bool) –> void
identity(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) -> bool
C++: core::chemical::AtomRefMapping<void *, void *>::identity() const –> bool
- invalid_entry(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) capsule ¶
C++: core::chemical::AtomRefMapping<void *, void *>::invalid_entry() const –> void *const &
- invalid_key(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) capsule ¶
C++: core::chemical::AtomRefMapping<void *, void *>::invalid_key() const –> void *const &
- invalidate(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, in: capsule) None ¶
C++: core::chemical::AtomRefMapping<void *, void *>::invalidate(void *const &) –> void
- reverse(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t) pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t ¶
C++: core::chemical::AtomRefMapping<void *, void *>::reverse() const –> class core::chemical::AtomRefMapping<void *, void *>
- reverse_lookup(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, out: capsule) capsule ¶
C++: core::chemical::AtomRefMapping<void *, void *>::reverse_lookup(void *const &) const –> void *const &
- show(self: pyrosetta.rosetta.core.chemical.AtomRefMapping_void__star__void__star__t, output: pyrosetta.rosetta.std.ostream) None ¶
C++: core::chemical::AtomRefMapping<void *, void *>::show(std::ostream &) const –> void
- class pyrosetta.rosetta.core.chemical.AtomType¶
Bases:
pybind11_object
basic atom type
name, element, certain properties and parameters
- add_property(self: pyrosetta.rosetta.core.chemical.AtomType, property: str) None ¶
set standard property to true, or set the specified hybridization
C++: core::chemical::AtomType::add_property(const std::string &) –> void
- assign(self: pyrosetta.rosetta.core.chemical.AtomType, : pyrosetta.rosetta.core.chemical.AtomType) pyrosetta.rosetta.core.chemical.AtomType ¶
C++: core::chemical::AtomType::operator=(const class core::chemical::AtomType &) –> class core::chemical::AtomType &
- atom_has_orbital(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
atom has an orbital attached
C++: core::chemical::AtomType::atom_has_orbital() const –> bool
- atom_type_name(self: pyrosetta.rosetta.core.chemical.AtomType) str ¶
- Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB.
You want pose.residue(i).atom_name(j) for that.
C++: core::chemical::AtomType::atom_type_name() const –> std::string
- clear_properties(self: pyrosetta.rosetta.core.chemical.AtomType) None ¶
set all standard properties to false, set hybridization to UNKNOWN_HYBRID, and clear extra properties
C++: core::chemical::AtomType::clear_properties() –> void
- element(self: pyrosetta.rosetta.core.chemical.AtomType) str ¶
returns the one- or two-letter element type
C++: core::chemical::AtomType::element() const –> std::string
- extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, index: int) float ¶
return an additional, non-hardcoded property
C++: core::chemical::AtomType::extra_parameter(const unsigned long) const –> double
- get_all_properties(self: pyrosetta.rosetta.core.chemical.AtomType) pyrosetta.rosetta.utility.vector1_std_string ¶
C++: core::chemical::AtomType::get_all_properties() const –> class utility::vector1<std::string, class std::allocator<std::string > >
- hybridization(self: pyrosetta.rosetta.core.chemical.AtomType) pyrosetta.rosetta.core.chemical.Hybridization ¶
retrieve an atom’s hybridization status.
C++: core::chemical::AtomType::hybridization() const –> const enum core::chemical::Hybridization &
- is_acceptor(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a hydrogen bond acceptor
C++: core::chemical::AtomType::is_acceptor() const –> bool
- is_aromatic(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is aromatic
C++: core::chemical::AtomType::is_aromatic() const –> bool
- is_donor(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a hydrogen bond donor
C++: core::chemical::AtomType::is_donor() const –> bool
- is_h2o(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a water
C++: core::chemical::AtomType::is_h2o() const –> bool
- is_haro(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
is the H atom aromatic?
C++: core::chemical::AtomType::is_haro() const –> bool
- is_heavyatom(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a heavy atom
C++: core::chemical::AtomType::is_heavyatom() const –> bool
- is_hydrogen(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a hydrogen atom
C++: core::chemical::AtomType::is_hydrogen() const –> bool
- is_polar_hydrogen(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
whether atom is a polar hydrogen atom
C++: core::chemical::AtomType::is_polar_hydrogen() const –> bool
- is_repulsive(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
is atom type repulsive (REPL, REPLS, HREPS)
C++: core::chemical::AtomType::is_repulsive() const –> bool
- is_virtual(self: pyrosetta.rosetta.core.chemical.AtomType) bool ¶
is atom type virtual?
C++: core::chemical::AtomType::is_virtual() const –> bool
- lj_radius(self: pyrosetta.rosetta.core.chemical.AtomType) float ¶
Lennard-Jones 6-12 potential parameter – atom radius
There are two functionally identical versions of the Lennard-Jones potential:
- E ~ 4eps(sigma1/d)^12 - (sigma1/d)^6 and
and
E ~ eps(sigma2/d)^12 - 2*(sigma2/d)^6
where sigma1 and sigma2 represent two different interpretations of the radius. eps represents the depth of the potential well. Sigma1 represents the distance between the two atoms where the Lennard-Jones energy is 0, i.e. where a collision is just forming/resolving. Sigma2 represents the distance between the two atoms where the derivative of the Lennard-Jones energy is 0, i.e. the minimum of the well depth.
- In rosetta, we mean sigma2 when we talk about radii, but PyMOL usually sets the radii to sigma1.
If you see two atoms overlapping using the Rosetta radii, they’re not necessarily in collision. They are just not at their minimum value.
The distances are related as sigma2 = 2^(1.0/6)*sigma1; sigma2 ~= 1.22*sigma1
C++: core::chemical::AtomType::lj_radius() const –> double
- lj_wdepth(self: pyrosetta.rosetta.core.chemical.AtomType) float ¶
Lennard-Jones 6-12 potential parameter – well depth
C++: core::chemical::AtomType::lj_wdepth() const –> double
- lk_dgfree(self: pyrosetta.rosetta.core.chemical.AtomType) float ¶
Lazaridis and Karplus solvation parameter – dgfree
C++: core::chemical::AtomType::lk_dgfree() const –> double
- lk_lambda(self: pyrosetta.rosetta.core.chemical.AtomType) float ¶
Lazaridis and Karplus solvation parameter – lambda
C++: core::chemical::AtomType::lk_lambda() const –> double
- lk_volume(self: pyrosetta.rosetta.core.chemical.AtomType) float ¶
Lazaridis and Karplus solvation parameter – volume
C++: core::chemical::AtomType::lk_volume() const –> double
- name(*args, **kwargs)¶
Overloaded function.
name(self: pyrosetta.rosetta.core.chemical.AtomType, setting: str) -> None
C++: core::chemical::AtomType::name(const std::string &) –> void
name(self: pyrosetta.rosetta.core.chemical.AtomType) -> str
- Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB.
You want pose.residue(i).atom_name(j) for that.
