core::scoring::MultipoleElecResidueInfo Class Reference

#include <MultipoleElecPotential.hh>

Inheritance diagram for core::scoring::MultipoleElecResidueInfo:

Public Types
typedef conformation::Residue	Residue
typedef numeric::xyzMatrix< Real >	Matrix
typedef numeric::xyzVector< Real >	Vector

Public Member Functions
	~MultipoleElecResidueInfo () override
MultipoleElecResidueInfoOP	copy_clone () const
basic::datacache::CacheableDataOP	clone () const override
	MultipoleElecResidueInfo ()
	MultipoleElecResidueInfo (Residue const &rsd)
utility::vector1< Size > const &	type () const
Size	type (Size const atm) const
void	set_type (Size const atm, Size in_val)
utility::vector1< id::AtomID > const &	coord_frame_ref () const
id::AtomID	coord_frame_ref (Size const atm) const
void	set_coord_frame_ref (Size const atm, id::AtomID in_val)
Real	monopole (Size const atm) const
Real	rKirkwood (Size const atm) const
Real &	nonconst_rKirkwood (Size const atm)
Vector const &	dipole (Size const atm) const
Vector const &	induced_dipole (Size const atm) const
Vector const &	stored_induced_dipole (Size const atm) const
Vector const &	induced_rf_dipole (Size const atm) const
Vector const &	stored_induced_rf_dipole (Size const atm) const
Matrix const &	quadrupole (Size const atm) const
Real &	nonconst_monopole (Size const atm)
Vector &	nonconst_stored_induced_dipole (Size const atm)
Vector &	nonconst_induced_dipole (Size const atm)
Vector &	nonconst_stored_induced_rf_dipole (Size const atm)
Vector &	nonconst_induced_rf_dipole (Size const atm)
Vector &	Efield_fixed (Size const atm)
utility::vector1< Vector > &	Efield_fixed ()
Vector &	Efield_induced (Size const atm)
utility::vector1< Vector > &	Efield_induced ()
Vector &	Efield_rf_fixed (Size const atm)
utility::vector1< Vector > &	Efield_rf_fixed ()
Vector &	Efield_rf_induced (Size const atm)
utility::vector1< Vector > &	Efield_rf_induced ()
Vector &	nonconst_dipole (Size const atm)
Matrix &	nonconst_quadrupole (Size const atm)
utility::vector1< id::AtomID > &	my_group (Size const atm)
utility::vector1< id::AtomID > const &	const_my_group (Size const atm) const
utility::vector1< id::AtomID > &	my_local_coord_frame (Size const atm)
Matrix &	local_coord_matrix (Size const atm)
MultipoleParameterOP const &	mp_param (Size atm1) const
MultipoleParameterOP &	nonconst_mp_param (Size atm1)
std::string const &	rosetta_res_type () const
std::string &	nonconst_rosetta_res_type ()
void	initialize (Residue const &rsd)

Private Attributes
utility::vector1< Size >	type_
utility::vector1< id::AtomID >	coord_frame_ref_
utility::vector1< Real >	monopole_
utility::vector1< Real >	rKirkwood_
utility::vector1< Vector >	dipole_
utility::vector1< Vector >	induced_dipole_
utility::vector1< Vector >	stored_induced_dipole_
utility::vector1< Vector >	induced_rf_dipole_
utility::vector1< Vector >	stored_induced_rf_dipole_
utility::vector1< Vector >	Efield_fixed_
utility::vector1< Vector >	Efield_induced_
utility::vector1< Vector >	Efield_rf_fixed_
utility::vector1< Vector >	Efield_rf_induced_
utility::vector1< Matrix >	quadrupole_
utility::vector1< Matrix >	local_coord_matrix_
utility::vector1 < utility::vector1< id::AtomID > >	my_group_
utility::vector1 < utility::vector1< id::AtomID > >	my_local_coord_frame_
utility::vector1 < MultipoleParameterOP >	mp_param_
std::string	rosetta_res_type_

Member Typedef Documentation

typedef numeric::xyzMatrix< Real > core::scoring::MultipoleElecResidueInfo::Matrix

typedef conformation::Residue core::scoring::MultipoleElecResidueInfo::Residue

typedef numeric::xyzVector< Real > core::scoring::MultipoleElecResidueInfo::Vector

Constructor & Destructor Documentation

core::scoring::MultipoleElecResidueInfo::~MultipoleElecResidueInfo ( )

overridedefault

core::scoring::MultipoleElecResidueInfo::MultipoleElecResidueInfo ( )

inline

core::scoring::MultipoleElecResidueInfo::MultipoleElecResidueInfo ( Residue const &  rsd )

inline

References initialize().

Member Function Documentation

basic::datacache::CacheableDataOP core::scoring::MultipoleElecResidueInfo::clone ( ) const

inlineoverride

utility::vector1< id::AtomID > const& core::scoring::MultipoleElecResidueInfo::const_my_group ( Size const  atm ) const

inline

References my_group_.

