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core::scoring::constraints::ConstraintSet Class Reference

#include <ConstraintSet.hh>

Inheritance diagram for core::scoring::constraints::ConstraintSet:
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Public Types

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

 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 ConstraintSetOP clone () const
 Clone operator – performs a shallow copy of the contained constraints. 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 ConstraintSetOP detached_clone () const
 Clone operator – performs a shallow copy of the contained constraints. 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 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_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_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &respair_data_cache) const
 Cache the ConstraintsCOP for a particular residue pair in the respair_data_cache, under the "cst_respair_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated between this pair of residues, 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 residue_pair_energy (Residue const &rsd1, Residue const &rsd2, Pose const &pose, ScoreFunction const &scorefxn, EnergyMap &emap) 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_constraint_exists (int const pos1, int const pos2) const
 uses the dof constraints 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
 

Protected Member Functions

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

void add_residue_pair_constraint (Size const pos1, Size const pos2, ConstraintCOP cst)
 
bool remove_residue_pair_constraint (Size const pos1, Size const pos2, ConstraintCOP cst, bool object_comparison)
 Returns true iff the constraint was successfully found and removed. More...
 
void add_sequence_constraint (aa_composition_energy::SequenceConstraintCOP cst)
 Add a sequence constraint to the sequence_constraints_ list. More...
 

Private Attributes

Size total_residue_
 
utility::vector1
< aa_composition_energy::SequenceConstraintCOP
sequence_constraints_
 List of sequence constraints. More...
 
ResiduePairConstraints residue_pair_constraints_
 constraints are added symmetrically More...
 
ResidueConstraints intra_residue_constraints_
 
Constraints non_residue_pair_constraints_
 
ResidueConstraints empty_rsdcst_
 
DOF_ConstraintOPs dof_constraints_
 
Size revision_id_
 
bool revision_id_current_
 
core::conformation::ConformationCAP conformation_pt_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::constraints::ConstraintSet::ConstraintSet ( )
core::scoring::constraints::ConstraintSet::ConstraintSet ( ConstraintSet const &  other)

References shallow_copy(), and total_residue_.

core::scoring::constraints::ConstraintSet::ConstraintSet ( ConstraintSet const &  other,
core::Size  start_residue,
core::Size  end_residue 
)

References shallow_copy().

core::scoring::constraints::ConstraintSet::~ConstraintSet ( )
override

Destructor must detach from conformation.

References detach_from_conformation().

Member Function Documentation

void core::scoring::constraints::ConstraintSet::add_constraint ( ConstraintCOP  cst)
void core::scoring::constraints::ConstraintSet::add_constraints ( ConstraintCOPs  cst_list)

References add_constraint().

Referenced by add_constraints().

void core::scoring::constraints::ConstraintSet::add_constraints ( ConstraintSetCOP const  cst_set)

add another constraint set to this constraint set

copy another constraint set into this one

References add_constraints().

void core::scoring::constraints::ConstraintSet::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.

References dof_constraints_, and mark_revision_id_expired().

void core::scoring::constraints::ConstraintSet::add_residue_pair_constraint ( Size const  pos1,
Size const  pos2,
ConstraintCOP  cst 
)
private
void core::scoring::constraints::ConstraintSet::add_sequence_constraint ( aa_composition_energy::SequenceConstraintCOP  cst)
private

Add a sequence constraint to the sequence_constraints_ list.

References sequence_constraints_.

Referenced by add_constraint().

void core::scoring::constraints::ConstraintSet::attach_to_conformation ( core::conformation::ConformationCAP  conformation)
void core::scoring::constraints::ConstraintSet::clear ( )
void core::scoring::constraints::ConstraintSet::clear_sequence_constraints ( )

Discard any and all sequence constraints in the sequence_constraints_ list.

References sequence_constraints_.

ConstraintSetOP core::scoring::constraints::ConstraintSet::clone ( ) const
virtual

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

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

void core::scoring::constraints::ConstraintSet::deep_copy ( ConstraintSet const &  other)
protected

Clone all of the constraints from other into this so that the two sets do not point at any shared data

References add_constraint(), clear(), and get_all_constraints().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_copy(), protocols::constraints_additional::MaxSeqSepConstraintSet::detached_copy(), and detached_copy().

void core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative ( id::AtomID const &  atom_id,
pose::Pose const &  pose,
ScoreFunction const &  scfxn,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const
virtual

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.

This could be made much more efficient by a mapping from AtomID's to constraints.

