#include <ConstraintSet.hh>

Inheritance diagram for core::scoring::constraints::ConstraintSet:

Collaboration diagram for core::scoring::constraints::ConstraintSet:

Public Types
typedef id::AtomID	AtomID

typedef id::DOF_ID	DOF_ID

typedef conformation::Residue	Residue

typedef pose::Pose	Pose

typedef utility::vector1 < ResidueConstraintsOP >	ResiduePairConstraints

typedef ResidueConstraints::const_iterator	ResiduePairConstraintsIterator

Public Member Functions
	ConstraintSet ()

	ConstraintSet (ConstraintSet const &other)

	ConstraintSet (ConstraintSet const &other, core::Size start_residue, core::Size end_residue)

virtual	~ConstraintSet ()
	Destructor so far only detaches from conformation. More...

virtual ConstraintSetOP	clone () const

virtual ConstraintSetOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP smap=NULL) const
	Copies the data from this ConstraintSet into a new object and returns its OP; atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. This will really clone all constraints since they have to change their atom-numbers and residue-numbers. More...

virtual ConstraintSetOP	steal_def_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP smap=NULL) const
	like remapped_clone, but constraints also steal_def from src-pose use, e.g., to get a new set of CoordinateConstraints for given xyz coordinates in src-pose More...

void	remap_residue_positions (id::SequenceMapping const &smap)
	remaps the constraints in this particular constraint set according to brief the passed in sequence mapping — redundant with remapped_clone!!! More...

virtual void	setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &res_data_cache) const
	Cache the ConstraintsCOP for a particular residue in the res_data_cache, under the "cst_res_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated for this residue, since, once a ConstraintsOP is added to the minimization graph, the derived class looses the chance to veto the evaluation of that constraint. More...

virtual void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &respair_data_cache) const
	Cache the ConstraintsCOP for a particular residue pair in the respair_data_cache, under the "cst_respair_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated between this pair of residues, since, once a ConstraintsOP is added to the minimization graph, the derived class looses the chance to veto the evaluation of that constraint. More...

virtual void	setup_for_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const

virtual void	setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const

virtual void	residue_pair_energy (Residue const &rsd1, Residue const &rsd2, Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) const

virtual void	deprecated_eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
	Switching over to a pairwise decomposable eval-atom-deriv system for RTMin means deprecating the old "evaluate an atom's derivative wrt the entire structure" This function is preserved (for now) for use by the RNA_TorsionEnergy. More...

virtual void	eval_multibody_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
	evaluate the derivatives for an atom that contains 3- or higher-body constraints. Such derivatives cannot be evalauated in an extra-posal context (e.g. such as in RTMin). More...

virtual bool	residue_pair_constraint_exists (int const pos1, int const pos2) const
	uses the dof constraints More...

virtual bool	residue_pair_constraints_exists (Size const pos) const

virtual void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

void	eval_intrares_energy (conformation::Residue const &rsd, EnergyMap &emap) const

virtual void	eval_non_residue_pair_energy (Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const

void	add_constraint (ConstraintCOP cst)

void	add_constraints (ConstraintCOPs cst_list)

bool	remove_constraint (ConstraintCOP cst, bool object_comparison)
	Returns true if the constraint was successfully found and removed. if object comparison is set to true, the constraint to be removed is found through the Constraint::== operator and not through pointer comparison. More...

bool	remove_constraints (ConstraintCOPs cst_list, bool object_comparison)

void	add_dof_constraint (DOF_ID const &id, FuncOP func, ScoreType const &t=dof_constraint)
	Note – still hacky. Will not be included in packing, just scoring and minimization. More...

ConstraintCOPs	get_all_constraints () const
	Returns all constraints in the set as a flat list, regardless of type. More...

