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core::scoring::mm Namespace Reference

Namespaces

 mmtrie
 

Classes

class  MMBondAngleLibrary
 
class  MMBondAngleResidueTypeParam
 
class  MMBondAngleResidueTypeParamSet
 
class  MMBondAngleScore
 Calculates scores of mm bond angle paramater sets given an angle. More...
 
class  MMBondLengthLibrary
 
class  MMBondLengthScore
 
class  MMLJEnergyTable
 blah More...
 
class  MMLJLibrary
 A class to maintain a set of MM LJ paramaters. More...
 
class  MMLJScore
 Calculates scores of mm lj paramater sets given two mm atom types, the path distance of the 2 atoms and actual distance between the two atoms. More...
 
class  MMTorsionLibrary
 A class to maintain a set of MM torsion paramaters. More...
 
class  MMTorsionScore
 Calculates scores of mm torsion paramater sets given an angle. More...
 

Typedefs

typedef utility::pointer::weak_ptr< MMBondAngleLibraryMMBondAngleLibraryAP
 
typedef utility::pointer::weak_ptr< MMBondAngleLibrary const > MMBondAngleLibraryCAP
 
typedef utility::pointer::shared_ptr< MMBondAngleLibraryMMBondAngleLibraryOP
 
typedef utility::pointer::shared_ptr< MMBondAngleLibrary const > MMBondAngleLibraryCOP
 
typedef utility::keys::Key3Tuple< int, int, int > mm_bondangle_atom_tri
 
typedef utility::keys::Key2Tuple< core::Real, core::Realmm_bondangle_param_set
 
typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_setmm_bondangle_library
 
typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_set >::const_iterator mm_bondangle_library_citer
 
typedef std::pair< mm_bondangle_library_citer, mm_bondangle_library_citermm_bondangle_library_citer_pair
 
typedef utility::keys::Key2Tuple< Size, Sizetwo_atom_set
 
typedef utility::keys::Key3Tuple< Size, Size, Sizethree_atom_set
 
typedef utility::pointer::weak_ptr< MMBondAngleResidueTypeParamSetMMBondAngleResidueTypeParamSetAP
 
typedef utility::pointer::weak_ptr< MMBondAngleResidueTypeParamSet const > MMBondAngleResidueTypeParamSetCAP
 
typedef utility::pointer::shared_ptr< MMBondAngleResidueTypeParamSetMMBondAngleResidueTypeParamSetOP
 
typedef utility::pointer::shared_ptr< MMBondAngleResidueTypeParamSet const > MMBondAngleResidueTypeParamSetCOP
 
typedef utility::pointer::weak_ptr< MMBondAngleScoreMMBondAngleScoreAP
 
typedef utility::pointer::weak_ptr< MMBondAngleScore const > MMBondAngleScoreCAP
 
typedef utility::pointer::shared_ptr< MMBondAngleScoreMMBondAngleScoreOP
 
typedef utility::pointer::shared_ptr< MMBondAngleScore const > MMBondAngleScoreCOP
 
typedef utility::pointer::weak_ptr< MMBondLengthLibraryMMBondLengthLibraryAP
 
typedef utility::pointer::weak_ptr< MMBondLengthLibrary const > MMBondLengthLibraryCAP
 
typedef utility::pointer::shared_ptr< MMBondLengthLibraryMMBondLengthLibraryOP
 
typedef utility::pointer::shared_ptr< MMBondLengthLibrary const > MMBondLengthLibraryCOP
 
typedef utility::keys::Key2Tuple< int, int > mm_bondlength_atom_pair
 
typedef utility::keys::Key2Tuple< core::Real, core::Realmm_bondlength_param_set
 
typedef std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_setmm_bondlength_library
 
typedef std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_set >::const_iterator mm_bondlength_library_citer
 
typedef std::pair< mm_bondlength_library_citer, mm_bondlength_library_citermm_bondlength_library_citer_pair
 
typedef utility::pointer::weak_ptr< MMBondLengthScoreMMBondLengthScoreAP
 
typedef utility::pointer::weak_ptr< MMBondLengthScore const > MMBondLengthScoreCAP
 
typedef utility::pointer::shared_ptr< MMBondLengthScoreMMBondLengthScoreOP
 
typedef utility::pointer::shared_ptr< MMBondLengthScore const > MMBondLengthScoreCOP
 
