#include <MaxSeqSepConstraintSet.hh>

Inheritance diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:

Collaboration diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:

Public Member Functions
	MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::FoldTree const &f)

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

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

ConstraintSetOP	clone () const

virtual ConstraintSetOP	remapped_clone (core::pose::Pose const &src, core::pose::Pose const &dest, core::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...

Size	max_seq_sep () const

void	set_max_seq_sep (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

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

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

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

virtual 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
	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...

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

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

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

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)

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

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
	MaxSeqSepConstraintSet (ConstraintSet const &other, core::kinematics::ShortestPathInFoldTreeOP 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

Private Types
typedef ConstraintSet	Parent

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

Private Attributes
Size	max_seq_sep_

core::kinematics::ShortestPathInFoldTreeOP	shortest_path_

Additional Inherited Members
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

Detailed Description

Definition at line 57 of file MaxSeqSepConstraintSet.hh.

Member Typedef Documentation

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

private

Definition at line 60 of file MaxSeqSepConstraintSet.hh.

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

private

Definition at line 59 of file MaxSeqSepConstraintSet.hh.

Constructor & Destructor Documentation

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

Definition at line 83 of file MaxSeqSepConstraintSet.cc.

References shortest_path_, and tr().

Referenced by clone(), and remapped_clone().

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

constructor. Does nothing.

Definition at line 95 of file MaxSeqSepConstraintSet.cc.

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

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

Definition at line 82 of file MaxSeqSepConstraintSet.cc.

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

protected

Member Function Documentation

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

inlinevirtual

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

Definition at line 70 of file MaxSeqSepConstraintSet.hh.

References MaxSeqSepConstraintSet().

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

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

Definition at line 200 of file MaxSeqSepConstraintSet.cc.

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().

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

Definition at line 192 of file MaxSeqSepConstraintSet.cc.

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

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

inline

Definition at line 80 of file MaxSeqSepConstraintSet.hh.

References max_seq_sep_.

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

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::remapped_clone	(	core::pose::Pose const &	src,
		core::pose::Pose const &	dest,
		core::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 from core::scoring::constraints::ConstraintSet.

Definition at line 106 of file MaxSeqSepConstraintSet.cc.

References max_seq_sep(), MaxSeqSepConstraintSet(), core::scoring::constraints::ConstraintSet::remapped_clone(), and shortest_path_.

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

inlinevirtual

uses the dof constraints

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

Definition at line 106 of file MaxSeqSepConstraintSet.hh.

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

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

virtual

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

Definition at line 143 of file MaxSeqSepConstraintSet.cc.

References core::scoring::constraints::ConstraintSet::residue_pair_energy(), core::conformation::Residue::seqpos(), and too_far().

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

inline

Definition at line 84 of file MaxSeqSepConstraintSet.hh.

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

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

virtual

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.

Definition at line 162 of file MaxSeqSepConstraintSet.cc.

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

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

inline

Definition at line 137 of file MaxSeqSepConstraintSet.hh.

References shortest_path_.

Referenced by eval_non_residue_pair_energy().

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