ResiduePairConstraintsIterator	residue_pair_constraints_begin (Size resid) const

ResiduePairConstraintsIterator	residue_pair_constraints_end (Size resid) const

void	on_length_change (conformation::signals::LengthEvent const &event)

void	on_connection_change (core::conformation::signals::ConnectionEvent const &event)

void	attach_to_conformation (core::conformation::Conformation *conformation)

void	detach_from_conformation ()

Size	revision_id () const

virtual void	show (std::ostream &out) const

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

virtual void	show_numbers (std::ostream &out) const

virtual Size	show_violations (std::ostream &out, pose::Pose &, Size verbose_level, Real threshold=1) const

bool	has_residue_pair_constraints () const

bool	has_intra_residue_constraints () const

bool	has_dof_constraints () const

bool	has_non_residue_pair_constraints () const

bool	has_constraints () const

void	clear ()

bool	is_empty () const

Protected Member Functions
virtual void	deprecated_eval_atom_derivative_for_residue_pairs (id::AtomID const &atom_id, pose::Pose const &pose, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const

void	mark_revision_id_expired ()

ResiduePairConstraints const &	residue_pair_constraints () const

Constraints const &	non_residue_pair_constraints () const

Private Member Functions
void	add_residue_pair_constraint (Size const pos1, Size const pos2, ConstraintCOP cst)
	private More...

bool	remove_residue_pair_constraint (Size const pos1, Size const pos2, ConstraintCOP cst, bool object_comparison)
	Returns true iff the constraint was successfully found and removed. More...

Private Attributes
ResiduePairConstraints	residue_pair_constraints_
	constraints are added symmetrically More...

ResidueConstraints	intra_residue_constraints_

Constraints	non_residue_pair_constraints_

ResidueConstraints	empty_rsdcst_

DOF_ConstraintOPs	dof_constraints_

Size	revision_id_

bool	revision_id_current_

core::conformation::Conformation *	conformation_pt_

Detailed Description

Definition at line 139 of file ConstraintSet.hh.

Member Typedef Documentation

typedef id::AtomID core::scoring::constraints::ConstraintSet::AtomID

Definition at line 141 of file ConstraintSet.hh.

typedef id::DOF_ID core::scoring::constraints::ConstraintSet::DOF_ID

Definition at line 142 of file ConstraintSet.hh.

typedef pose::Pose core::scoring::constraints::ConstraintSet::Pose

Definition at line 145 of file ConstraintSet.hh.

typedef conformation::Residue core::scoring::constraints::ConstraintSet::Residue

Definition at line 144 of file ConstraintSet.hh.

typedef utility::vector1< ResidueConstraintsOP > core::scoring::constraints::ConstraintSet::ResiduePairConstraints

Definition at line 147 of file ConstraintSet.hh.

typedef ResidueConstraints::const_iterator core::scoring::constraints::ConstraintSet::ResiduePairConstraintsIterator

Definition at line 148 of file ConstraintSet.hh.

Constructor & Destructor Documentation

core::scoring::constraints::ConstraintSet::ConstraintSet ( )

Definition at line 55 of file ConstraintSet.cc.

Referenced by clone(), remapped_clone(), and steal_def_clone().

core::scoring::constraints::ConstraintSet::ConstraintSet ( ConstraintSet const & other)

Definition at line 62 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and residue_pair_constraints_exists().

core::scoring::constraints::ConstraintSet::ConstraintSet	(	ConstraintSet const &	other,
		core::Size	start_residue,
		core::Size	end_residue
	)

Definition at line 105 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and residue_pair_constraints_exists().

virtual core::scoring::constraints::ConstraintSet::~ConstraintSet ( )

inlinevirtual

Destructor so far only detaches from conformation.

Definition at line 161 of file ConstraintSet.hh.

References detach_from_conformation().

Member Function Documentation

void core::scoring::constraints::ConstraintSet::add_constraint ( ConstraintCOP cst)

Definition at line 517 of file ConstraintSet.cc.

References core::scoring::constraints::Constraints::add_constraint(), core::scoring::constraints::add_constraint_to_residue_constraints(), add_residue_pair_constraint(), intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, and core::scoring::constraints::tr().

