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IMP Reference Guide
develop.549d75e6f4,2024/11/20
The Integrative Modeling Platform
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#include <IMP/atom/protein_ligand_score.h>
Inheritance diagram for IMP::atom::ProteinLigandAtomPairScore:add_protein_ligand_score_data() must be called on the molecules containing the atoms before the PairScore is used in order to properly initialize the particles.
The default library to use is protein_ligand_rank_score.lib. IMP also provides protein_ligand_pose_score.lib which can be found at IMP::atom::get_data_path("protein_ligand_pose_score.lib").
Definition at line 52 of file protein_ligand_score.h.
Public Member Functions | |
| ProteinLigandAtomPairScore (double threshold=std::numeric_limits< double >::max()) | |
| ProteinLigandAtomPairScore (double threshold, TextInput data_file) | |
| double | get_maximum_distance () const |
| Public Member Functions inherited from IMP::core::StatisticalPairScore< ProteinLigandType, true, false > | |
| StatisticalPairScore (IntKey k, double threshold, TextInput data_file) | |
| StatisticalPairScore (IntKey k, double threshold, TextInput data_file, unsigned int shift) | |
| Public Member Functions inherited from IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > > | |
| DistancePairScore (const DistanceScore &t0, std::string name="FunctorDistancePairScore %1%") | |
| virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const override |
| Overload this method to specify the inputs. More... | |
| double | evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const override |
| virtual double | evaluate_index (Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const override |
| Compute the score and the derivative if needed. More... | |
| double | evaluate_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const overridefinal |
| Compute the score and the derivative if needed over a set. More... | |
| double | evaluate_indexes_delta (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const overridefinal |
| Compute the change in score and the derivative if needed over a set. More... | |
| double | evaluate_indexes_scores (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const overridefinal |
| Compute the score and the derivative if needed over a set. More... | |
| score_functor::Statistical < ProteinLigandType, BIPARTITE, INTERPOLATE, false > & | get_score_functor () |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| Public Member Functions inherited from IMP::PairScore | |
| PairScore (std::string name="PairScore %1%") | |
| Restraints | create_current_decomposition (Model *m, const ParticleIndexPair &vt) const |
| virtual double | evaluate_if_good_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const |
| Compute the score and the derivative if needed, only if "good". More... | |
| Public Member Functions inherited from IMP::ParticleInputs | |
| ModelObjectsTemp | get_inputs (Model *m, const ParticleIndexes &pis) const |
| Get the ModelObjects read when the given list of particles is used. 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 | |
| Public Types inherited from IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > > | |
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typedef score_functor::Statistical < ProteinLigandType, BIPARTITE, INTERPOLATE, false > | DistanceScore |
| Public Types inherited from IMP::PairScore | |
| typedef ParticlePair | Argument |
| typedef ParticleIndexPair | IndexArgument |
| typedef PairModifier | Modifier |
| typedef const ParticlePair & | PassArgument |
| typedef const ParticleIndexPair & | PassIndexArgument |
| Protected Member Functions inherited from IMP::PairScore | |
| virtual Restraints | do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const |
| Override this to return your own decomposition. More... | |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |