#include <MaxSeqSepConstraintSet.hh>

Inheritance diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:

Public Types
typedef ConstraintSet	Parent

typedef core::scoring::constraints::ConstraintSetOP	ConstraintSetOP

Public Types inherited from core::scoring::constraints::ConstraintSet
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
	MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::FoldTree const &f)

	MaxSeqSepConstraintSet (MaxSeqSepConstraintSet const &other)
	@copy constructor. Performs a shallow copy of the constraints and the ShortestPathInFoldTree object More...

	~MaxSeqSepConstraintSet () override
	a ConstraintsSet whose constraints can be switched off, according to sequence separation in residues between residue pair constraints. More...

ConstraintSet &	operator= (ConstraintSet const &rhs) override

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

void	detached_copy (ConstraintSet const &src) override

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

bool	same_type_as_me (ConstraintSet const &other, bool recurse=true) const override

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

core::Size	max_seq_sep () const

void	set_max_seq_sep (core::Size setting)

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

bool	too_far (int const pos1, int const pos2) const

core::Size	largest_possible_sequence_sep (core::pose::Pose const &pose) const

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

void	setup_for_minimizing_for_residue_pair (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap, core::scoring::ResSingleMinimizationData const &res1_data_cache, core::scoring::ResSingleMinimizationData const &res2_data_cache, core::scoring::ResPairMinimizationData &respair_data_cache) const override
	If a pair of residues are not too far, then let the parent class implementation add the constraints for this respair to the respair_data_cache. This is the only opportunity the MaxSeqSepConstraint set has to influence how constraints are evaluated during minimization. More...

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

core::kinematics::ShortestPathInFoldTree const &	shortest_path () const

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

Public Member Functions inherited from core::scoring::constraints::ConstraintSet
	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 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 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	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_scoring (pose::Pose &pose, ScoreFunction const &scfxn) const

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

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
	MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::ShortestPathInFoldTreeCOP sp)

Protected Member Functions inherited from core::scoring::constraints::ConstraintSet
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
	MaxSeqSepConstraintSet ()

Private Attributes
core::Size	max_seq_sep_

core::kinematics::ShortestPathInFoldTreeCOP	shortest_path_

Member Typedef Documentation

◆ ConstraintSetOP

typedef core::scoring::constraints::ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::ConstraintSetOP

◆ Parent

typedef ConstraintSet protocols::constraints_additional::MaxSeqSepConstraintSet::Parent

Constructor & Destructor Documentation

◆ MaxSeqSepConstraintSet() [1/4]

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet	(	ConstraintSet const &	other,
		core::kinematics::FoldTree const &	f
	)

References shortest_path_, and tr().

◆ MaxSeqSepConstraintSet() [2/4]

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet ( MaxSeqSepConstraintSet const & other )

default

@copy constructor. Performs a shallow copy of the constraints and the ShortestPathInFoldTree object

◆ ~MaxSeqSepConstraintSet()

protocols::constraints_additional::MaxSeqSepConstraintSet::~MaxSeqSepConstraintSet ( )

overridedefault

a ConstraintsSet whose constraints can be switched off, according to sequence separation in residues between residue pair constraints.

◆ MaxSeqSepConstraintSet() [3/4]

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet	(	ConstraintSet const &	other,
		core::kinematics::ShortestPathInFoldTreeCOP	sp
	)

protected

◆ MaxSeqSepConstraintSet() [4/4]

protocols::constraints_additional::MaxSeqSepConstraintSet::MaxSeqSepConstraintSet ( )

privatedefault

Referenced by remapped_clone().

Member Function Documentation

◆ clone()

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::clone ( ) const

overridevirtual

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

Reimplemented from core::scoring::constraints::ConstraintSet.

◆ detached_clone()

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::detached_clone ( ) const

overridevirtual

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

Reimplemented from core::scoring::constraints::ConstraintSet.

◆ detached_copy()

void protocols::constraints_additional::MaxSeqSepConstraintSet::detached_copy ( ConstraintSet const & src )

override

References core::scoring::constraints::ConstraintSet::deep_copy(), max_seq_sep_, and shortest_path_.

◆ eval_non_residue_pair_energy()

void protocols::constraints_additional::MaxSeqSepConstraintSet::eval_non_residue_pair_energy	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::scoring::EnergyMap &	emap
	)		const

overridevirtual

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 from core::scoring::constraints::ConstraintSet.

References core::pose::Pose::conformation(), core::scoring::constraints::Constraint::effective_sequence_separation(), max_seq_sep(), core::scoring::constraints::ConstraintSet::non_residue_pair_constraints(), core::scoring::constraints::Constraint::score(), shortest_path(), and core::scoring::ScoreFunction::weights().

◆ largest_possible_sequence_sep()

Size protocols::constraints_additional::MaxSeqSepConstraintSet::largest_possible_sequence_sep ( core::pose::Pose const & pose ) const

References shortest_path_, and core::pose::Pose::size().

