#include <IgnoreSubsetConstraintSet.hh>

Inheritance diagram for protocols::comparative_modeling::IgnoreSubsetConstraintSet:

Public Types
typedef core::scoring::constraints::ConstraintSetOP	ConstraintSetOP

typedef core::scoring::constraints::ConstraintSet	ConstraintSet

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
	IgnoreSubsetConstraintSet (IgnoreSubsetConstraintSet const &other)
	constructor. Does nothing. More...

	IgnoreSubsetConstraintSet (std::set< int > const &residues_to_ignore, ConstraintSet const &other)

ConstraintSet &	operator= (ConstraintSet const &rhs) override
	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...

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

void	detached_copy (ConstraintSet const &src) override
	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...

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
	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...

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

void	setup_for_minimizing_for_residue (core::conformation::Residue const &rsd, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MinimizerMapBase const &minmap, core::scoring::ResSingleMinimizationData &res_data_cache) const override
	Allow the parent class implementation to add the residue constraints for this residue to the res_data_cache if this residue is not being ignored. 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
	Allow the parent class implenetation to add the residue-pair constraints for this residue pair to the respair_data_cache if neither residues are being ignored. More...

bool	ignore (int const pos) const
	Returns true if we're supposed to ignore this sequence position, false otherwise. More...

void	ignore_residue (int const pos)

std::set< int >	ignore_list () const

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

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 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_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

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

Private Attributes
std::set< int >	ignore_list_

Additional Inherited Members
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)

Member Typedef Documentation

typedef core::scoring::constraints::ConstraintSet protocols::comparative_modeling::IgnoreSubsetConstraintSet::ConstraintSet

typedef core::scoring::constraints::ConstraintSetOP protocols::comparative_modeling::IgnoreSubsetConstraintSet::ConstraintSetOP

Constructor & Destructor Documentation

protocols::comparative_modeling::IgnoreSubsetConstraintSet::IgnoreSubsetConstraintSet ( IgnoreSubsetConstraintSet const & other )

constructor. Does nothing.

Referenced by detached_clone().

protocols::comparative_modeling::IgnoreSubsetConstraintSet::IgnoreSubsetConstraintSet	(	std::set< int > const &	residues_to_ignore,
		ConstraintSet const &	other
	)

Member Function Documentation

ConstraintSetOP protocols::comparative_modeling::IgnoreSubsetConstraintSet::clone ( ) const

overridevirtual

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

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

ConstraintSetOP protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_clone ( ) const

overridevirtual

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

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

References IgnoreSubsetConstraintSet().

void protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_copy ( ConstraintSet const & src )

overridevirtual

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

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

bool protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore ( int const pos ) const

Returns true if we're supposed to ignore this sequence position, false otherwise.

References ignore_list_.

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

std::set< int > protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_list ( ) const

References ignore_list_.

void protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_residue ( int const pos )

References ignore_list_.

ConstraintSet & protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator= ( ConstraintSet const & rhs )

overridevirtual

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

References ignore_list_, and core::scoring::constraints::ConstraintSet::operator=().

bool protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_constraint_exists	(	int const	pos1,
		int const	pos2
	)		const

inlineoverridevirtual

uses the dof constraints

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

References ignore(), and core::scoring::constraints::ConstraintSet::residue_pair_constraint_exists().

void protocols::comparative_modeling::IgnoreSubsetConstraintSet::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 ignore(), core::scoring::constraints::ConstraintSet::residue_pair_energy(), and core::conformation::Residue::seqpos().

bool protocols::comparative_modeling::IgnoreSubsetConstraintSet::same_type_as_me	(	ConstraintSet const &	other,
		bool	recurse = `true`
	)		const

overridevirtual

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

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

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

overridevirtual

Allow the parent class implementation to add the residue constraints for this residue to the res_data_cache if this residue is not being ignored.

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

References ignore(), core::conformation::Residue::seqpos(), and core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue().

void protocols::comparative_modeling::IgnoreSubsetConstraintSet::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

Allow the parent class implenetation to add the residue-pair constraints for this residue pair to the respair_data_cache if neither residues are being ignored.

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

References ignore(), core::conformation::Residue::seqpos(), and core::scoring::constraints::ConstraintSet::setup_for_minimizing_for_residue_pair().

Member Data Documentation

std::set< int > protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_list_

private

Referenced by detached_copy(), ignore(), ignore_list(), ignore_residue(), and operator=().

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

src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.hh
src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.cc

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation