Rosetta Core  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::constraints::ConstraintSet Class Reference

#include <ConstraintSet.hh>

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)
 
virtual ~ConstraintSet ()
 Destructor so far only detaches from conformation. More...
 
virtual ConstraintSetOP clone () const
 
virtual ConstraintSetOP remapped_clone (pose::Pose const &src, pose::Pose const &dest, 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...
 
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_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, core::scoring::func::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

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 Member Functions

void add_residue_pair_constraint (Size const pos1, Size const pos2, ConstraintCOP cst)
 private More...
 
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...
 

Private Attributes

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::Conformationconformation_pt_
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

Destructor so far only detaches 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,
core::scoring::func::FuncOP  func,
ScoreType const &  t = 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::attach_to_conformation ( core::conformation::Conformation conformation)
void core::scoring::constraints::ConstraintSet::clear ( )
ConstraintSetOP core::scoring::constraints::ConstraintSet::clone ( ) const
virtual

References ConstraintSet().

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().

Referenced by core::scoring::rna::RNA_SugarCloseEnergy::eval_atom_derivative().

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 ( )
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)

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
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
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)
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 = 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.

References ConstraintSet(), and 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(), residue_pair_constraints_, and core::io::serialization::size().

Referenced by remove_constraint().

virtual bool core::scoring::constraints::ConstraintSet::residue_pair_constraint_exists ( int const  pos1,
int const  pos2 
) const
inlinevirtual

uses the dof constraints

References residue_pair_constraints_.

Referenced by show(), show_definition(), show_numbers(), and show_violations().

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
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.

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().

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.

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

void core::scoring::constraints::ConstraintSet::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &  scfxn 
) const
virtual
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 = NULL 
) 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 ConstraintSet(), and get_all_constraints().

Member Data Documentation

core::conformation::Conformation* 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

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