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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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#include <IMP/npctransport/AnchorToCylindricalPorePairScore.h>
Inheritance diagram for IMP::npctransport::AnchorToCylidnricalPorePairScore:a score for anchoring a bead to a reference point defined relatively to the surface of a cylindrical pore. The reference point is at a fixed angle about the pore central axis, radial distance from the pore edge, and z coordinate.
Definition at line 24 of file AnchorToCylindricalPorePairScore.h.
Public Member Functions | |
| AnchorToCylidnricalPorePairScore (Float rot_angle, Float pore_radial_d, Float z, Float k) | |
| AnchorToCylidnricalPorePairScore (SlabWithCylindricalPore scp, algebra::Vector3D initial_anchor_point, Float k) | |
| 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 &pip, DerivativeAccumulator *da) const override |
| Evaluate score for particle pair pip in model m. 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... | |
| 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... | |
| 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 () |
| IMP::npctransport::AnchorToCylidnricalPorePairScore::AnchorToCylidnricalPorePairScore | ( | Float | rot_angle, |
| Float | pore_radial_d, | ||
| Float | z, | ||
| Float | k | ||
| ) |
Initialize a harmonic distance score between an anchor bead and an equilibrium reference point that is evaluated according to the specified equilibrium values, relative to the cylindrical pore at the time of score evaluation.
| rot_angle | equilibrium counter-clockwise angle of the anchor bead in the x,y plane relative to the x axis, in Radians |
| radial_d | equilibrium radial distance from the pore surface (positive = inside pore; negative = outside) |
| z | equilibrium z coordinate |
| k | the harmonic force coefficient between the bead and the equilibrium reference point |
| IMP::npctransport::AnchorToCylidnricalPorePairScore::AnchorToCylidnricalPorePairScore | ( | SlabWithCylindricalPore | scp, |
| algebra::Vector3D | initial_anchor_point, | ||
| Float | k | ||
| ) |
initialized the score using current anchor_bead orientation relative to scp for initializing the values of the equilibrium rotation angle of the anchor about the pore central axis, its radial distance from the pore surface, and its z coordinate
| scp | The porus slab |
| initial_anchor_point | The coordinates that are used as reference for initializing the anchor equilibrium values relative to the slab |
| k | The harmonic force coefficient between the bead and the equilibrium reference point |
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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 86 of file AnchorToCylindricalPorePairScore.h.
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overridevirtual |
Evaluate score for particle pair pip in model m.
Evaluate score for particle pair pip in model m, where pip[0] is a SlabWithCylindricalPore and pip[1] is the anchored bead. The score is a harmonic distance restraint between the anchored bead and the equilibrium reference point relative to the porous slab (see constructors for details).
If da is not null, use it to accumulate derivatives in model.
Implements IMP::PairScore.
Definition at line 112 of file AnchorToCylindricalPorePairScore.h.
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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 86 of file AnchorToCylindricalPorePairScore.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 86 of file AnchorToCylindricalPorePairScore.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 86 of file AnchorToCylindricalPorePairScore.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 AnchorToCylindricalPorePairScore.h.