typedef utility::pointer::weak_ptr< MMLJEnergyTableMMLJEnergyTableAP
 
typedef utility::pointer::weak_ptr< MMLJEnergyTable const > MMLJEnergyTableCAP
 
typedef utility::pointer::shared_ptr< MMLJEnergyTableMMLJEnergyTableOP
 
typedef utility::pointer::shared_ptr< MMLJEnergyTable const > MMLJEnergyTableCOP
 
typedef utility::pointer::weak_ptr< MMLJLibraryMMLJLibraryAP
 
typedef utility::pointer::weak_ptr< MMLJLibrary const > MMLJLibraryCAP
 
typedef utility::pointer::shared_ptr< MMLJLibraryMMLJLibraryOP
 
typedef utility::pointer::shared_ptr< MMLJLibrary const > MMLJLibraryCOP
 
typedef Size mm_lj_atom
 
typedef utility::keys::Key2Tuple< Real, Realmm_lj_param_set
 
typedef utility::pointer::weak_ptr< MMLJScoreMMLJScoreAP
 
typedef utility::pointer::weak_ptr< MMLJScore const > MMLJScoreCAP
 
typedef utility::pointer::shared_ptr< MMLJScoreMMLJScoreOP
 
typedef utility::pointer::shared_ptr< MMLJScore const > MMLJScoreCOP
 
typedef utility::pointer::weak_ptr< MMTorsionLibraryMMTorsionLibraryAP
 
typedef utility::pointer::weak_ptr< MMTorsionLibrary const > MMTorsionLibraryCAP
 
typedef utility::pointer::shared_ptr< MMTorsionLibraryMMTorsionLibraryOP
 
typedef utility::pointer::shared_ptr< MMTorsionLibrary const > MMTorsionLibraryCOP
 
typedef utility::keys::Key4Tuple< int, int, int, int > mm_torsion_atom_quad
 
typedef utility::keys::Key3Tuple< core::Real, int, core::Realmm_torsion_param_set
 
typedef std::multimap< mm_torsion_atom_quad, mm_torsion_param_setmm_torsion_library
 
typedef std::multimap< mm_torsion_atom_quad, mm_torsion_param_set >::const_iterator mm_torsion_library_citer
 
typedef std::pair< mm_torsion_library_citer, mm_torsion_library_citermm_torsion_library_citer_pair
 
typedef utility::pointer::weak_ptr< MMTorsionScoreMMTorsionScoreAP
 
typedef utility::pointer::weak_ptr< MMTorsionScore const > MMTorsionScoreCAP
 
typedef utility::pointer::shared_ptr< MMTorsionScoreMMTorsionScoreOP
 
typedef utility::pointer::shared_ptr< MMTorsionScore const > MMTorsionScoreCOP
 

Functions

static basic::Tracer TR ("core.mm.MMBondAngleLibrary")
 
bool score_atom_centrally (core::chemical::ResidueType const &restype, utility::vector1< std::string > const &central_atoms_to_score, Size atomno)
 
std::ostream & operator<< (std::ostream &os, MMBondAngleResidueTypeParam const &residue_type_param)
 stream << MMBondAngleResidueTypeParam More...
 
static basic::Tracer TR ("core.mm.MMBondAngleResidueTypeParamSet")
 
bool connection_indices (core::conformation::Residue const &residue, core::conformation::Residue const &other_residue, core::Size const my_atomno, core::Size const other_atomno, core::Size &my_connection, core::Size &other_connection)
 get the indices of the connections that connects one of my atoms to an atom on another residue More...
 
MMBondAngleResidueTypeParamSetCOP mm_bond_angle_residue_type_param_set (core::scoring::ScoreFunction const &scorefxn)
 extract a MMBondAngleResidueTypeParamSet from a ScoreFunction, returning NULL if none exists More...
 
static basic::Tracer TR ("core.mm.MMBondLengthLibrary")
 
static basic::Tracer TR ("core.scoring.mm.MMLJEnergyTable")
 
static basic::Tracer TR ("core.mm.MMLJLibrary")
 
static basic::Tracer TR ("core.mm.MMTorsionLibrary")
 

Typedef Documentation

◆ mm_bondangle_atom_tri

typedef utility::keys::Key3Tuple< int, int, int > core::scoring::mm::mm_bondangle_atom_tri

◆ mm_bondangle_library

◆ mm_bondangle_library_citer

◆ mm_bondangle_library_citer_pair

◆ mm_bondangle_param_set

typedef utility::keys::Key2Tuple< core::Real, core::Real > core::scoring::mm::mm_bondangle_param_set

