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protocols::constraints_additional::MaxSeqSepConstraintSet Class Reference

#include <MaxSeqSepConstraintSet.hh>

Inheritance diagram for protocols::constraints_additional::MaxSeqSepConstraintSet:
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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)
 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...
 
ConstraintSetoperator= (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 ConstraintSetoperator= (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

Constructor & Destructor Documentation

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

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

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

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

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

Referenced by remapped_clone().

Member Function Documentation

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

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

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

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.

void protocols::constraints_additional::MaxSeqSepConstraintSet::detached_copy ( ConstraintSet const &  src)
override
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
Size protocols::constraints_additional::MaxSeqSepConstraintSet::largest_possible_sequence_sep ( core::pose::Pose const &  pose) const
core::Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep ( ) const
inline
ConstraintSet & protocols::constraints_additional::MaxSeqSepConstraintSet::operator= ( ConstraintSet const &  rhs)
override
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_.

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().

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
bool protocols::constraints_additional::MaxSeqSepConstraintSet::same_type_as_me ( ConstraintSet const &  other,
bool  recurse = true 
) const
override
void protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep ( core::Size  setting)
inline
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().

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

References shortest_path_.

Referenced by eval_non_residue_pair_energy().

Size protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations ( std::ostream &  out,
core::pose::Pose pose,
core::Size  verbose_level,
core::Real  threshold = 1 
)
bool protocols::constraints_additional::MaxSeqSepConstraintSet::too_far ( int const  pos1,
int const  pos2 
) const

Member Data Documentation

core::Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep_
private
core::kinematics::ShortestPathInFoldTreeCOP protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path_
private

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