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IMP Reference Guide
2.16.0
The Integrative Modeling Platform
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Enforce CHARMM stereochemistry on the given Hierarchy. More...
#include <IMP/atom/CHARMMStereochemistryRestraint.h>
Inheritance diagram for IMP::atom::CHARMMStereochemistryRestraint:Enforce CHARMM stereochemistry on the given Hierarchy.
It is assumed that the Hierarchy has already had CHARMM atom types assigned and conforms with the CHARMM topology information (for example, by calling CHARMMTopology::setup_hierarchy() first).
Definition at line 40 of file CHARMMStereochemistryRestraint.h.
Public Member Functions | |
| CHARMMStereochemistryRestraint (Hierarchy h, CHARMMTopology *topology) | |
| CHARMMStereochemistryRestraint (Hierarchy h, CHARMMTopology *topology, ParticlesTemp limit_to_these_particles) | |
| Initialize the restraint and limit to a set of particles. More... | |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const |
| StereochemistryPairFilter * | get_full_pair_filter () |
| Get a PairFilter including everything from original topology. More... | |
| StereochemistryPairFilter * | get_pair_filter () |
| Get a PairFilter that excludes all stereochemical pairs. More... | |
| virtual std::string | get_type_name () const |
| virtual ::IMP::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Perform the actual restraint scoring. More... | |
| void | add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| Create a scoring function with only this restraint. More... | |
| virtual RestraintInfo * | get_dynamic_info () const |
| virtual double | get_last_last_score () const |
| Get the unweighted score from the last-but-one time it was evaluated. More... | |
| virtual double | get_last_score () const |
| double | get_score () const |
| virtual RestraintInfo * | get_static_info () const |
| bool | get_was_good () const |
| void | set_weight (Float weight) |
| Float | get_weight () const |
| double | get_maximum_score () const |
| void | set_maximum_score (double s) |
| Public Member Functions inherited from IMP::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. More... | |
| bool | get_has_required_score_states () const |
| Return whether score states are computed. More... | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Get the interacting sets induced by this ModelObject. More... | |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| Get the score states that are ancestors of this in the dependency graph. More... | |
| void | set_has_dependencies (bool tf) |
| Either invalidate the dependencies or ensure they are correct. More... | |
| void | set_has_required_score_states (bool tf) |
| Compute the required score states. More... | |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual void | do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint | ( | Hierarchy | h, |
| CHARMMTopology * | topology, | ||
| ParticlesTemp | limit_to_these_particles | ||
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Initialize the restraint and limit to a set of particles.
Will only create restraints where every particle in the restraint is in the provided list.
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virtual |
Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.
Implements IMP::ModelObject.
| StereochemistryPairFilter* IMP::atom::CHARMMStereochemistryRestraint::get_full_pair_filter | ( | ) |
Get a PairFilter including everything from original topology.
| StereochemistryPairFilter* IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter | ( | ) |
Get a PairFilter that excludes all stereochemical pairs.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 75 of file CHARMMStereochemistryRestraint.h.