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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
< MMBondAngleLibrary
MMBondAngleLibraryAP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleLibrary const > 
MMBondAngleLibraryCAP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleLibrary
MMBondAngleLibraryOP
 
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::Real
mm_bondangle_param_set
 
typedef std::multimap
< mm_bondangle_atom_tri,
mm_bondangle_param_set
mm_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_citer
mm_bondangle_library_citer_pair
 
typedef
utility::keys::Key2Tuple< Size,
Size
two_atom_set
 
typedef
utility::keys::Key3Tuple< Size,
Size, Size
three_atom_set
 
typedef
utility::pointer::weak_ptr
< MMBondAngleResidueTypeParamSet
MMBondAngleResidueTypeParamSetAP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleResidueTypeParamSet
const > 
MMBondAngleResidueTypeParamSetCAP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleResidueTypeParamSet
MMBondAngleResidueTypeParamSetOP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleResidueTypeParamSet
const > 
MMBondAngleResidueTypeParamSetCOP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleScore
MMBondAngleScoreAP
 
typedef
utility::pointer::weak_ptr
< MMBondAngleScore const > 
MMBondAngleScoreCAP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleScore
MMBondAngleScoreOP
 
typedef
utility::pointer::shared_ptr
< MMBondAngleScore const > 
MMBondAngleScoreCOP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthLibrary
MMBondLengthLibraryAP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthLibrary const > 
MMBondLengthLibraryCAP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthLibrary
MMBondLengthLibraryOP
 
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::Real
mm_bondlength_param_set
 
typedef std::multimap
< mm_bondlength_atom_pair,
mm_bondlength_param_set
mm_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_citer
mm_bondlength_library_citer_pair
 
typedef
utility::pointer::weak_ptr
< MMBondLengthScore
MMBondLengthScoreAP
 
typedef
utility::pointer::weak_ptr
< MMBondLengthScore const > 
MMBondLengthScoreCAP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthScore
MMBondLengthScoreOP
 
typedef
utility::pointer::shared_ptr
< MMBondLengthScore const > 
MMBondLengthScoreCOP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyTable
MMLJEnergyTableAP
 
typedef
utility::pointer::weak_ptr
< MMLJEnergyTable const > 
MMLJEnergyTableCAP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyTable
MMLJEnergyTableOP
 
typedef
utility::pointer::shared_ptr
< MMLJEnergyTable const > 
MMLJEnergyTableCOP
 
typedef
utility::pointer::weak_ptr
< MMLJLibrary
MMLJLibraryAP
 
typedef
utility::pointer::weak_ptr
< MMLJLibrary const > 
MMLJLibraryCAP
 
typedef
utility::pointer::shared_ptr
< MMLJLibrary
MMLJLibraryOP
 
typedef
utility::pointer::shared_ptr
< MMLJLibrary const > 
MMLJLibraryCOP
 
typedef Size mm_lj_atom
 
typedef
utility::keys::Key2Tuple< Real,
Real
mm_lj_param_set
 
typedef
utility::pointer::weak_ptr
< MMLJScore
MMLJScoreAP
 
typedef
utility::pointer::weak_ptr
< MMLJScore const > 
MMLJScoreCAP
 
typedef
utility::pointer::shared_ptr
< MMLJScore
MMLJScoreOP
 
typedef
utility::pointer::shared_ptr
< MMLJScore const > 
MMLJScoreCOP
 
typedef
utility::pointer::weak_ptr
< MMTorsionLibrary
MMTorsionLibraryAP
 
typedef
utility::pointer::weak_ptr
< MMTorsionLibrary const > 
MMTorsionLibraryCAP
 
typedef
utility::pointer::shared_ptr
< MMTorsionLibrary
MMTorsionLibraryOP
 
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::Real
mm_torsion_param_set
 
typedef std::multimap
< mm_torsion_atom_quad,
mm_torsion_param_set
mm_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_citer
mm_torsion_library_citer_pair
 
