gasteiger

Bindings for core::chemical::gasteiger namespace

class pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

Bases: pybind11_object

contains hybridization and bond geometry data, which is used in Atom

AdditiveAtomicPolarizability = <Properties.AdditiveAtomicPolarizability: 11>
class AtomicOrbitalTypes

Bases: pybind11_object

Members:

S

Px

Py

Pz

Dxy

Dxz

Dyz

Dz2

Dx2y2

NumberOfAtomicOrbitalTypes

Dx2y2 = <AtomicOrbitalTypes.Dx2y2: 8>
Dxy = <AtomicOrbitalTypes.Dxy: 4>
Dxz = <AtomicOrbitalTypes.Dxz: 5>
Dyz = <AtomicOrbitalTypes.Dyz: 6>
Dz2 = <AtomicOrbitalTypes.Dz2: 7>
NumberOfAtomicOrbitalTypes = <AtomicOrbitalTypes.NumberOfAtomicOrbitalTypes: 9>
Px = <AtomicOrbitalTypes.Px: 1>
Py = <AtomicOrbitalTypes.Py: 2>
Pz = <AtomicOrbitalTypes.Pz: 3>
S = <AtomicOrbitalTypes.S: 0>
property name
property value
static AtomicOrbitalTypes_strings() → pyrosetta.rosetta.std.vector_std_string

C++: core::chemical::gasteiger::GasteigerAtomTypeData::AtomicOrbitalTypes_strings() –> const class std::vector<std::string, class std::allocator<std::string > > &

Clone(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

Clone function

pointer to new AtomTypeData

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

CovalentRadiusAromaticBond = <Properties.CovalentRadiusAromaticBond: 16>
CovalentRadiusDoubleBond = <Properties.CovalentRadiusDoubleBond: 14>
CovalentRadiusSingleBond = <Properties.CovalentRadiusSingleBond: 13>
CovalentRadiusTripleBond = <Properties.CovalentRadiusTripleBond: 15>
Dx2y2 = <AtomicOrbitalTypes.Dx2y2: 8>
Dxy = <AtomicOrbitalTypes.Dxy: 4>
Dxz = <AtomicOrbitalTypes.Dxz: 5>
Dyz = <AtomicOrbitalTypes.Dyz: 6>
Dz2 = <AtomicOrbitalTypes.Dz2: 7>
static GetPropertyName(PROPERTY: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties) → str

element type property as string

the property desired

the property as string

C++: core::chemical::gasteiger::GasteigerAtomTypeData::GetPropertyName(const enum core::chemical::gasteiger::GasteigerAtomTypeData::Properties) –> const std::string &

class HybridOrbitalType

Bases: pybind11_object

Members:

Unhybridized

SP

SP2

SP3

NumberHybridOrbitalType

NumberHybridOrbitalType = <HybridOrbitalType.NumberHybridOrbitalType: 4>
SP = <HybridOrbitalType.SP: 1>
SP2 = <HybridOrbitalType.SP2: 2>
SP3 = <HybridOrbitalType.SP3: 3>
Unhybridized = <HybridOrbitalType.Unhybridized: 0>
property name
property value
LonePairElectronAffinity = <Properties.LonePairElectronAffinity: 9>
LonePairElectronegativityMulliken = <Properties.LonePairElectronegativityMulliken: 10>
LonePairIonizationPotential = <Properties.LonePairIonizationPotential: 8>
None = <TypeDifference.None: 0>
NumberBondingPOrbitals = <TypeDifference.NumberBondingPOrbitals: 2>
NumberBondingSOrbitals = <TypeDifference.NumberBondingSOrbitals: 1>
NumberHybridOrbitalType = <HybridOrbitalType.NumberHybridOrbitalType: 4>
NumberLonePairOrbitals = <TypeDifference.NumberLonePairOrbitals: 3>
NumberOfAtomicOrbitalTypes = <AtomicOrbitalTypes.NumberOfAtomicOrbitalTypes: 9>
NumberOfProperties = <Properties.NumberOfProperties: 17>
NumberTypeDifferences = <TypeDifference.NumberTypeDifferences: 5>
One = <PiContributionType.One: 1>
Other = <TypeDifference.Other: 4>
class PiContributionType

