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

#include <AssignOrbitals.hh>

Collaboration diagram for core::chemical::orbitals::AssignOrbitals:
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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::SizeAObondedatoms_
 
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 
)
void core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom ( core::chemical::AtomType const &  atmtype)
void core::chemical::orbitals::AssignOrbitals::assign_orbitals ( )
void core::chemical::orbitals::AssignOrbitals::assign_sp2_orbitals_to_one_bonded_atom ( core::chemical::AtomType const &  atmtype)
void core::chemical::orbitals::AssignOrbitals::assign_sp2_sp_orbitals_to_one_bonded_atom ( core::chemical::AtomType const &  atmtype)
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 
)
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 
)
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 
)
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
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

Member Data Documentation

core::Size core::chemical::orbitals::AssignOrbitals::Aindex_
private
utility::vector1<core::Size> core::chemical::orbitals::AssignOrbitals::AObondedatoms_
private
core::Real core::chemical::orbitals::AssignOrbitals::AOdist_
private
core::Size core::chemical::orbitals::AssignOrbitals::AOhybridization_
private
core::Size core::chemical::orbitals::AssignOrbitals::n_orbitals_
private
core::Size core::chemical::orbitals::AssignOrbitals::Orbtype_
private

Referenced by assign_orbitals().

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

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