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protocols::constraints_additional::MaxSeqSepConstraintSet Class Reference

#include <MaxSeqSepConstraintSet.hh>

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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
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

References shortest_path_, and tr().

Referenced by clone(), and remapped_clone().

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

constructor. Does nothing.

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

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::ShortestPathInFoldTreeOP  sp 
)
protected

Member Function Documentation

ConstraintSetOP protocols::constraints_additional::MaxSeqSepConstraintSet::clone ( ) const
inlinevirtual
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
Size protocols::constraints_additional::MaxSeqSepConstraintSet::largest_possible_sequence_sep ( core::pose::Pose const &  pose) const
Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep ( ) const
inline
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.

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
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
void protocols::constraints_additional::MaxSeqSepConstraintSet::set_max_seq_sep ( 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
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.

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

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

Member Data Documentation

Size protocols::constraints_additional::MaxSeqSepConstraintSet::max_seq_sep_
private

Referenced by max_seq_sep(), and set_max_seq_sep().

core::kinematics::ShortestPathInFoldTreeOP protocols::constraints_additional::MaxSeqSepConstraintSet::shortest_path_
private

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