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IMP Reference Guide  2.20.1
The Integrative Modeling Platform
IMP::atom::OrientedSoapPairScore Class Reference

Score a pair of atoms using an orientation-dependent SOAP score. More...

#include <IMP/atom/OrientedSoapPairScore.h>

+ Inheritance diagram for IMP::atom::OrientedSoapPairScore:

Detailed Description

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)
 
SoapPairFilterget_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::OrientedSoapget_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 ParticlePairPassArgument
 
typedef const ParticleIndexPairPassIndexArgument
 
- 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 ()
 

Member Function Documentation

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.


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