#include <MMBondAngleResidueTypeParamSet.hh>

Inheritance diagram for core::scoring::mm::MMBondAngleResidueTypeParamSet:

Public Member Functions
	MMBondAngleResidueTypeParamSet ()
	ctor More...

MMBondAngleLibrary const *	mm_bondangle_library () const
	get bond angle library for newly created ResidueTypeParam objects More...

void	mm_bondangle_library (MMBondAngleLibrary const *value)
	set bond angle library for newly created ResidueTypeParam objects More...

bool	use_residue_type_theta0 () const
	get use of ResidueType theta0 in newly created ResidueTypeParam objects More...

void	use_residue_type_theta0 (bool value)
	set use of ResidueType theta0 in newly created ResidueTypeParam objects More...

utility::vector1< std::string > const &	central_atoms_to_score () const
	get central atoms to score in newly created ResidueTypeParam objects More...

void	central_atoms_to_score (utility::vector1< std::string > const &value)
	set central atoms to score in newly created ResidueTypeParam objects More...

MMBondAngleResidueTypeParam const &	get (core::chemical::ResidueType const &residue_type)
	lookup a param object for a given ResidueType More...

MMBondAngleResidueTypeParam const *	get (core::chemical::ResidueType const &residue_type) const
	lookup a param object for a given ResidueType, does not auto-create More...

void	lookup (core::conformation::Conformation const &conformation, core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, core::id::AtomID const &atomid3, core::Real &Ktheta, core::Real &theta0)
	lookup Ktheta and theta0 for any bond angle in a conformation More...

void	lookup (core::conformation::Conformation const &conformation, core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, core::id::AtomID const &atomid3, core::Real &Ktheta, core::Real &theta0) const
	lookup Ktheta and theta0 for any bond angle in a conformation More...

Private Member Functions
void	lookup (core::conformation::Conformation const &conformation, core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, core::id::AtomID const &atomid3, MMBondAngleResidueTypeParam const &residue_type_param, core::Real &Ktheta, core::Real &theta0) const
	lookup Ktheta and theta0 for any bond angle in a conformation More...

Private Attributes
MMBondAngleLibrary const *	mm_bondangle_library_
	bond angle library for deriving new ResidueTypeParam objects More...

bool	use_residue_type_theta0_
	use ResidueType defined theta0 in newly created ResidueTypeParam objects More...

utility::vector1< std::string >	central_atoms_to_score_
	only score certain central atoms in newly created ResidueTypeParam objects More...

std::map< std::string, MMBondAngleResidueTypeParam >	reside_type_param_map_
	mapping from ResidueType name to ResidueTypeParam More...

Constructor & Destructor Documentation

core::scoring::mm::MMBondAngleResidueTypeParamSet::MMBondAngleResidueTypeParamSet ( )

ctor

Member Function Documentation

utility::vector1<std::string> const& core::scoring::mm::MMBondAngleResidueTypeParamSet::central_atoms_to_score ( ) const

inline

get central atoms to score in newly created ResidueTypeParam objects

References central_atoms_to_score_.

void core::scoring::mm::MMBondAngleResidueTypeParamSet::central_atoms_to_score ( utility::vector1< std::string > const & value )

inline

set central atoms to score in newly created ResidueTypeParam objects

References central_atoms_to_score_.

MMBondAngleResidueTypeParam const & core::scoring::mm::MMBondAngleResidueTypeParamSet::get ( core::chemical::ResidueType const & residue_type )

lookup a param object for a given ResidueType

References central_atoms_to_score_, core::scoring::mm::MMBondAngleResidueTypeParam::init(), mm_bondangle_library_, core::chemical::ResidueTypeBase::name(), reside_type_param_map_, and use_residue_type_theta0_.

MMBondAngleResidueTypeParam const * core::scoring::mm::MMBondAngleResidueTypeParamSet::get ( core::chemical::ResidueType const & residue_type ) const

lookup a param object for a given ResidueType, does not auto-create

References core::chemical::ResidueTypeBase::name(), and reside_type_param_map_.

void core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup	(	core::conformation::Conformation const &	conformation,
		core::id::AtomID const &	atomid1,
		core::id::AtomID const &	atomid2,
		core::id::AtomID const &	atomid3,
		core::Real &	Ktheta,
		core::Real &	theta0
	)

lookup Ktheta and theta0 for any bond angle in a conformation

References core::conformation::Conformation::residue_type(), and core::id::AtomID::rsd().

