#include <VdWTinkerPotential.hh>

Inheritance diagram for core::scoring::VdWTinkerPotential:

Public Types
typedef core::conformation::Residue	Residue

Public Member Functions
	VdWTinkerPotential ()
	ctor More...

void	read_in_amoeba_parameters ()

void	read_in_vdw_tinker_parameters ()
	read in vdw parameters for amoeba types More...

core::Size	amoeba_type_lookup (std::string const &atomname, std::string const &resname, std::string const &variantname) const
	Look up Amoeba type by resname/atomname/variant name. More...

void	assign_residue_amoeba_type (Residue const &rsd, VdWTinkerResidueInfo &mp) const
	called prior to scoring, eg More...

void	assign_all_amoeba_types (pose::Pose &pose) const
	called prior to scoring, eg More...

void	get_rotamers_vdw_info (pose::Pose const &pose, conformation::RotamerSetBase &) const
	Get the amoeba info for rotamers. 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_vdw (Residue const &rsd1, VdWTinkerResidueInfo const &mp1, Residue const &rsd2, VdWTinkerResidueInfo const &mp2) const

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

Private Attributes
std::map< std::string, Size >	type_lookup_

std::string const	default_variant_

utility::vector1< Real >	vdw_radius_

utility::vector1< Real >	vdw_depth_

utility::vector1< Real >	vdw_reduce_

Member Typedef Documentation

typedef core::conformation::Residue core::scoring::VdWTinkerPotential::Residue

Constructor & Destructor Documentation

core::scoring::VdWTinkerPotential::VdWTinkerPotential ( )

inline

ctor

References read_in_amoeba_parameters(), and read_in_vdw_tinker_parameters().

Member Function Documentation

core::Size core::scoring::VdWTinkerPotential::amoeba_type_lookup	(	std::string const &	atomname,
		std::string const &	resname,
		std::string const &	variantname
	)		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::VdWTinkerPotential::assign_all_amoeba_types ( pose::Pose & pose ) const

called prior to scoring, eg

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

Referenced by setup_for_scoring().

void core::scoring::VdWTinkerPotential::assign_residue_amoeba_type	(	Residue const &	rsd,
		VdWTinkerResidueInfo &	mp
	)		const

called prior to scoring, eg

References amoeba_type_lookup(), core::conformation::Residue::atom_name(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), and core::scoring::VdWTinkerResidueInfo::nonconst_vdw_type().

Referenced by assign_all_amoeba_types(), get_rotamers_vdw_info(), core::energy_methods::VdWTinkerEnergy::setup_for_minimizing_for_residue(), core::energy_methods::VdWTinkerEnergy::setup_for_scoring_for_residue(), and update_residue_for_packing().

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

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::etable::count_pair::CP_CROSSOVER_3, 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(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), core::scoring::Energies::use_nblist(), vdw_depth_, vdw_radius_, vdw_reduce_, core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO, and core::conformation::Residue::xyz().

Referenced by core::energy_methods::VdWTinkerEnergy::eval_intrares_derivatives(), and core::energy_methods::VdWTinkerEnergy::eval_residue_pair_derivatives().

Real core::scoring::VdWTinkerPotential::get_res_res_vdw	(	Residue const &	rsd1,
		VdWTinkerResidueInfo const &	mp1,
		Residue const &	rsd2,
		VdWTinkerResidueInfo const &	mp2
	)		const

References core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function(), core::scoring::etable::count_pair::CountPairFactory::create_intrares_count_pair_function(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), vdw_depth_, vdw_radius_, vdw_reduce_, core::scoring::VdWTinkerResidueInfo::vdw_type(), and core::conformation::Residue::xyz().

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

void core::scoring::VdWTinkerPotential::get_rotamers_vdw_info	(	pose::Pose const &	pose,
		conformation::RotamerSetBase &	rotamer_set
	)		const

Get the amoeba info for rotamers.

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

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

void core::scoring::VdWTinkerPotential::read_in_amoeba_parameters ( )

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

References type_lookup_.

Referenced by VdWTinkerPotential().

void core::scoring::VdWTinkerPotential::read_in_vdw_tinker_parameters ( )

read in vdw parameters for amoeba types

References vdw_depth_, vdw_radius_, and vdw_reduce_.

Referenced by VdWTinkerPotential().

void core::scoring::VdWTinkerPotential::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::VDWTINKER_POSE_INFO.

void core::scoring::VdWTinkerPotential::setup_for_scoring ( pose::Pose & pose ) const

References assign_all_amoeba_types(), core::pose::Pose::data(), core::scoring::VdWTinkerPoseInfo::initialize(), and core::pose::datacache::CacheableDataType::VDWTINKER_POSE_INFO.

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