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 ¢ral_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") |