Bases: pybind11_object

how the atom type can contribute to a pi system

Members:

Zero

One

Two

ZeroOrTwo

One = <PiContributionType.One: 1>
Two = <PiContributionType.Two: 2>
Zero = <PiContributionType.Zero: 0>
ZeroOrTwo = <PiContributionType.ZeroOrTwo: 3>
property name
property value
PiOrbitalElectronegativityMulliken = <Properties.PiOrbitalElectronegativityMulliken: 6>
PiOrbitalElectronegativityPauling = <Properties.PiOrbitalElectronegativityPauling: 7>
PiValenceStateElectronAffinity = <Properties.PiValenceStateElectronAffinity: 5>
PiValenceStateIonizationPotential = <Properties.PiValenceStateIonizationPotential: 4>
class Properties

Bases: pybind11_object

enum properties for atom types

Members:

SigmaValenceStateIonizationPotential

SigmaValenceStateElectronAffinity

SigmaOrbitalElectronegativityMulliken

SigmaOrbitalElectronegativityPauling

PiValenceStateIonizationPotential

PiValenceStateElectronAffinity

PiOrbitalElectronegativityMulliken

PiOrbitalElectronegativityPauling

LonePairIonizationPotential

LonePairElectronAffinity

LonePairElectronegativityMulliken

AdditiveAtomicPolarizability

VdWaalsRadiusCSD

CovalentRadiusSingleBond

CovalentRadiusDoubleBond

CovalentRadiusTripleBond

CovalentRadiusAromaticBond

NumberOfProperties

AdditiveAtomicPolarizability = <Properties.AdditiveAtomicPolarizability: 11>
CovalentRadiusAromaticBond = <Properties.CovalentRadiusAromaticBond: 16>
CovalentRadiusDoubleBond = <Properties.CovalentRadiusDoubleBond: 14>
CovalentRadiusSingleBond = <Properties.CovalentRadiusSingleBond: 13>
CovalentRadiusTripleBond = <Properties.CovalentRadiusTripleBond: 15>
LonePairElectronAffinity = <Properties.LonePairElectronAffinity: 9>
LonePairElectronegativityMulliken = <Properties.LonePairElectronegativityMulliken: 10>
LonePairIonizationPotential = <Properties.LonePairIonizationPotential: 8>
NumberOfProperties = <Properties.NumberOfProperties: 17>
PiOrbitalElectronegativityMulliken = <Properties.PiOrbitalElectronegativityMulliken: 6>
PiOrbitalElectronegativityPauling = <Properties.PiOrbitalElectronegativityPauling: 7>
PiValenceStateElectronAffinity = <Properties.PiValenceStateElectronAffinity: 5>
PiValenceStateIonizationPotential = <Properties.PiValenceStateIonizationPotential: 4>
SigmaOrbitalElectronegativityMulliken = <Properties.SigmaOrbitalElectronegativityMulliken: 2>
SigmaOrbitalElectronegativityPauling = <Properties.SigmaOrbitalElectronegativityPauling: 3>
SigmaValenceStateElectronAffinity = <Properties.SigmaValenceStateElectronAffinity: 1>
SigmaValenceStateIonizationPotential = <Properties.SigmaValenceStateIonizationPotential: 0>
VdWaalsRadiusCSD = <Properties.VdWaalsRadiusCSD: 12>
property name
property value
Px = <AtomicOrbitalTypes.Px: 1>
Py = <AtomicOrbitalTypes.Py: 2>
Pz = <AtomicOrbitalTypes.Pz: 3>
S = <AtomicOrbitalTypes.S: 0>
SP = <HybridOrbitalType.SP: 1>
SP2 = <HybridOrbitalType.SP2: 2>
SP3 = <HybridOrbitalType.SP3: 3>
SigmaOrbitalElectronegativityMulliken = <Properties.SigmaOrbitalElectronegativityMulliken: 2>
SigmaOrbitalElectronegativityPauling = <Properties.SigmaOrbitalElectronegativityPauling: 3>
SigmaValenceStateElectronAffinity = <Properties.SigmaValenceStateElectronAffinity: 1>
SigmaValenceStateIonizationPotential = <Properties.SigmaValenceStateIonizationPotential: 0>
Two = <PiContributionType.Two: 2>
class TypeDifference

