IMP  2.2.0
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:

Public Member Functions

 OrientedSoapPairScore (std::string library)
 
SoapPairFilterget_pair_filter ()
 Get a filter that returns pairs that this score should use.
 
- Public Member Functions inherited from IMP::score_functor::DistancePairScore< score_functor::OrientedSoap >
 DistancePairScore (const DistanceScore &t0, std::string name="FunctorDistancePairScore %1%")
 
virtual kernel::ModelObjectsTemp do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
 
double evaluate_if_good_indexes (kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual double evaluate_index (kernel::Model *m, const kernel::ParticleIndexPair &pip, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
double evaluate_indexes (kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
 
virtual std::string get_type_name () const
 
virtual ::IMP::base::VersionInfo get_version_info () const
 Get information about the module and version of the object.
 
- Public Member Functions inherited from IMP::kernel::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (kernel::Model *m, const kernel::ParticleIndexPair &vt) const
 
virtual double evaluate (const kernel::ParticlePair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed. More...
 
virtual double evaluate_if_good_index (kernel::Model *m, const kernel::ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
 Compute the score and the derivative if needed.
 
- Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp get_input_containers (Particle *p) const
 
virtual ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual void do_destroy ()
 
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::OrientedSoap >
typedef score_functor::OrientedSoap DistanceScore
 
- Public Types inherited from IMP::kernel::PairScore
typedef kernel::ParticlePair Argument
 
typedef kernel::ParticleIndexPair IndexArgument
 
typedef PairModifier Modifier
 
typedef const
kernel::ParticlePair
PassArgument
 
typedef const
kernel::ParticleIndexPair
PassIndexArgument
 
- Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints do_create_current_decomposition (kernel::Model *m, const kernel::ParticleIndexPair &vt) const
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 

Detailed Description

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 http://salilab.org/SOAP/.

Definition at line 25 of file OrientedSoapPairScore.h.


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