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IMP Reference Guide
develop.27926d84dc,2024/04/19
The Integrative Modeling Platform
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Apply a function to the distance to a fixed point. More...
#include <IMP/spb/TiltSingletonScore.h>
Inheritance diagram for IMP::spb::TiltSingletonScore:Apply a function to the distance to a fixed point.
A particle is scored based on the distance between it and a constant point as passed to a UnaryFunction. This is useful for anchoring constraining particles within a sphere.
To restrain a set of particles store in SingletonContainer pc in a sphere do the following: ## \example core/restrain_in_sphere.py # This fragment shows how to restrain a set of points stored in a # SingletonContainer in a sphere of radius 'radius' centered around # 'center'. import IMP import IMP.core import sys IMP.setup_from_argv(sys.argv, "restrain in sphere") radius = 10 stiffness = 2 center = IMP.algebra.Vector3D(1, 2, 3) m = IMP.Model() p = m.add_particle("particle") IMP.core.XYZR.setup_particle( m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1)) ub = IMP.core.HarmonicUpperBound(radius, stiffness) # Restrain based on the distance to a single point (hence a ball ss = IMP.core.DistanceToSingletonScore(ub, center) r = IMP.core.SingletonRestraint(m, ss, p) r.evaluate(False)
Definition at line 29 of file TiltSingletonScore.h.
Public Member Functions | |
| TiltSingletonScore (UnaryFunction *f, const algebra::VectorD< 3 > &v1, const algebra::VectorD< 3 > &v2) | |
| virtual IMP::ModelObjectsTemp | do_get_inputs (IMP::Model *m, const IMP::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 (IMP::Model *m, const IMP::ParticleIndex p, 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... | |
| 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 | show (std::ostream &out=std::cout) const |
| 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 () |
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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 44 of file TiltSingletonScore.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 44 of file TiltSingletonScore.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 44 of file TiltSingletonScore.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 44 of file TiltSingletonScore.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 45 of file TiltSingletonScore.h.