Bases: pybind11_object

Type difference specifies the difference between two atom types

Members:

None

NumberBondingSOrbitals

NumberBondingPOrbitals

NumberLonePairOrbitals

Other

NumberTypeDifferences

None = <TypeDifference.None: 0>
NumberBondingPOrbitals = <TypeDifference.NumberBondingPOrbitals: 2>
NumberBondingSOrbitals = <TypeDifference.NumberBondingSOrbitals: 1>
NumberLonePairOrbitals = <TypeDifference.NumberLonePairOrbitals: 3>
NumberTypeDifferences = <TypeDifference.NumberTypeDifferences: 5>
Other = <TypeDifference.Other: 4>
property name
property value
Unhybridized = <HybridOrbitalType.Unhybridized: 0>
VdWaalsRadiusCSD = <Properties.VdWaalsRadiusCSD: 12>
Zero = <PiContributionType.Zero: 0>
ZeroOrTwo = <PiContributionType.ZeroOrTwo: 3>
assign(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, : pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

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

calculate_stability_metric(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → float
calculate the stability metric. Electronic stability is indicated by a larger number

This is used to decide between atom types when no other means are possible

C++: core::chemical::gasteiger::GasteigerAtomTypeData::calculate_stability_metric() const –> double

difference_from(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, OTHER: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference

determine the difference betweent his atom type data and another

the atom type data to compare this atom type data to

the corresponding TypeDifference

C++: core::chemical::gasteiger::GasteigerAtomTypeData::difference_from(const class core::chemical::gasteiger::GasteigerAtomTypeData &) –> enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference

get_atom_type_property(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, PROPERTY: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties) → float

atom type property as core::Real

the property desired

the property as core::Real

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_atom_type_property(const enum core::chemical::gasteiger::GasteigerAtomTypeData::Properties) const –> double

static get_average_cation_pi_ip_to_neutral_ip_ratio() → float

get_average_cation_pi_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

reference to a core::Real, which returns the ratio of Average(PiValenceStateIonizationPotential) for cations vs. neutral atoms

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_cation_pi_ip_to_neutral_ip_ratio() –> double

static get_average_cation_sigma_ip_to_neutral_ip_ratio() → float

get_average_cation_sigma_ip_to_neutral_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

reference to a core::Real, which returns the ratio of Average(SigmaValenceStateIonizationPotential) for cations vs. neutral atoms

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_cation_sigma_ip_to_neutral_ip_ratio() –> double

get_average_ip_change_cation_to_neutral(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → float

get the average ionization potential ratio between cation and neutral atom type that differ by TYPE_DIFFERENCE

the type difference to get the corresponding ratio for

the ratio

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_ip_change_cation_to_neutral(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) const –> double

get_average_ip_change_neutral_to_anion(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → float

get the average ionization potential ratio between neutral and cation atom type that differ by TYPE_DIFFERENCE

the type difference to get the corresponding ratio for

the ratio

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_ip_change_neutral_to_anion(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) const –> double

static get_average_neutral_pi_ip_to_anion_ip_ratio() → float

get_average_neutral_pi_ip_to_anion_ip_ratio helper function for AtomTypes::CalculateElectronegativityValues

reference to a core::Real, which returns the ratio of Average(PiValenceStateIonizationPotential) for neutral atoms vs. anions

