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Rosetta Core
2014.35
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Rosetta Core
2014.35
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#include <ConstraintSet.hh>
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::Conformation * | conformation_pt_ |
| typedef utility::vector1< ResidueConstraintsOP > core::scoring::constraints::ConstraintSet::ResiduePairConstraints |
| typedef ResidueConstraints::const_iterator core::scoring::constraints::ConstraintSet::ResiduePairConstraintsIterator |
| core::scoring::constraints::ConstraintSet::ConstraintSet | ( | ) |
Referenced by clone(), remapped_clone(), and steal_def_clone().
| core::scoring::constraints::ConstraintSet::ConstraintSet | ( | ConstraintSet const & | other | ) |
References core::scoring::constraints::ResidueConstraints::begin(), basic::CONSTRAINT_SET_COPY, dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and residue_pair_constraints_exists().
| core::scoring::constraints::ConstraintSet::ConstraintSet | ( | ConstraintSet const & | other, |
| core::Size | start_residue, | ||
| core::Size | end_residue | ||
| ) |
References core::scoring::constraints::ResidueConstraints::begin(), basic::CONSTRAINT_SET_COPY, dof_constraints_, core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::insert(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and residue_pair_constraints_exists().
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Destructor so far only detaches from conformation.
References detach_from_conformation().
| void core::scoring::constraints::ConstraintSet::add_constraint | ( | ConstraintCOP | cst | ) |
References core::scoring::constraints::Constraints::add_constraint(), core::scoring::constraints::add_constraint_to_residue_constraints(), add_residue_pair_constraint(), intra_residue_constraints_, mark_revision_id_expired(), and non_residue_pair_constraints_.
Referenced by add_constraints(), core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints(), core::scoring::dna::DNATorsionPotential::add_DNA_torsion_constraint(), core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(), core::scoring::rna::RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints(), core::scoring::constraints::ConstraintIO::read_cst_angles(), core::scoring::constraints::ConstraintIO::read_cst_atom_pairs(), core::scoring::constraints::ConstraintIO::read_cst_bindingsites(), core::scoring::constraints::ConstraintIO::read_cst_coordinates(), and remap_residue_positions().
| 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().
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private |
private
References core::scoring::constraints::add_constraint_to_residue_constraints(), and residue_pair_constraints_.
Referenced by add_constraint().
| void core::scoring::constraints::ConstraintSet::attach_to_conformation | ( | core::conformation::Conformation * | conformation | ) |
| void core::scoring::constraints::ConstraintSet::clear | ( | ) |
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References ConstraintSet().
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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().
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| void core::scoring::constraints::ConstraintSet::detach_from_conformation | ( | ) |
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References core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::ResidueConstraints::find(), intra_residue_constraints_, core::conformation::Residue::seqpos(), and core::scoring::ScoreFunction::weights().
Referenced by core::scoring::dna::DNATorsionEnergy::eval_intrares_energy(), and core::scoring::rna::RNA_SugarCloseEnergy::residue_energy().
| void core::scoring::constraints::ConstraintSet::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| EnergyMap & | emap | ||
| ) | const |
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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_.
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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 |
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 all, core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, and residue_pair_constraints_.
Referenced by remap_residue_positions(), remapped_clone(), and steal_def_clone().
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References has_dof_constraints(), has_intra_residue_constraints(), has_non_residue_pair_constraints(), and has_residue_pair_constraints().
Referenced by remap_residue_positions().
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References dof_constraints_.
Referenced by has_constraints().
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References intra_residue_constraints_, and core::scoring::constraints::ResidueConstraints::size().
Referenced by has_constraints().
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References non_residue_pair_constraints_, and core::scoring::constraints::Constraints::size().
Referenced by has_constraints().
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References residue_pair_constraints_.
Referenced by has_constraints().
| bool core::scoring::constraints::ConstraintSet::is_empty | ( | ) | const |
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References revision_id_current_.
Referenced by add_constraint(), add_dof_constraint(), clear(), and remove_constraint().
