core::scoring::etable::count_pair::CountPairGeneric Class Reference

#include <CountPairGeneric.hh>

Inheritance diagram for core::scoring::etable::count_pair::CountPairGeneric:

Public Types
typedef CountPairFunction	parent

Public Member Functions
	CountPairGeneric (conformation::Residue const &res1, conformation::Residue const &res2)
	CountPairGeneric (chemical::ResidueType const &restype1, chemical::ResidueType const &restype2, utility::vector1< std::pair< Size, Size > > bond_pairs)
	Create a count pair object that pretends there exist a chemical bond between some number of atoms in residue 1 and some number of atoms in residue2; the bond_pairs vector is a set of ordered-pairs of atom-indices, where the first is an atom from restype1 and the second is an atom of restype2. More...
void	set_crossover (Size)
	~CountPairGeneric () override
bool	operator() (int const at1, int const at2, Real &weight, Size &minpathdist) const
	function required by templated functions in atom_pair_energy_inline More...
int	path_distance (int const at1, int const at2) const
bool	count (int const at1, int const at2, Real &, Size &path_dist) const override
void	residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, etable::TableLookupEvaluator const &, EnergyMap &) const override
	Type Resolution Functions ///. More...
void	residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_sidechain_whole (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_backbone_backbone (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, etable::AnalyticEtableEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_sidechain_whole (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_backbone_backbone (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const override
void	residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const override
Public Member Functions inherited from core::scoring::etable::count_pair::CountPairFunction
	CountPairFunction ()
	~CountPairFunction () override
bool	operator() (int const at1, int const at2, Real &, Size &path_dist) const

Private Attributes
Size	n_connect_
utility::vector1 < utility::vector1< int > const * >	res1_conn_point_path_dists_
utility::vector1 < utility::vector1< int > const * >	res2_conn_point_path_dists_
Size	n_pconnect_
utility::vector1 < utility::vector1< int > const * >	res1_pbconn_point_path_dists_
utility::vector1 < utility::vector1< int > const * >	res2_pbconn_point_path_dists_
utility::vector1< int >	pb_lengths_
int	crossover_

Additional Inherited Members
Static Public Attributes inherited from core::scoring::etable::count_pair::CountPairFunction
static Real const	cp_half

Member Typedef Documentation

typedef CountPairFunction core::scoring::etable::count_pair::CountPairGeneric::parent

Constructor & Destructor Documentation

core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric	(	conformation::Residue const &	res1,
		conformation::Residue const &	res2
	)

References core::conformation::Residue::actual_residue_connection(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connections_to_residue(), core::chemical::ResConnID::connid(), core::conformation::Residue::get_pseudobonds_to_residue(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), n_connect_, n_pconnect_, core::conformation::Residue::path_distance(), pb_lengths_, res1_conn_point_path_dists_, res1_pbconn_point_path_dists_, res2_conn_point_path_dists_, res2_pbconn_point_path_dists_, core::conformation::Residue::residue_connection(), and core::conformation::Residue::seqpos().

core::scoring::etable::count_pair::CountPairGeneric::CountPairGeneric	(	chemical::ResidueType const &	restype1,
		chemical::ResidueType const &	restype2,
		utility::vector1< std::pair< Size, Size > >	bond_pairs
	)

Create a count pair object that pretends there exist a chemical bond between some number of atoms in residue 1 and some number of atoms in residue2; the bond_pairs vector is a set of ordered-pairs of atom-indices, where the first is an atom from restype1 and the second is an atom of restype2.

References n_connect_, core::chemical::ResidueType::path_distance(), res1_conn_point_path_dists_, and res2_conn_point_path_dists_.

core::scoring::etable::count_pair::CountPairGeneric::~CountPairGeneric ( )

overridedefault

Member Function Documentation

bool core::scoring::etable::count_pair::CountPairGeneric::count ( int const  at1, int const  at2, Real &  weight, Size &  path_dist  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References operator()().

bool core::scoring::etable::count_pair::CountPairGeneric::operator() ( int const  at1, int const  at2, Real &  weight, Size &  minpathdist  ) const

inline

function required by templated functions in atom_pair_energy_inline

References core::scoring::etable::count_pair::CountPairFunction::cp_half, crossover_, and path_distance().

Referenced by count().

int core::scoring::etable::count_pair::CountPairGeneric::path_distance ( int const  at1, int const  at2  ) const

inline

References n_connect_, n_pconnect_, pb_lengths_, res1_conn_point_path_dists_, res1_pbconn_point_path_dists_, res2_conn_point_path_dists_, and res2_pbconn_point_path_dists_.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance(), and operator()().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::TableLookupEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Type Resolution Functions ///.

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::AnalyticEtableEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::TableLookupEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_backbone_backbone().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_backbone_backbone ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::AnalyticEtableEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_backbone_backbone().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::TableLookupEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_backbone().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_backbone ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::AnalyticEtableEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_backbone().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::TableLookupEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_sidechain ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::AnalyticEtableEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_sidechain().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::TableLookupEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_whole().

void core::scoring::etable::count_pair::CountPairGeneric::residue_atom_pair_energy_sidechain_whole ( conformation::Residue const &  res1, conformation::Residue const &  res2, etable::AnalyticEtableEvaluator const &  etable_energy, EnergyMap &  emap  ) const

overridevirtual

Implements core::scoring::etable::count_pair::CountPairFunction.

References core::scoring::inline_residue_atom_pair_energy_sidechain_whole().

void core::scoring::etable::count_pair::CountPairGeneric::set_crossover

(

Size

xover

)

References crossover_.

Referenced by core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke().

Member Data Documentation

int core::scoring::etable::count_pair::CountPairGeneric::crossover_

private

Referenced by operator()(), and set_crossover().

Size core::scoring::etable::count_pair::CountPairGeneric::n_connect_

private

Referenced by CountPairGeneric(), and path_distance().

Size core::scoring::etable::count_pair::CountPairGeneric::n_pconnect_

private

Referenced by CountPairGeneric(), and path_distance().

utility::vector1< int > core::scoring::etable::count_pair::CountPairGeneric::pb_lengths_

private

Referenced by CountPairGeneric(), and path_distance().

utility::vector1< utility::vector1< int > const * > core::scoring::etable::count_pair::CountPairGeneric::res1_conn_point_path_dists_

private

Referenced by CountPairGeneric(), and path_distance().

utility::vector1< utility::vector1< int > const * > core::scoring::etable::count_pair::CountPairGeneric::res1_pbconn_point_path_dists_

private

Referenced by CountPairGeneric(), and path_distance().

utility::vector1< utility::vector1< int > const * > core::scoring::etable::count_pair::CountPairGeneric::res2_conn_point_path_dists_

private

Referenced by CountPairGeneric(), and path_distance().

utility::vector1< utility::vector1< int > const * > core::scoring::etable::count_pair::CountPairGeneric::res2_pbconn_point_path_dists_

private

Referenced by CountPairGeneric(), and path_distance().

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

• src/core/scoring/etable/count_pair/CountPairGeneric.hh
• src/core/scoring/etable/count_pair/CountPairGeneric.cc