#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

◆ Matrix

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

◆ Residue

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

◆ Vector

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

Constructor & Destructor Documentation

◆ ~MultipoleElecResidueInfo()

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

overridedefault

◆ MultipoleElecResidueInfo() [1/2]

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

inline

◆ MultipoleElecResidueInfo() [2/2]

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

inline

References initialize().

Member Function Documentation

◆ clone()

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

inlineoverride

◆ const_my_group()

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().

◆ coord_frame_ref() [1/2]

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(), and core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs().

◆ coord_frame_ref() [2/2]

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

inline

References coord_frame_ref_.

◆ copy_clone()

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

inline

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

◆ dipole()

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

inline

References dipole_.

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

◆ Efield_fixed() [1/2]

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

inline

References Efield_fixed_.

◆ Efield_fixed() [2/2]

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

inline

References Efield_fixed_.

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

◆ Efield_induced() [1/2]

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

inline

References Efield_induced_.

◆ Efield_induced() [2/2]

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(), core::scoring::MultipoleElecPotential::clear_induced_fields(), and core::scoring::MultipoleElecPotential::get_polarization_from_fields().

◆ Efield_rf_fixed() [1/2]

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

inline

References Efield_rf_fixed_.

◆ Efield_rf_fixed() [2/2]

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

inline

References Efield_rf_fixed_.

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

◆ Efield_rf_induced() [1/2]

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

inline

References Efield_rf_induced_.

◆ Efield_rf_induced() [2/2]

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

inline

References Efield_rf_induced_.

◆ induced_dipole()

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

inline

References induced_dipole_.

Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::MultipoleElecPotential::get_polarization_from_fields(), core::scoring::MultipoleElecPotential::get_res_res_elecE(), core::scoring::MultipoleElecPotential::induce_polarizable_dipoles(), core::scoring::MultipoleElecPotential::relax_induced_dipoles(), and core::scoring::MultipoleElecPotential::store_induced_dipoles().

◆ induced_rf_dipole()

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

inline

References induced_rf_dipole_.

◆ initialize()

void core::scoring::MultipoleElecResidueInfo::initialize ( conformation::Residue const & rsd )

◆ local_coord_matrix()

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

inline

References local_coord_matrix_.

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

◆ monopole()

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

inline

References monopole_.

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

◆ mp_param()

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

inline

References mp_param_.

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

◆ my_group()

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

inline

References my_group_.

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

◆ my_local_coord_frame()

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().

◆ nonconst_dipole()

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

inline

References dipole_.

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

◆ nonconst_induced_dipole()

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().

◆ nonconst_induced_rf_dipole()

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().

◆ nonconst_monopole()

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

inline

References monopole_.

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

◆ nonconst_mp_param()

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

inline

References mp_param_.

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

◆ nonconst_quadrupole()

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

inline

References quadrupole_.

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

◆ nonconst_rKirkwood()

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

inline

References rKirkwood_.

Referenced by core::scoring::MultipoleElecPotential::get_effective_radii(), and core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii().

◆ nonconst_rosetta_res_type()

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

inline

References rosetta_res_type_.

◆ nonconst_stored_induced_dipole()

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().

◆ nonconst_stored_induced_rf_dipole()

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

inline

References stored_induced_rf_dipole_.

◆ quadrupole()

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

inline

References quadrupole_.

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

◆ rKirkwood()

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

inline

References rKirkwood_.

Referenced by core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs(), 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().

◆ rosetta_res_type()

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

inline

References rosetta_res_type_.

◆ set_coord_frame_ref()

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().

◆ set_type()

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

inline

References type_.

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

◆ stored_induced_dipole()

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(), and core::scoring::MultipoleElecPotential::relax_induced_dipoles().

◆ stored_induced_rf_dipole()

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().

◆ type() [1/2]

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

inline

References type_.

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

◆ type() [2/2]

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

inline

References type_.

Member Data Documentation

◆ coord_frame_ref_

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

private

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

◆ dipole_

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

private

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

◆ Efield_fixed_

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

private

Referenced by Efield_fixed(), and initialize().

◆ Efield_induced_

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

private

Referenced by Efield_induced(), and initialize().

◆ Efield_rf_fixed_

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

private

Referenced by Efield_rf_fixed(), and initialize().

◆ Efield_rf_induced_

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

private

Referenced by Efield_rf_induced(), and initialize().

◆ induced_dipole_

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

private

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

◆ induced_rf_dipole_

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

private

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

◆ local_coord_matrix_

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

private

Referenced by initialize(), and local_coord_matrix().

◆ monopole_

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

private

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

◆ mp_param_

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

private

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

◆ my_group_

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

private

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

◆ my_local_coord_frame_

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

private

Referenced by initialize(), and my_local_coord_frame().

◆ quadrupole_

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

private

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

◆ rKirkwood_

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

private

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

◆ rosetta_res_type_

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

private

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

◆ stored_induced_dipole_

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

private

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

◆ stored_induced_rf_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().

◆ type_

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

Public Types

Public Member Functions

Private Attributes

Member Typedef Documentation

◆ Matrix

◆ Residue

◆ Vector

Constructor & Destructor Documentation

◆ ~MultipoleElecResidueInfo()

◆ MultipoleElecResidueInfo() [1/2]

◆ MultipoleElecResidueInfo() [2/2]

Member Function Documentation

◆ clone()

◆ const_my_group()

◆ coord_frame_ref() [1/2]

◆ coord_frame_ref() [2/2]

◆ copy_clone()

◆ dipole()

◆ Efield_fixed() [1/2]

◆ Efield_fixed() [2/2]

◆ Efield_induced() [1/2]

◆ Efield_induced() [2/2]

◆ Efield_rf_fixed() [1/2]

◆ Efield_rf_fixed() [2/2]

◆ Efield_rf_induced() [1/2]

◆ Efield_rf_induced() [2/2]

◆ induced_dipole()

◆ induced_rf_dipole()

◆ initialize()

◆ local_coord_matrix()

◆ monopole()

◆ mp_param()

◆ my_group()

◆ my_local_coord_frame()

◆ nonconst_dipole()

◆ nonconst_induced_dipole()

◆ nonconst_induced_rf_dipole()

◆ nonconst_monopole()

◆ nonconst_mp_param()

◆ nonconst_quadrupole()

◆ nonconst_rKirkwood()

◆ nonconst_rosetta_res_type()

◆ nonconst_stored_induced_dipole()

◆ nonconst_stored_induced_rf_dipole()

◆ quadrupole()

◆ rKirkwood()

◆ rosetta_res_type()

◆ set_coord_frame_ref()

◆ set_type()

◆ stored_induced_dipole()

◆ stored_induced_rf_dipole()

◆ type() [1/2]

◆ type() [2/2]

Member Data Documentation

◆ 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_

◆ quadrupole_

◆ rKirkwood_

◆ rosetta_res_type_

◆ stored_induced_dipole_

◆ stored_induced_rf_dipole_

◆ type_