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References non_residue_pair_constraints_.
| 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 | ) |
References core::conformation::signals::GeneralEvent::conformation, conformation_pt_, detach_from_conformation(), core::conformation::signals::LengthEvent::INVALIDATE, remap_residue_positions(), and core::conformation::signals::LengthEvent::tag.
Referenced by attach_to_conformation(), and detach_from_conformation().
| 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().
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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().
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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().
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uses the dof constraints
References residue_pair_constraints_.
Referenced by show(), show_definition(), show_numbers(), and show_violations().
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| 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 |
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References residue_pair_constraints_.
Referenced by ConstraintSet(), show(), show_definition(), show_numbers(), and show_violations().
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| Size core::scoring::constraints::ConstraintSet::revision_id | ( | ) | const |
References revision_id_, and revision_id_current_.
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References core::scoring::constraints::ResidueConstraints::begin(), core::pose::Pose::conformation(), core::scoring::constraints::ResidueConstraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and core::scoring::constraints::Constraints::setup_for_derivatives().
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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().
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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().
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References core::scoring::constraints::ResidueConstraints::begin(), core::pose::Pose::conformation(), core::scoring::constraints::ResidueConstraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraints_, and core::scoring::constraints::Constraints::setup_for_scoring().
Referenced by show_violations().
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References begin, residue_pair_constraint_exists(), residue_pair_constraints_, and residue_pair_constraints_exists().
Referenced by core::scoring::constraints::operator<<().
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References begin, core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraint_exists(), residue_pair_constraints_, and residue_pair_constraints_exists().
Referenced by core::scoring::constraints::ConstraintIO::write_constraints().
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References begin, core::scoring::constraints::ResidueConstraints::begin(), core::scoring::constraints::Constraints::begin(), core::scoring::constraints::ResidueConstraints::end(), core::scoring::constraints::Constraints::end(), intra_residue_constraints_, non_residue_pair_constraints_, residue_pair_constraint_exists(), residue_pair_constraints_, residue_pair_constraints_exists(), setup_for_scoring(), core::scoring::constraints::ResidueConstraints::size(), core::scoring::constraints::Constraints::size(), and viol.
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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().
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Referenced by attach_to_conformation(), detach_from_conformation(), on_connection_change(), and on_length_change().
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Referenced by add_dof_constraint(), clear(), ConstraintSet(), has_dof_constraints(), and is_empty().
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Referenced by residue_pair_constraints_begin(), and residue_pair_constraints_end().
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Referenced by add_constraint(), clear(), ConstraintSet(), deprecated_eval_atom_derivative(), eval_intrares_energy(), get_all_constraints(), has_intra_residue_constraints(), is_empty(), remove_constraint(), setup_for_derivatives(), setup_for_minimizing_for_residue(), setup_for_scoring(), show_definition(), show_numbers(), and show_violations().
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Referenced by add_constraint(), clear(), ConstraintSet(), deprecated_eval_atom_derivative(), eval_multibody_atom_derivative(), eval_non_residue_pair_energy(), get_all_constraints(), has_non_residue_pair_constraints(), is_empty(), non_residue_pair_constraints(), remove_constraint(), setup_for_derivatives(), setup_for_scoring(), show_definition(), show_numbers(), and show_violations().
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constraints are added symmetrically
Referenced by add_residue_pair_constraint(), clear(), ConstraintSet(), deprecated_eval_atom_derivative_for_residue_pairs(), get_all_constraints(), has_residue_pair_constraints(), is_empty(), remove_residue_pair_constraint(), residue_pair_constraint_exists(), residue_pair_constraints_begin(), residue_pair_constraints_end(), residue_pair_constraints_exists(), residue_pair_energy(), setup_for_derivatives(), setup_for_minimizing_for_residue_pair(), setup_for_scoring(), show(), show_definition(), show_numbers(), and show_violations().
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Referenced by revision_id().
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Referenced by mark_revision_id_expired(), and revision_id().
1.8.7