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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.
Examples: assess dope
Inheritance diagram for IMP::atom::DopePairScore:Public Member Functions | |
| DopePairScore (double threshold=std::numeric_limits< double >::max()) | |
| DopePairScore (double threshold, base::TextInput data_file) | |
| Public Member Functions inherited from IMP::core::StatisticalPairScore< DopeType, false, true > | |
| StatisticalPairScore (IntKey k, double threshold, base::TextInput data_file) | |
| StatisticalPairScore (IntKey k, double threshold, base::TextInput data_file, unsigned int shift) | |
| double | get_maximum_distance () const |
| Public Member Functions inherited from IMP::PairScore | |
| PairScore (std::string name="PairScore %1%") | |
| Restraints | create_current_decomposition (const ParticlePair &vt) const |
| virtual double | evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const =0 |
| Compute the score and the derivative if needed. | |
| virtual double | evaluate (const ParticlePairsTemp &o, DerivativeAccumulator *da) 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. | |
| virtual double | evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, double max) const |
| virtual double | evaluate_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const |
| Compute the score and the derivative if needed. | |
| virtual double | evaluate_indexes (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da) const |
| virtual ContainersTemp | get_input_containers (Particle *p) const =0 |
| virtual ParticlesTemp | get_input_particles (Particle *p) const =0 |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. | |
| 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 | |
| Static Public Member Functions inherited from IMP::core::StatisticalPairScore< DopeType, false, true > | |
| static StatisticalPairScore * | get_from (IMP::base::Object *o) |
