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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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#include <IMP/isd/CrossLinkMSRestraint.h>
Inheritance diagram for IMP::isd::CrossLinkMSRestraint:A restraint for ambiguous cross-linking MS data and multiple state approach. It marginalizes the false positive rate and depends on the expected fpr and an uncertainty parameter beta.
Definition at line 22 of file CrossLinkMSRestraint.h.
Public Member Functions | |
| CrossLinkMSRestraint (IMP::kernel::Model *m, double length, std::string name="CrossLinkMSRestraint%1%") | |
| Create the restraint. More... | |
| CrossLinkMSRestraint (IMP::kernel::Model *m, IMP::kernel::ParticleIndexAdaptor lengthi, std::string name="CrossLinkMSRestraint%1%") | |
| CrossLinkMSRestraint (IMP::kernel::Model *m, double length, double slope, std::string name="CrossLinkMSRestraint%1%") | |
| void | add_contribution (const IMP::kernel::ParticleIndexPair &pps, const IMP::kernel::ParticleIndexPair &sigmas, const IMP::kernel::ParticleIndex &psi) |
| virtual IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| unsigned int | get_number_of_contributions () const |
| double | get_probability () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| virtual double | unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Perform the actual restraint scoring. 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 double | get_last_score () const |
| double | get_score () const |
| bool | get_was_good () 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::kernel::ModelObject | |
| ModelObject (kernel::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::base::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::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint | ( | IMP::kernel::Model * | m, |
| double | length, | ||
| std::string | name = "CrossLinkMSRestraint%1%" |
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Create the restraint.
Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.
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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::kernel::ModelObject.
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Get information about the module and version of the object.
Reimplemented from IMP::base::Object.
Definition at line 67 of file CrossLinkMSRestraint.h.
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This macro declares the basic needed methods: evaluate and show