core::scoring::GenericBondedPotential Class Reference

Potential for core/scoring/methods/GenericBondedEnergy method. More...

#include <GenericBondedPotential.hh>

Inheritance diagram for core::scoring::GenericBondedPotential:

Public Member Functions
	GenericBondedPotential ()
	Default Constructor. More...
void	setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &sfxn, bool const &score_full=false, bool const &score_hybrid=true) const
	Constructor with exclusion behaviors. More...
void	residue_energy (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap &emap, bool const &score_full, bool const &score_hybrid) const
	interface with same named function in GenericBondedEnergy More...
void	residue_derivatives (conformation::Residue const &rsd, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs, bool const &score_full, bool const &score_hybrid) const
	interface with same named function in GenericBondedEnergy More...
void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap &emap, bool const &score_full, bool const &score_hybrid) const
	interface with same named function in GenericBondedEnergy More...
void	residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, bool const &score_full, bool const &score_hybrid) const
	interface with same named function in GenericBondedEnergy More...

Private Member Functions
void	modify_tors_params (std::string const atm1, std::string const atm2, std::string bondtype, std::string const atm3, std::string const atm4, core::Real k1_in, core::Real k2_in, core::Real k3_in, core::Real k4_in, core::Real f1_in=0.0, core::Real f2_in=0.0, core::Real f3_in=0.0, core::Real f4_in=0.0, core::Real offset=0.0)
	modify torsional parameters "after the fact" More...
void	read_database (std::string filename)
	read database file located at database/scoring/score_function/generic_potential More...
void	modify_torsion_params_from_cmd_line ()
	read flags or command line and apply modify_tors_params funciton More...
SpringParams const &	lookup_bond_params (Size type1, Size type2) const
	fast database lookup; bond/angles (currently) keyed on type only More...
SpringParams const &	lookup_angle_params (Size type1, Size type2, Size type3) const
GenTorsionParams const &	lookup_tors_params (core::chemical::BondName bn, core::chemical::BondRingness br, Size type1, Size type2, Size type3, Size type4) const
	fast database lookup; torsions conditioned on types + 2-3 bond More...
SpringParams const &	lookup_improper_params (Size type1, Size type2, Size type3, Size type4, int &idx2, int &idx3, int &idx4) const
	fast database lookup; improper keyed on types only More...
Real	eval_residue_energy_and_derivative_bond (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (1-body) for bond-length term More...
Real	eval_residue_energy_and_derivative_angle (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (1-body) for bond-angle term More...
Real	eval_residue_energy_and_derivative_torsion (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, ResidueExclParamsCOP excl_params, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (1-body) for regular torsion term More...
Real	eval_residue_energy_and_derivative_improper (conformation::Residue const &rsd, utility::vector1< DerivVectorPair > &atom_derivs, ResidueExclParamsCOP excl_params, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (1-body) for improper-torsion term More...
Real	eval_residue_pair_energy_and_derivative_bond (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (2-body) for bond-length term More...
Real	eval_residue_pair_energy_and_derivative_angle (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (2-body) for bond-angle term More...
Real	eval_residue_pair_energy_and_derivative_torsion (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, ResidueExclParamsCOP excl_info_res1, ResidueExclParamsCOP excl_info_res2, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (2-body) for regular torsion term More...
Real	eval_residue_pair_energy_and_derivative_improper (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &atom_derivs_r1, utility::vector1< DerivVectorPair > &atom_derivs_r2, ResidueExclParamsCOP excl_info_res1, ResidueExclParamsCOP excl_info_res2, Real const weight=0.0, bool const calc_deriv=false) const
	evaluate each component (2-body) for improper-torsion term More...

Private Attributes
utility::vector1< int >	defined_atom_types_
std::map< std::string, utility::vector1< core::Size > >	name_index_map
core::Size	natomtypes
utility::vector1< SpringParams >	bond_pot_
utility::vector1< SpringParams >	angle_pot_
utility::vector1< SpringParams >	improper_pot_
utility::vector1< GenTorsionParams >	tors_pot_
std::unordered_map< uint64_t, Size >	bond_lookup_
std::unordered_map< uint64_t, Size >	angle_lookup_
std::unordered_map< uint64_t, Size >	improper_lookup_
std::unordered_map< uint64_t, Size >	tors_lookup_
bool	quick_lookup_

Static Private Attributes
static const SpringParams	null_sp_param
static const GenTorsionParams	null_tors_param

Detailed Description

Potential for core/scoring/methods/GenericBondedEnergy method.

