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::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
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...
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...

Variables
static basic::Tracer	TR ("core.mm.MMBondAngleLibrary")
static basic::Tracer	TR ("core.mm.MMBondAngleResidueTypeParamSet")
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 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< double, double > 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< double, double > 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< double, int, double > core::scoring::mm::mm_torsion_param_set

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::owning_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
	)

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_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(), and core::scoring::ScoreFunction::ci_2b_intrares_end().

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_, numeric::conversions::degrees(), 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(), and utility::same_ignoring_spaces().

Referenced by core::scoring::mm::MMBondAngleResidueTypeParam::init().

Variable Documentation

basic::Tracer core::scoring::mm::TR("core.mm.MMLJLibrary")

static

basic::Tracer core::scoring::mm::TR("core.scoring.mm.MMLJEnergyTable")

static

basic::Tracer core::scoring::mm::TR("core.mm.MMBondAngleResidueTypeParamSet")

static

basic::Tracer core::scoring::mm::TR("core.mm.MMTorsionLibrary")

static

basic::Tracer core::scoring::mm::TR("core.mm.MMBondLengthLibrary")

static

basic::Tracer core::scoring::mm::TR("core.mm.MMBondAngleLibrary")

static

Referenced by core::scoring::mm::MMBondLengthLibrary::lookup(), core::scoring::mm::MMBondAngleLibrary::lookup(), core::scoring::mm::MMTorsionLibrary::lookup(), core::scoring::mm::MMBondAngleLibrary::MMBondAngleLibrary(), core::scoring::mm::MMBondLengthLibrary::MMBondLengthLibrary(), core::scoring::mm::MMLJEnergyTable::MMLJEnergyTable(), core::scoring::mm::MMLJLibrary::MMLJLibrary(), core::scoring::mm::MMTorsionLibrary::MMTorsionLibrary(), core::scoring::mm::MMBondLengthLibrary::pretty_print(), and core::scoring::mm::MMBondAngleLibrary::pretty_print().