core::scoring::MultipoleElecPotential Class Reference

#include <MultipoleElecPotential.hh>

Inheritance diagram for core::scoring::MultipoleElecPotential:

Public Types
typedef core::conformation::Residue	Residue

Public Member Functions
	MultipoleElecPotential ()
	ctor More...
	MultipoleElecPotential (methods::EnergyMethodOptions const &options)
	Options constructor. More...
void	read_in_amoeba_parameters ()
void	read_in_multipole_parameters ()
	read in multipole parameters for amoeba types More...
void	find_params_and_neighbors (core::pose::Pose const &pose, MultipoleParameterOP &mp_param, MultipoleElecResidueInfo &mp, core::conformation::Residue const &rsd, Size const j, Size const this_type) const
	Find the appropriate multipole params and axis atoms. More...
void	build_frame_and_rotate (core::pose::Pose const &pose, MultipoleParameterOP &mp_param, Size orig_atom, MultipoleElecResidueInfo &mp, core::conformation::Residue const &rsd) const
core::Size	amoeba_type_lookup (std::string const &atomname, std::string const &resname, std::string const &variantname, std::string const &variantname2) const
	Look up Amoeba type by resname/atomname/variant name. More...
void	align_residue_multipole_axes (core::pose::Pose const &pose, Residue const &rsd, MultipoleElecResidueInfo &mp) const
	called prior to scoring, eg More...
void	align_multipole_axes (pose::Pose &pose) const
	called prior to scoring, eg More...
void	assign_residue_amoeba_type (Residue const &rsd, MultipoleElecResidueInfo &mp) const
	called prior to scoring, eg More...
void	assign_all_amoeba_types (pose::Pose &pose) const
	called prior to scoring, eg More...
void	determine_polarization_groups (pose::Pose &pose) const
	called prior to scoring, eg More...
void	induce_polarizable_dipoles (pose::Pose &pose) const
	called prior to scoring, eg More...
void	store_induced_dipoles (pose::Pose &pose) const
	Copies over induced dipoles to storage. More...
core::Real	relax_induced_dipoles (pose::Pose &pose, Real relax) const
	Copies over induced dipoles to storage. More...
void	calculate_fixed_fields_for_polarization (pose::Pose &pose) const
	Get the electric field due to permanent multipoles. More...
void	clear_induced_fields (pose::Pose &pose) const
	Zero out the fields due to induced dipoles. More...
void	calculate_induced_fields_for_polarization (pose::Pose &pose) const
	Get the electric field due to permanent multipoles. More...
void	get_polarization_from_fields (pose::Pose &pose) const
	Get the electric field due to permanent multipoles. More...
void	get_effective_radii (pose::Pose &pose) const
	Get the effective radii for Generalized Kirkwood. More...
void	get_rotamers_multipole_info (pose::Pose const &pose, conformation::RotamerSetBase &) const
	Get the amoeba info for rotamers. More...
void	get_rotamers_effective_radii (pose::Pose const &pose, conformation::RotamerSetBase &) const
	Get the effective radii for Generalized Kirkwood. More...
void	get_single_rotamer_effective_radii (Residue const &rsd1, pose::Pose const &pose, MultipoleElecPoseInfoCOP mp_info, MultipoleElecResidueInfo &mp1) const
	Get the effective radii for Generalized Kirkwood. More...
void	setup_for_scoring (pose::Pose &pose) const
void	setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &repacking_residues) const
	Note: when called at the beginning of rotamer_trials, task.being_packed(i) will be false for all i this ensures that we use all the information we have to compute the current set of radii. More...
void	update_residue_for_packing (pose::Pose &pose, Size const seqpos) const
	called eg after a rotamer substitution is accepted during rotamer trials More...
Real	get_res_res_elecE (Residue const &rsd1, MultipoleElecResidueInfo const &mp1, Residue const &rsd2, MultipoleElecResidueInfo const &mp2) const
void	calculate_res_res_fixed_fields_for_polarization (Residue const &rsd1, MultipoleElecResidueInfo &mp1, Residue const &rsd2, MultipoleElecResidueInfo &mp2) const
void	calculate_res_res_induced_fields_for_polarization (Residue const &rsd1, MultipoleElecResidueInfo &mp1, Residue const &rsd2, MultipoleElecResidueInfo &mp2) const
void	calculate_and_store_all_derivs (pose::Pose const &pose) const
void	eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, MultipoleElecResidueInfo const &mp1, MultipoleElecResidueInfo const &mp2, pose::Pose const &pose, Real const &factor, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const