References core::pose::Pose::conformation(), deprecated_eval_atom_derivative_for_residue_pairs(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::eval_ws_atom_derivative(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, non_residue_pair_constraints_, and core::id::AtomID::rsd().

void core::scoring::constraints::ConstraintSet::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
protectedvirtual
void core::scoring::constraints::ConstraintSet::detach_from_conformation ( )
ConstraintSetOP core::scoring::constraints::ConstraintSet::detached_clone ( ) const
virtual

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

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

void core::scoring::constraints::ConstraintSet::detached_copy ( ConstraintSet const &  src)
virtual

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 in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References deep_copy().

void core::scoring::constraints::ConstraintSet::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const
virtual
void core::scoring::constraints::ConstraintSet::eval_intrares_energy ( conformation::Residue const &  rsd,
EnergyMap emap 
) const
void core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative ( id::AtomID const &  atom_id,
pose::Pose const &  pose,
ScoreFunction const &  ,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const
virtual

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).

References core::pose::Pose::conformation(), core::scoring::constraints::Constraints::eval_ws_atom_derivative(), and non_residue_pair_constraints_.

void core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy ( Pose const &  pose,
ScoreFunction const &  sfxn,
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 in protocols::constraints_additional::MaxSeqSepConstraintSet.

References core::pose::Pose::conformation(), core::scoring::constraints::Constraints::conformation_energy(), non_residue_pair_constraints_, and core::scoring::ScoreFunction::weights().

utility::vector1< ConstraintCOP > core::scoring::constraints::ConstraintSet::get_all_constraints ( ) const

Returns all constraints in the set as a flat list, regardless of type.

This will be fairly inefficient if there are many, many constraints.

References intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and sequence_constraints_.

Referenced by deep_copy(), remap_residue_positions(), remapped_clone(), protocols::constraints_additional::MaxSeqSepConstraintSet::show_violations(), and steal_def_clone().

bool core::scoring::constraints::ConstraintSet::has_constraints ( ) const
inline
bool core::scoring::constraints::ConstraintSet::has_dof_constraints ( ) const
inline

References dof_constraints_.

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::has_intra_residue_constraints ( ) const
inline
bool core::scoring::constraints::ConstraintSet::has_non_residue_pair_constraints ( ) const
inline
bool core::scoring::constraints::ConstraintSet::has_residue_pair_constraints ( ) const
inline

References residue_pair_constraints_.

Referenced by has_constraints().

bool core::scoring::constraints::ConstraintSet::is_empty ( ) const
void core::scoring::constraints::ConstraintSet::mark_revision_id_expired ( )
protected
core::Size core::scoring::constraints::ConstraintSet::n_sequence_constraints ( ) const

Get the number of sequence constraints.

References sequence_constraints_.

Constraints const& core::scoring::constraints::ConstraintSet::non_residue_pair_constraints ( ) const
inlineprotected
void core::scoring::constraints::ConstraintSet::on_connection_change ( core::conformation::signals::ConnectionEvent const &  event)
void core::scoring::constraints::ConstraintSet::on_length_change ( conformation::signals::LengthEvent const &  event)
ConstraintSet & core::scoring::constraints::ConstraintSet::operator= ( ConstraintSet const &  rhs)
virtual

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 in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References core::scoring::constraints::ResidueConstraints::begin(), dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::erase(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, residue_pair_constraints_, sequence_constraints_, and total_residue_.

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=().

void core::scoring::constraints::ConstraintSet::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!!!

References add_constraint(), clear(), get_all_constraints(), has_constraints(), and core::scoring::constraints::tr().

Referenced by on_length_change().

ConstraintSetOP core::scoring::constraints::ConstraintSet::remapped_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
id::SequenceMappingCOP  smap = nullptr 
) 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 .. 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 in protocols::constraints_additional::MaxSeqSepConstraintSet.

References get_all_constraints().

bool core::scoring::constraints::ConstraintSet::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.

References intra_residue_constraints_, mark_revision_id_expired(), non_residue_pair_constraints_, core::scoring::constraints::Constraints::remove_constraint(), core::scoring::constraints::remove_constraint_from_residue_constraints(), remove_residue_pair_constraint(), and core::scoring::constraints::tr().

Referenced by remove_constraints().

bool core::scoring::constraints::ConstraintSet::remove_constraints ( ConstraintCOPs  cst_list,
bool  object_comparison 
)

References remove_constraint().

bool core::scoring::constraints::ConstraintSet::remove_residue_pair_constraint ( Size const  pos1,
Size const  pos2,
ConstraintCOP  cst,
bool  object_comparison 
)
private

Returns true iff the constraint was successfully found and removed.

private

References core::scoring::constraints::remove_constraint_from_residue_constraints(), and residue_pair_constraints_.

