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IMP Reference Guide
2.20.1
The Integrative Modeling Platform
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#include <IMP/npctransport/linear_distance_pair_scores.h>
Inheritance diagram for IMP::npctransport::LinearInteractionPairScore:A soft linear attractive / repulsive score between two spheres. The score is 0 if the spheres are beyond the attractive range. Within the attractive range, the score decreases linearly (= attraction) with slope k_attr_ until the spheres touch. Once the spheres begin to penetrate each other, the score rises linearly with slope k_rep_ (= repulsion), though it may be negative for small penetration.
Definition at line 206 of file linear_distance_pair_scores.h.
Classes | |
| struct | EvaluationCache |
Public Member Functions | |
| LinearInteractionPairScore (double k_rep, double range_attr, double k_attr, std::string name="LinearIDPairScore%1%") | |
| ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const override |
| Overload this method to specify the inputs. More... | |
| double | evaluate_if_good_index (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
| virtual double | evaluate_indexes (Model *m, const ParticleIndexPairs &pips, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const override |
| EvaluationCache const & | get_evaluation_cache () const |
| double | get_k_attraction () const |
| returns the k for sphere-sphere attraction in kcal/mol/A units More... | |
| double | get_k_repulsion () const |
| returns the k for sphere-sphere repulsion in kcal/mol/A units More... | |
| double | get_range_attraction () const |
| returns the range for sphere-sphere attraction in A More... | |
| 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... | |
| void | set_k_attraction (double k_attr) |
| set k for sphere-sphere attraction in kcal/mol/A units More... | |
| void | set_k_repulsion (double k_rep) |
| set k for sphere-sphere repulsion in kcal/mol/A units 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... | |
| 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 =0 |
| Compute the score and the derivative if needed. More... | |
| virtual double | evaluate_indexes_delta (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const |
| Compute the change in score and the derivative if needed over a set. More... | |
| virtual double | evaluate_indexes_scores (Model *m, const ParticleIndexPairs &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const |
| Compute the score and the derivative if needed over a set. 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) |
Protected Member Functions | |
| double | evaluate_index (algebra::Sphere3D const &s0, algebra::Sphere3D const &s1, algebra::Sphere3D &ds0, algebra::Sphere3D &ds1, DerivativeAccumulator *da) const |
| 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 () |
Additional Inherited Members | |
| Public Types inherited from IMP::PairScore | |
| typedef ParticlePair | Argument |
| typedef ParticleIndexPair | IndexArgument |
| typedef PairModifier | Modifier |
| typedef const ParticlePair & | PassArgument |
| typedef const ParticleIndexPair & | PassIndexArgument |
| IMP::npctransport::LinearInteractionPairScore::LinearInteractionPairScore | ( | double | k_rep, |
| double | range_attr, | ||
| double | k_attr, | ||
| std::string | name = "LinearIDPairScore%1%" |
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| ) |
The score is 0 if the spheres are beyond the attractive range. Within the attractive range, the score decreases linearly (= attraction) with slope k_attr_ until the spheres touch. Once the spheres begin to penetrate each other, the score rises linearly with slope k_rep_ (= repulsion), though it may be negative for small penetration.
The energy potential difference between the unbound state and when the beads touch is: DELTA-U=0.5*k_attr*range_attr [kcal/mol]
| k_rep | repulsion force constant in kcal/mol/A units |
| range_attr | attraction range between sphere surfaces |
| k_attr | attraction force constant in kcal/mol/A unit |
| name | score object names |
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overridevirtual |
Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
Reimplemented in IMP::npctransport::SitesPairScore.
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protected |
evaluates the linear interaction score, for spheres s0 and s1, outputting derivatives to ds0 and ds1 scaled by da, if da is not null
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overridevirtual |
evaluate all index pairs between pips[lower_bound] and pis[upper_bound] and update their coordinate derivatives scaled by da, if da is not null
Reimplemented from IMP::PairScore.
Reimplemented in IMP::npctransport::SitesPairScore.
| double IMP::npctransport::LinearInteractionPairScore::get_k_attraction | ( | ) | const |
returns the k for sphere-sphere attraction in kcal/mol/A units
Definition at line 303 of file linear_distance_pair_scores.h.
| double IMP::npctransport::LinearInteractionPairScore::get_k_repulsion | ( | ) | const |
returns the k for sphere-sphere repulsion in kcal/mol/A units
Definition at line 311 of file linear_distance_pair_scores.h.
| double IMP::npctransport::LinearInteractionPairScore::get_range_attraction | ( | ) | const |
returns the range for sphere-sphere attraction in A
Definition at line 300 of file linear_distance_pair_scores.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Reimplemented in IMP::npctransport::SitesPairScore.
Definition at line 318 of file linear_distance_pair_scores.h.
| void IMP::npctransport::LinearInteractionPairScore::set_k_attraction | ( | double | k_attr | ) |
set k for sphere-sphere attraction in kcal/mol/A units
Definition at line 306 of file linear_distance_pair_scores.h.
| void IMP::npctransport::LinearInteractionPairScore::set_k_repulsion | ( | double | k_rep | ) |
set k for sphere-sphere repulsion in kcal/mol/A units
Definition at line 314 of file linear_distance_pair_scores.h.