◆ mm_bondlength_atom_pair

typedef utility::keys::Key2Tuple< int, int > core::scoring::mm::mm_bondlength_atom_pair

◆ mm_bondlength_library

◆ mm_bondlength_library_citer

◆ mm_bondlength_library_citer_pair

◆ mm_bondlength_param_set

◆ mm_lj_atom

◆ mm_lj_param_set

typedef utility::keys::Key2Tuple< Real, Real > core::scoring::mm::mm_lj_param_set

◆ mm_torsion_atom_quad

typedef utility::keys::Key4Tuple< int, int, int, int > core::scoring::mm::mm_torsion_atom_quad

◆ mm_torsion_library

◆ mm_torsion_library_citer

◆ mm_torsion_library_citer_pair

◆ mm_torsion_param_set

typedef utility::keys::Key3Tuple< core::Real, int, core::Real > core::scoring::mm::mm_torsion_param_set

◆ MMBondAngleLibraryAP

typedef utility::pointer::weak_ptr< MMBondAngleLibrary > core::scoring::mm::MMBondAngleLibraryAP

◆ MMBondAngleLibraryCAP

typedef utility::pointer::weak_ptr< MMBondAngleLibrary const > core::scoring::mm::MMBondAngleLibraryCAP

◆ MMBondAngleLibraryCOP

typedef utility::pointer::shared_ptr< MMBondAngleLibrary const > core::scoring::mm::MMBondAngleLibraryCOP

◆ MMBondAngleLibraryOP

typedef utility::pointer::shared_ptr< MMBondAngleLibrary > core::scoring::mm::MMBondAngleLibraryOP

◆ MMBondAngleResidueTypeParamSetAP

◆ MMBondAngleResidueTypeParamSetCAP

◆ MMBondAngleResidueTypeParamSetCOP

◆ MMBondAngleResidueTypeParamSetOP

◆ MMBondAngleScoreAP

typedef utility::pointer::weak_ptr< MMBondAngleScore > core::scoring::mm::MMBondAngleScoreAP

◆ MMBondAngleScoreCAP

typedef utility::pointer::weak_ptr< MMBondAngleScore const > core::scoring::mm::MMBondAngleScoreCAP

◆ MMBondAngleScoreCOP

typedef utility::pointer::shared_ptr< MMBondAngleScore const > core::scoring::mm::MMBondAngleScoreCOP

◆ MMBondAngleScoreOP

typedef utility::pointer::shared_ptr< MMBondAngleScore > core::scoring::mm::MMBondAngleScoreOP

◆ MMBondLengthLibraryAP

typedef utility::pointer::weak_ptr< MMBondLengthLibrary > core::scoring::mm::MMBondLengthLibraryAP

◆ MMBondLengthLibraryCAP

typedef utility::pointer::weak_ptr< MMBondLengthLibrary const > core::scoring::mm::MMBondLengthLibraryCAP

◆ MMBondLengthLibraryCOP

typedef utility::pointer::shared_ptr< MMBondLengthLibrary const > core::scoring::mm::MMBondLengthLibraryCOP

◆ MMBondLengthLibraryOP

typedef utility::pointer::shared_ptr< MMBondLengthLibrary > core::scoring::mm::MMBondLengthLibraryOP

◆ MMBondLengthScoreAP

typedef utility::pointer::weak_ptr< MMBondLengthScore > core::scoring::mm::MMBondLengthScoreAP

◆ MMBondLengthScoreCAP

typedef utility::pointer::weak_ptr< MMBondLengthScore const > core::scoring::mm::MMBondLengthScoreCAP

◆ MMBondLengthScoreCOP

typedef utility::pointer::shared_ptr< MMBondLengthScore const > core::scoring::mm::MMBondLengthScoreCOP

◆ MMBondLengthScoreOP

typedef utility::pointer::shared_ptr< MMBondLengthScore > core::scoring::mm::MMBondLengthScoreOP

◆ MMLJEnergyTableAP

typedef utility::pointer::weak_ptr< MMLJEnergyTable > core::scoring::mm::MMLJEnergyTableAP

◆ MMLJEnergyTableCAP

typedef utility::pointer::weak_ptr< MMLJEnergyTable const > core::scoring::mm::MMLJEnergyTableCAP

◆ MMLJEnergyTableCOP

typedef utility::pointer::shared_ptr< MMLJEnergyTable const > core::scoring::mm::MMLJEnergyTableCOP

