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::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 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

Definition at line 45 of file MMBondAngleLibrary.hh.

typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_set > core::scoring::mm::mm_bondangle_library

Definition at line 47 of file MMBondAngleLibrary.hh.

typedef std::multimap< mm_bondangle_atom_tri, mm_bondangle_param_set >::const_iterator core::scoring::mm::mm_bondangle_library_citer

Definition at line 48 of file MMBondAngleLibrary.hh.

typedef std::pair< mm_bondangle_library_citer, mm_bondangle_library_citer > core::scoring::mm::mm_bondangle_library_citer_pair

Definition at line 49 of file MMBondAngleLibrary.hh.

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

Definition at line 46 of file MMBondAngleLibrary.hh.

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

Definition at line 37 of file MMBondLengthLibrary.hh.

typedef std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_set > core::scoring::mm::mm_bondlength_library

Definition at line 39 of file MMBondLengthLibrary.hh.

typedef std::multimap< mm_bondlength_atom_pair, mm_bondlength_param_set >::const_iterator core::scoring::mm::mm_bondlength_library_citer

Definition at line 40 of file MMBondLengthLibrary.hh.

typedef std::pair< mm_bondlength_library_citer, mm_bondlength_library_citer > core::scoring::mm::mm_bondlength_library_citer_pair

Definition at line 41 of file MMBondLengthLibrary.hh.

typedef utility::keys::Key2Tuple< double, double > core::scoring::mm::mm_bondlength_param_set

Definition at line 38 of file MMBondLengthLibrary.hh.

typedef Size core::scoring::mm::mm_lj_atom

Definition at line 41 of file MMLJLibrary.hh.

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

Definition at line 42 of file MMLJLibrary.hh.

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

Definition at line 41 of file MMTorsionLibrary.hh.

typedef std::multimap< mm_torsion_atom_quad, mm_torsion_param_set > core::scoring::mm::mm_torsion_library

Definition at line 43 of file MMTorsionLibrary.hh.

typedef std::multimap< mm_torsion_atom_quad, mm_torsion_param_set >::const_iterator core::scoring::mm::mm_torsion_library_citer

Definition at line 44 of file MMTorsionLibrary.hh.

typedef std::pair< mm_torsion_library_citer, mm_torsion_library_citer > core::scoring::mm::mm_torsion_library_citer_pair

Definition at line 45 of file MMTorsionLibrary.hh.

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

Definition at line 42 of file MMTorsionLibrary.hh.

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

Definition at line 27 of file MMBondAngleLibrary.fwd.hh.

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

Definition at line 30 of file MMBondAngleLibrary.fwd.hh.

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

Definition at line 32 of file MMBondAngleLibrary.fwd.hh.

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

Definition at line 31 of file MMBondAngleLibrary.fwd.hh.

typedef utility::pointer::access_ptr< MMBondAngleResidueTypeParamSet > core::scoring::mm::MMBondAngleResidueTypeParamSetAP

Definition at line 27 of file MMBondAngleResidueTypeParamSet.fwd.hh.

typedef utility::pointer::access_ptr< MMBondAngleResidueTypeParamSet const > core::scoring::mm::MMBondAngleResidueTypeParamSetCAP

Definition at line 30 of file MMBondAngleResidueTypeParamSet.fwd.hh.

typedef utility::pointer::owning_ptr< MMBondAngleResidueTypeParamSet const > core::scoring::mm::MMBondAngleResidueTypeParamSetCOP

Definition at line 32 of file MMBondAngleResidueTypeParamSet.fwd.hh.

typedef utility::pointer::owning_ptr< MMBondAngleResidueTypeParamSet > core::scoring::mm::MMBondAngleResidueTypeParamSetOP

Definition at line 31 of file MMBondAngleResidueTypeParamSet.fwd.hh.

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

Definition at line 27 of file MMBondAngleScore.fwd.hh.

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

Definition at line 30 of file MMBondAngleScore.fwd.hh.

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

Definition at line 32 of file MMBondAngleScore.fwd.hh.

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

Definition at line 31 of file MMBondAngleScore.fwd.hh.

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

Definition at line 27 of file MMBondLengthLibrary.fwd.hh.

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

Definition at line 30 of file MMBondLengthLibrary.fwd.hh.

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

Definition at line 32 of file MMBondLengthLibrary.fwd.hh.

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

Definition at line 31 of file MMBondLengthLibrary.fwd.hh.

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

Definition at line 27 of file MMBondLengthScore.fwd.hh.

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

Definition at line 30 of file MMBondLengthScore.fwd.hh.

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

Definition at line 32 of file MMBondLengthScore.fwd.hh.

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

Definition at line 31 of file MMBondLengthScore.fwd.hh.

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

Definition at line 27 of file MMLJEnergyTable.fwd.hh.

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

Definition at line 30 of file MMLJEnergyTable.fwd.hh.

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

Definition at line 32 of file MMLJEnergyTable.fwd.hh.

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

Definition at line 31 of file MMLJEnergyTable.fwd.hh.

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

Definition at line 27 of file MMLJLibrary.fwd.hh.

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

Definition at line 30 of file MMLJLibrary.fwd.hh.

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

Definition at line 32 of file MMLJLibrary.fwd.hh.

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

Definition at line 31 of file MMLJLibrary.fwd.hh.

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

Definition at line 28 of file MMLJScore.fwd.hh.

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

Definition at line 31 of file MMLJScore.fwd.hh.

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

Definition at line 33 of file MMLJScore.fwd.hh.

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

Definition at line 32 of file MMLJScore.fwd.hh.

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

Definition at line 27 of file MMTorsionLibrary.fwd.hh.

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

Definition at line 30 of file MMTorsionLibrary.fwd.hh.

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

Definition at line 32 of file MMTorsionLibrary.fwd.hh.

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

Definition at line 31 of file MMTorsionLibrary.fwd.hh.

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

Definition at line 27 of file MMTorsionScore.fwd.hh.

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

Definition at line 30 of file MMTorsionScore.fwd.hh.

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

Definition at line 32 of file MMTorsionScore.fwd.hh.

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

Definition at line 31 of file MMTorsionScore.fwd.hh.

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

Definition at line 43 of file MMBondAngleResidueTypeParam.hh.

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

Definition at line 42 of file MMBondAngleResidueTypeParam.hh.

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
	)

get the indices of the connections that connects one of my atoms to an atom on another residue

Definition at line 108 of file MMBondAngleResidueTypeParamSet.cc.

References core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_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

Definition at line 256 of file MMBondAngleResidueTypeParamSet.cc.

References core::scoring::ScoreFunction::ci_2b_intrares_begin(), and core::scoring::ScoreFunction::ci_2b_intrares_end().

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

stream << MMBondAngleResidueTypeParam

Definition at line 181 of file MMBondAngleResidueTypeParam.cc.

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
	)