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IMP Reference Guide
develop.d4e9f3251e,2024/04/26
The Integrative Modeling Platform
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#include <IMP/npctransport/HarmonicSpringSingletonScore.h>
Inheritance diagram for IMP::npctransport::HarmonicSpringSingletonScore:A harmonic score between two bonded spheres connected by a spring whose resting length is dynamic
Definition at line 28 of file HarmonicSpringSingletonScore.h.
Public Member Functions | |
| HarmonicSpringSingletonScore (double k1, double k2, std::string name="HarmonicSpringSingletonScore%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 ParticleIndexes &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const override |
| virtual double | evaluate_index (Model *m, ParticleIndex pi, DerivativeAccumulator *da) const override |
| Compute the score and the derivative if needed. More... | |
| double | evaluate_indexes (Model *m, const ParticleIndexes &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 ParticleIndexes &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 ParticleIndexes &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_k1 () const |
| double | get_k2 () 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_k1 (double k1) |
| void | set_k2 (double k2) |
| Public Member Functions inherited from IMP::SingletonScore | |
| SingletonScore (std::string name="SingletonScore %1%") | |
| Restraints | create_current_decomposition (Model *m, ParticleIndex vt) const |
| virtual double | evaluate_if_good_index (Model *m, ParticleIndex 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::SingletonScore | |
| typedef Particle * | Argument |
| typedef ParticleIndex | IndexArgument |
| typedef SingletonModifier | Modifier |
| typedef Particle * | PassArgument |
| typedef ParticleIndex | PassIndexArgument |
| Protected Member Functions inherited from IMP::SingletonScore | |
| virtual Restraints | do_create_current_decomposition (Model *m, ParticleIndex 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 () |
| IMP::npctransport::HarmonicSpringSingletonScore::HarmonicSpringSingletonScore | ( | double | k1, |
| double | k2, | ||
| std::string | name = "HarmonicSpringSingletonScore%1%" |
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| ) |
a harmonic well pair potential that keeps two particles connected by a spring particle whose resting length itself is dynamic
| k1 | the force constant applied by the string on tethered particles in units of kcal/mol/A^2 - attractive if spring is longer than rest length, repulsive if shorter than rest length. The spring applies a force of k1*dX on each particle, and a counter force of 2*k1*dX acts on the spring, where dX=|distance(p1,p2)-(rest_length)| |
| k2 | the force constant for relaxation of the spring rest length to its equilibrium value in kcal/mol/A^2. The force equals k2*dX where dX=|(rest_length)-(equilibrium length)| |
| name | the name of the score |
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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::SingletonScore.
Definition at line 85 of file HarmonicSpringSingletonScore.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 Particle |
| da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implements IMP::SingletonScore.
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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 Particle, 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::SingletonScore.
Definition at line 85 of file HarmonicSpringSingletonScore.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::SingletonScore.
Definition at line 85 of file HarmonicSpringSingletonScore.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::SingletonScore.
Definition at line 85 of file HarmonicSpringSingletonScore.h.
| double IMP::npctransport::HarmonicSpringSingletonScore::get_k1 | ( | ) | const |
returns the force constant to bring particles to the current rest length in kcal/mol/A^2
Definition at line 63 of file HarmonicSpringSingletonScore.h.
| double IMP::npctransport::HarmonicSpringSingletonScore::get_k2 | ( | ) | const |
returns the force constant to bring the current rest length to equilibrium in kcal/mol/A^2
Definition at line 73 of file HarmonicSpringSingletonScore.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 87 of file HarmonicSpringSingletonScore.h.
| void IMP::npctransport::HarmonicSpringSingletonScore::set_k1 | ( | double | k1 | ) |
sets the force constant to bring particles to the current rest length in kcal/mol/A^2
Definition at line 58 of file HarmonicSpringSingletonScore.h.
| void IMP::npctransport::HarmonicSpringSingletonScore::set_k2 | ( | double | k2 | ) |
sets the force constant to bring the current rest length to equilibrium in kcal/mol/A^2
Definition at line 68 of file HarmonicSpringSingletonScore.h.