C++: core::chemical::AtomType::name() const –> const std::string &
- print(self: pyrosetta.rosetta.core.chemical.AtomType, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::chemical::AtomType::print(std::ostream &) const –> void
- set_all_extra_parameters(self: pyrosetta.rosetta.core.chemical.AtomType, extra_parameters: pyrosetta.rosetta.utility.vector1_double) None ¶
all the extra parameters at once
C++: core::chemical::AtomType::set_all_extra_parameters(const class utility::vector1<double, class std::allocator<double> > &) –> void
- set_extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, index: int, setting: float) None ¶
return an additional, non-hardcoded property
C++: core::chemical::AtomType::set_extra_parameter(const unsigned long, const double) –> void
- set_parameter(self: pyrosetta.rosetta.core.chemical.AtomType, param: str, setting: float) None ¶
set LJ and LK solvation parameter for this atom type
C++: core::chemical::AtomType::set_parameter(const std::string &, const double) –> void
- set_property(self: pyrosetta.rosetta.core.chemical.AtomType, property: str, setting: bool) None ¶
set relevant properties for this atom type hh
C++: core::chemical::AtomType::set_property(const std::string &, const bool) –> void
- class pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, : pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO) pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO ¶
C++: core::chemical::AtomTypeDatabaseIO::operator=(const class core::chemical::AtomTypeDatabaseIO &) –> class core::chemical::AtomTypeDatabaseIO &
- get_all_atom_types_in_database(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) pyrosetta.rosetta.utility.vector1_std_string ¶
C++: core::chemical::AtomTypeDatabaseIO::get_all_atom_types_in_database(class std::shared_ptr<class utility::sql_database::session>) const –> class utility::vector1<std::string, class std::allocator<std::string > >
- initialize(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) None ¶
write the schema
C++: core::chemical::AtomTypeDatabaseIO::initialize(class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_atom_type_set_to_database(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, atom_type_set: core::chemical::AtomTypeSet, db_session: utility::sql_database::session) None ¶
C++: core::chemical::AtomTypeDatabaseIO::write_atom_type_set_to_database(const class core::chemical::AtomTypeSet &, class std::shared_ptr<class utility::sql_database::session>) const –> void
- write_schema_to_db(self: pyrosetta.rosetta.core.chemical.AtomTypeDatabaseIO, db_session: utility::sql_database::session) None ¶
generate the table schemas and write them to the database
C++: core::chemical::AtomTypeDatabaseIO::write_schema_to_db(class std::shared_ptr<class utility::sql_database::session>) const –> void
- class pyrosetta.rosetta.core.chemical.AtomTypeSet¶
Bases:
pybind11_object
a set of AtomTypes
a vector of pointers each of which points to an AtomType and the vector index is looked up by an atom_name string in a map
- add_parameters_from_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) None ¶
additional file I/O
C++: core::chemical::AtomTypeSet::add_parameters_from_file(const std::string &) –> void
- assign(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, : pyrosetta.rosetta.core.chemical.AtomTypeSet) pyrosetta.rosetta.core.chemical.AtomTypeSet ¶
C++: core::chemical::AtomTypeSet::operator=(const class core::chemical::AtomTypeSet &) –> class core::chemical::AtomTypeSet &
- atom_type_index(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, atom_type_name: str) int ¶
lookup the atom_type by the atom_type_name string
C++: core::chemical::AtomTypeSet::atom_type_index(const std::string &) const –> int
- directory(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) str ¶
Get the source directory, eg to open an additional file in that directory
C++: core::chemical::AtomTypeSet::directory() const –> const std::string &
- extra_parameter_index(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, name: str) int ¶
SLOW
C++: core::chemical::AtomTypeSet::extra_parameter_index(const std::string &) const –> int
- extra_parameter_indices(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) pyrosetta.rosetta.std.map_std_string_int ¶
C++: core::chemical::AtomTypeSet::extra_parameter_indices() const –> const class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > > &
- has_atom(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, atom_type_name: str) bool ¶
Check if atom is present
C++: core::chemical::AtomTypeSet::has_atom(const std::string &) const –> bool
- has_extra_parameter(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, name: str) bool ¶
C++: core::chemical::AtomTypeSet::has_extra_parameter(const std::string &) const –> bool
- mode(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) pyrosetta.rosetta.core.chemical.TypeSetMode ¶
The mode of the AtomTypeSet
C++: core::chemical::AtomTypeSet::mode() const –> enum core::chemical::TypeSetMode
- n_atomtypes(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) int ¶
number of atom types in the set
C++: core::chemical::AtomTypeSet::n_atomtypes() const –> unsigned long
- name(self: pyrosetta.rosetta.core.chemical.AtomTypeSet) str ¶
the name of the AtomTypeSet
C++: core::chemical::AtomTypeSet::name() const –> std::string
- read_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) None ¶
file I/O
C++: core::chemical::AtomTypeSet::read_file(const std::string &) –> void
- read_meta_file(self: pyrosetta.rosetta.core.chemical.AtomTypeSet, filename: str) None ¶
- Read in meta information from the given file
Meta information is info about the AtomTypeSet as a whole
C++: core::chemical::AtomTypeSet::read_meta_file(const std::string &) –> void
- class pyrosetta.rosetta.core.chemical.AutomorphismIterator¶
Bases:
pybind11_object
Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations.
Common automorphisms include flipping a phenyl ring (think Phe chi2) or rotating a methyl group (or CF3, if you don’t care about H). However, they can be much more complicated than that, and some cannot be imitated by rotation about a bond. Examples include labeling a -CF3 clockwise vs. counterclockwise, or swapping the -CF3 branches of -C(CF3)2R. See the ligand of PDB 1PQC for a reasonably complex example.
Formally, a graph automorphism is an isomorphism of that graph with itself: given a graph G(V,E) and a mapping M that relabels the vertices according to M(v) -> v’, then M is an automorphism iff (M(u),M(v)) is an edge if and only if (u,v) is an edge. If the vertices are “colored” (in our case, have atom types), it must also be true that M(v) and v have the same color, for all v in V.
Thus you can re-label a phenyl ring
2 3 6 5 6 3
- 1 4 or 1 4 but not 1 4
6 5 2 3 2 5
because in the last case, there are new bonds 6-3 and 2-5, and missing bonds 6-5 and 2-3.
See also: OpenEye’s OEChem library and its OERMSD() function.
- next(self: pyrosetta.rosetta.core.chemical.AutomorphismIterator) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
- Returns the next automorphism for this residue type
as a vector that maps “old” atom indices to “new” atom indices. Returns an empty vector when no more automorphisms remain.