Private Attributes
Real	Ep
Real	Ew
Real const	bohr
bool	use_polarization
bool	use_gen_kirkwood
std::map< std::string, Size >	type_lookup_
std::string const	default_variant_
std::multimap< Size, MultipoleParameter::MultipoleParameterOP >	multipole_info_
utility::vector1< utility::vector1< DerivVectorPair > >	cached_atom_derivs_

Member Typedef Documentation

Residue

typedef core::conformation::Residue core::scoring::MultipoleElecPotential::Residue

Constructor & Destructor Documentation

MultipoleElecPotential() [1/2]

core::scoring::MultipoleElecPotential::MultipoleElecPotential ( )

inline

ctor

References read_in_amoeba_parameters(), and read_in_multipole_parameters().

MultipoleElecPotential() [2/2]

core::scoring::MultipoleElecPotential::MultipoleElecPotential

(

methods::EnergyMethodOptions const &

options

)

Options constructor.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References read_in_amoeba_parameters(), and read_in_multipole_parameters().

Member Function Documentation

align_multipole_axes()

void core::scoring::MultipoleElecPotential::align_multipole_axes

(

pose::Pose &

pose

)

const

called prior to scoring, eg

References align_residue_multipole_axes(), core::conformation::Residue::atom_name(), core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::dipole(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), and core::scoring::TR().

Referenced by setup_for_scoring().

align_residue_multipole_axes()

void core::scoring::MultipoleElecPotential::align_residue_multipole_axes	(	core::pose::Pose const &	pose,
		Residue const &	rsd,
		MultipoleElecResidueInfo &	mp
	)		const

called prior to scoring, eg

References core::kinematics::AtomTree::atom(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::pose::Pose::atom_tree(), core::id::AtomID::atomno(), core::conformation::Residue::bonded_neighbor(), build_frame_and_rotate(), core::conformation::Residue::chi_atoms(), core::scoring::MultipoleElecResidueInfo::coord_frame_ref(), find_params_and_neighbors(), core::conformation::Residue::is_virtual(), core::conformation::Residue::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::conformation::Residue::nchi(), core::scoring::MultipoleElecResidueInfo::nonconst_mp_param(), core::kinematics::tree::Atom::parent(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), core::scoring::MultipoleElecResidueInfo::set_coord_frame_ref(), core::scoring::TR(), core::conformation::Residue::type(), core::scoring::MultipoleElecResidueInfo::type(), and core::conformation::Residue::xyz().

Referenced by align_multipole_axes(), get_rotamers_multipole_info(), core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue(), core::energy_methods::MultipoleElecEnergy::setup_for_scoring_for_residue(), and update_residue_for_packing().

amoeba_type_lookup()

core::Size core::scoring::MultipoleElecPotential::amoeba_type_lookup	(	std::string const &	atomname,
		std::string const &	resname,
		std::string const &	variantname,
		std::string const &	variantname2
	)		const

Look up Amoeba type by resname/atomname/variant name.

References core::scoring::TR(), and type_lookup_.