Referenced by add_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), core::scoring::dna::DNATorsionPotential::add_DNA_torsion_constraint(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), protocols::toolbox::DecoySetEvaluation::create_dist_constraints(), protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_bindingsites(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), and remap_residue_positions().

void core::scoring::constraints::ConstraintSet::add_constraints ( ConstraintCOPs cst_list)

Definition at line 507 of file ConstraintSet.cc.

References add_constraint().

void core::scoring::constraints::ConstraintSet::add_dof_constraint	(	DOF_ID const &	id,
		FuncOP	func,
		ScoreType const &	t = `dof_constraint`
	)

Note – still hacky. Will not be included in packing, just scoring and minimization.

Definition at line 645 of file ConstraintSet.cc.

References dof_constraints_, and mark_revision_id_expired().

void core::scoring::constraints::ConstraintSet::add_residue_pair_constraint	(	Size const	pos1,
		Size const	pos2,
		ConstraintCOP	cst
	)

private

Definition at line 497 of file ConstraintSet.cc.

References core::scoring::constraints::add_constraint_to_residue_constraints(), and residue_pair_constraints_.

Referenced by add_constraint().

void core::scoring::constraints::ConstraintSet::attach_to_conformation ( core::conformation::Conformation * conformation)

Definition at line 754 of file ConstraintSet.cc.

References core::conformation::Conformation::attach_connection_obs(), core::conformation::Conformation::attach_length_obs(), conformation_pt_, detach_from_conformation(), on_connection_change(), and on_length_change().

void core::scoring::constraints::ConstraintSet::clear ( )

Definition at line 958 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::clear(), core::scoring::constraints::Constraints::clear(), dof_constraints_, intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, and residue_pair_constraints_.

Referenced by remap_residue_positions().

ConstraintSetOP core::scoring::constraints::ConstraintSet::clone ( ) const

virtual

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

Definition at line 161 of file ConstraintSet.cc.

References ConstraintSet().

void core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		ScoreFunction const &	scfxn,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

virtual

Switching over to a pairwise decomposable eval-atom-deriv system for RTMin means deprecating the old "evaluate an atom's derivative wrt the entire structure" This function is preserved (for now) for use by the RNA_TorsionEnergy.

This could be made much more efficient by a mapping from AtomID's to constraints.

Definition at line 337 of file ConstraintSet.cc.

References core::pose::Pose::conformation(), deprecated_eval_atom_derivative_for_residue_pairs(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::eval_ws_atom_derivative(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, non_residue_pair_constraints_, and core::id::AtomID::rsd().

void core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative_for_residue_pairs	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

protectedvirtual

Definition at line 379 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::pose::Pose::conformation(), core::scoring::constraints::ResidueConstraints::end(), residue_pair_constraints_, and core::id::AtomID::rsd().

Referenced by deprecated_eval_atom_derivative().

void core::scoring::constraints::ConstraintSet::detach_from_conformation ( )

Definition at line 766 of file ConstraintSet.cc.

References conformation_pt_, core::conformation::Conformation::detach_connection_obs(), core::conformation::Conformation::detach_length_obs(), on_connection_change(), and on_length_change().

Referenced by attach_to_conformation(), on_connection_change(), on_length_change(), and ~ConstraintSet().

void core::scoring::constraints::ConstraintSet::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

Definition at line 402 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ScoreFunction::weights().

Referenced by core::scoring::dna::DNATorsionEnergy::eval_intrares_energy(), and core::scoring::rna::RNA_SugarCloseEnergy::residue_energy().

void core::scoring::constraints::ConstraintSet::eval_intrares_energy	(	conformation::Residue const &	rsd,
		EnergyMap &	emap
	)		const

Definition at line 417 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, and core::conformation::Residue::seqpos().

void core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap const &	weights,
		Vector &	F1,
		Vector &	F2
	)		const

virtual

evaluate the derivatives for an atom that contains 3- or higher-body constraints. Such derivatives cannot be evalauated in an extra-posal context (e.g. such as in RTMin).

Definition at line 366 of file ConstraintSet.cc.