typedef
utility::pointer::weak_ptr
< MMTorsionScore
MMTorsionScoreAP
 
typedef
utility::pointer::weak_ptr
< MMTorsionScore const > 
MMTorsionScoreCAP
 
typedef
utility::pointer::shared_ptr
< MMTorsionScore
MMTorsionScoreOP
 
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

typedef utility::keys::Key3Tuple< int, int, int > core::scoring::mm::mm_bondangle_atom_tri
typedef utility::keys::Key2Tuple< core::Real, core::Real > core::scoring::mm::mm_bondangle_param_set
typedef utility::keys::Key2Tuple< int, int > core::scoring::mm::mm_bondlength_atom_pair
typedef utility::keys::Key2Tuple< Real, Real > core::scoring::mm::mm_lj_param_set
typedef utility::keys::Key4Tuple< int, int, int, int > core::scoring::mm::mm_torsion_atom_quad
typedef utility::keys::Key3Tuple< core::Real, int, core::Real > core::scoring::mm::mm_torsion_param_set
typedef utility::pointer::weak_ptr< MMBondAngleLibrary > core::scoring::mm::MMBondAngleLibraryAP
typedef utility::pointer::weak_ptr< MMBondAngleLibrary const > core::scoring::mm::MMBondAngleLibraryCAP
typedef utility::pointer::shared_ptr< MMBondAngleLibrary const > core::scoring::mm::MMBondAngleLibraryCOP
typedef utility::pointer::shared_ptr< MMBondAngleLibrary > core::scoring::mm::MMBondAngleLibraryOP
typedef utility::pointer::weak_ptr< MMBondAngleScore > core::scoring::mm::MMBondAngleScoreAP
typedef utility::pointer::weak_ptr< MMBondAngleScore const > core::scoring::mm::MMBondAngleScoreCAP
typedef utility::pointer::shared_ptr< MMBondAngleScore const > core::scoring::mm::MMBondAngleScoreCOP
typedef utility::pointer::shared_ptr< MMBondAngleScore > core::scoring::mm::MMBondAngleScoreOP
typedef utility::pointer::weak_ptr< MMBondLengthLibrary > core::scoring::mm::MMBondLengthLibraryAP
typedef utility::pointer::weak_ptr< MMBondLengthLibrary const > core::scoring::mm::MMBondLengthLibraryCAP
typedef utility::pointer::shared_ptr< MMBondLengthLibrary const > core::scoring::mm::MMBondLengthLibraryCOP
typedef utility::pointer::shared_ptr< MMBondLengthLibrary > core::scoring::mm::MMBondLengthLibraryOP
typedef utility::pointer::weak_ptr< MMBondLengthScore > core::scoring::mm::MMBondLengthScoreAP
typedef utility::pointer::weak_ptr< MMBondLengthScore const > core::scoring::mm::MMBondLengthScoreCAP
typedef utility::pointer::shared_ptr< MMBondLengthScore const > core::scoring::mm::MMBondLengthScoreCOP
typedef utility::pointer::shared_ptr< MMBondLengthScore > core::scoring::mm::MMBondLengthScoreOP
typedef utility::pointer::weak_ptr< MMLJEnergyTable > core::scoring::mm::MMLJEnergyTableAP
typedef utility::pointer::weak_ptr< MMLJEnergyTable const > core::scoring::mm::MMLJEnergyTableCAP
typedef utility::pointer::shared_ptr< MMLJEnergyTable const > core::scoring::mm::MMLJEnergyTableCOP
typedef utility::pointer::shared_ptr< MMLJEnergyTable > core::scoring::mm::MMLJEnergyTableOP
typedef utility::pointer::weak_ptr< MMLJLibrary > core::scoring::mm::MMLJLibraryAP
typedef utility::pointer::weak_ptr< MMLJLibrary const > core::scoring::mm::MMLJLibraryCAP
typedef utility::pointer::shared_ptr< MMLJLibrary const > core::scoring::mm::MMLJLibraryCOP
typedef utility::pointer::shared_ptr< MMLJLibrary > core::scoring::mm::MMLJLibraryOP
typedef utility::pointer::weak_ptr< MMLJScore > core::scoring::mm::MMLJScoreAP
typedef utility::pointer::weak_ptr< MMLJScore const > core::scoring::mm::MMLJScoreCAP
typedef utility::pointer::shared_ptr< MMLJScore const > core::scoring::mm::MMLJScoreCOP
typedef utility::pointer::shared_ptr< MMLJScore > core::scoring::mm::MMLJScoreOP
typedef utility::pointer::weak_ptr< MMTorsionLibrary > core::scoring::mm::MMTorsionLibraryAP
typedef utility::pointer::weak_ptr< MMTorsionLibrary const > core::scoring::mm::MMTorsionLibraryCAP
typedef utility::pointer::shared_ptr< MMTorsionLibrary const > core::scoring::mm::MMTorsionLibraryCOP
typedef utility::pointer::shared_ptr< MMTorsionLibrary > core::scoring::mm::MMTorsionLibraryOP
typedef utility::pointer::weak_ptr< MMTorsionScore > core::scoring::mm::MMTorsionScoreAP
typedef utility::pointer::weak_ptr< MMTorsionScore const > core::scoring::mm::MMTorsionScoreCAP
typedef utility::pointer::shared_ptr< MMTorsionScore const > core::scoring::mm::MMTorsionScoreCOP
typedef utility::pointer::shared_ptr< MMTorsionScore > core::scoring::mm::MMTorsionScoreOP
typedef utility::keys::Key3Tuple< Size, Size, Size > core::scoring::mm::three_atom_set
typedef utility::keys::Key2Tuple< Size, Size > core::scoring::mm::two_atom_set

Function Documentation

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 
)
MMBondAngleResidueTypeParamSetCOP core::scoring::mm::mm_bond_angle_residue_type_param_set ( core::scoring::ScoreFunction const &  scorefxn)
std::ostream& core::scoring::mm::operator<< ( std::ostream &  os,
MMBondAngleResidueTypeParam const &  residue_type_param 
)
bool core::scoring::mm::score_atom_centrally ( core::chemical::ResidueType const &  restype,
utility::vector1< std::string > const &  central_atoms_to_score,
Size  atomno 
)
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMLJLibrary"  )
static
static basic::Tracer core::scoring::mm::TR ( "core.scoring.mm.MMLJEnergyTable"  )
static
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondLengthLibrary"  )
static
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMTorsionLibrary"  )
static
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondAngleLibrary"  )
static
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMBondAngleResidueTypeParamSet"  )
static