C++: core::chemical::AutomorphismIterator::next() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- class pyrosetta.rosetta.core.chemical.Bond¶
Bases:
pybind11_object
basic chemical Bond
name, element, certain properties and parameters from .params file
- GetMaximumElectrons(self: pyrosetta.rosetta.core.chemical.Bond) int ¶
C++: core::chemical::Bond::GetMaximumElectrons() const –> unsigned long
- GetMinimumElectrons(self: pyrosetta.rosetta.core.chemical.Bond) int ¶
C++: core::chemical::Bond::GetMinimumElectrons() const –> unsigned long
- GetNumberOfElectrons(self: pyrosetta.rosetta.core.chemical.Bond) int ¶
C++: core::chemical::Bond::GetNumberOfElectrons() const –> unsigned long
- GetSDAltFileID(self: pyrosetta.rosetta.core.chemical.Bond) int ¶
C++: core::chemical::Bond::GetSDAltFileID() const –> unsigned long
- GetSDFileID(self: pyrosetta.rosetta.core.chemical.Bond) int ¶
C++: core::chemical::Bond::GetSDFileID() const –> unsigned long
- IsBondInRing(self: pyrosetta.rosetta.core.chemical.Bond) bool ¶
C++: core::chemical::Bond::IsBondInRing() const –> bool
- IsBondOrderKnown(self: pyrosetta.rosetta.core.chemical.Bond) bool ¶
C++: core::chemical::Bond::IsBondOrderKnown() const –> bool
- SetSDFType(self: pyrosetta.rosetta.core.chemical.Bond, SDF_ID: int) None ¶
Reset the internal data such that it matches the appropriate value for the SDF datatype.
Substitution (taken from) for BCL’s FindBondTypeFromSDFInfo( const std::size_t &SDF_ID)
C++: core::chemical::Bond::SetSDFType(const unsigned long) –> void
- aromaticity(*args, **kwargs)¶
Overloaded function.
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
/ Getters
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
- 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(std::ostream &) 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_object
- Proper aromaticity implies participation in a 4n+2 electron ring system.
For simple single-double alternation, see conjugatable bond.
Members:
UnknownAromaticity
NonaromaticBond
IsAromaticBond
- IsAromaticBond = <BondAromaticity.IsAromaticBond: 2>¶
- NonaromaticBond = <BondAromaticity.NonaromaticBond: 1>¶
- UnknownAromaticity = <BondAromaticity.UnknownAromaticity: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.BondConjugability¶
Bases:
pybind11_object
- As with the BCL, bond conjugability is more about the atom types on
either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems
Members:
UnknownConjugability
NotConjugableBond
ConjugableBond
- ConjugableBond = <BondConjugability.ConjugableBond: 2>¶
- NotConjugableBond = <BondConjugability.NotConjugableBond: 1>¶
- UnknownConjugability = <BondConjugability.UnknownConjugability: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.BondIsometry¶
Bases:
pybind11_object
Members:
UnknownIsometry
NoBondIsometry
EIsometry
ZIsometry
- EIsometry = <BondIsometry.EIsometry: 2>¶
- NoBondIsometry = <BondIsometry.NoBondIsometry: 1>¶
- UnknownIsometry = <BondIsometry.UnknownIsometry: 0>¶
- ZIsometry = <BondIsometry.ZIsometry: 3>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.BondName¶
Bases:
pybind11_object
Members:
UnknownBond
SingleBond
DoubleBond
TripleBond
AromaticBond
OrbitalBond
PseudoBond
- AromaticBond = <BondName.AromaticBond: 4>¶
- DoubleBond = <BondName.DoubleBond: 2>¶
- OrbitalBond = <BondName.OrbitalBond: 5>¶
- PseudoBond = <BondName.PseudoBond: 99>¶
- SingleBond = <BondName.SingleBond: 1>¶
- TripleBond = <BondName.TripleBond: 3>¶
- UnknownBond = <BondName.UnknownBond: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.BondOrder¶
Bases:
pybind11_object
Members:
UnknownBondOrder
SingleBondOrder
DoubleBondOrder
TripleBondOrder
OrbitalBondOrder
DeleteBondOrder
PseudoBondOrder
- DeleteBondOrder = <BondOrder.DeleteBondOrder: 5>¶
- DoubleBondOrder = <BondOrder.DoubleBondOrder: 2>¶
- OrbitalBondOrder = <BondOrder.OrbitalBondOrder: 4>¶
- PseudoBondOrder = <BondOrder.PseudoBondOrder: 99>¶
- SingleBondOrder = <BondOrder.SingleBondOrder: 1>¶
- TripleBondOrder = <BondOrder.TripleBondOrder: 3>¶
- UnknownBondOrder = <BondOrder.UnknownBondOrder: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.BondRingness¶
Bases:
pybind11_object
Members:
UnknownRingness
BondNotInRing
BondInRing
- BondInRing = <BondRingness.BondInRing: 2>¶
- BondNotInRing = <BondRingness.BondNotInRing: 1>¶
- UnknownRingness = <BondRingness.UnknownRingness: 0>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets¶
Bases:
CacheableData
A (Pose-cacheable) container for ResidueTypeSets
- assign(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, src: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets ¶
C++: core::chemical::CacheableResidueTypeSets::operator=(const class core::chemical::CacheableResidueTypeSets &) –> class core::chemical::CacheableResidueTypeSets &
- clear(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) None ¶
C++: core::chemical::CacheableResidueTypeSets::clear() –> void
- clone(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets) pyrosetta.rosetta.basic.datacache.CacheableData ¶
C++: core::chemical::CacheableResidueTypeSets::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>
- get_res_type_set(*args, **kwargs)¶
Overloaded function.
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, non-const version
If one doesn’t already exist, return a null pointer.
C++: core::chemical::CacheableResidueTypeSets::get_res_type_set(enum core::chemical::TypeSetMode) –> class std::shared_ptr<class core::chemical::PoseResidueTypeSet>
- get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData ¶
C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>
- get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t ¶
C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>
- has_res_type_set(self: pyrosetta.rosetta.core.chemical.CacheableResidueTypeSets, mode: pyrosetta.rosetta.core.chemical.TypeSetMode) bool ¶
Do we have a ‘mode’ ResidueTypeSet already instantiated?
C++: core::chemical::CacheableResidueTypeSets::has_res_type_set(enum core::chemical::TypeSetMode) const –> bool
- set_res_type_set(*args, **kwargs)¶
Overloaded function.
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.ChangeAncestory¶
Bases:
PatchOperation
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ChangeAncestory, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
change the ancestory, but leave the icoors intact.
C++: core::chemical::ChangeAncestory::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ChangeAncestory, : pyrosetta.rosetta.core.chemical.ChangeAncestory) pyrosetta.rosetta.core.chemical.ChangeAncestory ¶
C++: core::chemical::ChangeAncestory::operator=(const class core::chemical::ChangeAncestory &) –> class core::chemical::ChangeAncestory &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ChangeAncestory) str ¶
Return the name of this PatchOperation (“ChangeAncestory”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ChangeAncestory::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ChangeBondType¶
Bases:
PatchOperation
A patch operation for changing the bond type of a given bond.
See residue_io.cc for a description of bond types.
Labonte <JWLabonte.edu>
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ChangeBondType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Apply this patch to the given ResidueType.
C++: core::chemical::ChangeBondType::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ChangeBondType, : pyrosetta.rosetta.core.chemical.ChangeBondType) pyrosetta.rosetta.core.chemical.ChangeBondType ¶
C++: core::chemical::ChangeBondType::operator=(const class core::chemical::ChangeBondType &) –> class core::chemical::ChangeBondType &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ChangeBondType) str ¶
Return the name of this PatchOperation (“ChangeBondType”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ChangeBondType::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ChemicalManager¶
Bases:
SingletonBase_core_chemical_ChemicalManager_t
a class managing different sets of atom_type_set and residue_type_set
make it as a singleton class so that atom_type_set and residue_type_set are only
input and initialized once. They can be later retrieved by querying this class.