References core::pose::Pose::conformation(), core::scoring::constraints::Constraints::eval_ws_atom_derivative(), and non_residue_pair_constraints_.

void core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy	(	Pose const &	pose,
		ScoreFunction const &	sfxn,
		EnergyMap &	emap
	)		const

virtual

Does NOT zero the emap values, just adds the additional contribution to the existing emap energies (so can be called inside finalize_total_energies)

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet.

Definition at line 433 of file ConstraintSet.cc.

References core::pose::Pose::conformation(), core::scoring::constraints::Constraints::conformation_energy(), non_residue_pair_constraints_, and core::scoring::ScoreFunction::weights().

utility::vector1< ConstraintCOP > core::scoring::constraints::ConstraintSet::get_all_constraints ( ) const

Returns all constraints in the set as a flat list, regardless of type.

This will be fairly inefficient if there are many, many constraints.

Definition at line 655 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, and residue_pair_constraints_.

Referenced by remap_residue_positions(), remapped_clone(), protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations(), and steal_def_clone().

bool core::scoring::constraints::ConstraintSet::has_constraints ( ) const

inline

Definition at line 434 of file ConstraintSet.hh.

References has_dof_constraints(), has_intra_residue_constraints(), has_non_residue_pair_constraints(), and has_residue_pair_constraints().

Referenced by remap_residue_positions().

bool core::scoring::constraints::ConstraintSet::has_dof_constraints ( ) const

inline

Definition at line 424 of file ConstraintSet.hh.

References dof_constraints_.

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::has_intra_residue_constraints ( ) const

inline

Definition at line 419 of file ConstraintSet.hh.

References intra_residue_constraints_, and core::scoring::constraints::ResidueConstraints::size().

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::has_non_residue_pair_constraints ( ) const

inline

Definition at line 429 of file ConstraintSet.hh.

References non_residue_pair_constraints_, and core::scoring::constraints::Constraints::size().

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::has_residue_pair_constraints ( ) const

inline

Definition at line 414 of file ConstraintSet.hh.

References residue_pair_constraints_.

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::is_empty ( ) const

Definition at line 970 of file ConstraintSet.cc.

References dof_constraints_, intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, core::scoring::constraints::ResidueConstraints::size(), and core::scoring::constraints::Constraints::size().

void core::scoring::constraints::ConstraintSet::mark_revision_id_expired ( )

protected

Definition at line 788 of file ConstraintSet.cc.

References revision_id_current_.

Referenced by add_constraint(), add_dof_constraint(), clear(), remove_constraint(), and protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep().

Constraints const& core::scoring::constraints::ConstraintSet::non_residue_pair_constraints ( ) const

inlineprotected

Definition at line 485 of file ConstraintSet.hh.

References non_residue_pair_constraints_.

Referenced by protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy().

void core::scoring::constraints::ConstraintSet::on_connection_change ( core::conformation::signals::ConnectionEvent const & event)

Definition at line 730 of file ConstraintSet.cc.

References core::conformation::signals::ConnectionEvent::conformation, conformation_pt_, detach_from_conformation(), core::conformation::signals::ConnectionEvent::tag, and core::scoring::constraints::tr().

Referenced by attach_to_conformation(), and detach_from_conformation().

void core::scoring::constraints::ConstraintSet::on_length_change ( conformation::signals::LengthEvent const & event)

Definition at line 707 of file ConstraintSet.cc.

References core::conformation::signals::GeneralEvent::conformation, conformation_pt_, detach_from_conformation(), core::conformation::signals::LengthEvent::INVALIDATE, remap_residue_positions(), and core::conformation::signals::LengthEvent::tag.

Referenced by attach_to_conformation(), and detach_from_conformation().

void core::scoring::constraints::ConstraintSet::remap_residue_positions ( id::SequenceMapping const & smap)

remaps the constraints in this particular constraint set according to brief the passed in sequence mapping — redundant with remapped_clone!!!

Definition at line 205 of file ConstraintSet.cc.

