core::scoring::mm::MMBondAngleResidueTypeParam Class Reference

#include <MMBondAngleResidueTypeParam.hh>

Public Member Functions
	MMBondAngleResidueTypeParam ()
	Default ctor. More...
void	init (core::chemical::ResidueType const &residue_type, MMBondAngleLibrary const &mm_bondangle_library, bool use_residue_type_theta0, utility::vector1< std::string > const &central_atoms_to_score)
	initialize the parameters More...
Size	num_bondangles () const
	get number of intraresidue bond angles More...
three_atom_set const &	bondangle (Size const bondang) const
	Return the indices for the set of atoms that define a particular intraresidue angle. More...
core::Real	Ktheta (Size const bondang) const
	get Ktheta for a particular intraresidue angle More...
core::Real	theta0 (Size const bondang) const
	get Ktheta for a particular intraresidue angle More...
utility::vector1< Size > const &	bondangles_for_atom (Size atomno) const
	Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom. More...
core::Size	bondangle_index (three_atom_set const &atom_set) const
	Returns the index of the intraresidue bond angle, 0 if not found. More...
Size	n_possible_residue_connections () const
	number of ResidueConnections, counting polymeric residue connections More...
Size	n_connection_pairs (Size const connection) const
	number of ResidueConnections, counting polymeric residue connections More...
two_atom_set const &	connection_pair (Size const connection, Size const bondang) const
	Return the indices for the set of two atoms that form part of a interresidue bond angle. More...
core::Real	connection_theta0 (Size const connection, Size const bondang) const
	Return ResidueType derived theta0 for a interresidue bond angle. More...
bool	connection_use_theta0 (Size const connection, Size const bondang) const
	Return whether to use ResidueType derived theta0 for a interresidue bond angle. More...
core::Size	connection_index (Size const connection, two_atom_set const &atom_set) const
	Returns the index of the interresidue bond angle, 0 if not found. More...

Private Attributes
utility::vector1< three_atom_set >	bondangle_atom_sets_
	vector of sets of atoms that make up bond angles in the residue More...
utility::vector1< core::Real >	Ktheta_
	vector of Ktheta values for each set More...
utility::vector1< core::Real >	theta0_
	vector of theta0 values for each set More...
utility::vector1 < utility::vector1< Size > >	bondangles_for_atom_
	all intra-residue bond angles that each atom "participates" in. More...
std::map< three_atom_set, core::Size >	bondangle_index_
	map to lookup a bondangle given its three atoms More...
utility::vector1 < utility::vector1 < two_atom_set > >	connection_atom_sets_
	vector of vector of pairs of atoms that take part in interresidue bond angles More...
utility::vector1 < utility::vector1< core::Real > >	connection_theta0_
	vector of vector of theta0 values for pairs of atoms that take part in interresidue bond angles More...
utility::vector1 < utility::vector1< bool > >	connection_use_theta0_
	vector of vector of booleans indicating whether to use theta0_ or lookup on the fly More...
utility::vector1< std::map < two_atom_set, core::Size > >	connection_index_
	vector of maps for lookup of interresidue theta0 parameters More...

Friends
std::ostream &	operator<< (std::ostream &os, MMBondAngleResidueTypeParam const &residue_type_param)
	stream << MMBondAngleResidueTypeParam More...

Constructor & Destructor Documentation

core::scoring::mm::MMBondAngleResidueTypeParam::MMBondAngleResidueTypeParam ( )

default

Default ctor.

Member Function Documentation

three_atom_set const& core::scoring::mm::MMBondAngleResidueTypeParam::bondangle ( Size const  bondang ) const

inline

Return the indices for the set of atoms that define a particular intraresidue angle.

References bondangle_atom_sets_.

core::Size core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_index ( three_atom_set const &  atom_set ) const

inline

Returns the index of the intraresidue bond angle, 0 if not found.

References bondangle_index_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

utility::vector1< Size > const& core::scoring::mm::MMBondAngleResidueTypeParam::bondangles_for_atom ( Size  atomno ) const

inline

Returns the list of all of the indices of all the intraresidue bond angles a particular atom is involved in. Useful for calculating the derivatives for an atom.

References bondangles_for_atom_.

core::Size core::scoring::mm::MMBondAngleResidueTypeParam::connection_index ( Size const  connection, two_atom_set const &  atom_set  ) const

inline

Returns the index of the interresidue bond angle, 0 if not found.