- atom_type_set(*args, **kwargs)¶
Overloaded function.
atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, type_set_type: pyrosetta.rosetta.core.chemical.TypeSetMode) -> pyrosetta.rosetta.core.chemical.AtomTypeSet
query atom_type_set by mode
C++: core::chemical::ChemicalManager::atom_type_set(enum core::chemical::TypeSetMode) –> class std::shared_ptr<const class core::chemical::AtomTypeSet>
atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) -> pyrosetta.rosetta.core.chemical.AtomTypeSet
query atom_type_set by a name tag
C++: core::chemical::ChemicalManager::atom_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::AtomTypeSet>
- element_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) core::chemical::ElementSet ¶
query atom_type_set by a name tag
C++: core::chemical::ChemicalManager::element_set(const std::string &) –> class std::shared_ptr<const class core::chemical::ElementSet>
- gasteiger_atom_type_set(*args, **kwargs)¶
Overloaded function.
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 std::string &) –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>
- static get_instance() core::chemical::ChemicalManager ¶
C++: utility::SingletonBase<core::chemical::ChemicalManager>::get_instance() –> class core::chemical::ChemicalManager *
- has_residue_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) bool ¶
Check if residue_type_set is instantiated…
C++: core::chemical::ChemicalManager::has_residue_type_set(const std::string &) –> bool
- ideal_bond_length_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) core::chemical::IdealBondLengthSet ¶
query ideal_bond_lengths
C++: core::chemical::ChemicalManager::ideal_bond_length_set(const std::string &) –> class std::shared_ptr<const class core::chemical::IdealBondLengthSet>
- mm_atom_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) core::chemical::MMAtomTypeSet ¶
query mm_atom_type_set by a name tag
C++: core::chemical::ChemicalManager::mm_atom_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::MMAtomTypeSet>
- orbital_type_set(self: pyrosetta.rosetta.core.chemical.ChemicalManager, tag: str) core::chemical::orbitals::OrbitalTypeSet ¶
query orbital_type_set by a name tag
C++: core::chemical::ChemicalManager::orbital_type_set(const std::string &) –> class std::shared_ptr<const class core::chemical::orbitals::OrbitalTypeSet>
- residue_type_set(*args, **kwargs)¶
Overloaded function.
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 std::string &) –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>
- class pyrosetta.rosetta.core.chemical.ChiralFlipAtoms¶
Bases:
PatchOperation
Execute chiral flip (primarily: at CA)
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
set the NCAA rotamer library path in the residue type
C++: core::chemical::ChiralFlipAtoms::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms, : pyrosetta.rosetta.core.chemical.ChiralFlipAtoms) pyrosetta.rosetta.core.chemical.ChiralFlipAtoms ¶
C++: core::chemical::ChiralFlipAtoms::operator=(const class core::chemical::ChiralFlipAtoms &) –> class core::chemical::ChiralFlipAtoms &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ChiralFlipAtoms) str ¶
Return the name of this PatchOperation (“ChiralFlipAtoms”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ChiralFlipAtoms::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ChiralFlipNaming¶
Bases:
PatchOperation
Execute chiral flip (primarily: at CA)
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) bool ¶
C++: core::chemical::ChiralFlipNaming::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
set the NCAA rotamer library path in the residue type
C++: core::chemical::ChiralFlipNaming::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming, : pyrosetta.rosetta.core.chemical.ChiralFlipNaming) pyrosetta.rosetta.core.chemical.ChiralFlipNaming ¶
C++: core::chemical::ChiralFlipNaming::operator=(const class core::chemical::ChiralFlipNaming &) –> class core::chemical::ChiralFlipNaming &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) bool ¶
This patch operaton DOES result in a new base residue type.
C++: core::chemical::ChiralFlipNaming::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) bool ¶
Generates a new aa
C++: core::chemical::ChiralFlipNaming::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ChiralFlipNaming) str ¶
Return the name of this PatchOperation (“ChiralFlipNaming”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ChiralFlipNaming::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ClearChiRotamers¶
Bases:
PatchOperation
A patch operation for clearing all rotamer bins from the chi of a ResidueType.
This is useful if one has redefined a chi.
Labonte <JWLabonte.edu>
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Apply this patch to the given ResidueType.
C++: core::chemical::ClearChiRotamers::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers, : pyrosetta.rosetta.core.chemical.ClearChiRotamers) pyrosetta.rosetta.core.chemical.ClearChiRotamers ¶
C++: core::chemical::ClearChiRotamers::operator=(const class core::chemical::ClearChiRotamers &) –> class core::chemical::ClearChiRotamers &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ClearChiRotamers) str ¶
Return the name of this PatchOperation (“ClearChiRotamers”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ClearChiRotamers::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton¶
Bases:
PatchOperation
Add a connection to the residue’s sulfur and make a virtual proton to track the position of the connection atom
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::ConnectSulfurAndMakeVirtualProton::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, : pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton) pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton ¶
C++: core::chemical::ConnectSulfurAndMakeVirtualProton::operator=(const class core::chemical::ConnectSulfurAndMakeVirtualProton &) –> class core::chemical::ConnectSulfurAndMakeVirtualProton &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton, rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, atom: str) bool ¶
C++: core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton) str ¶
Return the name of this PatchOperation (“ConnectSulfurAndMakeVirtualProton”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ConnectSulfurAndMakeVirtualProton::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteActCoordAtom¶
Bases:
PatchOperation
- Delete an act coord atom
Added by Andrew M. Watkins in April 2015
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::DeleteActCoordAtom::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom, : pyrosetta.rosetta.core.chemical.DeleteActCoordAtom) pyrosetta.rosetta.core.chemical.DeleteActCoordAtom ¶
C++: core::chemical::DeleteActCoordAtom::operator=(const class core::chemical::DeleteActCoordAtom &) –> class core::chemical::DeleteActCoordAtom &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteActCoordAtom) str ¶
Return the name of this PatchOperation (“DeleteActCoordAtom”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteActCoordAtom::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteAtom¶
Bases:
PatchOperation
delete an atom
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
delete an atom from ResidueType rsd
C++: core::chemical::DeleteAtom::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteAtom, : pyrosetta.rosetta.core.chemical.DeleteAtom) pyrosetta.rosetta.core.chemical.DeleteAtom ¶
C++: core::chemical::DeleteAtom::operator=(const class core::chemical::DeleteAtom &) –> class core::chemical::DeleteAtom &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.DeleteAtom) str ¶
C++: core::chemical::DeleteAtom::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteAtom) str ¶
Return the name of this PatchOperation (“DeleteAtom”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteAtom::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteChildProton¶
Bases:
PatchOperation
delete child proton
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteChildProton, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::DeleteChildProton::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteChildProton, : pyrosetta.rosetta.core.chemical.DeleteChildProton) pyrosetta.rosetta.core.chemical.DeleteChildProton ¶
C++: core::chemical::DeleteChildProton::operator=(const class core::chemical::DeleteChildProton &) –> class core::chemical::DeleteChildProton &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteChildProton) str ¶
Return the name of this PatchOperation (“DeleteChildProton”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteChildProton::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom¶
Bases:
PatchOperation
- Delete a metal binding atom
Added by Andrew M. Watkins in April 2015
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
C++: core::chemical::DeleteMetalbindingAtom::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom, : pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom) pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom ¶
C++: core::chemical::DeleteMetalbindingAtom::operator=(const class core::chemical::DeleteMetalbindingAtom &) –> class core::chemical::DeleteMetalbindingAtom &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom) str ¶
Return the name of this PatchOperation (“DeleteMetalbindingAtom”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteMetalbindingAtom::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteProperty¶
Bases:
PatchOperation
- delete a property from ResidueType
Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM’s (e.g. methylation) Rewritten by Vikram K. Mulligan on 25 Aug. 2016 to use enums wherever possible for speed.