References add_constraint(), clear(), get_all_constraints(), has_constraints(), and core::scoring::constraints::tr().

Referenced by on_length_change().

ConstraintSetOP core::scoring::constraints::ConstraintSet::remapped_clone	(	pose::Pose const &	src,
		pose::Pose const &	dest,
		id::SequenceMappingCOP	smap = `NULL`
	)		const

virtual

Copies the data from this ConstraintSet into a new object and returns its OP; atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. This will really clone all constraints since they have to change their atom-numbers and residue-numbers.

Copies the data from this ConstraintSet into a new object and returns an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. This will really clone all constraints since they have to change their atom-numbers and residue-numbers.

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet.

Definition at line 171 of file ConstraintSet.cc.

References ConstraintSet(), and get_all_constraints().

Referenced by protocols::constraints_additional::MaxSeqSepConstraintSet::remapped_clone().

bool core::scoring::constraints::ConstraintSet::remove_constraint	(	ConstraintCOP	cst,
		bool	object_comparison
	)

Returns true if the constraint was successfully found and removed. if object comparison is set to true, the constraint to be removed is found through the Constraint::== operator and not through pointer comparison.

Definition at line 616 of file ConstraintSet.cc.

References intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, core::scoring::constraints::Constraints::remove_constraint(), core::scoring::constraints::remove_constraint_from_residue_constraints(), remove_residue_pair_constraint(), and core::scoring::constraints::tr().

Referenced by remove_constraints().

bool core::scoring::constraints::ConstraintSet::remove_constraints	(	ConstraintCOPs	cst_list,
		bool	object_comparison
	)

Definition at line 597 of file ConstraintSet.cc.

References remove_constraint().

bool core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint	(	Size const	pos1,
		Size const	pos2,
		ConstraintCOP	cst,
		bool	object_comparison
	)

private

Returns true iff the constraint was successfully found and removed.

private

Definition at line 568 of file ConstraintSet.cc.

References core::scoring::constraints::remove_constraint_from_residue_constraints(), residue_pair_constraints_, and core::io::serialization::size().

Referenced by remove_constraint().

virtual bool core::scoring::constraints::ConstraintSet::residue_pair_constraint_exists	(	int const	pos1,
		int const	pos2
	)		const

inlinevirtual

uses the dof constraints

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

Definition at line 294 of file ConstraintSet.hh.

References residue_pair_constraints_.

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_constraint_exists(), protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_constraint_exists(), show(), show_definition(), show_numbers(), and show_violations().

ResiduePairConstraints const& core::scoring::constraints::ConstraintSet::residue_pair_constraints ( ) const

protected

ConstraintSet::ResiduePairConstraintsIterator core::scoring::constraints::ConstraintSet::residue_pair_constraints_begin ( Size resid) const

Definition at line 692 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), empty_rsdcst_, and residue_pair_constraints_.

ConstraintSet::ResiduePairConstraintsIterator core::scoring::constraints::ConstraintSet::residue_pair_constraints_end ( Size resid) const

Definition at line 699 of file ConstraintSet.cc.

References empty_rsdcst_, core::scoring::constraints::ResidueConstraints::end(), and residue_pair_constraints_.

virtual bool core::scoring::constraints::ConstraintSet::residue_pair_constraints_exists ( Size const pos) const

inlinevirtual

Definition at line 303 of file ConstraintSet.hh.

References residue_pair_constraints_.

Referenced by ConstraintSet(), show(), show_definition(), show_numbers(), and show_violations().

void core::scoring::constraints::ConstraintSet::residue_pair_energy	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Pose const &	pose,
		ScoreFunction const &	scorefxn,
		EnergyMap &	emap
	)		const

virtual

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

Definition at line 318 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), residue_pair_constraints_, core::scoring::constraints::Constraints::residue_pair_energy(), core::conformation::Residue::seqpos(), and core::scoring::ScoreFunction::weights().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(), and protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy().

Size core::scoring::constraints::ConstraintSet::revision_id ( ) const

Definition at line 778 of file ConstraintSet.cc.