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_neutral_pi_ip_to_anion_ip_ratio() –> double

static get_average_neutral_sigma_ip_to_anion_ip_ratio() → float

GetAverageNeutralSigmaIVToEARatio helper function for AtomTypes::CalculateElectronegativityValues

reference to a core::Real, which returns the ratio of Average(SigmaValenceStateIonizationPotential) for neutral atoms vs. anions

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_average_neutral_sigma_ip_to_anion_ip_ratio() –> double

get_electron_affinity(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → float

get the electron affinity type corresponding to a TypeDifference

the type difference to get the corresponding electron affinity for

the electron affinity type corresponding to TypeDifference

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_electron_affinity(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) const –> double

get_electronegativity(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → float

get the electronegativity type corresponding to a TypeDifference

the type difference to get the corresponding electronegativity for

the electronegativity type corresponding to TypeDifference

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_electronegativity(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) const –> double

get_element_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.Element

return ElementType

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

get_formal_charge(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Charge

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_formal_charge() const –> short

get_hybrid_orbital_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType

returns the hybridization of the atom type

the type of hybrid orbital

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_hybrid_orbital_type() const –> enum core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType

get_ionization_potential(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → float

get the ionization potential type corresponding to a TypeDifference

the type difference to get the corresponding ionization potential for

the ionization potential type corresponding to TypeDifference

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_ionization_potential(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) const –> double

get_maxE_contribution_to_pi_system(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Get the max number of electrons available for contribution to an aromatic ring

the max electrons contributed by this atom type to a pi system

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_maxE_contribution_to_pi_system() const –> unsigned long

get_name(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → str

return Name

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_name() const –> const std::string &

get_number_bonds(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of bonds

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_bonds() const –> unsigned long

get_number_electrons_in_bonds(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

get_number_electrons_in_bonds calculates the total number of electrons in pi-orbital and sigma bonds

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_electrons_in_bonds() const –> unsigned long

get_number_electrons_in_p_orbitals(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of electrons in p orbitals (whether hybridized or not)

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_electrons_in_p_orbitals() const –> unsigned long

get_number_hybrid_bonds(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of hybridized bonds

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_hybrid_bonds() const –> unsigned long

get_number_hybrid_lone_pairs(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

returns the number of lone pairs in hybrid orbitals

the number of lone pairs in hybrid orbitals

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_hybrid_lone_pairs() const –> unsigned long

get_number_hybrid_orbitals(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

returns the number of hybridized orbitals

the number of hybridized orbitals

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_hybrid_orbitals() const –> unsigned long

get_number_pi_orbitals(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of pi-orbitals

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_pi_orbitals() const –> unsigned long

get_number_sigma_orbitals(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of Sigma orbitals

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_sigma_orbitals() const –> unsigned long

get_number_unhybridized_lone_pairs(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

return Number of unhybridized lone pairs

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_unhybridized_lone_pairs() const –> unsigned long

get_number_unhybridized_sigma_orbitals(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

Number of Sigma orbitals that are not hybridized

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_number_unhybridized_sigma_orbitals() const –> unsigned long

get_orbital_E_neg_pos(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → float

the orbital electronegativity associated with the charged state

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_orbital_E_neg_pos() const –> double

get_pi_electron_contribution_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.PiContributionType

Get the type of contribution this atom type can make to a pi system

the type of contribution this atom type can make to a pi system

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_pi_electron_contribution_type() const –> enum core::chemical::gasteiger::GasteigerAtomTypeData::PiContributionType

get_stability_metric(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → float
Get the stability metric. Electronic stability is indicated by a larger number