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteProperty, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
delete a property
C++: core::chemical::DeleteProperty::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteProperty, : pyrosetta.rosetta.core.chemical.DeleteProperty) pyrosetta.rosetta.core.chemical.DeleteProperty ¶
C++: core::chemical::DeleteProperty::operator=(const class core::chemical::DeleteProperty &) –> class core::chemical::DeleteProperty &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.DeleteProperty) str ¶
Which property, if any, is deleted.
C++: core::chemical::DeleteProperty::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.DeleteProperty) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
Returns NO_PROPERTY if this PatchOperation deletes a custom, on-the-fly property.
C++: core::chemical::DeleteProperty::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteProperty) str ¶
Return the name of this PatchOperation (“DeleteProperty”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteProperty::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteTerminalChi¶
Bases:
PatchOperation
- Delete terminal chi angle
Added by Andrew M. Watkins in April 2015
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
redefine a chi angle
C++: core::chemical::DeleteTerminalChi::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi, : pyrosetta.rosetta.core.chemical.DeleteTerminalChi) pyrosetta.rosetta.core.chemical.DeleteTerminalChi ¶
C++: core::chemical::DeleteTerminalChi::operator=(const class core::chemical::DeleteTerminalChi &) –> class core::chemical::DeleteTerminalChi &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which variant, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::PatchOperation::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteTerminalChi) str ¶
Return the name of this PatchOperation (“DeleteTerminalChi”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteTerminalChi::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.DeleteVariantType¶
Bases:
PatchOperation
A patch operation for deleting a VariantType from a ResidueType.
Labonte <JWLabonte.edu>
Vikram K. Mulligan (vmullig.edu) – modified to primarily use enums instead of strings.
- adds_atoms(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.utility.vector1_std_string ¶
Which atom(s), if any, is/are added. Used for fast matching of ResidueType/Patches to PDB residues.
This includes both atoms and all possible aliases for those atoms.
C++: core::chemical::PatchOperation::adds_atoms() –> class utility::vector1<std::string, class std::allocator<std::string > >
- adds_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is added.
C++: core::chemical::PatchOperation::adds_property() const –> std::string
- adds_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is added.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::adds_property_enum() const –> enum core::chemical::ResidueProperty
- applies_to_placeholder(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Special – does this apply to ‘minimal’, placeholder types? Generally true, unless updating aa or name3.
C++: core::chemical::PatchOperation::applies_to_placeholder() const –> bool
- apply(self: pyrosetta.rosetta.core.chemical.DeleteVariantType, rsd: pyrosetta.rosetta.core.chemical.MutableResidueType) bool ¶
Apply this patch to the given ResidueType.
C++: core::chemical::DeleteVariantType::apply(class core::chemical::MutableResidueType &) const –> bool
- assign(self: pyrosetta.rosetta.core.chemical.DeleteVariantType, : pyrosetta.rosetta.core.chemical.DeleteVariantType) pyrosetta.rosetta.core.chemical.DeleteVariantType ¶
C++: core::chemical::DeleteVariantType::operator=(const class core::chemical::DeleteVariantType &) –> class core::chemical::DeleteVariantType &
- changes_connections_on(self: pyrosetta.rosetta.core.chemical.PatchOperation, : pyrosetta.rosetta.core.chemical.ResidueType, : str) bool ¶
Can this case change connections for the atom on the residue?
Be a little careful, as the passed atom name string may not have the same
whitespace padding as any internal atom name.
C++: core::chemical::PatchOperation::changes_connections_on(const class core::chemical::ResidueType &, const std::string &) const –> bool
- deletes_atom(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which atom, if any, is deleted. Used for fast matching of ResidueType/Patches to PDB residues.
C++: core::chemical::PatchOperation::deletes_atom() –> std::string
- deletes_property(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Which property, if any, is deleted.
C++: core::chemical::PatchOperation::deletes_property() const –> std::string
- deletes_property_enum(self: pyrosetta.rosetta.core.chemical.PatchOperation) pyrosetta.rosetta.core.chemical.ResidueProperty ¶
Which property, if any, is deleted.
This returns an enum value.
Vikram K. Mulligan (vmullig.edu)
C++: core::chemical::PatchOperation::deletes_property_enum() const –> enum core::chemical::ResidueProperty
- deletes_variant(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) str ¶
Which variant, if any, is deleted.
C++: core::chemical::DeleteVariantType::deletes_variant() const –> std::string
- deletes_variant_enum(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) pyrosetta.rosetta.core.chemical.VariantType ¶
Which variant, if any, is deleted, by enum.
C++: core::chemical::DeleteVariantType::deletes_variant_enum() const –> enum core::chemical::VariantType
- generates_base_residue_type(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates base residue – legacy for D_AA – do not use otherwise.
C++: core::chemical::PatchOperation::generates_base_residue_type() const –> bool
- generates_interchangeability_group(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates interchangeability_group.
C++: core::chemical::PatchOperation::generates_interchangeability_group() –> std::string
- generates_name3(self: pyrosetta.rosetta.core.chemical.PatchOperation) str ¶
Generates name3.
C++: core::chemical::PatchOperation::generates_name3() –> std::string
- may_change_aa(self: pyrosetta.rosetta.core.chemical.PatchOperation) bool ¶
Generates a new aa
C++: core::chemical::PatchOperation::may_change_aa() –> bool
- name(self: pyrosetta.rosetta.core.chemical.DeleteVariantType) str ¶
Return the name of this PatchOperation (“DeleteVariantType”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::DeleteVariantType::name() const –> std::string
- class pyrosetta.rosetta.core.chemical.ElectronConfiguration¶
Bases:
pybind11_object
describes the electron configuration of atoms
Describes the electron configuration of an atom on quantum chemistry level.