Main class calculating gen_bonded energy term. Consists of energy terms of bond-length, -angle, torsion, and improper torsions. Reads in database/scoring/score_function/generic_bonded/generic_bonded.XX.txt and stores it as SpringParams or GenTorsionParams as local variables for score enumeration.

Constructor & Destructor Documentation

GenericBondedPotential()

core::scoring::GenericBondedPotential::GenericBondedPotential

(

)

Default Constructor.

Member Function Documentation

eval_residue_energy_and_derivative_angle()

Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_angle ( conformation::Residue const &  rsd, utility::vector1< DerivVectorPair > &  atom_derivs, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (1-body) for bond-angle term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueType::bondangle(), core::scoring::SpringParams::delta(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_energy_and_derivative_bond()

Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_bond ( conformation::Residue const &  rsd, utility::vector1< DerivVectorPair > &  atom_derivs, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (1-body) for bond-length term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::scoring::SpringParams::delta(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), core::conformation::Residue::natoms(), core::chemical::ResidueType::nbrs(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_energy_and_derivative_improper()

Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_improper ( conformation::Residue const &  rsd, utility::vector1< DerivVectorPair > &  atom_derivs, ResidueExclParamsCOP  excl_params, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (1-body) for improper-torsion term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), core::chemical::ResidueType::nbrs(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_energy_and_derivative_torsion()

Real core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion ( conformation::Residue const &  rsd, utility::vector1< DerivVectorPair > &  atom_derivs, ResidueExclParamsCOP  excl_params, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (1-body) for regular torsion term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), core::scoring::GenTorsionParams::deriv(), core::chemical::ResidueType::dihedral(), core::scoring::GenTorsionParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::GenTorsionParams::is_null(), core::scoring::GenTorsionParams::k(), core::scoring::GenTorsionParams::offset(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::GenTorsionParams::torsion_type(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_pair_energy_and_derivative_angle()

Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_angle ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, utility::vector1< DerivVectorPair > &  atom_derivs_r1, utility::vector1< DerivVectorPair > &  atom_derivs_r2, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (2-body) for bond-angle term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::conformation::Residue::connections_to_residue(), core::scoring::SpringParams::delta(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_pair_energy_and_derivative_bond()

Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_bond ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, utility::vector1< DerivVectorPair > &  atom_derivs_r1, utility::vector1< DerivVectorPair > &  atom_derivs_r2, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (2-body) for bond-length term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connections_to_residue(), core::scoring::SpringParams::delta(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), and core::conformation::Residue::xyz().

eval_residue_pair_energy_and_derivative_improper()

Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_improper ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, utility::vector1< DerivVectorPair > &  atom_derivs_r1, utility::vector1< DerivVectorPair > &  atom_derivs_r2, ResidueExclParamsCOP  excl_info_res1, ResidueExclParamsCOP  excl_info_res2, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (2-body) for improper-torsion term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::conformation::Residue::connections_to_residue(), core::scoring::SpringParams::deriv(), core::scoring::SpringParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::SpringParams::is_null(), core::scoring::SpringParams::k(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

eval_residue_pair_energy_and_derivative_torsion()

Real core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, utility::vector1< DerivVectorPair > &  atom_derivs_r1, utility::vector1< DerivVectorPair > &  atom_derivs_r2, ResidueExclParamsCOP  excl_info_res1, ResidueExclParamsCOP  excl_info_res2, Real const  weight = 0.0, bool const  calc_deriv = false  ) const

private

evaluate each component (2-body) for regular torsion term

References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::chemical::ResidueType::atoms_within_two_bonds_of_a_residue_connection(), core::chemical::ResidueType::bond_ringness(), core::chemical::ResidueType::bond_type(), core::chemical::BondNotInRing, core::conformation::Residue::connections_to_residue(), core::scoring::GenTorsionParams::deriv(), core::chemical::DoubleBond, core::scoring::GenTorsionParams::energy(), core::chemical::element::F, core::chemical::element::I, core::scoring::GenTorsionParams::is_null(), core::conformation::Residue::is_protein(), core::scoring::GenTorsionParams::k(), core::conformation::Residue::last_backbone_atom(), core::scoring::GenTorsionParams::offset(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), protocols::hybridization::score, core::conformation::Residue::seqpos(), core::chemical::SingleBond, core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

lookup_angle_params()