This is used to decide between atom types when no other means are possible

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_stability_metric() const –> double

static get_type_difference_name(TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.TypeDifference) → str

type difference as string

the type difference for which a string is desired

the type difference as a string

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_type_difference_name(const enum core::chemical::gasteiger::GasteigerAtomTypeData::TypeDifference) –> const std::string &

get_valence_electrons_sp(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → int

valence electrons in sp orbitals

C++: core::chemical::gasteiger::GasteigerAtomTypeData::get_valence_electrons_sp() const –> unsigned long

is_conjugated(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → bool

determine if this atom type can participate in pi-bond conjugation

true iff this atom type has any non-single bonds or lone pairs

C++: core::chemical::gasteiger::GasteigerAtomTypeData::is_conjugated() const –> bool

is_gasteiger_atom_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → bool

is this a well characterized gasteiger atom type

true iff this atom type is this a well characterized gasteiger atom type

C++: core::chemical::gasteiger::GasteigerAtomTypeData::is_gasteiger_atom_type() const –> bool

read(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, ISTREAM: pyrosetta.rosetta.std.istream, ele_set: pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t) → pyrosetta.rosetta.std.istream

read from std::istream

input stream

istream which was read from

C++: core::chemical::gasteiger::GasteigerAtomTypeData::read(std::istream &, class std::weak_ptr<const class core::chemical::ElementSet>) –> std::istream &

set_property(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, DATA: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties, VALUE: float) → None

set a particular data

the property to set

the value to set the property to

C++: core::chemical::gasteiger::GasteigerAtomTypeData::set_property(const enum core::chemical::gasteiger::GasteigerAtomTypeData::Properties, const double) –> void

write(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, OSTREAM: pyrosetta.rosetta.std.ostream) → pyrosetta.rosetta.std.ostream

write to std::ostream

output stream to write to

number of indentations

output stream which was written to

C++: core::chemical::gasteiger::GasteigerAtomTypeData::write(std::ostream &) const –> std::ostream &

class pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet

Bases: pybind11_object

A set of Bcl Atom types

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

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

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

atom_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, atom_type_name: str) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

Lookup the element index by the element_symbol string

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::atom_type(const std::string &) const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>

atom_type_index(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, atom_type_name: str) → int

Lookup the element index by the element_symbol string

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::atom_type_index(const std::string &) const –> unsigned long

contains_atom_type(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, atom_type_name: str) → bool

Check if there is an element_type associated with an element_symbol string

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::contains_atom_type(const std::string &) const –> bool

element_set(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t

Return the associated element type set.

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::element_set() const –> class std::weak_ptr<const class core::chemical::ElementSet>

n_types(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet) → int

Number of atom types in the set

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::n_types() const –> unsigned long

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

What does the ChemicalManger call this TypeSet?

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

read_bond_file(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, filename: str) → None

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::read_bond_file(const std::string &) –> void

read_file(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, filename: str) → None

Load the AtomSet from a file

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::read_file(const std::string &) –> void

type_for_fake_atoms(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

Return the type that’s assigned for fake atoms. (Virtual atoms and the like.)

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

class pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom

Bases: pybind11_object

A helper class by which AtomTypes can return all possible atom types for a given atom in a structure

that is easily accessed by orbital type

AddAromaticAtomType(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, ATOM_TYPE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, DESIRED_CHARGE: int) → None

add an atom type to the search using a set of rules for atom types in aromatic rings

the type of atom to consider

the charge desired The atom type will be ordered using the distance from the desired charge as the first sort key, second by the stability. Unlike AddAtomType, AddAromaticAtomType always adds the type to the considered list

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::AddAromaticAtomType(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>, const int) –> void

AddAtomType(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, ATOM_TYPE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → None

add an atom type to be considered

the type of atom to consider

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

CouldHaveHybridization(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, HYBRID: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType) → bool

tell whether a particular hybrid orbital type is possible given what we know about this atom

the type of hybrid orbital

true iff there is a possible atom type for that hybrid orbital

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::CouldHaveHybridization(const enum core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType) const –> bool

Finalize(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom) → None

Select the best choice for the atom type wherever possible

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::Finalize() –> void

FinalizeAromatic(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, DESIRED_CHARGE: int) → None

only keep the most stable types for the atom that span the set of desired pi orbital electrons (0-2)

the preferred charge used during construction of the maps when there is no part of standardization that should edit this class

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeAromatic(const int) –> void

FinalizeUnhybridized(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom) → None

choose the preferred atom type (using VSEPR theory) assuming that the orbitals do not hybridize