- class AngularMomentumQuantumNumber¶
Bases:
pybind11_object
Members:
e_S
e_P
e_D
e_F
MaxAngularMomentumQuantumNumber
- MaxAngularMomentumQuantumNumber = <AngularMomentumQuantumNumber.MaxAngularMomentumQuantumNumber: 4>¶
- e_D = <AngularMomentumQuantumNumber.e_D: 2>¶
- e_F = <AngularMomentumQuantumNumber.e_F: 3>¶
- e_P = <AngularMomentumQuantumNumber.e_P: 1>¶
- e_S = <AngularMomentumQuantumNumber.e_S: 0>¶
- property name¶
- property value¶
- static AngularMomentumQuantumNumber_strings() pyrosetta.rosetta.std.vector_std_string ¶
C++: core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber_strings() –> const class std::vector<std::string, class std::allocator<std::string > > &
- MaxAngularMomentumQuantumNumber = <AngularMomentumQuantumNumber.MaxAngularMomentumQuantumNumber: 4>¶
- MaxPrincipleQuantumNumber = <PrincipalQuantumNumber.MaxPrincipleQuantumNumber: 7>¶
- class PrincipalQuantumNumber¶
Bases:
pybind11_object
Members:
e_1
e_2
e_3
e_4
e_5
e_6
e_7
MaxPrincipleQuantumNumber
- MaxPrincipleQuantumNumber = <PrincipalQuantumNumber.MaxPrincipleQuantumNumber: 7>¶
- e_1 = <PrincipalQuantumNumber.e_1: 0>¶
- e_2 = <PrincipalQuantumNumber.e_2: 1>¶
- e_3 = <PrincipalQuantumNumber.e_3: 2>¶
- e_4 = <PrincipalQuantumNumber.e_4: 3>¶
- e_5 = <PrincipalQuantumNumber.e_5: 4>¶
- e_6 = <PrincipalQuantumNumber.e_6: 5>¶
- e_7 = <PrincipalQuantumNumber.e_7: 6>¶
- property name¶
- property value¶
- static PrincipalQuantumNumber_strings() pyrosetta.rosetta.std.vector_std_string ¶
C++: core::chemical::ElectronConfiguration::PrincipalQuantumNumber_strings() –> const class std::vector<std::string, class std::allocator<std::string > > &
- assign(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, : pyrosetta.rosetta.core.chemical.ElectronConfiguration) pyrosetta.rosetta.core.chemical.ElectronConfiguration ¶
C++: core::chemical::ElectronConfiguration::operator=(const class core::chemical::ElectronConfiguration &) –> class core::chemical::ElectronConfiguration &
- e_1 = <PrincipalQuantumNumber.e_1: 0>¶
- e_2 = <PrincipalQuantumNumber.e_2: 1>¶
- e_3 = <PrincipalQuantumNumber.e_3: 2>¶
- e_4 = <PrincipalQuantumNumber.e_4: 3>¶
- e_5 = <PrincipalQuantumNumber.e_5: 4>¶
- e_6 = <PrincipalQuantumNumber.e_6: 5>¶
- e_7 = <PrincipalQuantumNumber.e_7: 6>¶
- e_D = <AngularMomentumQuantumNumber.e_D: 2>¶
- e_F = <AngularMomentumQuantumNumber.e_F: 3>¶
- e_P = <AngularMomentumQuantumNumber.e_P: 1>¶
- e_S = <AngularMomentumQuantumNumber.e_S: 0>¶
- static get_angular_momentum_quantum_number(STR: str) pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber ¶
AngularMomentumQuantumNumber as string
NUM the AngularMomentumQuantumNumber desired
AngularMomentumQuantumNumber as string
C++: core::chemical::ElectronConfiguration::get_angular_momentum_quantum_number(const std::string &) –> enum core::chemical::ElectronConfiguration::AngularMomentumQuantumNumber
- static get_descriptor(*args, **kwargs)¶
Overloaded function.
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 &
- static get_principal_quantum_number(STR: str) pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber ¶
PrincipalQuantumNumber from string
NUM the PrincipalQuantumNumber desired
PrincipalQuantumNumber as string
C++: core::chemical::ElectronConfiguration::get_principal_quantum_number(const std::string &) –> enum core::chemical::ElectronConfiguration::PrincipalQuantumNumber
- max_valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
the maximum number of electrons in SP orbitals for the noble gas in this period
C++: core::chemical::ElectronConfiguration::max_valence_electrons_sp() const –> unsigned long
- read(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, ISTREAM: pyrosetta.rosetta.std.istream) pyrosetta.rosetta.std.istream ¶
read from std::istream
input stream
istream which was read from
C++: core::chemical::ElectronConfiguration::read(std::istream &) –> std::istream &
- unpaired_valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
return the number of valence electrons in SP orbitals
C++: core::chemical::ElectronConfiguration::unpaired_valence_electrons_sp() const –> unsigned long
- valence_electrons_p(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
number ValenceElectrons in the pi valence orbitals
C++: core::chemical::ElectronConfiguration::valence_electrons_p() const –> unsigned long
- valence_electrons_s(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
return number ValenceElectrons in the sigma valence orbitals
C++: core::chemical::ElectronConfiguration::valence_electrons_s() const –> unsigned long
- valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
number valence_electrons_sp
C++: core::chemical::ElectronConfiguration::valence_electrons_sp() const –> unsigned long
- valence_electrons_spd(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration) int ¶
number valence_electrons_spd
C++: core::chemical::ElectronConfiguration::valence_electrons_spd() const –> unsigned long
- write(self: pyrosetta.rosetta.core.chemical.ElectronConfiguration, OSTREAM: pyrosetta.rosetta.std.ostream) pyrosetta.rosetta.std.ostream ¶
write to std::ostream
output stream
number of indentations
ostream which was written to
C++: core::chemical::ElectronConfiguration::write(std::ostream &) const –> std::ostream &
- class pyrosetta.rosetta.core.chemical.Element¶
Bases:
pybind11_object
stores element properties
This is a low level helper class to store element properties
- Clone(self: pyrosetta.rosetta.core.chemical.Element) pyrosetta.rosetta.core.chemical.Element ¶
virtual copy constructor
C++: core::chemical::Element::Clone() const –> class std::shared_ptr<class core::chemical::Element>
- CovalentRadius = <Properties.CovalentRadius: 1>¶
- Mass = <Properties.Mass: 0>¶
- NumberOfProperties = <Properties.NumberOfProperties: 3>¶
- class Properties¶
Bases:
pybind11_object
enum properties for element types
Members:
Mass
CovalentRadius
VDWaalsRadius
NumberOfProperties
- CovalentRadius = <Properties.CovalentRadius: 1>¶
- Mass = <Properties.Mass: 0>¶
- NumberOfProperties = <Properties.NumberOfProperties: 3>¶
- VDWaalsRadius = <Properties.VDWaalsRadius: 2>¶
- property name¶
- property value¶
- VDWaalsRadius = <Properties.VDWaalsRadius: 2>¶
- assign(self: pyrosetta.rosetta.core.chemical.Element, : pyrosetta.rosetta.core.chemical.Element) pyrosetta.rosetta.core.chemical.Element ¶
C++: core::chemical::Element::operator=(const class core::chemical::Element &) –> class core::chemical::Element &
- element(self: pyrosetta.rosetta.core.chemical.Element) pyrosetta.rosetta.core.chemical.element.Elements ¶
The element enumeration
C++: core::chemical::Element::element() const –> enum core::chemical::element::Elements
- get_atomic_number(self: pyrosetta.rosetta.core.chemical.Element) int ¶
atomic number
atomic number
C++: core::chemical::Element::get_atomic_number() const –> unsigned long
- get_chemical_name(self: pyrosetta.rosetta.core.chemical.Element) str ¶
GetChemicalName
full chemical name
C++: core::chemical::Element::get_chemical_name() const –> const std::string &
- get_chemical_symbol(self: pyrosetta.rosetta.core.chemical.Element) str ¶
GetChemicalSymbol
chemical symbol one or two letters as AtomName
C++: core::chemical::Element::get_chemical_symbol() const –> const std::string &
- get_electron_configuration(self: pyrosetta.rosetta.core.chemical.Element) pyrosetta.rosetta.core.chemical.ElectronConfiguration ¶
electron configuration
the ElectronConfiguration
C++: core::chemical::Element::get_electron_configuration() const –> const class core::chemical::ElectronConfiguration &
- get_index(self: pyrosetta.rosetta.core.chemical.Element) int ¶
- Get the index of this element in the parent Element set
Will be zero if it’s not a member.