◆ MMLJEnergyTableOP

typedef utility::pointer::shared_ptr< MMLJEnergyTable > core::scoring::mm::MMLJEnergyTableOP

◆ MMLJLibraryAP

typedef utility::pointer::weak_ptr< MMLJLibrary > core::scoring::mm::MMLJLibraryAP

◆ MMLJLibraryCAP

typedef utility::pointer::weak_ptr< MMLJLibrary const > core::scoring::mm::MMLJLibraryCAP

◆ MMLJLibraryCOP

typedef utility::pointer::shared_ptr< MMLJLibrary const > core::scoring::mm::MMLJLibraryCOP

◆ MMLJLibraryOP

typedef utility::pointer::shared_ptr< MMLJLibrary > core::scoring::mm::MMLJLibraryOP

◆ MMLJScoreAP

typedef utility::pointer::weak_ptr< MMLJScore > core::scoring::mm::MMLJScoreAP

◆ MMLJScoreCAP

typedef utility::pointer::weak_ptr< MMLJScore const > core::scoring::mm::MMLJScoreCAP

◆ MMLJScoreCOP

typedef utility::pointer::shared_ptr< MMLJScore const > core::scoring::mm::MMLJScoreCOP

◆ MMLJScoreOP

typedef utility::pointer::shared_ptr< MMLJScore > core::scoring::mm::MMLJScoreOP

◆ MMTorsionLibraryAP

typedef utility::pointer::weak_ptr< MMTorsionLibrary > core::scoring::mm::MMTorsionLibraryAP

◆ MMTorsionLibraryCAP

typedef utility::pointer::weak_ptr< MMTorsionLibrary const > core::scoring::mm::MMTorsionLibraryCAP

◆ MMTorsionLibraryCOP

typedef utility::pointer::shared_ptr< MMTorsionLibrary const > core::scoring::mm::MMTorsionLibraryCOP

◆ MMTorsionLibraryOP

typedef utility::pointer::shared_ptr< MMTorsionLibrary > core::scoring::mm::MMTorsionLibraryOP

◆ MMTorsionScoreAP

typedef utility::pointer::weak_ptr< MMTorsionScore > core::scoring::mm::MMTorsionScoreAP

◆ MMTorsionScoreCAP

typedef utility::pointer::weak_ptr< MMTorsionScore const > core::scoring::mm::MMTorsionScoreCAP

◆ MMTorsionScoreCOP

typedef utility::pointer::shared_ptr< MMTorsionScore const > core::scoring::mm::MMTorsionScoreCOP

◆ MMTorsionScoreOP

typedef utility::pointer::shared_ptr< MMTorsionScore > core::scoring::mm::MMTorsionScoreOP

◆ three_atom_set

typedef utility::keys::Key3Tuple< Size, Size, Size > core::scoring::mm::three_atom_set

◆ two_atom_set

typedef utility::keys::Key2Tuple< Size, Size > core::scoring::mm::two_atom_set

Function Documentation

◆ connection_indices()

bool core::scoring::mm::connection_indices ( core::conformation::Residue const &  residue,
core::conformation::Residue const &  other_residue,
core::Size const  my_atomno,
core::Size const  other_atomno,
core::Size my_connection,
core::Size other_connection 
)

◆ mm_bond_angle_residue_type_param_set()

MMBondAngleResidueTypeParamSetCOP core::scoring::mm::mm_bond_angle_residue_type_param_set ( core::scoring::ScoreFunction const &  scorefxn)

◆ operator<<()

std::ostream& core::scoring::mm::operator<< ( std::ostream &  os,
MMBondAngleResidueTypeParam const &  residue_type_param 
)

◆ score_atom_centrally()

bool core::scoring::mm::score_atom_centrally ( core::chemical::ResidueType const &  restype,
utility::vector1< std::string > const &  central_atoms_to_score,
Size  atomno 
)

◆ TR() [1/6]

static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondAngleLibrary"  )
static

◆ TR() [2/6]

static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondAngleResidueTypeParamSet"  )
static

◆ TR() [3/6]

static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondLengthLibrary"  )
static

◆ TR() [4/6]

static basic::Tracer core::scoring::mm::TR ( "core.mm.MMLJLibrary"  )
static

◆ TR() [5/6]

static basic::Tracer core::scoring::mm::TR ( "core.mm.MMTorsionLibrary"  )
static

◆ TR() [6/6]

static basic::Tracer core::scoring::mm::TR ( "core.scoring.mm.MMLJEnergyTable"  )
static