#include <COMCoordinateConstraint.hh>

Public Member Functions
	COMCoordinateConstraint ()
	null constructor More...

	COMCoordinateConstraint (utility::vector1< AtomID > const &atms, Vector const &COM_target, Real stdv, Real interval, scoring::ScoreType scoretype=scoring::coordinate_constraint)
	ctor from atom list + input pose More...

	COMCoordinateConstraint (utility::vector1< AtomID > const &atms, Vector const &COM_target, Real stdv, scoring::ScoreType scoretype=scoring::coordinate_constraint)

	COMCoordinateConstraint (utility::vector1< AtomID > const &atms, Vector const &COM_target, scoring::ScoreType scoretype=scoring::coordinate_constraint)

virtual scoring::constraints::ConstraintOP	clone () const

virtual scoring::constraints::ConstraintOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP smap) const

void	score (scoring::func::XYZ_Func const &xyz, scoring::EnergyMap const &, scoring::EnergyMap &emap) const

void	setup_for_scoring (scoring::func::XYZ_Func const &xyz, scoring::ScoreFunction const &scfxn) const

void	setup_for_derivatives (scoring::func::XYZ_Func const &xyz, scoring::ScoreFunction const &scfxn) const

virtual void	fill_f1_f2 (AtomID const &atom, scoring::func::XYZ_Func const &xyz, Vector &F1, Vector &F2, scoring::EnergyMap const &weights) const

std::string	type () const

Size	natoms () const

virtual scoring::constraints::ConstraintOP	remap_resid (id::SequenceMapping const &) const

AtomID const &	atom (Size const n) const

void	show (std::ostream &out) const

void	show_def (std::ostream &out, pose::Pose const &pose) const

void	read_def (std::istream &in, pose::Pose const &pose, scoring::func::FuncFactory const &func_factory)
	Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_. More...

Size	show_violations (std::ostream &out, pose::Pose const &pose, Size verbose_level, Real threshold=1.0) const

Private Attributes
Vector	dCOM_

Vector	COM_target_

utility::vector1< AtomID >	atms_

Real	stdv_

Real	interval_

Constructor & Destructor Documentation

protocols::constraints_additional::COMCoordinateConstraint::COMCoordinateConstraint ( )

inline

null constructor

References constraints, coordinate_constraint, and scoring.

Referenced by remapped_clone().

protocols::constraints_additional::COMCoordinateConstraint::COMCoordinateConstraint	(	utility::vector1< AtomID > const &	atms,
		Vector const &	COM_target,
		Real	stdv,
		Real	interval,
		scoring::ScoreType	scoretype = `scoring::coordinate_constraint`
	)

ctor from atom list + input pose

c-tor

protocols::constraints_additional::COMCoordinateConstraint::COMCoordinateConstraint	(	utility::vector1< AtomID > const &	atms,
		Vector const &	COM_target,
		Real	stdv,
		scoring::ScoreType	scoretype = `scoring::coordinate_constraint`
	)

protocols::constraints_additional::COMCoordinateConstraint::COMCoordinateConstraint	(	utility::vector1< AtomID > const &	atms,
		Vector const &	COM_target,
		scoring::ScoreType	scoretype = `scoring::coordinate_constraint`
	)

Member Function Documentation

id::AtomID const & protocols::constraints_additional::COMCoordinateConstraint::atom ( Size const n ) const

virtual

Implements core::scoring::constraints::Constraint.

References atms_, and utility_exit_with_message.

Referenced by fill_f1_f2().

virtual scoring::constraints::ConstraintOP protocols::constraints_additional::COMCoordinateConstraint::clone ( ) const

inlinevirtual

void protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2	(	AtomID const &	atom,
		scoring::func::XYZ_Func const &	xyz,
		Vector &	F1,
		Vector &	F2,
		scoring::EnergyMap const &	weights
	)		const

virtual

References atms_, atom(), dCOM_, natoms(), score_type, and protocols::kinmatch::xyz().

Size protocols::constraints_additional::COMCoordinateConstraint::natoms ( ) const

virtual

Implements core::scoring::constraints::Constraint.

References atms_.

Referenced by fill_f1_f2(), and setup_for_scoring().

void protocols::constraints_additional::COMCoordinateConstraint::read_def	(	std::istream &	in,
		pose::Pose const &	pose,
		scoring::func::FuncFactory const &	func_factory
	)

Format should look like: Dunbrack seqpos_ rot_vec_pos_ rot_bin_ bonus_.

References atms_, core::chemical::ResidueType::atom_index(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and tr.

virtual scoring::constraints::ConstraintOP protocols::constraints_additional::COMCoordinateConstraint::remap_resid ( id::SequenceMapping const & ) const

inlinevirtual

scoring::constraints::ConstraintOP protocols::constraints_additional::COMCoordinateConstraint::remapped_clone	(	pose::Pose const &	src,
		pose::Pose const &	dest,
		id::SequenceMappingCOP	smap
	)		const

virtual

References atms_, atom_id_to_named_atom_id(), COM_target_, COMCoordinateConstraint(), interval_, named_atom_id_to_atom_id(), core::id::NamedAtomID::rsd(), stdv_, and core::id::AtomID::valid().

void protocols::constraints_additional::COMCoordinateConstraint::score	(	scoring::func::XYZ_Func const &	xyz,
		scoring::EnergyMap const &	,
		scoring::EnergyMap &	emap
	)		const

virtual

Implements core::scoring::constraints::Constraint.

References atms_, COM_target_, dCOM_, numeric::xyzVector< class >::dot_product(), interval_, score_type, stdv_, tr, and protocols::kinmatch::xyz().

void protocols::constraints_additional::COMCoordinateConstraint::setup_for_derivatives	(	scoring::func::XYZ_Func const &	xyz,
		scoring::ScoreFunction const &	scfxn
	)		const

References setup_for_scoring().

void protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring	(	scoring::func::XYZ_Func const &	xyz,
		scoring::ScoreFunction const &	scfxn
	)		const

References atms_, natoms(), and core::scoring::func::XYZ_Func::residue().

Referenced by setup_for_derivatives().

void protocols::constraints_additional::COMCoordinateConstraint::show ( std::ostream & out ) const

virtual

Reimplemented from core::scoring::constraints::Constraint.

void protocols::constraints_additional::COMCoordinateConstraint::show_def	(	std::ostream &	out,
		pose::Pose const &	pose
	)		const

Size protocols::constraints_additional::COMCoordinateConstraint::show_violations	(	std::ostream &	out,
		pose::Pose const &	pose,
		Size	verbose_level,
		Real	threshold = `1.0`
	)		const