C++: core::chemical::Element::get_index() const –> unsigned long
- get_main_group(self: pyrosetta.rosetta.core.chemical.Element) int ¶
main Group #
C++: core::chemical::Element::get_main_group() const –> unsigned long
- get_period(self: pyrosetta.rosetta.core.chemical.Element) int ¶
Period
C++: core::chemical::Element::get_period() const –> unsigned long
- get_property(self: pyrosetta.rosetta.core.chemical.Element, PROPERTY: pyrosetta.rosetta.core.chemical.Element.Properties) float ¶
element type property as core::Real
the property desired
the property as core::Real
C++: core::chemical::Element::get_property(const enum core::chemical::Element::Properties &) const –> double
- static get_property_name(PROPERTY: pyrosetta.rosetta.core.chemical.Element.Properties) str ¶
element type property as string
the property desired
the property as string
C++: core::chemical::Element::get_property_name(const enum core::chemical::Element::Properties &) –> const std::string &
- is_conjugatable(self: pyrosetta.rosetta.core.chemical.Element) bool ¶
tell whether this element type can participate in a conjugated system
true if this element can participate in a common conjugated system Specifically tests if the element has 1-4 valence electrons in P orbitals
C++: core::chemical::Element::is_conjugatable() const –> bool
- is_fake(self: pyrosetta.rosetta.core.chemical.Element) bool ¶
Return true unless the element actually exists in the periodic table.
C++: core::chemical::Element::is_fake() const –> bool
- read(self: pyrosetta.rosetta.core.chemical.Element, ISTREAM: pyrosetta.rosetta.std.istream) pyrosetta.rosetta.std.istream ¶
read from std::istream
input stream
istream which was read from
C++: core::chemical::Element::read(std::istream &) –> std::istream &
- set_index(self: pyrosetta.rosetta.core.chemical.Element, setting: int) None ¶
C++: core::chemical::Element::set_index(unsigned long) –> void
- weight(self: pyrosetta.rosetta.core.chemical.Element) float ¶
This is legacy code from old element set
Return the full name of the Element
C++: core::chemical::Element::weight() const –> double
- write(self: pyrosetta.rosetta.core.chemical.Element, OSTREAM: pyrosetta.rosetta.std.ostream) pyrosetta.rosetta.std.ostream ¶
write to std::ostream
output stream
ostream which was written to
C++: core::chemical::Element::write(std::ostream &) const –> std::ostream &
- class pyrosetta.rosetta.core.chemical.ElementSet¶
Bases:
pybind11_object
A set of Bcl Elements
This class contains a vector of pointers each of which points to an Element and the vector index is looked up by an element_name string in a map.
- assign(self: pyrosetta.rosetta.core.chemical.ElementSet, : pyrosetta.rosetta.core.chemical.ElementSet) pyrosetta.rosetta.core.chemical.ElementSet ¶
C++: core::chemical::ElementSet::operator=(const class core::chemical::ElementSet &) –> class core::chemical::ElementSet &
- contains_element_type(self: pyrosetta.rosetta.core.chemical.ElementSet, element_symbol: str) bool ¶
Check if there is an element_type associated with an element_symbol string
C++: core::chemical::ElementSet::contains_element_type(const std::string &) const –> bool
- element(*args, **kwargs)¶
Overloaded function.
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 std::string &) 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 std::string &) const –> unsigned long
- n_elements(self: pyrosetta.rosetta.core.chemical.ElementSet) int ¶
Number of elements in the set
C++: core::chemical::ElementSet::n_elements() const –> unsigned long
- name(self: pyrosetta.rosetta.core.chemical.ElementSet) str ¶
What the ChemicalManager knows this as, if relevant
C++: core::chemical::ElementSet::name() const –> const std::string &
- read_file(self: pyrosetta.rosetta.core.chemical.ElementSet, filename: str) None ¶
Load the ElementSet from a file
C++: core::chemical::ElementSet::read_file(const std::string &) –> void
- class pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet¶
Bases:
ResidueTypeSet
A collection of ResidueType defined
- atom_type_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.core.chemical.AtomTypeSet ¶
C++: core::chemical::ResidueTypeSet::atom_type_set() const –> class std::shared_ptr<const class core::chemical::AtomTypeSet>
- base_residue_types(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
The list of ResidueTypes that don’t have any patches, but can be patched.
C++: core::chemical::ResidueTypeSet::base_residue_types() const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- database_directory(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet) str ¶
accessor for database_directory
C++: core::chemical::GlobalResidueTypeSet::database_directory() const –> const std::string &
- element_set(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.core.chemical.ElementSet ¶
C++: core::chemical::ResidueTypeSet::element_set() const –> class std::shared_ptr<const class core::chemical::ElementSet>
- generates_patched_residue_type_with_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, interchangeability_group: str) bool ¶
- Check if a base type (like “CYS”) generates any types with a new interchangeability group (like “SCY” (via cys_acetylated))
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_interchangeability_group(const std::string &, const std::string &) const –> bool
- generates_patched_residue_type_with_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_residue_name: str, name3: str) bool ¶
- Check if a base type (like “SER”) generates any types with another name3 (like “SEP”)
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::generates_patched_residue_type_with_name3(const std::string &, const std::string &) const –> bool
- get_all_types_with_variants_aa(*args, **kwargs)¶
Overloaded function.
get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Gets all types with the given aa type and variants
The number of variants must match exactly. Variants can be custom variants. (It’s assumed that the passed VariantTypeList contains no duplicates.)
C++: core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
get_all_types_with_variants_aa(self: pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t
Gets all types with the given aa type and variants, making exceptions for some variants.
- The number of variants must match exactly. Variants can be custom variants, but exceptions must
be standard types, listed in VariantType.hh.
(It’s assumed that the passed VariantTypeList contains no duplicates.)
