#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

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

Constructor & Destructor Documentation

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

inline

ctor

References read_in_amoeba_parameters(), and read_in_multipole_parameters().

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

void core::scoring::MultipoleElecPotential::align_multipole_axes ( pose::Pose & pose ) const

called prior to scoring, eg

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

Referenced by setup_for_scoring().

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

called prior to scoring, eg

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().

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().

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().

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().

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.

Referenced by align_residue_multipole_axes().

void core::scoring::MultipoleElecPotential::calculate_and_store_all_derivs ( pose::Pose const & pose ) const

References cached_atom_derivs_, 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::pose::Pose::energies(), Ep, Ew, core::scoring::get_damped_scale_factors_with_derivs(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::conformation::Residue::natoms(), core::pose::num_atoms(), core::pose::Pose::residue(), core::scoring::same_polarization_group(), core::pose::Pose::size(), core::scoring::T(), use_gen_kirkwood, and core::scoring::Energies::use_nblist().

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

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

Referenced by induce_polarizable_dipoles().

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::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

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().

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().

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::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

void core::scoring::MultipoleElecPotential::determine_polarization_groups ( pose::Pose & pose ) const

called prior to scoring, eg

References core::id::AtomID::atomno(), core::conformation::Conformation::bonded_neighbor_all_res(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::sequence::end, core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::pose::Pose::residue(), core::id::AtomID::rsd(), core::pose::Pose::size(), and core::scoring::TR().

Referenced by setup_for_scoring(), and update_residue_for_packing().

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().

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.

Referenced by align_residue_multipole_axes().

void core::scoring::MultipoleElecPotential::get_effective_radii ( pose::Pose & pose ) const

Get the effective radii for Generalized Kirkwood.

References core::conformation::Residue::atom_type_set(), core::pose::Pose::data(), core::chemical::AtomTypeSet::extra_parameter_index(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by setup_for_scoring(), and update_residue_for_packing().

void core::scoring::MultipoleElecPotential::get_polarization_from_fields ( pose::Pose & pose ) const

Get the electric field due to permanent multipoles.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::scoring::TR().

Referenced by induce_polarizable_dipoles().

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().

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().

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().

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().

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::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, 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().

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().

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().

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::pose::datacache::CacheableDataType::MULTIPOLE_POSE_INFO, core::scoring::MultipoleElecResidueInfo::nonconst_induced_dipole(), protocols::antibody::design::relax, core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by induce_polarizable_dipoles().

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.

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::scoring::MultipoleElecPoseInfo::initialize(), 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().

void core::scoring::MultipoleElecPotential::store_induced_dipoles ( pose::Pose & pose ) const

Copies over induced dipoles to storage.

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

Referenced by induce_polarizable_dipoles().