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

#include <CountPairGeneric.hh>

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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)
 
virtual ~CountPairGeneric ()
 
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
 
virtual bool count (int const at1, int const at2, Real &, Size &path_dist) const
 
virtual void residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, etable::TableLookupEvaluator const &, EnergyMap &) const
 Type Resolution Functions ///. More...
 
virtual void residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_sidechain_whole (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_backbone_backbone (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &, conformation::Residue const &, etable::TableLookupEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy (conformation::Residue const &res1, conformation::Residue const &res2, etable::AnalyticEtableEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_sidechain_backbone (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_sidechain_whole (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_backbone_backbone (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const
 
virtual void residue_atom_pair_energy_sidechain_sidechain (conformation::Residue const &, conformation::Residue const &, etable::AnalyticEtableEvaluator const &, EnergyMap &) const
 
- Public Member Functions inherited from core::scoring::etable::count_pair::CountPairFunction
 CountPairFunction ()
 
virtual ~CountPairFunction ()
 
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
 

Detailed Description

Definition at line 37 of file CountPairGeneric.hh.

Member Typedef Documentation

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

Definition at line 41 of file CountPairGeneric.hh.

Constructor & Destructor Documentation

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

Definition at line 39 of file CountPairGeneric.cc.

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.

Definition at line 97 of file CountPairGeneric.cc.

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 ( )
virtual

Definition at line 125 of file CountPairGeneric.cc.

Member Function Documentation

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

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

Definition at line 136 of file CountPairGeneric.cc.

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

Definition at line 67 of file CountPairGeneric.hh.

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

Definition at line 88 of file CountPairGeneric.hh.

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 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
virtual

Type Resolution Functions ///.

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

Definition at line 147 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 208 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 184 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 244 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 158 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 219 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 197 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 255 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 171 of file CountPairGeneric.cc.

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
virtual

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

Definition at line 232 of file CountPairGeneric.cc.

References core::scoring::inline_residue_atom_pair_energy_sidechain_whole().

void core::scoring::etable::count_pair::CountPairGeneric::set_crossover ( Size  xover)

Definition at line 130 of file CountPairGeneric.cc.

References crossover_.

Referenced by core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), and protocols::match::Matcher::create_ds_builder().

Member Data Documentation

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

Definition at line 231 of file CountPairGeneric.hh.

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

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

Definition at line 222 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 226 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 229 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 223 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 227 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 224 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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

Definition at line 228 of file CountPairGeneric.hh.

Referenced by CountPairGeneric(), and path_distance().

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