#include <AssignOrbitals.hh>

Collaboration diagram for core::chemical::orbitals::AssignOrbitals:

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_

Detailed Description

Definition at line 35 of file AssignOrbitals.hh.

Constructor & Destructor Documentation

core::chemical::orbitals::AssignOrbitals::AssignOrbitals ( core::chemical::ResidueTypeOP const restype)

Definition at line 42 of file AssignOrbitals.cc.

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
	)

Definition at line 448 of file AssignOrbitals.cc.

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)

Definition at line 347 of file AssignOrbitals.cc.

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

Referenced by assign_orbitals().

void core::chemical::orbitals::AssignOrbitals::assign_orbitals ( )

Definition at line 50 of file AssignOrbitals.cc.

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_helper(), core::kinematics::distance(), core::chemical::ChemicalManager::get_instance(), make_orbital_element_name(), make_orbital_type_name(), Orbtype_, protocols::swa::phi(), restype_, set_orbital_type_and_bond(), and core::chemical::orbitals::strip_whitespace().

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)

Definition at line 392 of file AssignOrbitals.cc.

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)

Definition at line 368 of file AssignOrbitals.cc.

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
	)

Definition at line 514 of file AssignOrbitals.cc.

References core::kinematics::distance(), protocols::swa::phi(), 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
	)

Definition at line 632 of file AssignOrbitals.cc.

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
	)

Definition at line 567 of file AssignOrbitals.cc.

References protocols::match::upstream::b, core::pack::dunbrack::c, 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
	)

Definition at line 418 of file AssignOrbitals.cc.

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

Definition at line 486 of file AssignOrbitals.cc.

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

Definition at line 465 of file AssignOrbitals.cc.

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
	)