#include <ConstraintSet.hh>

Inheritance 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)

	~ConstraintSet () override
	Destructor must detach from conformation. More...

virtual ConstraintSet &	operator= (ConstraintSet const &rhs)
	Assignment operator – requires that "same_type_as_me" has already been called. This performs a shallow copy of all of the constraints held in the ConstraintSet, efficiently avoiding copy operations on ResidueConstraint objects that are already identical. More...

virtual ConstraintSetOP	clone () const
	Clone operator – performs a shallow copy of the contained constraints. More...

virtual void	detached_copy (ConstraintSet const &src)
	Perform a deep copy of the source ConstraintSet into this ConstraintSet so that the two do not share any data in common – and can thus this constraintSet can be safely handed to another thread; this function relies on the Constraint class's clone() method, which is required to create a deep copy of itself. More...

virtual ConstraintSetOP	detached_clone () const
	Clone operator – performs a shallow copy of the contained constraints. More...

virtual bool	same_type_as_me (ConstraintSet const &other, bool recurse=true) const
	Does this ConstraintSet class have the same type as the other ConstraintSet object? If so, then the assignment operator can be used to copy constraints from one ConstraintSet into the other. Always call this with recurse set to true or unspecified – derived classes should make sure that they set this variable to false in their implementations of this method to avoid infinite recursion. More...

virtual ConstraintSetOP	remapped_clone (pose::Pose const &src, pose::Pose const &dest, id::SequenceMappingCOP smap=nullptr) 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 .. nullptr = 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=nullptr) 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)

void	add_constraints (ConstraintSetCOP const cst_set)
	add another constraint set to this constraint set More...

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, func::FuncOP func, ScoreType const &t=core::scoring::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::ConformationCAP 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 ()

void	clear_sequence_constraints ()
	Discard any and all sequence constraints in the sequence_constraints_ list. More...

core::Size	n_sequence_constraints () const
	Get the number of sequence constraints. More...

aa_composition_energy::SequenceConstraintCOP	sequence_constraint (core::Size const index) const
	Get the owning pointer to the Nth sequence constraint. More...

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

void	shallow_copy (ConstraintSet const &other, Size start, Size end)

void	deep_copy (ConstraintSet const &other)

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

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...

void	add_sequence_constraint (aa_composition_energy::SequenceConstraintCOP cst)
	Add a sequence constraint to the sequence_constraints_ list. More...

Private Attributes
Size	total_residue_

utility::vector1 < aa_composition_energy::SequenceConstraintCOP >	sequence_constraints_
	List of sequence constraints. More...

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::ConformationCAP	conformation_pt_

Member Typedef Documentation

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

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

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

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

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

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

Constructor & Destructor Documentation

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

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

References shallow_copy(), and total_residue_.

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

References shallow_copy().

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

override

Destructor must detach from conformation.

References detach_from_conformation().

Member Function Documentation

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

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

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::energy_methods::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(), deep_copy(), 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(), remap_residue_positions(), and protocols::hbnet::HBNet::set_constraints().

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

References add_constraint().

Referenced by add_constraints().

void core::scoring::constraints::ConstraintSet::add_constraints ( ConstraintSetCOP const cst_set )

add another constraint set to this constraint set

copy another constraint set into this one

References add_constraints().

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

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

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

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

Referenced by add_constraint().

void core::scoring::constraints::ConstraintSet::add_sequence_constraint ( aa_composition_energy::SequenceConstraintCOP cst )

private

Add a sequence constraint to the sequence_constraints_ list.

References sequence_constraints_.

Referenced by add_constraint().

void core::scoring::constraints::ConstraintSet::attach_to_conformation ( core::conformation::ConformationCAP conformation )

References conformation_pt_, detach_from_conformation(), on_connection_change(), and on_length_change().

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

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

Referenced by deep_copy(), and remap_residue_positions().

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

Discard any and all sequence constraints in the sequence_constraints_ list.

