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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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Restrain atom pairs based on a set of crosslinks. More...
#include <IMP/isd/AtomicCrossLinkMSRestraint.h>
Inheritance diagram for IMP::isd::AtomicCrossLinkMSRestraint:Restrain atom pairs based on a set of crosslinks.
Definition at line 21 of file AtomicCrossLinkMSRestraint.h.
Public Member Functions | |
| AtomicCrossLinkMSRestraint (IMP::Model *m, double length, ParticleIndex psi, Float slope=0.0, bool part_of_log_score=false, std::string name="AtomicCrossLinkMSRestraint%1%") | |
| Constructor. More... | |
| void | add_contribution (const ParticleIndexPair &ppi, const ParticleIndexPair &sigmas) |
| Add a contribution to this xlink. More... | |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const override |
| Float | evaluate_for_contributions (Ints c, DerivativeAccumulator *accum) const |
| Evaluate the restraint just for a subset of contribution indexes. More... | |
| ParticleIndexPair | get_contribution (int i) const |
| Get the particles in a contribution. More... | |
| ParticleIndexPair | get_contribution_sigmas (int i) const |
| Get the sigma nuisances in a contribution. More... | |
| unsigned int | get_number_of_contributions () const |
| Get number of contributions added to the restraint. More... | |
| ParticleIndex | get_psi () const |
| Get the psi nuisance in a contribution. 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_part_of_log_score (bool hey) |
| void | set_slope (Float slope) |
| void | show (std::ostream &out) const |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override |
| Return the unweighted score for the restraint. More... | |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| Create a restraint and register it with the model. More... | |
| Restraint () | |
| Default constructor. More... | |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| Create a scoring function with only this restraint. More... | |
| virtual RestraintInfo * | get_dynamic_info () const |
| bool | get_is_aggregate () const |
| Return whether this restraint wraps a number of other restraints. More... | |
| double | get_last_last_score () const |
| Get the unweighted score from the last-but-one time it was evaluated. More... | |
| virtual double | get_last_score () const |
| double | get_score () const |
| virtual RestraintInfo * | get_static_info () const |
| bool | get_was_good () const |
| double | evaluate (bool calc_derivs) const |
| double | evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| double | evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
| double | evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| double | evaluate_if_good (bool calc_derivatives) const |
| double | evaluate_if_below (bool calc_derivatives, double max) const |
| virtual double | unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| Return the unweighted score, taking moving particles into account. More... | |
| virtual double | unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const |
| virtual double | unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const |
| The function calling this will treat any score >= max as bad. More... | |
| virtual double | unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
| virtual double | unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
| void | set_weight (Float weight) |
| Float | get_weight () const |
| double | get_maximum_score () const |
| void | set_maximum_score (double s) |
| Public Member Functions inherited from IMP::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. More... | |
| bool | get_has_required_score_states () const |
| Return whether score states are computed. More... | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Get the interacting sets induced by this ModelObject. More... | |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| Get the score states that are ancestors of this in the dependency graph. More... | |
| void | set_has_dependencies (bool tf) |
| Either invalidate the dependencies or ensure they are correct. More... | |
| void | set_has_required_score_states (bool tf) |
| Compute the required score states. 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 | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual void | do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const override |
| Protected Member Functions inherited from IMP::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| Protected Attributes inherited from IMP::Restraint | |
| bool | is_aggregate_ |
| IMP::isd::AtomicCrossLinkMSRestraint::AtomicCrossLinkMSRestraint | ( | IMP::Model * | m, |
| double | length, | ||
| ParticleIndex | psi, | ||
| Float | slope = 0.0, |
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| bool | part_of_log_score = false, |
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| std::string | name = "AtomicCrossLinkMSRestraint%1%" |
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| ) |
Constructor.
| [in] | m | The IMP model |
| [in] | length | The maximum length of the crosslinker |
| [in] | psi | The xlink uncertainty nuisance particle |
| [in] | slope | Exponential factor added to the score |
| [in] | part_of_log_score | If true, will return probability instead of score (but the derivative will still be for a log) |
| [in] | name | The restraint name |
| void IMP::isd::AtomicCrossLinkMSRestraint::add_contribution | ( | const ParticleIndexPair & | ppi, |
| const ParticleIndexPair & | sigmas | ||
| ) |
Add a contribution to this xlink.
| [in] | ppi | The particles to which you will apply the restraint |
| [in] | sigmas | Nuisance parameters (one per residue involved in the XL) |
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overridevirtual |
Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.
Implements IMP::ModelObject.
| Float IMP::isd::AtomicCrossLinkMSRestraint::evaluate_for_contributions | ( | Ints | c, |
| DerivativeAccumulator * | accum | ||
| ) | const |
Evaluate the restraint just for a subset of contribution indexes.
| ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution | ( | int | i | ) | const |
Get the particles in a contribution.
Definition at line 57 of file AtomicCrossLinkMSRestraint.h.
| ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_sigmas | ( | int | i | ) | const |
Get the sigma nuisances in a contribution.
Definition at line 60 of file AtomicCrossLinkMSRestraint.h.
| unsigned int IMP::isd::AtomicCrossLinkMSRestraint::get_number_of_contributions | ( | ) | const |
Get number of contributions added to the restraint.
Definition at line 54 of file AtomicCrossLinkMSRestraint.h.
| ParticleIndex IMP::isd::AtomicCrossLinkMSRestraint::get_psi | ( | ) | const |
Get the psi nuisance in a contribution.
Definition at line 63 of file AtomicCrossLinkMSRestraint.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 74 of file AtomicCrossLinkMSRestraint.h.
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overridevirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.