core::chemical::orbitals::AssignOrbitals Class Reference

#include <AssignOrbitals.hh>

Public Member Functions
	AssignOrbitals (core::chemical::ResidueTypeOP const restype)
void	assign_orbitals ()
void	assign_only_pi_orbitals_to_atom (core::chemical::AtomType const &atmtype)
void	assign_sp2_sp_orbitals_to_one_bonded_atom (core::chemical::AtomType const &atmtype)
void	add_orbitals_to_restype (core::Size const atm_index2, core::Size const atm_index3, core::chemical::AtomType const &atmtype, std::string const atom_hybridization, utility::vector1< numeric::xyzVector< core::Real > > const orbital_xyz_vectors)
void	assign_sp2_orbitals_to_one_bonded_atom (core::chemical::AtomType const &atmtype)
utility::vector1 < numeric::xyzVector < core::Real > >	cross_product_helper (core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Real const dist)
void	calculate_orbital_icoor (numeric::xyzVector< core::Real > const orbital_xyz, core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, std::string const orbital_element_name)
utility::vector1 < numeric::xyzVector < core::Real > >	Coordinates_TriganolPlanar_bondedto1atom_helper (core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Real const dist)
utility::vector1 < numeric::xyzVector < core::Real > >	Coordinates_Tetrahedral_bondedto3atoms_helper (core::Size const atm_index1, core::Size const atm_index2, core::Size const atm_index3, core::Size const atm_index4, core::Real const dist)

Private Member Functions
std::string	make_orbital_type_name (AtomType const &atmtype, std::string const orbitaltype, core::Size const hybridization)
std::string	make_orbital_element_name ()
void	set_orbital_type_and_bond (core::Size atom_index, std::string orbital_element_name, std::string orbital_type_full_name)

Private Attributes
core::Size	Aindex_
core::Size	AOhybridization_
core::Size	Orbtype_
core::Real	AOdist_
utility::vector1< core::Size >	AObondedatoms_
core::chemical::ResidueTypeOP	restype_
core::Size	n_orbitals_

Constructor & Destructor Documentation

core::chemical::orbitals::AssignOrbitals::AssignOrbitals

(

core::chemical::ResidueTypeOP const

restype

)

Member Function Documentation

void core::chemical::orbitals::AssignOrbitals::add_orbitals_to_restype	(	core::Size const	atm_index2,
		core::Size const	atm_index3,
		core::chemical::AtomType const &	atmtype,
		std::string const	atom_hybridization,
		utility::vector1< numeric::xyzVector< core::Real > > const	orbital_xyz_vectors
	)

References Aindex_, AOhybridization_, calculate_orbital_icoor(), make_orbital_element_name(), make_orbital_type_name(), and set_orbital_type_and_bond().

Referenced by assign_only_pi_orbitals_to_atom(), assign_orbitals(), assign_sp2_orbitals_to_one_bonded_atom(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

void core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom

(

core::chemical::AtomType const &

atmtype

)

References add_orbitals_to_restype(), Aindex_, AObondedatoms_, AOdist_, cross_product_helper(), core::chemical::AtomType::name(), and restype_.

Referenced by assign_orbitals().

void core::chemical::orbitals::AssignOrbitals::assign_orbitals

(

)

References core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, add_orbitals_to_restype(), Aindex_, AObondedatoms_, AOdist_, AOhybridization_, assign_only_pi_orbitals_to_atom(), assign_sp2_orbitals_to_one_bonded_atom(), assign_sp2_sp_orbitals_to_one_bonded_atom(), core::chemical::ChemicalManager::atom_type_set(), calculate_orbital_icoor(), Coordinates_Tetrahedral_bondedto3atoms_helper(), cross_product(), cross_product_helper(), core::kinematics::distance(), core::chemical::ChemicalManager::get_instance(), make_orbital_element_name(), make_orbital_type_name(), numeric::xyzVector< class >::normalized(), Orbtype_, numeric::NumericTraits< class >::pi(), numeric::conversions::radians(), restype_, set_orbital_type_and_bond(), core::chemical::orbitals::strip_whitespace(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), numeric::xyzVector< class >::z(), and numeric::xyzVector< class >::zero().

Referenced by core::chemical::ResidueTypeSet::add_residue_type(), and core::chemical::ResidueTypeSet::ResidueTypeSet().

void core::chemical::orbitals::AssignOrbitals::assign_sp2_orbitals_to_one_bonded_atom

(

core::chemical::AtomType const &

atmtype

)

References add_orbitals_to_restype(), Aindex_, AObondedatoms_, AOdist_, Coordinates_TriganolPlanar_bondedto1atom_helper(), and restype_.

