orbitals

Bindings for core::chemical::orbitals namespace

class pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals

Bases: pybind11_object

Coordinates_Tetrahedral_bondedto3atoms_helper(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atm_vd1: capsule, atm_vd2: capsule, atm_vd3: capsule, atm_vd4: capsule, dist: float) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::chemical::orbitals::AssignOrbitals::Coordinates_Tetrahedral_bondedto3atoms_helper(void *const, void *const, void *const, void *const, const double) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

Coordinates_TriganolPlanar_bondedto1atom_helper(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atm_vd1: capsule, atm_vd2: capsule, atm_vd3: capsule, dist: float) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(void *const, void *const, void *const, const double) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

add_orbitals_to_restype(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atm_vd2: capsule, atm_vd3: capsule, atmtype: pyrosetta.rosetta.core.chemical.AtomType, atom_hybridization: str, orbital_xyz_vectors: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: core::chemical::orbitals::AssignOrbitals::add_orbitals_to_restype(void *, void *, const class core::chemical::AtomType &, const std::string &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

assign_only_pi_orbitals_to_atom(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atmtype: pyrosetta.rosetta.core.chemical.AtomType) → None

C++: core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom(const class core::chemical::AtomType &) –> void

assign_orbitals(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals) → None

C++: core::chemical::orbitals::AssignOrbitals::assign_orbitals() –> void

assign_sp2_orbitals_to_one_bonded_atom(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atmtype: pyrosetta.rosetta.core.chemical.AtomType) → None

C++: core::chemical::orbitals::AssignOrbitals::assign_sp2_orbitals_to_one_bonded_atom(const class core::chemical::AtomType &) –> void

assign_sp2_sp_orbitals_to_one_bonded_atom(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atmtype: pyrosetta.rosetta.core.chemical.AtomType) → None

C++: core::chemical::orbitals::AssignOrbitals::assign_sp2_sp_orbitals_to_one_bonded_atom(const class core::chemical::AtomType &) –> void

calculate_orbital_icoor(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, orbital_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, atm_vd1: capsule, atm_vd2: capsule, atm_vd3: capsule, orbital_element_name: str) → None

C++: core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor(const class numeric::xyzVector<double> &, void *const, void *const, void *const, const std::string &) –> void

cross_product_helper(self: pyrosetta.rosetta.core.chemical.orbitals.AssignOrbitals, atm_vd1: capsule, atm_vd2: capsule, atm_vd3: capsule, dist: float) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::chemical::orbitals::AssignOrbitals::cross_product_helper(void *const, void *const, void *const, const double) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

class pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData, : pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData

C++: core::chemical::orbitals::ICoorOrbitalData::operator=(const class core::chemical::orbitals::ICoorOrbitalData &) –> class core::chemical::orbitals::ICoorOrbitalData &

build(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData, stub1_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, stub2_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, stub3_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::chemical::orbitals::ICoorOrbitalData::build(class numeric::xyzVector<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>) const –> class numeric::xyzVector<double>

distance(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → float

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

get_stub1(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → str

C++: core::chemical::orbitals::ICoorOrbitalData::get_stub1() const –> const std::string &

get_stub2(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → str

C++: core::chemical::orbitals::ICoorOrbitalData::get_stub2() const –> const std::string &

get_stub3(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → str

C++: core::chemical::orbitals::ICoorOrbitalData::get_stub3() const –> const std::string &

phi(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → float

C++: core::chemical::orbitals::ICoorOrbitalData::phi() const –> double

replace_stub1(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData, atom1: str) → None

C++: core::chemical::orbitals::ICoorOrbitalData::replace_stub1(const std::string &) –> void

replace_stub2(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData, atom2: str) → None

C++: core::chemical::orbitals::ICoorOrbitalData::replace_stub2(const std::string &) –> void

replace_stub3(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData, atom3: str) → None

C++: core::chemical::orbitals::ICoorOrbitalData::replace_stub3(const std::string &) –> void

theta(self: pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData) → float

C++: core::chemical::orbitals::ICoorOrbitalData::theta() const –> double

class pyrosetta.rosetta.core.chemical.orbitals.OrbitalType

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType, : pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → pyrosetta.rosetta.core.chemical.orbitals.OrbitalType

C++: core::chemical::orbitals::OrbitalType::operator=(const class core::chemical::orbitals::OrbitalType &) –> class core::chemical::orbitals::OrbitalType &

atom_type_name(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → pyrosetta.rosetta.utility.vector1_std_string

returns the atom_types associated with the orbital type. defined in orbital_properties.txt