Referenced by assign_residue_amoeba_type().

assign_all_amoeba_types()

void core::scoring::MultipoleElecPotential::assign_all_amoeba_types

(

pose::Pose &

pose

)

const

called prior to scoring, eg

References assign_residue_amoeba_type(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by setup_for_scoring().

assign_residue_amoeba_type()

void core::scoring::MultipoleElecPotential::assign_residue_amoeba_type	(	Residue const &	rsd,
		MultipoleElecResidueInfo &	mp
	)		const

called prior to scoring, eg

References amoeba_type_lookup(), core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::set_type(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by assign_all_amoeba_types(), get_rotamers_multipole_info(), core::energy_methods::MultipoleElecEnergy::setup_for_minimizing_for_residue(), core::energy_methods::MultipoleElecEnergy::setup_for_scoring_for_residue(), and update_residue_for_packing().

build_frame_and_rotate()

void core::scoring::MultipoleElecPotential::build_frame_and_rotate	(	core::pose::Pose const &	pose,
		MultipoleParameterOP &	mp_param,
		Size	orig_atom,
		MultipoleElecResidueInfo &	mp,
		core::conformation::Residue const &	rsd
	)		const

Build the matrix to rotate from the local frame to the global one.

References core::conformation::Residue::atom_name(), core::scoring::bisector, core::scoring::MultipoleElecResidueInfo::dipole(), core::scoring::MultipoleElecResidueInfo::local_coord_matrix(), core::scoring::MultipoleElecResidueInfo::my_local_coord_frame(), core::conformation::Residue::name3(), core::scoring::MultipoleElecResidueInfo::nonconst_dipole(), core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole(), core::scoring::MultipoleElecResidueInfo::nonconst_induced_rf_dipole(), core::scoring::MultipoleElecResidueInfo::nonconst_monopole(), core::scoring::MultipoleElecResidueInfo::nonconst_quadrupole(), core::scoring::none, protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), protocols::cluster::calibur::rotate(), core::conformation::Residue::seqpos(), core::scoring::MultipoleElecResidueInfo::stored_induced_dipole(), core::scoring::MultipoleElecResidueInfo::stored_induced_rf_dipole(), core::scoring::three_fold, core::scoring::TR(), core::conformation::Residue::xyz(), core::scoring::z_axis_only, core::scoring::z_then_bisector, and core::scoring::z_then_x.

Referenced by align_residue_multipole_axes().

calculate_and_store_all_derivs()

void core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs

(

pose::Pose const &

pose

)

const

References cached_atom_derivs_, core::scoring::MultipoleElecResidueInfo::coord_frame_ref(), core::scoring::etable::count_pair::CP_CROSSOVER_34, core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_intrares_count_pair_function(), core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::dipole(), core::pose::Pose::energies(), Ep, Ew, core::scoring::get_damped_scale_factors_with_derivs(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::scoring::MultipoleElecResidueInfo::monopole(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::scoring::MultipoleElecResidueInfo::quadrupole(), core::pose::Pose::residue(), core::scoring::MultipoleElecResidueInfo::rKirkwood(), core::scoring::same_polarization_group(), core::pose::Pose::size(), core::scoring::T(), use_gen_kirkwood, core::scoring::Energies::use_nblist(), and core::conformation::Residue::xyz().

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

calculate_fixed_fields_for_polarization()

void core::scoring::MultipoleElecPotential::calculate_fixed_fields_for_polarization

(

pose::Pose &

pose

)

const

Get the electric field due to permanent multipoles.

References calculate_res_res_fixed_fields_for_polarization(), core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::Efield_fixed(), core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

calculate_induced_fields_for_polarization()

void core::scoring::MultipoleElecPotential::calculate_induced_fields_for_polarization

(

pose::Pose &

pose

)

const

Get the electric field due to permanent multipoles.

References calculate_res_res_induced_fields_for_polarization(), core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::Efield_induced(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

calculate_res_res_fixed_fields_for_polarization()

void core::scoring::MultipoleElecPotential::calculate_res_res_fixed_fields_for_polarization	(	Residue const &	rsd1,
		MultipoleElecResidueInfo &	mp1,
		Residue const &	rsd2,
		MultipoleElecResidueInfo &	mp2
	)		const

References core::scoring::MultipoleElecResidueInfo::dipole(), core::scoring::MultipoleElecResidueInfo::Efield_fixed(), core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed(), Ep, Ew, core::scoring::get_damped_scale_factors(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::monopole(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::quadrupole(), core::scoring::MultipoleElecResidueInfo::rKirkwood(), core::scoring::same_polarization_group(), core::conformation::Residue::seqpos(), use_gen_kirkwood, and core::conformation::Residue::xyz().

