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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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Score a pair of atoms using an orientation-dependent SOAP score. More...
#include <IMP/atom/OrientedSoapPairScore.h>
Inheritance diagram for IMP::atom::OrientedSoapPairScore:Score a pair of atoms using an orientation-dependent SOAP score.
Orientation-dependent SOAP scores include those that score loops (SOAP-Loop), protein-peptide interfaces (SOAP-Peptide) and proteins (SOAP-Protein). The library files themselves, such as soap_loop.hdf5 or soap_protein_od.hdf5, are rather large (~1.5GB) and so are not included here. They can be downloaded separately from https://salilab.org/SOAP/.
Definition at line 26 of file OrientedSoapPairScore.h.
Public Member Functions | |
| OrientedSoapPairScore (std::string library) | |
| SoapPairFilter * | get_pair_filter () |
| Get a filter that returns pairs that this score should use. More... | |
| Public Member Functions inherited from IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap > | |
| DistancePairScoreWithCache (const DistanceScore &t0, std::string name="FunctorDistancePairScoreWithCache %1%") | |
| virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const override |
| Overload this method to specify the inputs. More... | |
| virtual double | evaluate_index (Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const override |
| Compute the score and the derivative if needed. More... | |
| virtual double | evaluate_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const override |
| Compute the score and the derivative if needed over a set. More... | |
| virtual double | evaluate_indexes_delta (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const override |
| Compute the change in score and the derivative if needed over a set. More... | |
| virtual double | evaluate_indexes_scores (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const override |
| Compute the score and the derivative if needed over a set. More... | |
| score_functor::OrientedSoap & | 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... | |
| virtual double | evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
| 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::DistancePairScoreWithCache< score_functor::OrientedSoap > | |
| typedef score_functor::OrientedSoap | 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 () |
| SoapPairFilter* IMP::atom::OrientedSoapPairScore::get_pair_filter | ( | ) |
Get a filter that returns pairs that this score should use.
Definition at line 38 of file OrientedSoapPairScore.h.