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Rosetta
2020.50
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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 ¢ral_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 utility::keys::Key3Tuple< int, int, int > core::scoring::mm::mm_bondangle_atom_tri |
typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_set > core::scoring::mm::mm_bondangle_library |
typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_set >::const_iterator core::scoring::mm::mm_bondangle_library_citer |
typedef std::pair< mm_bondangle_library_citer, mm_bondangle_library_citer > core::scoring::mm::mm_bondangle_library_citer_pair |
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 std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_set > core::scoring::mm::mm_bondlength_library |
typedef std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_set >::const_iterator core::scoring::mm::mm_bondlength_library_citer |
typedef std::pair< mm_bondlength_library_citer, mm_bondlength_library_citer > core::scoring::mm::mm_bondlength_library_citer_pair |
typedef utility::keys::Key2Tuple< core::Real, core::Real > core::scoring::mm::mm_bondlength_param_set |
typedef Size core::scoring::mm::mm_lj_atom |
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 std::multimap< mm_torsion_atom_quad, mm_torsion_param_set > core::scoring::mm::mm_torsion_library |
typedef std::multimap< mm_torsion_atom_quad, mm_torsion_param_set >::const_iterator core::scoring::mm::mm_torsion_library_citer |
typedef std::pair< mm_torsion_library_citer, mm_torsion_library_citer > core::scoring::mm::mm_torsion_library_citer_pair |
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< MMBondAngleResidueTypeParamSet > core::scoring::mm::MMBondAngleResidueTypeParamSetAP |
typedef utility::pointer::weak_ptr< MMBondAngleResidueTypeParamSet const > core::scoring::mm::MMBondAngleResidueTypeParamSetCAP |
typedef utility::pointer::shared_ptr< MMBondAngleResidueTypeParamSet const > core::scoring::mm::MMBondAngleResidueTypeParamSetCOP |
typedef utility::pointer::shared_ptr< MMBondAngleResidueTypeParamSet > core::scoring::mm::MMBondAngleResidueTypeParamSetOP |
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 |
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 | ||
) |
get the indices of the connections that connects one of my atoms to an atom on another residue
References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_possible_residue_connections(), core::chemical::ResConnID::resid(), core::conformation::Residue::residue_connection(), and core::conformation::Residue::seqpos().
Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().
MMBondAngleResidueTypeParamSetCOP core::scoring::mm::mm_bond_angle_residue_type_param_set | ( | core::scoring::ScoreFunction const & | scorefxn | ) |
extract a MMBondAngleResidueTypeParamSet from a ScoreFunction, returning NULL if none exists
References core::scoring::ScoreFunction::ci_2b_intrares_begin(), core::scoring::ScoreFunction::ci_2b_intrares_end(), and core::scoring::methods::MMBondAngleEnergy::residue_type_param_set().
std::ostream& core::scoring::mm::operator<< | ( | std::ostream & | os, |
MMBondAngleResidueTypeParam const & | residue_type_param | ||
) |
stream << MMBondAngleResidueTypeParam
References core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_atom_sets_, core::scoring::mm::MMBondAngleResidueTypeParam::connection_atom_sets_, core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0_, core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0_, core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta_, and core::scoring::mm::MMBondAngleResidueTypeParam::theta0_.
bool core::scoring::mm::score_atom_centrally | ( | core::chemical::ResidueType const & | restype, |
utility::vector1< std::string > const & | central_atoms_to_score, | ||
Size | atomno | ||
) |
References core::chemical::ResidueType::atom_name().
Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init().
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Referenced by core::scoring::mm::MMBondLengthLibrary::lookup(), core::scoring::mm::MMTorsionLibrary::lookup(), core::scoring::mm::MMBondLengthLibrary::MMBondLengthLibrary(), core::scoring::mm::MMLJLibrary::MMLJLibrary(), core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary(), and core::scoring::mm::MMBondLengthLibrary::pretty_print().
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