Referenced by calculate_fixed_fields_for_polarization().

calculate_res_res_induced_fields_for_polarization()

void core::scoring::MultipoleElecPotential::calculate_res_res_induced_fields_for_polarization	(	Residue const &	rsd1,
		MultipoleElecResidueInfo &	mp1,
		Residue const &	rsd2,
		MultipoleElecResidueInfo &	mp2
	)		const

References core::scoring::MultipoleElecResidueInfo::Efield_induced(), Ep, Ew, core::scoring::get_damped_scale_factors(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::rKirkwood(), core::conformation::Residue::seqpos(), use_gen_kirkwood, and core::conformation::Residue::xyz().

Referenced by calculate_induced_fields_for_polarization().

clear_induced_fields()

void core::scoring::MultipoleElecPotential::clear_induced_fields

(

pose::Pose &

pose

)

const

Zero out the fields due to induced dipoles.

References core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::Efield_induced(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

determine_polarization_groups()

void core::scoring::MultipoleElecPotential::determine_polarization_groups

(

pose::Pose &

pose

)

const

called prior to scoring, eg

References core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::sequence::end, core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::scoring::MultipoleElecResidueInfo::my_group(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), core::scoring::TR(), core::scoring::MultipoleElecResidueInfo::type(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring(), and update_residue_for_packing().

eval_residue_pair_derivatives()

void core::scoring::MultipoleElecPotential::eval_residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		MultipoleElecResidueInfo const &	mp1,
		MultipoleElecResidueInfo const &	mp2,
		pose::Pose const &	pose,
		Real const &	factor,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const

References cached_atom_derivs_, core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), and core::scoring::TR().

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

find_params_and_neighbors()

void core::scoring::MultipoleElecPotential::find_params_and_neighbors	(	core::pose::Pose const &	pose,
		MultipoleParameterOP &	mp_param,
		MultipoleElecResidueInfo &	mp,
		core::conformation::Residue const &	rsd,
		Size const	j,
		Size const	this_type
	)		const

Find the appropriate multipole params and axis atoms.

References core::conformation::Residue::atom_name(), core::scoring::bisector, core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::lower_connect_atom(), multipole_info_, core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::scoring::MultipoleElecResidueInfo::my_local_coord_frame(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::conformation::Residue::nbrs(), core::scoring::none, core::scoring::pair, core::conformation::Residue::path_distance(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::scoring::three_fold, core::scoring::TR(), core::scoring::MultipoleElecResidueInfo::type(), core::conformation::Residue::upper_connect_atom(), core::scoring::z_axis_only, core::scoring::z_then_bisector, and core::scoring::z_then_x.

Referenced by align_residue_multipole_axes().

get_effective_radii()

void core::scoring::MultipoleElecPotential::get_effective_radii

(

pose::Pose &

pose

)

const

Get the effective radii for Generalized Kirkwood.

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::pose::Pose::data(), core::chemical::AtomType::extra_parameter(), core::chemical::AtomTypeSet::extra_parameter_index(), core::conformation::Residue::is_virtual(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_rKirkwood(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring(), and update_residue_for_packing().

get_polarization_from_fields()

void core::scoring::MultipoleElecPotential::get_polarization_from_fields

(

pose::Pose &

pose

)

const

Get the electric field due to permanent multipoles.

References core::conformation::Residue::atom_name(), core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::Efield_fixed(), core::scoring::MultipoleElecResidueInfo::Efield_induced(), core::scoring::MultipoleElecResidueInfo::Efield_rf_fixed(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole(), core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by induce_polarizable_dipoles().

get_res_res_elecE()

Real core::scoring::MultipoleElecPotential::get_res_res_elecE	(	Residue const &	rsd1,
		MultipoleElecResidueInfo const &	mp1,
		Residue const &	rsd2,
		MultipoleElecResidueInfo const &	mp2
	)		const

References core::scoring::etable::count_pair::CP_CROSSOVER_34, core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_intrares_count_pair_function(), core::scoring::MultipoleElecResidueInfo::dipole(), Ep, Ew, core::scoring::get_damped_scale_factors(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::monopole(), core::scoring::MultipoleElecResidueInfo::mp_param(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::quadrupole(), core::scoring::MultipoleElecResidueInfo::rKirkwood(), core::scoring::same_polarization_group(), core::conformation::Residue::seqpos(), use_gen_kirkwood, and core::conformation::Residue::xyz().