References connection_index_, and core::sequence::end.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

two_atom_set const& core::scoring::mm::MMBondAngleResidueTypeParam::connection_pair ( Size const  connection, Size const  bondang  ) const

inline

Return the indices for the set of two atoms that form part of a interresidue bond angle.

References connection_atom_sets_.

core::Real core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0 ( Size const  connection, Size const  bondang  ) const

inline

Return ResidueType derived theta0 for a interresidue bond angle.

References connection_theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

bool core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0 ( Size const  connection, Size const  bondang  ) const

inline

Return whether to use ResidueType derived theta0 for a interresidue bond angle.

References connection_use_theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

void core::scoring::mm::MMBondAngleResidueTypeParam::init	(	core::chemical::ResidueType const &	residue_type,
		MMBondAngleLibrary const &	mm_bondangle_library,
		bool	use_residue_type_theta0,
		utility::vector1< std::string > const &	central_atoms_to_score
	)

initialize the parameters

References core::chemical::ResidueType::bondangle(), bondangle_atom_sets_, bondangle_index_, bondangles_for_atom_, core::chemical::ResidueType::bonded_neighbor(), connection_atom_sets_, connection_index_, connection_theta0_, connection_use_theta0_, core::chemical::ResidueType::ideal_xyz(), Ktheta_, core::scoring::mm::MMBondAngleLibrary::lookup(), core::chemical::ResidueType::mm_name(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::num_bondangles(), core::chemical::ResidueType::residue_connection(), core::scoring::mm::score_atom_centrally(), and theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), and core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

core::Real core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta ( Size const  bondang ) const

inline

get Ktheta for a particular intraresidue angle

References Ktheta_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

Size core::scoring::mm::MMBondAngleResidueTypeParam::n_connection_pairs ( Size const  connection ) const

inline

number of ResidueConnections, counting polymeric residue connections

References connection_atom_sets_.

Size core::scoring::mm::MMBondAngleResidueTypeParam::n_possible_residue_connections ( ) const

inline

number of ResidueConnections, counting polymeric residue connections

References connection_atom_sets_.

Size core::scoring::mm::MMBondAngleResidueTypeParam::num_bondangles ( ) const

inline

get number of intraresidue bond angles

References bondangle_atom_sets_.

core::Real core::scoring::mm::MMBondAngleResidueTypeParam::theta0 ( Size const  bondang ) const

inline

get Ktheta for a particular intraresidue angle

References theta0_.

Referenced by core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup().

Friends And Related Function Documentation

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

friend

stream << MMBondAngleResidueTypeParam

Member Data Documentation

utility::vector1< three_atom_set > core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_atom_sets_

private

vector of sets of atoms that make up bond angles in the residue

Referenced by bondangle(), init(), num_bondangles(), and core::scoring::mm::operator<<().

std::map< three_atom_set, core::Size > core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_index_

private

map to lookup a bondangle given its three atoms

Referenced by bondangle_index(), and init().

utility::vector1< utility::vector1< Size > > core::scoring::mm::MMBondAngleResidueTypeParam::bondangles_for_atom_

private

all intra-residue bond angles that each atom "participates" in.

Referenced by bondangles_for_atom(), and init().

utility::vector1< utility::vector1< two_atom_set > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_atom_sets_

private

vector of vector of pairs of atoms that take part in interresidue bond angles

Referenced by connection_pair(), init(), n_connection_pairs(), n_possible_residue_connections(), and core::scoring::mm::operator<<().

utility::vector1< std::map< two_atom_set, core::Size > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_index_

private

vector of maps for lookup of interresidue theta0 parameters

Referenced by connection_index(), and init().

utility::vector1< utility::vector1< core::Real > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0_

private

vector of vector of theta0 values for pairs of atoms that take part in interresidue bond angles

Referenced by connection_theta0(), init(), and core::scoring::mm::operator<<().

utility::vector1< utility::vector1< bool > > core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0_

private

vector of vector of booleans indicating whether to use theta0_ or lookup on the fly

Referenced by connection_use_theta0(), init(), and core::scoring::mm::operator<<().

utility::vector1< core::Real > core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta_

private

vector of Ktheta values for each set

Referenced by init(), Ktheta(), and core::scoring::mm::operator<<().

utility::vector1< core::Real > core::scoring::mm::MMBondAngleResidueTypeParam::theta0_

private

vector of theta0 values for each set

Referenced by init(), core::scoring::mm::operator<<(), and theta0().

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The documentation for this class was generated from the following files:

• src/core/scoring/mm/MMBondAngleResidueTypeParam.hh
• src/core/scoring/mm/MMBondAngleResidueTypeParam.cc