IMP  2.0.0
The Integrative Modeling Platform
IMP::atom::DopePairScore Class Reference

#include <IMP/atom/DopePairScore.h>

+ 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::score_functor::DistancePairScore< score_functor::Dope >
 DistancePairScore (const DistanceScore &t0, std::string name="FunctorDistancePairScore %1%")
 
virtual void do_show (std::ostream &out) const
 
- Public Member Functions inherited from IMP::kernel::PairScore
 PairScore (std::string name="PairScore %1%")
 
Restraints create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual double evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const
 Compute the score and the derivative if needed.
 
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, unsigned int lower_bound, unsigned int upper_bound) 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, unsigned int lower_bound, unsigned int upper_bound) const
 
ContainersTemp get_input_containers (Particle *p) const
 
ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
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. 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
 
- Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints do_create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
 
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 

Detailed Description

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.


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