Referenced by assign_orbitals().

void core::chemical::orbitals::AssignOrbitals::assign_sp2_sp_orbitals_to_one_bonded_atom

(

core::chemical::AtomType const &

atmtype

)

References add_orbitals_to_restype(), Aindex_, AObondedatoms_, AOdist_, Coordinates_TriganolPlanar_bondedto1atom_helper(), cross_product_helper(), and restype_.

Referenced by assign_orbitals().

void core::chemical::orbitals::AssignOrbitals::calculate_orbital_icoor	(	numeric::xyzVector< core::Real > const	orbital_xyz,
		core::Size const	atm_index1,
		core::Size const	atm_index2,
		core::Size const	atm_index3,
		std::string const	orbital_element_name
	)

References numeric::xyzVector< class >::distance(), core::kinematics::distance(), numeric::NumericTraits< class >::pi(), restype_, and core::chemical::orbitals::strip_whitespace().

Referenced by add_orbitals_to_restype(), and assign_orbitals().

utility::vector1< numeric::xyzVector< core::Real > > core::chemical::orbitals::AssignOrbitals::Coordinates_Tetrahedral_bondedto3atoms_helper	(	core::Size const	atm_index1,
		core::Size const	atm_index2,
		core::Size const	atm_index3,
		core::Size const	atm_index4,
		core::Real const	dist
	)

References restype_.

Referenced by assign_orbitals().

utility::vector1< numeric::xyzVector< core::Real > > core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper	(	core::Size const	atm_index1,
		core::Size const	atm_index2,
		core::Size const	atm_index3,
		core::Real const	dist
	)

References core::pack::dunbrack::c, cross_product(), numeric::constants::r::pi, numeric::constants::r::pi_over_3, and restype_.

Referenced by assign_sp2_orbitals_to_one_bonded_atom(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

utility::vector1< numeric::xyzVector< core::Real > > core::chemical::orbitals::AssignOrbitals::cross_product_helper	(	core::Size const	atm_index1,
		core::Size const	atm_index2,
		core::Size const	atm_index3,
		core::Real const	dist
	)

References cross_product(), and numeric::xyzVector< class >::normalized().

Referenced by assign_only_pi_orbitals_to_atom(), assign_orbitals(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

std::string core::chemical::orbitals::AssignOrbitals::make_orbital_element_name ( )

private

References n_orbitals_.

Referenced by add_orbitals_to_restype(), and assign_orbitals().

std::string core::chemical::orbitals::AssignOrbitals::make_orbital_type_name ( AtomType const &  atmtype, std::string const  orbitaltype, core::Size const  hybridization  )

private

References core::chemical::AtomType::element().

Referenced by add_orbitals_to_restype(), and assign_orbitals().

void core::chemical::orbitals::AssignOrbitals::set_orbital_type_and_bond ( core::Size  atom_index, std::string  orbital_element_name, std::string  orbital_type_full_name  )

private

References restype_, and core::chemical::orbitals::strip_whitespace().

Referenced by add_orbitals_to_restype(), and assign_orbitals().

Member Data Documentation

core::Size core::chemical::orbitals::AssignOrbitals::Aindex_

private

Referenced by add_orbitals_to_restype(), assign_only_pi_orbitals_to_atom(), assign_orbitals(), assign_sp2_orbitals_to_one_bonded_atom(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

utility::vector1<core::Size> core::chemical::orbitals::AssignOrbitals::AObondedatoms_

private

Referenced by assign_only_pi_orbitals_to_atom(), assign_orbitals(), assign_sp2_orbitals_to_one_bonded_atom(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

core::Real core::chemical::orbitals::AssignOrbitals::AOdist_

private

Referenced by assign_only_pi_orbitals_to_atom(), assign_orbitals(), assign_sp2_orbitals_to_one_bonded_atom(), and assign_sp2_sp_orbitals_to_one_bonded_atom().

core::Size core::chemical::orbitals::AssignOrbitals::AOhybridization_

private

Referenced by add_orbitals_to_restype(), and assign_orbitals().

core::Size core::chemical::orbitals::AssignOrbitals::n_orbitals_

private

Referenced by make_orbital_element_name().

core::Size core::chemical::orbitals::AssignOrbitals::Orbtype_

private

Referenced by assign_orbitals().

core::chemical::ResidueTypeOP core::chemical::orbitals::AssignOrbitals::restype_

private

Referenced by assign_only_pi_orbitals_to_atom(), assign_orbitals(), assign_sp2_orbitals_to_one_bonded_atom(), assign_sp2_sp_orbitals_to_one_bonded_atom(), calculate_orbital_icoor(), Coordinates_Tetrahedral_bondedto3atoms_helper(), Coordinates_TriganolPlanar_bondedto1atom_helper(), and set_orbital_type_and_bond().

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The documentation for this class was generated from the following files:

• src/core/chemical/orbitals/AssignOrbitals.hh
• src/core/chemical/orbitals/AssignOrbitals.cc