C++: core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_all_types_with_variants_by_basetype(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_type: pyrosetta.rosetta.core.chemical.ResidueType, variants: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, variant_strings: pyrosetta.rosetta.utility.vector1_std_string, exceptions: pyrosetta.rosetta.utility.vector1_core_chemical_VariantType, no_metapatches: bool) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Given a base residue type, desired variants, and undesired variants, retrieve a list
of cached ResidueTypeCOPs. If not cached, generate the data and cache them.
A ResidueTypeCOP to a base residue type, used for looking up the variant.
A list of VariantTypes that the returned ResidueTypes must have, used for looking up the variant.
A list of custom VariantTypes (that don’t have enums) that the returned ResidueTypes must have, used for looking up the variant.
A list of VariantTypes that are ignored in matching.
If true, metapatches are ignored.
A list of ResidueTypeCOPs matching the desired variants, with the desired base type.
This function is threadsafe. Caching and retrieveal are handled with a ReadWriteMutex.
Vikram K. Mulligan (vmulligan.org).
C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_by_basetype(class std::shared_ptr<const class core::chemical::ResidueType>, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<enum core::chemical::VariantType, class std::allocator<enum core::chemical::VariantType> > &, const bool) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_all_types_with_variants_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Get all non-patched ResidueTypes with the given name1
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)
C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_all_types_with_variants_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Get all non-patched ResidueTypes with the given name3
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
The number of variants must match exactly. (It’s assumed that the passed VariantTypeList contains no duplicates.)
C++: core::chemical::ResidueTypeSet::get_all_types_with_variants_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_base_types_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Gets all non-patched types with the given aa type
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_base_types_aa(enum core::chemical::AA) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_base_types_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Get all non-patched ResidueTypes with the given name1
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_base_types_name1(char) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_base_types_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_ResidueType_t ¶
- Get all non-patched ResidueTypes with the given name3
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_base_types_name3(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::ResidueType>, class std::allocator<class std::shared_ptr<const class core::chemical::ResidueType> > >
- get_d_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, l_rsd: pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.chemical.ResidueType ¶
Given a D-residue, get its L-equivalent.
Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not a D-residue. Preserves variant types. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
Works for L-amino acids and L-peptoids (peptoids with chiral “L” sidechains”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ResidueTypeSet::get_d_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_l_equivalent(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, d_rsd: pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Given an L-residue, get its D-equivalent.
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
Returns NULL if there is no equivalent, true otherwise. Throws an error if this is not an L-residue. Preserves variant types.
Works for D-amino acids and D-peptoids (peptoids with chiral “D” sidechains”).
Vikram K. Mulligan (vmullig.edu).
C++: core::chemical::ResidueTypeSet::get_l_equivalent(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_mirrored_type(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, original_rsd: pyrosetta.rosetta.core.chemical.ResidueType) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Given a residue, get its mirror-image type.
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
Returns the same residue if this is an ACHIRAL type (e.g. gly), the D-equivalent for an L-residue, the L-equivalent of a D-residue, or NULL if this is an L-residue with no D-equivalent (or a D- with no L-equivalent). Preserves variant types.
C++: core::chemical::ResidueTypeSet::get_mirrored_type(class std::shared_ptr<const class core::chemical::ResidueType>) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_patches(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_chemical_Patch_t ¶
- Get the patches corresponding to a patch name.
Will get both regular an metapatches
C++: core::chemical::ResidueTypeSet::get_patches(const std::string &) const –> class utility::vector1<class std::shared_ptr<const class core::chemical::Patch>, class std::allocator<class std::shared_ptr<const class core::chemical::Patch> > >
- get_representative_type_aa(*args, **kwargs)¶
Overloaded function.
get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType
Get the base ResidueType with the given aa type and variants
Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>
get_representative_type_aa(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, aa: pyrosetta.rosetta.core.chemical.AA) -> pyrosetta.rosetta.core.chemical.ResidueType
- Note for derived classes: this method will obtain a read lock, and possibly
a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_aa(enum core::chemical::AA) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_representative_type_base_name(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, base_name: str) pyrosetta.rosetta.core.chemical.ResidueType ¶
- Note for derived classes: this method will obtain a read lock, and possibly
a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_base_name(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_representative_type_name1(*args, **kwargs)¶
Overloaded function.
get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType
Get the base ResidueType with the given name1 and variants
Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>
get_representative_type_name1(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name1: str) -> pyrosetta.rosetta.core.chemical.ResidueType
- Note for derived classes: this method will obtain a read lock, and possibly
a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_name1(char) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_representative_type_name3(*args, **kwargs)¶
Overloaded function.
get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str, variants: pyrosetta.rosetta.utility.vector1_std_string) -> pyrosetta.rosetta.core.chemical.ResidueType
Get the base ResidueType with the given name3 and variants
Returns 0 if one does not exist. The returned type will have at least all the variants given, but may have more if a minimal variant type isn’t availible. Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class core::chemical::ResidueType>
get_representative_type_name3(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name3: str) -> pyrosetta.rosetta.core.chemical.ResidueType
- Note for derived classes: this method will obtain a read lock, and possibly
a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_representative_type_name3(const std::string &) const –> class std::shared_ptr<const class core::chemical::ResidueType>
- get_residue_type_with_custom_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) pyrosetta.rosetta.core.chemical.ResidueType ¶
C++: core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &
- get_residue_type_with_variant_added(*args, **kwargs)¶
Overloaded function.
get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: pyrosetta.rosetta.core.chemical.VariantType) -> pyrosetta.rosetta.core.chemical.ResidueType
- Query a variant ResidueType by its base ResidueType and VariantType
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &
get_residue_type_with_variant_added(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, new_type: str) -> pyrosetta.rosetta.core.chemical.ResidueType
C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(const class core::chemical::ResidueType &, const std::string &) const –> const class core::chemical::ResidueType &
- get_residue_type_with_variant_removed(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, init_rsd: pyrosetta.rosetta.core.chemical.ResidueType, old_type: pyrosetta.rosetta.core.chemical.VariantType) pyrosetta.rosetta.core.chemical.ResidueType ¶
- return the residuetype we get from variant rsd type after removing the desired variant type
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(const class core::chemical::ResidueType &, const enum core::chemical::VariantType) const –> const class core::chemical::ResidueType &
- get_self_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.core.chemical.ResidueTypeSet ¶
C++: core::chemical::ResidueTypeSet::get_self_ptr() const –> class std::shared_ptr<const class core::chemical::ResidueTypeSet>
- get_self_weak_ptr(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t ¶
C++: core::chemical::ResidueTypeSet::get_self_weak_ptr() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>
- has_interchangeability_group(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) bool ¶
- Does this ResidueTypeSet have ResidueTypes with the given interchangeability group?
Note for derived classes: this method will obtain a read lock, and possibly a write lock on the ResidueTypeSetCache.
C++: core::chemical::ResidueTypeSet::has_interchangeability_group(const std::string &) const –> bool
- has_metapatch(self: pyrosetta.rosetta.core.chemical.ResidueTypeSet, name: str) bool ¶
Do we have this metapatch?
C++: core::chemical::ResidueTypeSet::has_metapatch(const std::string &) const –> bool
-
has_name(self: