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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Score atoms based on the Fiser/Melo loop modeling statistical potential. More...
#include <IMP/atom/LoopStatisticalPairScore.h>
Inheritance diagram for IMP::atom::LoopStatisticalPairScore:Score atoms based on the Fiser/Melo loop modeling statistical potential.
See Fiser et al, Modeling of loops in protein structures. Protein Science 9, 1753-1773, 2000.
Like DOPE, this potential 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 LoopStatisticalPairScore.h.
Public Member Functions | |
| LoopStatisticalPairScore (double threshold=std::numeric_limits< double >::max()) | |
| LoopStatisticalPairScore (double threshold, TextInput data_file) | |
| Public Member Functions inherited from IMP::score_functor::DistancePairScore< score_functor::LoopStatistical > | |
| DistancePairScore (const DistanceScore &t0, std::string name="FunctorDistancePairScore %1%") | |
| virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const override |
| Overload this method to specify the inputs. More... | |
| double | evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const override |
| virtual double | evaluate_index (Model *m, const ParticleIndexPair &pip, DerivativeAccumulator *da) const override |
| Compute the score and the derivative if needed. More... | |
| double | evaluate_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const overridefinal |
| Compute the score and the derivative if needed over a set. More... | |
| double | evaluate_indexes_delta (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const overridefinal |
| Compute the change in score and the derivative if needed over a set. More... | |
| double | evaluate_indexes_scores (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const overridefinal |
| Compute the score and the derivative if needed over a set. More... | |
| score_functor::LoopStatistical & | get_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... | |
| 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::DistancePairScore< score_functor::LoopStatistical > | |
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typedef score_functor::LoopStatistical | DistanceScore |
| Public Types inherited from IMP::PairScore | |
| typedef ParticlePair | Argument |
| typedef ParticleIndexPair | IndexArgument |
| typedef PairModifier | Modifier |
| typedef const ParticlePair & | PassArgument |
| typedef const ParticleIndexPair & | PassIndexArgument |
| 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 () |