Referenced by core::energy_methods::MultipoleElecEnergy::eval_intrares_energy(), core::energy_methods::MultipoleElecEnergy::eval_intrares_energy_ext(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::MultipoleElecEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::MultipoleElecEnergy::residue_pair_energy(), and core::energy_methods::MultipoleElecEnergy::residue_pair_energy_ext().

get_rotamers_effective_radii()

void core::scoring::MultipoleElecPotential::get_rotamers_effective_radii	(	pose::Pose const &	pose,
		conformation::RotamerSetBase &	rotamer_set
	)		const

Get the effective radii for Generalized Kirkwood.

References core::conformation::RotamerSetBase::data(), core::pose::Pose::data(), get_single_rotamer_effective_radii(), core::conformation::RotamerSetCacheableDataType::MULTIPOLE_ELEC_ROTAMER_SET_INFO, core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().

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

get_rotamers_multipole_info()

void core::scoring::MultipoleElecPotential::get_rotamers_multipole_info	(	pose::Pose const &	pose,
		conformation::RotamerSetBase &	rotamer_set
	)		const

Get the amoeba info for rotamers.

References align_residue_multipole_axes(), assign_residue_amoeba_type(), core::conformation::RotamerSetBase::data(), core::conformation::RotamerSetCacheableDataType::MULTIPOLE_ELEC_ROTAMER_SET_INFO, core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().

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

get_single_rotamer_effective_radii()

void core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii	(	Residue const &	rsd1,
		pose::Pose const &	pose,
		MultipoleElecPoseInfoCOP	mp_info,
		MultipoleElecResidueInfo &	mp1
	)		const

Get the effective radii for Generalized Kirkwood.

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::chemical::AtomType::extra_parameter(), core::chemical::AtomTypeSet::extra_parameter_index(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_rKirkwood(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), core::pose::Pose::size(), core::scoring::TR(), and core::conformation::Residue::xyz().

Referenced by get_rotamers_effective_radii().

induce_polarizable_dipoles()

void core::scoring::MultipoleElecPotential::induce_polarizable_dipoles

(

pose::Pose &

pose

)

const

called prior to scoring, eg

References calculate_fixed_fields_for_polarization(), calculate_induced_fields_for_polarization(), clear_induced_fields(), core::pose::Pose::data(), get_polarization_from_fields(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::conformation::Residue::is_virtual(), core::scoring::MultipoleElecResidueInfo::local_coord_matrix(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_stored_induced_dipole(), protocols::antibody::design::relax, relax_induced_dipoles(), core::pose::Pose::residue(), core::pose::Pose::size(), store_induced_dipoles(), core::scoring::TR(), and use_polarization.

Referenced by setup_for_scoring().

read_in_amoeba_parameters()

void core::scoring::MultipoleElecPotential::read_in_amoeba_parameters

(

)

read in parameters for amoeba and mappings between Rosetta residues/atoms and Amoeba types

References type_lookup_.

Referenced by MultipoleElecPotential().

read_in_multipole_parameters()

void core::scoring::MultipoleElecPotential::read_in_multipole_parameters

(

)

read in multipole parameters for amoeba types

References core::scoring::bisector, bohr, multipole_info_, core::scoring::none, core::scoring::pair, core::scoring::three_fold, core::scoring::z_axis_only, core::scoring::z_then_bisector, and core::scoring::z_then_x.