Referenced by remove_constraint().

virtual bool core::scoring::constraints::ConstraintSet::residue_pair_constraint_exists ( int const  pos1,
int const  pos2 
) const
inlinevirtual
ResiduePairConstraints const& core::scoring::constraints::ConstraintSet::residue_pair_constraints ( ) const
protected
ConstraintSet::ResiduePairConstraintsIterator core::scoring::constraints::ConstraintSet::residue_pair_constraints_begin ( Size  resid) const
ConstraintSet::ResiduePairConstraintsIterator core::scoring::constraints::ConstraintSet::residue_pair_constraints_end ( Size  resid) const
virtual bool core::scoring::constraints::ConstraintSet::residue_pair_constraints_exists ( Size const  pos) const
inlinevirtual
void core::scoring::constraints::ConstraintSet::residue_pair_energy ( Residue const &  rsd1,
Residue const &  rsd2,
Pose const &  pose,
ScoreFunction const &  scorefxn,
EnergyMap emap 
) const
virtual
Size core::scoring::constraints::ConstraintSet::revision_id ( ) const
bool core::scoring::constraints::ConstraintSet::same_type_as_me ( ConstraintSet const &  other,
bool  recurse = true 
) const
virtual

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 in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References same_type_as_me().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::same_type_as_me(), protocols::constraints_additional::MaxSeqSepConstraintSet::same_type_as_me(), and same_type_as_me().

core::scoring::aa_composition_energy::SequenceConstraintCOP core::scoring::constraints::ConstraintSet::sequence_constraint ( core::Size const  index) const

Get the owning pointer to the Nth sequence constraint.

References sequence_constraints_.

void core::scoring::constraints::ConstraintSet::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual
void core::scoring::constraints::ConstraintSet::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
virtual

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.

Reimplemented in protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References core::scoring::cst_res_data, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ResSingleMinimizationData::set_data().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue().

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

Cache the ConstraintsCOP for a particular residue pair in the respair_data_cache, under the "cst_respair_data" element of the data-cache's CachableDataOP array. Derived ConstraintSet classes should decide HERE whether any constraints should be evaluated between this pair of residues, since, once a ConstraintsOP is added to the minimization graph, the derived class looses the chance to veto the evaluation of that constraint.

Reimplemented in protocols::constraints_additional::MaxSeqSepConstraintSet, and protocols::comparative_modeling::IgnoreSubsetConstraintSet.

References core::scoring::cst_respair_data, core::sequence::end, residue_pair_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ResPairMinimizationData::set_data().

Referenced by protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair().

void core::scoring::constraints::ConstraintSet::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual
void core::scoring::constraints::ConstraintSet::shallow_copy ( ConstraintSet const &  other,
Size  start_residue,
Size  end_residue 
)
protected

Copy all of the Constraint pointers from other into this so that the two sets points to the same Constraint objects, but different Constraints. (Reminder, a Constraint is a single constraint and a Constraints is a container of Constraint objects). All of the Constraints objects must be cloned – cloning a Constraints object creates a shallow copy. Only constraints that have at least one residue between start_residue and end_residue will be copied.

References core::scoring::constraints::ResidueConstraints::clear(), dof_constraints_, core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, residue_pair_constraints_exists(), and sequence_constraints_.

Referenced by ConstraintSet().

void core::scoring::constraints::ConstraintSet::show ( std::ostream &  out) const
virtual
void core::scoring::constraints::ConstraintSet::show_definition ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
virtual
void core::scoring::constraints::ConstraintSet::show_numbers ( std::ostream &  out) const
virtual
Size core::scoring::constraints::ConstraintSet::show_violations ( std::ostream &  out,
pose::Pose pose,
Size  verbose_level,
Real  threshold = 1 
) const
virtual
ConstraintSetOP core::scoring::constraints::ConstraintSet::steal_def_clone ( pose::Pose const &  src,
pose::Pose const &  dest,
id::SequenceMappingCOP  smap = nullptr 
) const
virtual

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

same as remapped clone, but it also steals coordinates from src pose

References get_all_constraints().

Member Data Documentation

core::conformation::ConformationCAP core::scoring::constraints::ConstraintSet::conformation_pt_
private
DOF_ConstraintOPs core::scoring::constraints::ConstraintSet::dof_constraints_
private
ResidueConstraints core::scoring::constraints::ConstraintSet::empty_rsdcst_
private
ResidueConstraints core::scoring::constraints::ConstraintSet::intra_residue_constraints_
private
Constraints core::scoring::constraints::ConstraintSet::non_residue_pair_constraints_
private
ResiduePairConstraints core::scoring::constraints::ConstraintSet::residue_pair_constraints_
private
Size core::scoring::constraints::ConstraintSet::revision_id_
mutableprivate

Referenced by revision_id().

bool core::scoring::constraints::ConstraintSet::revision_id_current_
mutableprivate
utility::vector1< aa_composition_energy::SequenceConstraintCOP > core::scoring::constraints::ConstraintSet::sequence_constraints_
private

List of sequence constraints.

Sequence constraints constrain the sequence, just as geometric constraints constrain the geometry.

Referenced by add_sequence_constraint(), clear(), clear_sequence_constraints(), get_all_constraints(), n_sequence_constraints(), operator=(), sequence_constraint(), and shallow_copy().

Size core::scoring::constraints::ConstraintSet::total_residue_
private

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