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IMP Reference Guide
2.19.0
The Integrative Modeling Platform
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Lennard-Jones score between a pair of particles. More...
#include <IMP/atom/LennardJonesPairScore.h>
Inheritance diagram for IMP::atom::LennardJonesPairScore:Lennard-Jones score between a pair of particles.
The two particles in the pair must be LennardJones particles. The form of the potential is
\[ -\epsilon \left[ w_{rep} \left(\frac{r_{min}}{r}\right)^{12} - 2 w_{att} \left(\frac{r_{min}}{r}\right)^{6}\right] \]
where \(\epsilon\) is the depth of the well between the two particles, \(r_{min}\) the sum of the particles' radii, \(r\) the inter-particle distance, and \(w_{rep}\) and \(w_{att}\) the weights on the repulsive and attractive parts of the potential respectively; both weights are 1.0 by default.
The well depth is the geometric mean of the individual particles' well depths (as extracted by LennardJones::get_well_depth).
Note that because this score uses radii and well depths set in the particles themselves, the strength of the interaction cannot be changed for a particular pair of atoms (as is done in the CHARMM forcefield with the rarely-used NBFIX directive, for example). If the well depth or radius of a single particle is modified, that will affect its interaction with all particles.
Definition at line 41 of file LennardJonesPairScore.h.
Public Member Functions | |
| LennardJonesPairScore (SmoothingFunction *f) | |
| 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 &p, 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... | |
| double | get_attractive_weight () const |
| double | get_repulsive_weight () const |
| 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_attractive_weight (double attractive_weight) |
| void | set_repulsive_weight (double repulsive_weight) |
| 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::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 () |
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overridevirtual |
Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
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overridevirtual |
Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), but may terminate the computation early if the total score is higher than max.
Reimplemented from IMP::PairScore.
Definition at line 84 of file LennardJonesPairScore.h.
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overridevirtual |
Compute the score and the derivative if needed.
| m | the model of vt |
| vt | the index in m of an object of type ParticlePair |
| da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implements IMP::PairScore.
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finaloverridevirtual |
Compute the score and the derivative if needed over a set.
| m | the model of o |
| o | objects of type ParticlePair, specified by index |
| da | a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
| lower_bound | index of first item in o to evaluate |
| upper_bound | index one past last item in o to evaluate |
Reimplemented from IMP::PairScore.
Definition at line 84 of file LennardJonesPairScore.h.
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finaloverridevirtual |
Compute the change in score and the derivative if needed over a set.
The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.
Reimplemented from IMP::PairScore.
Definition at line 84 of file LennardJonesPairScore.h.
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finaloverridevirtual |
Compute the score and the derivative if needed over a set.
Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].
Reimplemented from IMP::PairScore.
Definition at line 84 of file LennardJonesPairScore.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 85 of file LennardJonesPairScore.h.