Referenced by lookup().

void core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup	(	core::conformation::Conformation const &	conformation,
		core::id::AtomID const &	atomid1,
		core::id::AtomID const &	atomid2,
		core::id::AtomID const &	atomid3,
		core::Real &	Ktheta,
		core::Real &	theta0
	)		const

lookup Ktheta and theta0 for any bond angle in a conformation

References central_atoms_to_score_, core::scoring::mm::MMBondAngleResidueTypeParam::init(), lookup(), mm_bondangle_library_, core::conformation::Conformation::residue_type(), core::id::AtomID::rsd(), and use_residue_type_theta0_.

void core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup	(	core::conformation::Conformation const &	conformation,
		core::id::AtomID const &	atomid1,
		core::id::AtomID const &	atomid2,
		core::id::AtomID const &	atomid3,
		MMBondAngleResidueTypeParam const &	residue_type_param,
		core::Real &	Ktheta,
		core::Real &	theta0
	)		const

private

lookup Ktheta and theta0 for any bond angle in a conformation

References core::id::AtomID::atomno(), core::scoring::mm::MMBondAngleResidueTypeParam::bondangle_index(), core::scoring::mm::MMBondAngleResidueTypeParam::connection_index(), core::scoring::mm::connection_indices(), core::scoring::mm::MMBondAngleResidueTypeParam::connection_theta0(), core::scoring::mm::MMBondAngleResidueTypeParam::connection_use_theta0(), core::scoring::mm::MMBondAngleResidueTypeParam::Ktheta(), core::scoring::mm::MMBondAngleLibrary::lookup(), mm_bondangle_library_, core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::id::AtomID::rsd(), and core::scoring::mm::MMBondAngleResidueTypeParam::theta0().

MMBondAngleLibrary const* core::scoring::mm::MMBondAngleResidueTypeParamSet::mm_bondangle_library ( ) const

inline

get bond angle library for newly created ResidueTypeParam objects

References mm_bondangle_library_.

void core::scoring::mm::MMBondAngleResidueTypeParamSet::mm_bondangle_library ( MMBondAngleLibrary const * value )

inline

set bond angle library for newly created ResidueTypeParam objects

References mm_bondangle_library_.

bool core::scoring::mm::MMBondAngleResidueTypeParamSet::use_residue_type_theta0 ( ) const

inline

get use of ResidueType theta0 in newly created ResidueTypeParam objects

References use_residue_type_theta0_.

void core::scoring::mm::MMBondAngleResidueTypeParamSet::use_residue_type_theta0 ( bool value )

inline

set use of ResidueType theta0 in newly created ResidueTypeParam objects

References use_residue_type_theta0_.

Member Data Documentation

utility::vector1<std::string> core::scoring::mm::MMBondAngleResidueTypeParamSet::central_atoms_to_score_

private

only score certain central atoms in newly created ResidueTypeParam objects

Referenced by central_atoms_to_score(), get(), and lookup().

MMBondAngleLibrary const* core::scoring::mm::MMBondAngleResidueTypeParamSet::mm_bondangle_library_

private

bond angle library for deriving new ResidueTypeParam objects

Referenced by get(), lookup(), and mm_bondangle_library().

std::map<std::string, MMBondAngleResidueTypeParam> core::scoring::mm::MMBondAngleResidueTypeParamSet::reside_type_param_map_

private

mapping from ResidueType name to ResidueTypeParam

Referenced by get().

bool core::scoring::mm::MMBondAngleResidueTypeParamSet::use_residue_type_theta0_

private

use ResidueType defined theta0 in newly created ResidueTypeParam objects

Referenced by get(), lookup(), and use_residue_type_theta0().

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

src/core/scoring/mm/MMBondAngleResidueTypeParamSet.hh
src/core/scoring/mm/MMBondAngleResidueTypeParamSet.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation