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IMP
2.3.0
The Integrative Modeling Platform
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IMP
2.3.0
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 http://salilab.org/SOAP/.
Definition at line 25 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::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. More... | |
| double | evaluate_indexes (kernel::Model *m, const kernel::ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const |
| 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 |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| 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. More... | |
| 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 () |
| 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 |
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typedef const kernel::ParticlePair & | PassArgument |
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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... | |
| 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 35 of file OrientedSoapPairScore.h.