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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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#include <IMP/atom/DopePairScore.h>
Inheritance diagram for IMP::atom::DopePairScore:Score pair of atoms based on DOPE.
See M.-y. Shen and A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Science 15, 2507–2524, 2006.
DOPE should not be applied to two atoms from the same residue. You may need to use the SameResiduePairFilter to filter these out.
Definition at line 41 of file DopePairScore.h.
Public Member Functions | |
| DopePairScore (double threshold=std::numeric_limits< double >::max()) | |
| DopePairScore (double threshold, base::TextInput data_file) | |
| Public Member Functions inherited from IMP::score_functor::DistancePairScore< score_functor::Dope > | |
| 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::Dope & | 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::Dope > | |
| typedef score_functor::Dope | 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 () |