This is used for elements in group 1, 2, & 7, which do hybridize in the gasteiger scheme

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeUnhybridized() –> void

static FindPossibleAtomTypesForAtom(GASTEIGER_ATOM_TYPE_SET: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, ELEMENT: pyrosetta.rosetta.core.chemical.Element, NUMBER_ELECTRONS_IN_BONDS: int, NUMBER_BONDS: int, SUSPECTED_CHARGE: int, IN_AROMATIC_RING: bool) → pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom

constructor from the known information about the atom

element type,

number of electrons in bonds for the atom type

number of bonds for the atom

expected charge, ignored if no atom type matching the other criteria if found

true iff the atom has bonds of the aromatic unspecified type

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>, const class core::chemical::Element &, const unsigned long, const unsigned long, const int, const bool) –> class core::chemical::gasteiger::PossibleAtomTypesForAtom

GetMostStableType(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData

return the most stable type

the most stable type - NULL if no such type exists

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

GetNumberPossibleTypes(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom) → int

return the number of types that the atom has the potential to become

the number of types that the atom has the potential to become

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::GetNumberPossibleTypes() const –> unsigned long

RemoveHybridization(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, HYBRID: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType) → None

remove a particular hybrid orbital type from the possible types, unless that would remove all possibilities

the type of hybrid orbital to remove

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::RemoveHybridization(const enum core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType) –> void

SetToType(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, ATOM_TYPE: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) → None

set this object to only consider the given atom type

the atom type desired

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

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

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

gasteiger_atom_type_set(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, GASTEIGER_ATOM_TYPE_SET: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet) → None

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::gasteiger_atom_type_set(class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>) –> void

hybridization_rank(self: pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom, hybrid: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.HybridOrbitalType) → int

C++: core::chemical::gasteiger::PossibleAtomTypesForAtom::hybridization_rank(const enum core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType) –> unsigned long

pyrosetta.rosetta.core.chemical.gasteiger.assign_gasteiger_atom_types(*args, **kwargs)

Overloaded function.

  1. assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, gasteiger_atom_type_set: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, keep_existing: bool) -> None

  2. assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, gasteiger_atom_type_set: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, keep_existing: bool, allow_unknown: bool) -> None

C++: core::chemical::gasteiger::assign_gasteiger_atom_types(class core::chemical::MutableResidueType &, class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>, bool, bool) –> void

  1. assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.MutableResidueType) -> None

  2. assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, keep_existing: bool) -> None

  3. assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.MutableResidueType, keep_existing: bool, allow_unknown: bool) -> None

Version which gets typeset from ResidueType, or just uses default

C++: core::chemical::gasteiger::assign_gasteiger_atom_types(class core::chemical::MutableResidueType &, bool, bool) –> void

pyrosetta.rosetta.core.chemical.gasteiger.safe_read(*args, **kwargs)

Overloaded function.

  1. safe_read(in: pyrosetta.rosetta.std.istream, val: int) -> None

C++: core::chemical::gasteiger::safe_read(std::istream &, unsigned long &) –> void

  1. safe_read(in: pyrosetta.rosetta.std.istream, val: float) -> None

C++: core::chemical::gasteiger::safe_read(std::istream &, double &) –> void

pyrosetta.rosetta.core.chemical.gasteiger.safe_write(*args, **kwargs)

Overloaded function.

  1. safe_write(out: pyrosetta.rosetta.std.ostream, val: int) -> None

  2. safe_write(out: pyrosetta.rosetta.std.ostream, val: int, sep: bool) -> None

C++: core::chemical::gasteiger::safe_write(std::ostream &, const unsigned long &, bool) –> void

  1. safe_write(out: pyrosetta.rosetta.std.ostream, val: float) -> None

  2. safe_write(out: pyrosetta.rosetta.std.ostream, val: float, sep: bool) -> None

C++: core::chemical::gasteiger::safe_write(std::ostream &, const double &, bool) –> void