gasteiger¶

Bindings for core::chemical::gasteiger namespace

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

Bases: pybind11_builtins.pybind11_object

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

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>

GetPropertyName(PROPERTY: pyrosetta.rosetta.core.chemical.gasteiger.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 PiContributionType¶

Bases: pybind11_builtins.pybind11_object

how the atom type can contribute to a pi system

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) -> bool
__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) → int¶

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: int) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) -> bool
__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: int) -> bool

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.PiContributionType, arg0: tuple) → None¶

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class Properties¶

Bases: pybind11_builtins.pybind11_object

enum properties for atom types

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: pyrosetta.rosetta.core.chemical.gasteiger.Properties) -> bool
__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties) → int¶

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: int) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: pyrosetta.rosetta.core.chemical.gasteiger.Properties) -> bool
__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: int) -> bool

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.Properties, arg0: tuple) → None¶

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class TypeDifference¶

Bases: pybind11_builtins.pybind11_object

Type difference specifies the difference between two atom types

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__(*args, **kwargs)¶

Overloaded function.

__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) -> bool
__eq__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: int) -> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) → tuple¶

__gt__¶: Return self>value.

__hash__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) → int¶

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: int) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__int__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) → int¶

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__(*args, **kwargs)¶

Overloaded function.

__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) -> bool
__ne__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: int) -> bool

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference) → str¶

__setattr__¶: Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.core.chemical.gasteiger.TypeDifference, arg0: tuple) → None¶

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) -> None
__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, NAME: str, ELEMENT_TYPE: pyrosetta.rosetta.core.chemical.Element, HYBRIDIZATION: core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType, HYBRID_ORBITALS_IN_SIGMA_BONDS: int, HYBRID_ORBITALS_NONBINDING: int, PI_ORBITALS_IN_BONDS: pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t, ATOMIC_ORBITALS_NONBINDING: pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t, SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL: float, SIGMA_VALENCE_STATE_ELECTRON_AFFINITY: float, PI_VALENCE_STATE_IONIZATION_POTENTIAL: float, PI_VALENCE_STATE_ELECTRON_AFFINITY: float, LONE_PAIR_IONIZATION_POTENTIAL: float, LONE_PAIR_ELECTRON_AFFINITY: float, ATOMIC_POLARIZABILITY: float) -> None
__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, NAME: str, ELEMENT: str, HYBRIDIZATION: core::chemical::gasteiger::GasteigerAtomTypeData::HybridOrbitalType, HYBRID_ORBITALS_IN_SIGMA_BONDS: int, HYBRID_ORBITALS_NONBINDING: int, PI_ORBITALS_IN_BONDS: pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t, ATOMIC_ORBITALS_NONBINDING: pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t, SIGMA_VALENCE_STATE_IONIZATION_POTENTIAL: float, SIGMA_VALENCE_STATE_ELECTRON_AFFINITY: float, PI_VALENCE_STATE_IONIZATION_POTENTIAL: float, PI_VALENCE_STATE_ELECTRON_AFFINITY: float, LONE_PAIR_IONIZATION_POTENTIAL: float, LONE_PAIR_ELECTRON_AFFINITY: float, ATOMIC_POLARIZABILITY: float, ele_set: pyrosetta.rosetta.core.chemical.ElementSet) -> None
__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, NAME: str, ELEMENT_TYPE: pyrosetta.rosetta.core.chemical.Element, CHARGE: int) -> None
__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, arg0: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

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

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.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.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

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

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.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.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

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

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.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.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.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.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_nNumber_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_nNumber_hybrid_lone_pairs() 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_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.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

get_type_difference_name(TYPE_DIFFERENCE: pyrosetta.rosetta.core.chemical.gasteiger.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(class std::basic_istream<char> &, class std::weak_ptr<const class core::chemical::ElementSet>) –> class std::basic_istream<char> &

set_property(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData, DATA: pyrosetta.rosetta.core.chemical.gasteiger.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(class std::basic_ostream<char> &) const –> std::ostream &

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

Bases: pybind11_builtins.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, index: int) → pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData¶

Lookup an Atom by 1-based indexing

C++: core::chemical::gasteiger::GasteigerAtomTypeSet::operator[](const unsigned long) const –> class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeData>

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, arg0: pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t) -> None

doc

__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, element_set: pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ElementSet_t, name: str) -> None
__init__(self: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, arg0: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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.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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

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

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.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.

assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.ResidueType, gasteiger_atom_type_set: pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet, keep_existing: bool) -> None
assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.ResidueType, 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::ResidueType &, class std::shared_ptr<const class core::chemical::gasteiger::GasteigerAtomTypeSet>, bool, bool) –> void

assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.ResidueType) -> None
assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.ResidueType, keep_existing: bool) -> None
assign_gasteiger_atom_types(restype: pyrosetta.rosetta.core.chemical.ResidueType, 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::ResidueType &, bool, bool) –> void

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

Overloaded function.

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

C++: core::chemical::gasteiger::safe_read(class std::basic_istream<char> &, unsigned long &) –> void

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

C++: core::chemical::gasteiger::safe_read(class std::basic_istream<char> &, double &) –> void

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

Overloaded function.

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

C++: core::chemical::gasteiger::safe_write(class std::basic_ostream<char> &, const unsigned long &, bool) –> void

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

C++: core::chemical::gasteiger::safe_write(class std::basic_ostream<char> &, const double &, bool) –> void