◆ max_seq_sep()

core::Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep ( ) const

inline

References max_seq_sep_.

Referenced by eval_non_residue_pair_energy(), remapped_clone(), show_violations(), and too_far().

◆ operator=()

ConstraintSet & protocols::constraints_additional::MaxSeqSepConstraintSet::operator= ( ConstraintSet const & rhs )

override

References core::scoring::constraints::ConstraintSet::mark_revision_id_expired(), max_seq_sep_, and shortest_path_.

◆ remapped_clone()

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::remapped_clone	(	core::pose::Pose const &	src,
		core::pose::Pose const &	dest,
		core::id::SequenceMappingCOP	smap = `nullptr`
	)		const

overridevirtual

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 from core::scoring::constraints::ConstraintSet.

References max_seq_sep(), MaxSeqSepConstraintSet(), and shortest_path_.

◆ residue_pair_constraint_exists()

bool protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_constraint_exists	(	int const	pos1,
		int const	pos2
	)		const

inlineoverridevirtual

uses the dof constraints

Reimplemented from core::scoring::constraints::ConstraintSet.

References too_far().

◆ residue_pair_energy()

void protocols::constraints_additional::MaxSeqSepConstraintSet::residue_pair_energy	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Pose const &	pose,
		core::scoring::ScoreFunction const &	scorefxn,
		core::scoring::EnergyMap &	emap
	)		const

overridevirtual

Reimplemented from core::scoring::constraints::ConstraintSet.

References core::conformation::Residue::seqpos(), and too_far().

◆ same_type_as_me()

bool protocols::constraints_additional::MaxSeqSepConstraintSet::same_type_as_me	(	ConstraintSet const &	other,
		bool	recurse = `true`
	)		const

override

References core::scoring::constraints::ConstraintSet::same_type_as_me().

◆ set_max_seq_sep()

void protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep ( core::Size setting )

inline

References core::scoring::constraints::ConstraintSet::mark_revision_id_expired(), and max_seq_sep_.

◆ setup_for_minimizing_for_residue_pair()

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

overridevirtual

If a pair of residues are not too far, then let the parent class implementation add the constraints for this respair to the respair_data_cache. This is the only opportunity the MaxSeqSepConstraint set has to influence how constraints are evaluated during minimization.

Reimplemented from core::scoring::constraints::ConstraintSet.

References core::conformation::Residue::seqpos(), and too_far().

◆ shortest_path()

core::kinematics::ShortestPathInFoldTree const& protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path ( ) const

inline

References shortest_path_.

Referenced by eval_non_residue_pair_energy().

◆ show_violations()

Size protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations	(	std::ostream &	out,
		core::pose::Pose &	pose,
		core::Size	verbose_level,
		core::Real	threshold = `1`
	)

References core::scoring::constraints::ConstraintSet::get_all_constraints(), max_seq_sep(), and core::conformation::membrane::out.

◆ too_far()

bool protocols::constraints_additional::MaxSeqSepConstraintSet::too_far	(	int const	pos1,
		int const	pos2
	)		const

References max_seq_sep(), and shortest_path_.

Referenced by residue_pair_constraint_exists(), residue_pair_energy(), and setup_for_minimizing_for_residue_pair().

Member Data Documentation

◆ max_seq_sep_

core::Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep_

private

Referenced by detached_copy(), max_seq_sep(), operator=(), and set_max_seq_sep().

◆ shortest_path_

core::kinematics::ShortestPathInFoldTreeCOP protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path_

private

Referenced by detached_copy(), largest_possible_sequence_sep(), MaxSeqSepConstraintSet(), operator=(), remapped_clone(), shortest_path(), and too_far().

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

src/protocols/constraints_additional/MaxSeqSepConstraintSet.hh
src/protocols/constraints_additional/MaxSeqSepConstraintSet.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ ConstraintSetOP

◆ Parent

Constructor & Destructor Documentation

◆ MaxSeqSepConstraintSet() [1/4]

◆ MaxSeqSepConstraintSet() [2/4]

◆ ~MaxSeqSepConstraintSet()

◆ MaxSeqSepConstraintSet() [3/4]

◆ MaxSeqSepConstraintSet() [4/4]

Member Function Documentation

◆ clone()

◆ detached_clone()

◆ detached_copy()

◆ eval_non_residue_pair_energy()

◆ largest_possible_sequence_sep()

◆ max_seq_sep()

◆ operator=()

◆ remapped_clone()

◆ residue_pair_constraint_exists()

◆ residue_pair_energy()

◆ same_type_as_me()

◆ set_max_seq_sep()

◆ setup_for_minimizing_for_residue_pair()

◆ shortest_path()

◆ show_violations()

◆ too_far()

Member Data Documentation

◆ max_seq_sep_

◆ shortest_path_