Referenced by core::scoring::same_polarization_group().

utility::vector1< id::AtomID > const& core::scoring::MultipoleElecResidueInfo::coord_frame_ref ( ) const

inline

References coord_frame_ref_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes().

id::AtomID core::scoring::MultipoleElecResidueInfo::coord_frame_ref ( Size const  atm ) const

inline

References coord_frame_ref_.

MultipoleElecResidueInfoOP core::scoring::MultipoleElecResidueInfo::copy_clone ( ) const

inline

Referenced by core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue().

Vector const& core::scoring::MultipoleElecResidueInfo::dipole ( Size const  atm ) const

inline

References dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

Vector& core::scoring::MultipoleElecResidueInfo::Efield_fixed ( Size const  atm )

inline

References Efield_fixed_.

Referenced by core::scoring::MultipoleElecPotential::calculate_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization().

utility::vector1< Vector >& core::scoring::MultipoleElecResidueInfo::Efield_fixed ( )

inline

References Efield_fixed_.

Vector& core::scoring::MultipoleElecResidueInfo::Efield_induced ( Size const  atm )

inline

References Efield_induced_.

Referenced by core::scoring::MultipoleElecPotential::calculate_induced_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::clear_induced_fields().

utility::vector1< Vector >& core::scoring::MultipoleElecResidueInfo::Efield_induced ( )

inline

References Efield_induced_.

Vector& core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed ( Size const  atm )

inline

References Efield_rf_fixed_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization().

utility::vector1< Vector >& core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed ( )

inline

References Efield_rf_fixed_.

Vector& core::scoring::MultipoleElecResidueInfo::Efield_rf_induced ( Size const  atm )

inline

References Efield_rf_induced_.

utility::vector1< Vector >& core::scoring::MultipoleElecResidueInfo::Efield_rf_induced ( )

inline

References Efield_rf_induced_.

Vector const& core::scoring::MultipoleElecResidueInfo::induced_dipole ( Size const  atm ) const

inline

References induced_dipole_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

Vector const& core::scoring::MultipoleElecResidueInfo::induced_rf_dipole ( Size const  atm ) const

inline

References induced_rf_dipole_.

void core::scoring::MultipoleElecResidueInfo::initialize

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::atom_name(), coord_frame_ref_, dipole_, Efield_fixed_, Efield_induced_, Efield_rf_fixed_, Efield_rf_induced_, induced_dipole_, induced_rf_dipole_, local_coord_matrix_, monopole_, mp_param_, my_group_, my_local_coord_frame_, core::conformation::Residue::name(), core::conformation::Residue::natoms(), quadrupole_, rKirkwood_, rosetta_res_type_, core::conformation::Residue::seqpos(), stored_induced_dipole_, stored_induced_rf_dipole_, core::scoring::TR(), type_, and core::conformation::Residue::xyz().

Referenced by MultipoleElecResidueInfo().

Matrix& core::scoring::MultipoleElecResidueInfo::local_coord_matrix ( Size const  atm )

inline

References local_coord_matrix_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

Real core::scoring::MultipoleElecResidueInfo::monopole ( Size const  atm ) const

inline

References monopole_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

MultipoleParameterOP const& core::scoring::MultipoleElecResidueInfo::mp_param ( Size  atm1 ) const

inline

References mp_param_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

utility::vector1< id::AtomID >& core::scoring::MultipoleElecResidueInfo::my_group ( Size const  atm )

inline

References my_group_.

utility::vector1< id::AtomID >& core::scoring::MultipoleElecResidueInfo::my_local_coord_frame ( Size const  atm )

inline

References my_local_coord_frame_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate(), and core::scoring::MultipoleElecPotential::find_params_and_neighbors().

Vector& core::scoring::MultipoleElecResidueInfo::nonconst_dipole ( Size const  atm )

inline

References dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

Vector& core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole ( Size const  atm )

inline

References induced_dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), and core::scoring::MultipoleElecPotential::relax_induced_dipoles().

Vector& core::scoring::MultipoleElecResidueInfo::nonconst_induced_rf_dipole ( Size const  atm )

inline

References induced_rf_dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

Real& core::scoring::MultipoleElecResidueInfo::nonconst_monopole ( Size const  atm )

inline

References monopole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

MultipoleParameterOP& core::scoring::MultipoleElecResidueInfo::nonconst_mp_param ( Size  atm1 )

inline

References mp_param_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes().

Matrix& core::scoring::MultipoleElecResidueInfo::nonconst_quadrupole ( Size const  atm )

inline

References quadrupole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

Real& core::scoring::MultipoleElecResidueInfo::nonconst_rKirkwood ( Size const  atm )

inline

References rKirkwood_.

Referenced by core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii().

std::string& core::scoring::MultipoleElecResidueInfo::nonconst_rosetta_res_type ( )

inline

References rosetta_res_type_.