SpringParams const & core::scoring::GenericBondedPotential::lookup_angle_params ( Size  type1, Size  type2, Size  type3  ) const

private

References core::scoring::get_parameter_hash().

lookup_bond_params()

SpringParams const & core::scoring::GenericBondedPotential::lookup_bond_params ( Size  type1, Size  type2  ) const

private

fast database lookup; bond/angles (currently) keyed on type only

References core::scoring::get_parameter_hash().

lookup_improper_params()

SpringParams const & core::scoring::GenericBondedPotential::lookup_improper_params ( Size  type1, Size  type2, Size  type3, Size  type4, int &  idx2, int &  idx3, int &  idx4  ) const

private

fast database lookup; improper keyed on types only

References core::scoring::get_parameter_hash().

lookup_tors_params()

GenTorsionParams const & core::scoring::GenericBondedPotential::lookup_tors_params ( core::chemical::BondName  bn, core::chemical::BondRingness  br, Size  type1, Size  type2, Size  type3, Size  type4  ) const

private

fast database lookup; torsions conditioned on types + 2-3 bond

References core::scoring::bin_from_bond(), core::scoring::get_parameter_hash(), and core::scoring::TR().

modify_tors_params()

void core::scoring::GenericBondedPotential::modify_tors_params ( std::string const  atm1, std::string const  atm2, std::string  bondtype, std::string const  atm3, std::string const  atm4, core::Real  k1_in, core::Real  k2_in, core::Real  k3_in, core::Real  k4_in, core::Real  f1_in = 0.0, core::Real  f2_in = 0.0, core::Real  f3_in = 0.0, core::Real  f4_in = 0.0, core::Real  offset = 0.0  )

private

modify torsional parameters "after the fact"

References core::scoring::bondorders_map(), core::scoring::get_parameter_hash(), core::scoring::GenTorsionParams::set_offset(), and core::scoring::TR().

modify_torsion_params_from_cmd_line()

void core::scoring::GenericBondedPotential::modify_torsion_params_from_cmd_line ( )

private

read flags or command line and apply modify_tors_params funciton

References core::scoring::TR().

read_database()

void core::scoring::GenericBondedPotential::read_database ( std::string  filename )

private

read database file located at database/scoring/score_function/generic_potential

References core::scoring::bondorders_map(), protocols::abinitio::filename(), core::scoring::get_parameter_hash(), core::scoring::GenTorsionParams::k6(), core::scoring::rmANGLE, core::scoring::rmATOM, core::scoring::rmBOND, core::scoring::rmIMPROPER, core::scoring::rmNONE, core::scoring::rmTORSION, core::scoring::GenTorsionParams::set_offset(), and core::scoring::TR().

residue_derivatives()

void core::scoring::GenericBondedPotential::residue_derivatives	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	atom_derivs,
		bool const &	score_full,
		bool const &	score_hybrid
	)		const

interface with same named function in GenericBondedEnergy

References core::pose::Pose::data(), core::scoring::gen_bonded, core::scoring::gen_bonded_angle, core::scoring::gen_bonded_bond, core::pose::datacache::CacheableDataType::GEN_BONDED_EXCL_INFO, core::scoring::gen_bonded_improper, core::scoring::gen_bonded_torsion, core::conformation::Residue::is_metal(), core::conformation::Residue::is_water(), core::conformation::Residue::type(), and core::conformation::Residue::type_ptr().