Referenced by MultipoleElecPotential().

relax_induced_dipoles()

core::Real core::scoring::MultipoleElecPotential::relax_induced_dipoles	(	pose::Pose &	pose,
		Real	relax
	)		const

Copies over induced dipoles to storage.

References core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole(), protocols::antibody::design::relax, core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::MultipoleElecResidueInfo::stored_induced_dipole().

Referenced by induce_polarizable_dipoles().

setup_for_packing()

void core::scoring::MultipoleElecPotential::setup_for_packing	(	pose::Pose &	pose,
		utility::vector1< bool > const &	repacking_residues
	)		const

Note: when called at the beginning of rotamer_trials, task.being_packed(i) will be false for all i this ensures that we use all the information we have to compute the current set of radii.

References core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO.

setup_for_scoring()

void core::scoring::MultipoleElecPotential::setup_for_scoring

(

pose::Pose &

pose

)

const

References align_multipole_axes(), assign_all_amoeba_types(), core::pose::Pose::data(), determine_polarization_groups(), core::pose::Pose::energies(), get_effective_radii(), induce_polarizable_dipoles(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, and core::scoring::Energies::use_nblist().

Referenced by core::energy_methods::MultipoleElecEnergy::setup_for_derivatives(), core::energy_methods::MultipoleElecEnergy::setup_for_packing(), and core::energy_methods::MultipoleElecEnergy::setup_for_scoring().

store_induced_dipoles()

void core::scoring::MultipoleElecPotential::store_induced_dipoles

(

pose::Pose &

pose

)

const

Copies over induced dipoles to storage.

References core::pose::Pose::data(), core::scoring::MultipoleElecResidueInfo::induced_dipole(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::scoring::MultipoleElecResidueInfo::nonconst_stored_induced_dipole(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

update_residue_for_packing()

void core::scoring::MultipoleElecPotential::update_residue_for_packing	(	pose::Pose &	pose,
		Size const	seqpos
	)		const

called eg after a rotamer substitution is accepted during rotamer trials

References align_residue_multipole_axes(), assign_residue_amoeba_type(), core::pose::Pose::data(), determine_polarization_groups(), get_effective_radii(), core::scoring::MultipoleElecResidueInfo::initialize(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, and core::pose::Pose::residue().

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

Member Data Documentation

bohr

Real const core::scoring::MultipoleElecPotential::bohr

private

Referenced by read_in_multipole_parameters().

cached_atom_derivs_

utility::vector1< utility::vector1< DerivVectorPair > > core::scoring::MultipoleElecPotential::cached_atom_derivs_

mutableprivate

Referenced by calculate_and_store_all_derivs(), and eval_residue_pair_derivatives().

default_variant_

std::string const core::scoring::MultipoleElecPotential::default_variant_

private

Ep

Real core::scoring::MultipoleElecPotential::Ep

private

Referenced by calculate_and_store_all_derivs(), calculate_res_res_fixed_fields_for_polarization(), calculate_res_res_induced_fields_for_polarization(), and get_res_res_elecE().

Ew

Real core::scoring::MultipoleElecPotential::Ew

private

Referenced by calculate_and_store_all_derivs(), calculate_res_res_fixed_fields_for_polarization(), calculate_res_res_induced_fields_for_polarization(), and get_res_res_elecE().

multipole_info_

std::multimap< Size, MultipoleParameter::MultipoleParameterOP > core::scoring::MultipoleElecPotential::multipole_info_

private

Referenced by find_params_and_neighbors(), and read_in_multipole_parameters().

type_lookup_

std::map< std::string, Size > core::scoring::MultipoleElecPotential::type_lookup_

private

Referenced by amoeba_type_lookup(), and read_in_amoeba_parameters().

use_gen_kirkwood

bool core::scoring::MultipoleElecPotential::use_gen_kirkwood

private

Referenced by calculate_and_store_all_derivs(), calculate_res_res_fixed_fields_for_polarization(), calculate_res_res_induced_fields_for_polarization(), and get_res_res_elecE().

use_polarization

bool core::scoring::MultipoleElecPotential::use_polarization

private

Referenced by induce_polarizable_dipoles().

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

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