References sequence_constraints_.

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

virtual

Clone operator – performs a shallow copy of the contained constraints.

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

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

protected

Clone all of the constraints from other into this so that the two sets do not point at any shared data

References add_constraint(), clear(), and get_all_constraints().

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

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.

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

References core::pose::Pose::conformation(), residue_pair_constraints_, and core::id::AtomID::rsd().

Referenced by deprecated_eval_atom_derivative().

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

References conformation_pt_, on_connection_change(), and on_length_change().

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

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

virtual

Clone operator – performs a shallow copy of the contained constraints.

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

void core::scoring::constraints::ConstraintSet::detached_copy ( ConstraintSet const & src )

virtual

Perform a deep copy of the source ConstraintSet into this ConstraintSet so that the two do not share any data in common – and can thus this constraintSet can be safely handed to another thread; this function relies on the Constraint class's clone() method, which is required to create a deep copy of itself.

Reimplemented in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References deep_copy().

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

virtual

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::energy_methods::DNATorsionEnergy::eval_intrares_energy(), and core::energy_methods::RNA_SugarCloseEnergy::residue_energy().

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

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).

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.

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.

References intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and sequence_constraints_.

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

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

inline

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

References dof_constraints_.

Referenced by has_constraints().

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

inline

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

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

References residue_pair_constraints_.

Referenced by has_constraints().

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

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

References revision_id_current_.

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

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

Get the number of sequence constraints.

References sequence_constraints_.

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

inlineprotected

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 )

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 )

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().

ConstraintSet & core::scoring::constraints::ConstraintSet::operator= ( ConstraintSet const & rhs )

virtual

Assignment operator – requires that "same_type_as_me" has already been called. This performs a shallow copy of all of the constraints held in the ConstraintSet, efficiently avoiding copy operations on ResidueConstraint objects that are already identical.

This can be called by derived classes to make sure that all of the base class data is efficiently copied.

Reimplemented in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References core::scoring::constraints::ResidueConstraints::begin(), dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::erase(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, residue_pair_constraints_, sequence_constraints_, and total_residue_.

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=().

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!!!

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 = `nullptr`
	)		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 .. nullptr = 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.

References get_all_constraints().

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.

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
	)

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

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

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.

References residue_pair_constraints_.

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::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

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

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

References residue_pair_constraints_.

Referenced by shallow_copy(), 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.

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().

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

References revision_id_, and revision_id_current_.

bool core::scoring::constraints::ConstraintSet::same_type_as_me	(	ConstraintSet const &	other,
		bool	recurse = `true`
	)		const

virtual

Does this ConstraintSet class have the same type as the other ConstraintSet object? If so, then the assignment operator can be used to copy constraints from one ConstraintSet into the other. Always call this with recurse set to true or unspecified – derived classes should make sure that they set this variable to false in their implementations of this method to avoid infinite recursion.

Reimplemented in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References same_type_as_me().

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

core::scoring::aa_composition_energy::SequenceConstraintCOP core::scoring::constraints::ConstraintSet::sequence_constraint ( core::Size const index ) const

Get the owning pointer to the Nth sequence constraint.

References sequence_constraints_.

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

virtual

References core::pose::Pose::conformation(), 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.

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.

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().

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

virtual

References core::pose::Pose::conformation(), 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::shallow_copy	(	ConstraintSet const &	other,
		Size	start_residue,
		Size	end_residue
	)

protected

Copy all of the Constraint pointers from other into this so that the two sets points to the same Constraint objects, but different Constraints. (Reminder, a Constraint is a single constraint and a Constraints is a container of Constraint objects). All of the Constraints objects must be cloned – cloning a Constraints object creates a shallow copy. Only constraints that have at least one residue between start_residue and end_residue will be copied.

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

Referenced by ConstraintSet().

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

virtual

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().

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

References 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

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

References 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().

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

References get_all_constraints().