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

residue_energy()

void core::scoring::GenericBondedPotential::residue_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		EnergyMap &	emap,
		bool const &	score_full,
		bool const &	score_hybrid
	)		const

interface with same named function in GenericBondedEnergy

References core::pose::Pose::data(), core::chemical::element::F, core::scoring::gen_bonded, core::scoring::gen_bonded_angle, core::scoring::gen_bonded_bond, core::pose::datacache::CacheableDataType::GEN_BONDED_EXCL_INFO, core::scoring::gen_bonded_improper, core::scoring::gen_bonded_torsion, core::chemical::element::I, core::conformation::Residue::is_metal(), core::conformation::Residue::is_water(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), and core::conformation::Residue::type_ptr().

Referenced by core::energy_methods::GenericBondedEnergy::eval_intrares_energy().

residue_pair_derivatives()

void core::scoring::GenericBondedPotential::residue_pair_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		EnergyMap const &	weights,
		utility::vector1< DerivVectorPair > &	atom_derivs_r1,
		utility::vector1< DerivVectorPair > &	atom_derivs_r2,
		bool const &	score_full,
		bool const &	score_hybrid
	)		const

interface with same named function in GenericBondedEnergy

References core::conformation::Residue::connected_residue_at_resconn(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::data(), core::scoring::gen_bonded, core::scoring::gen_bonded_angle, core::scoring::gen_bonded_bond, core::pose::datacache::CacheableDataType::GEN_BONDED_EXCL_INFO, core::scoring::gen_bonded_improper, core::scoring::gen_bonded_torsion, core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::chemical::ResidueType::upper_connect_id().

Referenced by core::energy_methods::GenericBondedEnergy::eval_residue_pair_derivatives().

residue_pair_energy()

void core::scoring::GenericBondedPotential::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		EnergyMap &	emap,
		bool const &	score_full,
		bool const &	score_hybrid
	)		const

interface with same named function in GenericBondedEnergy

References core::conformation::Residue::connected_residue_at_resconn(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::data(), core::chemical::element::F, core::scoring::gen_bonded, core::scoring::gen_bonded_angle, core::scoring::gen_bonded_bond, core::pose::datacache::CacheableDataType::GEN_BONDED_EXCL_INFO, core::scoring::gen_bonded_improper, core::scoring::gen_bonded_torsion, core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::element::I, core::conformation::Residue::name(), core::conformation::Residue::seqpos(), core::scoring::TR(), core::conformation::Residue::type(), core::conformation::Residue::type_ptr(), and core::chemical::ResidueType::upper_connect_id().

Referenced by core::energy_methods::GenericBondedEnergy::residue_pair_energy().

setup_for_scoring()

void core::scoring::GenericBondedPotential::setup_for_scoring	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	sfxn,
		bool const &	score_full = false,
		bool const &	score_hybrid = true
	)		const

Constructor with exclusion behaviors.

interface with same named function in GenericBondedEnergy

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::GEN_BONDED_EXCL_INFO, core::conformation::Residue::is_metal(), core::conformation::Residue::is_water(), core::chemical::ResidueTypeBase::name(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

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

Member Data Documentation

angle_lookup_

std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::angle_lookup_

private

angle_pot_

utility::vector1< SpringParams > core::scoring::GenericBondedPotential::angle_pot_

private

bond_lookup_

std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::bond_lookup_

private

bond_pot_

utility::vector1< SpringParams > core::scoring::GenericBondedPotential::bond_pot_

private

defined_atom_types_

utility::vector1< int > core::scoring::GenericBondedPotential::defined_atom_types_

private

improper_lookup_

std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::improper_lookup_

private

improper_pot_

utility::vector1< SpringParams > core::scoring::GenericBondedPotential::improper_pot_

private

name_index_map

std::map< std::string, utility::vector1< core::Size > > core::scoring::GenericBondedPotential::name_index_map

private

natomtypes

core::Size core::scoring::GenericBondedPotential::natomtypes

private

null_sp_param

const SpringParams core::scoring::GenericBondedPotential::null_sp_param

staticprivate

null_tors_param

const GenTorsionParams core::scoring::GenericBondedPotential::null_tors_param

staticprivate

quick_lookup_

bool core::scoring::GenericBondedPotential::quick_lookup_

private

tors_lookup_

std::unordered_map< uint64_t, Size > core::scoring::GenericBondedPotential::tors_lookup_

private

tors_pot_

utility::vector1< GenTorsionParams > core::scoring::GenericBondedPotential::tors_pot_

private

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

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