Vector& core::scoring::MultipoleElecResidueInfo::nonconst_stored_induced_dipole ( Size const  atm )

inline

References stored_induced_dipole_.

Referenced by core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), and core::scoring::MultipoleElecPotential::store_induced_dipoles().

Vector& core::scoring::MultipoleElecResidueInfo::nonconst_stored_induced_rf_dipole ( Size const  atm )

inline

References stored_induced_rf_dipole_.

Matrix const& core::scoring::MultipoleElecResidueInfo::quadrupole ( Size const  atm ) const

inline

References quadrupole_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

Real core::scoring::MultipoleElecResidueInfo::rKirkwood ( Size const  atm ) const

inline

References rKirkwood_.

Referenced by core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), and core::scoring::MultipoleElecPotential::get_res_res_elecE().

std::string const& core::scoring::MultipoleElecResidueInfo::rosetta_res_type ( ) const

inline

References rosetta_res_type_.

void core::scoring::MultipoleElecResidueInfo::set_coord_frame_ref ( Size const  atm, id::AtomID  in_val  )

inline

References coord_frame_ref_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes().

void core::scoring::MultipoleElecResidueInfo::set_type ( Size const  atm, Size  in_val  )

inline

References type_.

Referenced by core::scoring::MultipoleElecPotential::assign_residue_amoeba_type().

Vector const& core::scoring::MultipoleElecResidueInfo::stored_induced_dipole ( Size const  atm ) const

inline

References stored_induced_dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

Vector const& core::scoring::MultipoleElecResidueInfo::stored_induced_rf_dipole ( Size const  atm ) const

inline

References stored_induced_rf_dipole_.

Referenced by core::scoring::MultipoleElecPotential::build_frame_and_rotate().

utility::vector1< Size > const& core::scoring::MultipoleElecResidueInfo::type ( ) const

inline

References type_.

Referenced by core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), and core::scoring::MultipoleElecPotential::find_params_and_neighbors().

Size core::scoring::MultipoleElecResidueInfo::type ( Size const  atm ) const

inline

References type_.

Member Data Documentation

utility::vector1< id::AtomID > core::scoring::MultipoleElecResidueInfo::coord_frame_ref_

private

Referenced by coord_frame_ref(), initialize(), and set_coord_frame_ref().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::dipole_

private

Referenced by dipole(), initialize(), and nonconst_dipole().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::Efield_fixed_

private

Referenced by Efield_fixed(), and initialize().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::Efield_induced_

private

Referenced by Efield_induced(), and initialize().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed_

private

Referenced by Efield_rf_fixed(), and initialize().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::Efield_rf_induced_

private

Referenced by Efield_rf_induced(), and initialize().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::induced_dipole_

private

Referenced by induced_dipole(), initialize(), and nonconst_induced_dipole().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::induced_rf_dipole_

private

Referenced by induced_rf_dipole(), initialize(), and nonconst_induced_rf_dipole().

utility::vector1< Matrix > core::scoring::MultipoleElecResidueInfo::local_coord_matrix_

private

Referenced by initialize(), and local_coord_matrix().

utility::vector1< Real > core::scoring::MultipoleElecResidueInfo::monopole_

private

Referenced by initialize(), monopole(), and nonconst_monopole().

utility::vector1< MultipoleParameterOP > core::scoring::MultipoleElecResidueInfo::mp_param_

private

Referenced by initialize(), mp_param(), and nonconst_mp_param().

utility::vector1< utility::vector1< id::AtomID > > core::scoring::MultipoleElecResidueInfo::my_group_

private

Referenced by const_my_group(), initialize(), and my_group().

utility::vector1< utility::vector1< id::AtomID > > core::scoring::MultipoleElecResidueInfo::my_local_coord_frame_

private

Referenced by initialize(), and my_local_coord_frame().

utility::vector1< Matrix > core::scoring::MultipoleElecResidueInfo::quadrupole_

private

Referenced by initialize(), nonconst_quadrupole(), and quadrupole().

utility::vector1< Real > core::scoring::MultipoleElecResidueInfo::rKirkwood_

private

Referenced by initialize(), nonconst_rKirkwood(), and rKirkwood().

std::string core::scoring::MultipoleElecResidueInfo::rosetta_res_type_

private

Referenced by initialize(), nonconst_rosetta_res_type(), and rosetta_res_type().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::stored_induced_dipole_

private

Referenced by initialize(), nonconst_stored_induced_dipole(), and stored_induced_dipole().

utility::vector1< Vector > core::scoring::MultipoleElecResidueInfo::stored_induced_rf_dipole_

private

Referenced by initialize(), nonconst_stored_induced_rf_dipole(), and stored_induced_rf_dipole().

utility::vector1< Size > core::scoring::MultipoleElecResidueInfo::type_

private

Referenced by initialize(), set_type(), and type().

---

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

• src/core/scoring/MultipoleElecPotential.hh
• src/core/scoring/MultipoleElecPotential.cc