References revision_id_, and revision_id_current_.

void core::scoring::constraints::ConstraintSet::setup_for_derivatives	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

Definition at line 295 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::pose::Pose::conformation(), core::scoring::constraints::ResidueConstraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and core::scoring::constraints::Constraints::setup_for_derivatives().

void core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap,
		ResSingleMinimizationData &	res_data_cache
	)		const

virtual

Cache the ConstraintsCOP for a particular residue in the res_data_cache, under the "cst_res_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated for this residue, since, once a ConstraintsOP is added to the minimization graph, the derived class looses the chance to veto the evaluation of that constraint.

Reimplemented in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

Definition at line 231 of file ConstraintSet.cc.

References core::scoring::cst_res_data, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ResSingleMinimizationData::set_data().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue().

void core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	minmap,
		ResSingleMinimizationData const &	res1_data_cache,
		ResSingleMinimizationData const &	res2_data_cache,
		ResPairMinimizationData &	respair_data_cache
	)		const

virtual

Cache the ConstraintsCOP for a particular residue pair in the respair_data_cache, under the "cst_respair_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated between this pair of residues, since, once a ConstraintsOP is added to the minimization graph, the derived class looses the chance to veto the evaluation of that constraint.

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

Definition at line 247 of file ConstraintSet.cc.

References core::scoring::cst_respair_data, core::sequence::end, residue_pair_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ResPairMinimizationData::set_data().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(), and protocols::constraints_additional::MaxSeqSepConstraintSet::setup_for_minimizing_for_residue_pair().

void core::scoring::constraints::ConstraintSet::setup_for_scoring	(	pose::Pose &	pose,
		ScoreFunction const &	scfxn
	)		const

virtual

Definition at line 268 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::pose::Pose::conformation(), core::scoring::constraints::ResidueConstraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and core::scoring::constraints::Constraints::setup_for_scoring().

Referenced by show_violations().

void core::scoring::constraints::ConstraintSet::show ( std::ostream & out) const

virtual

Definition at line 796 of file ConstraintSet.cc.

References residue_pair_constraint_exists(), residue_pair_constraints_, and residue_pair_constraints_exists().

Referenced by protocols::fldsgn::BluePrintBDR::centroid_build(), and core::scoring::constraints::operator<<().

void core::scoring::constraints::ConstraintSet::show_definition	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

virtual

Definition at line 823 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraint_exists(), residue_pair_constraints_, and residue_pair_constraints_exists().

Referenced by core::scoring::constraints::ConstraintIO::write_constraints().

void core::scoring::constraints::ConstraintSet::show_numbers ( std::ostream & out) const

virtual

Definition at line 864 of file ConstraintSet.cc.

References intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraint_exists(), residue_pair_constraints_, residue_pair_constraints_exists(), core::scoring::constraints::ResidueConstraints::size(), and core::scoring::constraints::Constraints::size().

Size core::scoring::constraints::ConstraintSet::show_violations	(	std::ostream &	out,
		pose::Pose &	pose,
		Size	verbose_level,
		Real	threshold = `1`
	)		const

virtual

Definition at line 894 of file ConstraintSet.cc.

References core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraint_exists(), residue_pair_constraints_, residue_pair_constraints_exists(), setup_for_scoring(), core::scoring::constraints::ResidueConstraints::size(), and core::scoring::constraints::Constraints::size().

Referenced by protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations().

ConstraintSetOP core::scoring::constraints::ConstraintSet::steal_def_clone	(	pose::Pose const &	src,
		pose::Pose const &	dest,
		id::SequenceMappingCOP	smap = `NULL`
	)		const

virtual

like remapped_clone, but constraints also steal_def from src-pose use, e.g., to get a new set of CoordinateConstraints for given xyz coordinates in src-pose

same as remapped clone, but it also steals coordinates from src pose

Definition at line 187 of file ConstraintSet.cc.

References ConstraintSet(), and get_all_constraints().