C++: core::chemical::orbitals::OrbitalType::atom_type_name() const –> class utility::vector1<std::string, class std::allocator<std::string > >

distance(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → float

returns the distance from the atom the orbital comes off. defined in orbital_properties.txt

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

hybridization(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → str

returns hybrdiziation of atom the orbital is attached to

C++: core::chemical::orbitals::OrbitalType::hybridization() const –> std::string

name(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → str

returns the name of the orbital type. defined in orbital_properties.txt

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

orbital_enum(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum

C++: core::chemical::orbitals::OrbitalType::orbital_enum() const –> enum core::chemical::orbitals::orbital_type_enum

orbital_name(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType) → str

returns the orbital associated with the type

C++: core::chemical::orbitals::OrbitalType::orbital_name() const –> std::string

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

The parameters are the actual headings in the orbital_properties.txt. If you want to add more paramters,

you must edit orbital_properties.txt and add another heading. You also need to edit AtomTypeSet.txt so that it recognizes that parameter and parses it. The parameters are different form the properties in that they are Reals/Size and properties are strings.

C++: core::chemical::orbitals::OrbitalType::set_parameter(const std::string &, const double) –> void

set_property(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalType, property: str, setting: bool) → None

Currently, these properties are not actually in the orbital_properties.txt. I have them here

as an example on how to add properties. This is also a place holder as the ligand code will soon be using these properties. The Acceptor/Donor could refer to orbitals that have a lone pair and are donating to a hydrogen, or an electron defficient region. In order to add properties, one must add the properties to the last line of orbital_properties.txt and make a private member variable for that property in the header file. Then do a string match comparision, like seen below. These properties are set via OrbitalTypeSet.hh

C++: core::chemical::orbitals::OrbitalType::set_property(const std::string &, const bool) –> void

class pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeMapper

Bases: SingletonBase_core_chemical_orbitals_OrbitalTypeMapper_t

static get_instance() → core::chemical::orbitals::OrbitalTypeMapper

C++: utility::SingletonBase<core::chemical::orbitals::OrbitalTypeMapper>::get_instance() –> class core::chemical::orbitals::OrbitalTypeMapper *

get_orbital_enum(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeMapper, orbital_type_name: str) → pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum

C++: core::chemical::orbitals::OrbitalTypeMapper::get_orbital_enum(std::string &) –> enum core::chemical::orbitals::orbital_type_enum

class pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet, : pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet) → pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet

C++: core::chemical::orbitals::OrbitalTypeSet::operator=(const class core::chemical::orbitals::OrbitalTypeSet &) –> class core::chemical::orbitals::OrbitalTypeSet &

name(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet) → str

What the ChemicalManager knows this as, if relevant

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

orbital_type_index(*args, **kwargs)

Overloaded function.

1. orbital_type_index(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet, orbital_type_name: str) -> int

lookup the orbital type by the orbital type name string

C++: core::chemical::orbitals::OrbitalTypeSet::orbital_type_index(const std::string &) const –> int

2. orbital_type_index(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet, orbital_type_name: str) -> int

lookup the orbital type by the orbital type name string

C++: core::chemical::orbitals::OrbitalTypeSet::orbital_type_index(std::string &) const –> int

read_file(self: pyrosetta.rosetta.core.chemical.orbitals.OrbitalTypeSet, filename: str) → None

C++: core::chemical::orbitals::OrbitalTypeSet::read_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.orbitals.orbital_type_enum

Bases: pybind11_object

Members:

C_pi_sp2

N_pi_sp2

N_p_sp2

O_pi_sp2

O_p_sp2

O_p_sp3

S_p_sp3

O_pi_sp2_bb

O_p_sp2_bb

num_orbital_types

C_pi_sp2 = <orbital_type_enum.C_pi_sp2: 1>

N_p_sp2 = <orbital_type_enum.N_p_sp2: 3>

N_pi_sp2 = <orbital_type_enum.N_pi_sp2: 2>

O_p_sp2 = <orbital_type_enum.O_p_sp2: 5>

O_p_sp2_bb = <orbital_type_enum.O_p_sp2_bb: 9>

O_p_sp3 = <orbital_type_enum.O_p_sp3: 6>

O_pi_sp2 = <orbital_type_enum.O_pi_sp2: 4>

O_pi_sp2_bb = <orbital_type_enum.O_pi_sp2_bb: 8>

S_p_sp3 = <orbital_type_enum.S_p_sp3: 7>

property name

num_orbital_types = <orbital_type_enum.O_p_sp2_bb: 9>

property value