Rosetta 3.4
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core::scoring::mm Namespace Reference

Namespaces

namespace  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::access_ptr
< MMBondAngleLibrary
MMBondAngleLibraryAP
typedef
utility::pointer::access_ptr
< MMBondAngleLibrary const > 
MMBondAngleLibraryCAP
typedef
utility::pointer::owning_ptr
< MMBondAngleLibrary
MMBondAngleLibraryOP
typedef
utility::pointer::owning_ptr
< MMBondAngleLibrary const > 
MMBondAngleLibraryCOP
typedef
utility::keys::Key3Tuple< int,
int, int
mm_bondangle_atom_tri
typedef
utility::keys::Key2Tuple
< double, double > 
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::access_ptr
< MMBondAngleResidueTypeParamSet
MMBondAngleResidueTypeParamSetAP
typedef
utility::pointer::access_ptr
< MMBondAngleResidueTypeParamSet
const > 
MMBondAngleResidueTypeParamSetCAP
typedef
utility::pointer::owning_ptr
< MMBondAngleResidueTypeParamSet
MMBondAngleResidueTypeParamSetOP
typedef
utility::pointer::owning_ptr
< MMBondAngleResidueTypeParamSet
const > 
MMBondAngleResidueTypeParamSetCOP
typedef
utility::pointer::access_ptr
< MMBondAngleScore
MMBondAngleScoreAP
typedef
utility::pointer::access_ptr
< MMBondAngleScore const > 
MMBondAngleScoreCAP
typedef
utility::pointer::owning_ptr
< MMBondAngleScore
MMBondAngleScoreOP
typedef
utility::pointer::owning_ptr
< MMBondAngleScore const > 
MMBondAngleScoreCOP
typedef
utility::pointer::access_ptr
< MMBondLengthLibrary
MMBondLengthLibraryAP
typedef
utility::pointer::access_ptr
< MMBondLengthLibrary const > 
MMBondLengthLibraryCAP
typedef
utility::pointer::owning_ptr
< MMBondLengthLibrary
MMBondLengthLibraryOP
typedef
utility::pointer::owning_ptr
< MMBondLengthLibrary const > 
MMBondLengthLibraryCOP
typedef
utility::keys::Key2Tuple< int,
int
mm_bondlength_atom_pair
typedef
utility::keys::Key2Tuple
< double, double > 
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::access_ptr
< MMBondLengthScore
MMBondLengthScoreAP
typedef
utility::pointer::access_ptr
< MMBondLengthScore const > 
MMBondLengthScoreCAP
typedef
utility::pointer::owning_ptr
< MMBondLengthScore
MMBondLengthScoreOP
typedef
utility::pointer::owning_ptr
< MMBondLengthScore const > 
MMBondLengthScoreCOP
typedef
utility::pointer::access_ptr
< MMLJEnergyTable
MMLJEnergyTableAP
typedef
utility::pointer::access_ptr
< MMLJEnergyTable const > 
MMLJEnergyTableCAP
typedef
utility::pointer::owning_ptr
< MMLJEnergyTable
MMLJEnergyTableOP
typedef
utility::pointer::owning_ptr
< MMLJEnergyTable const > 
MMLJEnergyTableCOP
typedef
utility::pointer::access_ptr
< MMLJLibrary
MMLJLibraryAP
typedef
utility::pointer::access_ptr
< MMLJLibrary const > 
MMLJLibraryCAP
typedef
utility::pointer::owning_ptr
< MMLJLibrary
MMLJLibraryOP
typedef
utility::pointer::owning_ptr
< MMLJLibrary const > 
MMLJLibraryCOP
typedef Size mm_lj_atom
typedef
utility::keys::Key2Tuple< Real,
Real
mm_lj_param_set
typedef
utility::pointer::access_ptr
< MMLJScore
MMLJScoreAP
typedef
utility::pointer::access_ptr
< MMLJScore const > 
MMLJScoreCAP
typedef
utility::pointer::owning_ptr
< MMLJScore
MMLJScoreOP
typedef
utility::pointer::owning_ptr
< MMLJScore const > 
MMLJScoreCOP
typedef
utility::pointer::access_ptr
< MMTorsionLibrary
MMTorsionLibraryAP
typedef
utility::pointer::access_ptr
< MMTorsionLibrary const > 
MMTorsionLibraryCAP
typedef
utility::pointer::owning_ptr
< MMTorsionLibrary
MMTorsionLibraryOP
typedef
utility::pointer::owning_ptr
< MMTorsionLibrary const > 
MMTorsionLibraryCOP
typedef
utility::keys::Key4Tuple< int,
int, int, int
mm_torsion_atom_quad
typedef
utility::keys::Key3Tuple
< double, int, double > 
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::access_ptr
< MMTorsionScore
MMTorsionScoreAP
typedef
utility::pointer::access_ptr
< MMTorsionScore const > 
MMTorsionScoreCAP
typedef
utility::pointer::owning_ptr
< MMTorsionScore
MMTorsionScoreOP
typedef
utility::pointer::owning_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
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
MMBondAngleResidueTypeParamSetCOP mm_bond_angle_residue_type_param_set (core::scoring::ScoreFunction const &scorefxn)
 extract a MMBondAngleResidueTypeParamSet from a ScoreFunction, returning NULL if none exists
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< double, double > core::scoring::mm::mm_bondangle_param_set
typedef utility::keys::Key2Tuple< int, int > core::scoring::mm::mm_bondlength_atom_pair
typedef utility::keys::Key2Tuple< double, double > core::scoring::mm::mm_bondlength_param_set
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< double, int, double > core::scoring::mm::mm_torsion_param_set
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.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]
static basic::Tracer core::scoring::mm::TR ( "core.scoring.mm.MMLJEnergyTable"  ) [static]
static basic::Tracer core::scoring::mm::TR ( "core.mm.MMLJLibrary"  ) [static]
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