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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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A restraint for ambiguous cross-linking MS data and multiple state approach. More...
#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 27 of file CrossLinkMSRestraint.h.
Public Member Functions | |
| CrossLinkMSRestraint (IMP::Model *m, double length, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%") | |
| Create the restraint. More... | |
| CrossLinkMSRestraint (IMP::Model *m, IMP::ParticleIndexAdaptor lengthi, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%") | |
| CrossLinkMSRestraint (IMP::Model *m, double length, double slope, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%") | |
| void | add_contribution (const IMP::ParticleIndexPair &pps, const IMP::ParticleIndexPair &sigmas, IMP::ParticleIndex psi) |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const override |
| ParticleIndexPair | get_contribution_particle_indexes (int i) const |
| Get the particle indexes from a contribution. More... | |
| ParticleIndex | get_contribution_psi_index (int i) const |
| Get the psi particle index from a contribution. More... | |
| ParticleIndexPair | get_contribution_sigma_indexes (int i) const |
| Get the sigma particle indexes from a contribution. More... | |
| bool | get_has_slope () const |
| Return true iff the restraint has a slope. More... | |
| bool | get_is_length_variable () const |
| Return true iff the length is variable (stored in a Scale) More... | |
| double | get_length () const |
| Get the length of this restraint. More... | |
| bool | get_log_prob () const |
| unsigned int | get_number_of_contributions () const |
| double | get_probability () const |
| double | get_slope () const |
| RestraintInfo * | get_static_info () const override |
| 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... | |
| 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 |
| 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) |
Source information | |
These methods get or set the protein name and residue index of each end of the cross-link, as identified in the experiment (typically these will correspond to the information in a CSV file or similar). This information is not used in modeling, but is written into output RMF files and is needed to generate mmCIF files. %{ | |
| void | set_source_protein1 (std::string protein1) |
| Set protein name for one end of the cross-link. More... | |
| std::string | get_source_protein1 () const |
| Get protein name for one end of the cross-link. More... | |
| void | set_source_protein2 (std::string protein2) |
| Set protein name for one end of the cross-link. More... | |
| std::string | get_source_protein2 () const |
| Get protein name for one end of the cross-link. More... | |
| void | set_source_residue1 (int residue1) |
| Set residue number for one end of the cross-link. More... | |
| int | get_source_residue1 () const |
| Get residue number for one end of the cross-link. More... | |
| void | set_source_residue2 (int residue2) |
| Set residue number for one end of the cross-link. More... | |
| int | get_source_residue2 () const |
| Get residue number for one end of the cross-link. More... | |
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::CrossLinkMSRestraint::CrossLinkMSRestraint | ( | IMP::Model * | m, |
| double | length, | ||
| bool | get_log_prob = false, |
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| std::string | name = "CrossLinkMSRestraint%1%" |
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| ) |
Create the restraint.
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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.
| ParticleIndexPair IMP::isd::CrossLinkMSRestraint::get_contribution_particle_indexes | ( | int | i | ) | const |
Get the particle indexes from a contribution.
Definition at line 148 of file CrossLinkMSRestraint.h.
| ParticleIndex IMP::isd::CrossLinkMSRestraint::get_contribution_psi_index | ( | int | i | ) | const |
Get the psi particle index from a contribution.
Definition at line 143 of file CrossLinkMSRestraint.h.
| ParticleIndexPair IMP::isd::CrossLinkMSRestraint::get_contribution_sigma_indexes | ( | int | i | ) | const |
Get the sigma particle indexes from a contribution.
Definition at line 138 of file CrossLinkMSRestraint.h.
| bool IMP::isd::CrossLinkMSRestraint::get_has_slope | ( | ) | const |
Return true iff the restraint has a slope.
Definition at line 129 of file CrossLinkMSRestraint.h.
| bool IMP::isd::CrossLinkMSRestraint::get_is_length_variable | ( | ) | const |
Return true iff the length is variable (stored in a Scale)
Definition at line 124 of file CrossLinkMSRestraint.h.
| double IMP::isd::CrossLinkMSRestraint::get_length | ( | ) | const |
Get the length of this restraint.
Note that if the restraint was constructed with a length Scale, this can change during sampling.
Definition at line 115 of file CrossLinkMSRestraint.h.
| std::string IMP::isd::CrossLinkMSRestraint::get_source_protein1 | ( | ) | const |
Get protein name for one end of the cross-link.
Definition at line 81 of file CrossLinkMSRestraint.h.
| std::string IMP::isd::CrossLinkMSRestraint::get_source_protein2 | ( | ) | const |
Get protein name for one end of the cross-link.
Definition at line 87 of file CrossLinkMSRestraint.h.
| int IMP::isd::CrossLinkMSRestraint::get_source_residue1 | ( | ) | const |
Get residue number for one end of the cross-link.
Definition at line 93 of file CrossLinkMSRestraint.h.
| int IMP::isd::CrossLinkMSRestraint::get_source_residue2 | ( | ) | const |
Get residue number for one end of the cross-link.
Definition at line 99 of file CrossLinkMSRestraint.h.
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overridevirtual |
Reimplemented from IMP::Restraint.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 161 of file CrossLinkMSRestraint.h.
| void IMP::isd::CrossLinkMSRestraint::set_source_protein1 | ( | std::string | protein1 | ) |
Set protein name for one end of the cross-link.
Definition at line 78 of file CrossLinkMSRestraint.h.
| void IMP::isd::CrossLinkMSRestraint::set_source_protein2 | ( | std::string | protein2 | ) |
Set protein name for one end of the cross-link.
Definition at line 84 of file CrossLinkMSRestraint.h.
| void IMP::isd::CrossLinkMSRestraint::set_source_residue1 | ( | int | residue1 | ) |
Set residue number for one end of the cross-link.
Definition at line 90 of file CrossLinkMSRestraint.h.
| void IMP::isd::CrossLinkMSRestraint::set_source_residue2 | ( | int | residue2 | ) |
Set residue number for one end of the cross-link.
Definition at line 96 of file CrossLinkMSRestraint.h.
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overridevirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.