#include <BindingSiteConstraint.hh>

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

	BindingSiteConstraint (utility::vector1< AtomID > const &atms, core::pose::Pose const &start_pose, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
	ctor from atom list + input pose More...

	BindingSiteConstraint (utility::vector1< AtomID > const &atms, ObjexxFCL::FArray2D< core::Real > tgt_pos, ObjexxFCL::FArray2D< core::Real > tgt_pos_centroid, core::scoring::ScoreType scoretype=core::scoring::atom_pair_constraint)
	ctor from a vector of atom positions (in lieu of a pose) More...

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

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

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

void	pre_align (utility::vector1< numeric::xyzVector< core::Real > > const &templ_atms, utility::vector1< bool > const &) const

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

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

std::string	type () const

Size	natoms () const

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

AtomID const &	atom (Size const n) const

void	show (std::ostream &out) const

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

void	read_def (std::istream &in, core::pose::Pose const &pose, core::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, core::pose::Pose const &pose, core::Size verbose_level, core::Real threshold=1.0) const

Protected Member Functions
void	init (core::pose::Pose const &start_pose)

Private Attributes
utility::vector1< AtomID >	atms_

ObjexxFCL::FArray2D< core::Real >	tgt_pos_

ObjexxFCL::FArray2D< core::Real >	tgt_pos_centroid_

Static Private Attributes
static std::map< AtomID, numeric::xyzVector< core::Real > >	rot_db

Constructor & Destructor Documentation

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint ( )

inline

null constructor

References atom_pair_constraint, constraints, and scoring.

Referenced by clone(), and remap_resid().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint	(	utility::vector1< AtomID > const &	atms,
		core::pose::Pose const &	start_pose,
		core::scoring::ScoreType	scoretype = `core::scoring::atom_pair_constraint`
	)

ctor from atom list + input pose

c-tor

Parameters

scoretype ? TO DO – give own scoretype

References init().

protocols::constraints_additional::BindingSiteConstraint::BindingSiteConstraint	(	utility::vector1< AtomID > const &	atms,
		ObjexxFCL::FArray2D< core::Real >	tgt_pos,
		ObjexxFCL::FArray2D< core::Real >	tgt_pos_centroid,
		core::scoring::ScoreType	scoretype = `core::scoring::atom_pair_constraint`
	)

ctor from a vector of atom positions (in lieu of a pose)

Parameters

scoretype ? TO DO – give own scoretype

Member Function Documentation

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

virtual

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

References atms_, and utility_exit_with_message.

Referenced by fill_f1_f2().

virtual core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::clone ( ) const

inlinevirtual

References atms_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

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

virtual

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

void protocols::constraints_additional::BindingSiteConstraint::init ( core::pose::Pose const & start_pose )

protected

References atms_, core::chemical::CENTROID, core::chemical::ResidueTypeSet::name(), natoms(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::util::switch_to_residue_type_set(), tgt_pos_, tgt_pos_centroid_, and core::pose::Pose::xyz().

Referenced by BindingSiteConstraint(), and read_def().

core::Size protocols::constraints_additional::BindingSiteConstraint::natoms ( ) const

virtual

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

References atms_.

Referenced by init(), pre_align(), and setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::pre_align	(	utility::vector1< numeric::xyzVector< core::Real > > const &	templ_atms,
		utility::vector1< bool > const &	align_centroid
	)		const

References atms_, numeric::model_quality::findUU(), natoms(), rot_db, tgt_pos_, tgt_pos_centroid_, utility_exit_with_message, numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

Referenced by setup_for_scoring().

void protocols::constraints_additional::BindingSiteConstraint::read_def	(	std::istream &	in,
		core::pose::Pose const &	pose,
		core::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(), init(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and tr.

core::scoring::constraints::ConstraintOP protocols::constraints_additional::BindingSiteConstraint::remap_resid ( core::id::SequenceMapping const & seqmap ) const

virtual

References atms_, BindingSiteConstraint(), tgt_pos_, and tgt_pos_centroid_.

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

virtual

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

References atms_, rot_db, and score_type.

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

References setup_for_scoring().

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

References atms_, core::chemical::CENTROID, core::chemical::ResidueTypeSet::name(), natoms(), pre_align(), core::scoring::func::XYZ_Func::residue(), core::chemical::ResidueType::residue_type_set(), and protocols::kinmatch::xyz().

Referenced by setup_for_derivatives().

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

virtual

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

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

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

std::string protocols::constraints_additional::BindingSiteConstraint::type ( ) const

virtual

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

Member Data Documentation

utility::vector1< AtomID > protocols::constraints_additional::BindingSiteConstraint::atms_

private

Referenced by atom(), clone(), fill_f1_f2(), init(), natoms(), pre_align(), read_def(), remap_resid(), score(), and setup_for_scoring().

std::map< core::id::AtomID, numeric::xyzVector< core::Real > > protocols::constraints_additional::BindingSiteConstraint::rot_db

staticprivate

Referenced by fill_f1_f2(), pre_align(), and score().

ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_

private

Referenced by clone(), init(), pre_align(), and remap_resid().

ObjexxFCL::FArray2D< core::Real > protocols::constraints_additional::BindingSiteConstraint::tgt_pos_centroid_

private

Referenced by clone(), init(), pre_align(), and remap_resid().

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

symlinks/rosetta/src/protocols/constraints_additional/BindingSiteConstraint.hh
symlinks/rosetta/src/protocols/constraints_additional/BindingSiteConstraint.cc

Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation