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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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#include <IMP/isd/LognormalAmbiguousRestraint.h>
Inheritance diagram for IMP::isd::LognormalAmbiguousRestraint:A restraint for ambiguous cross-linking MS data. \( z_i \) is the discrete classifier, \( \sigma_G \) is the uncertainty estimate for good data points, \( \sigma_B \) is the uncertainty estimate for bad data points, \( k_i \) is the index of the restraint to be picked up from the ambiguous set, and \( \lambda_0 \) is the maximum length for the cross-linker.
Usage: Construct the ambiguous set using LognormalAmbiguousRestraint( \( z_i \), \( sigma_G \), \( sigma_B \), \( k_i \), \( \lambda_0 \)). Pass individual cross-linked particles to add_contribution(part0, part1). The marginal likelihood is modeled by a sigmoid function:
\[p(D|X,I) = \frac{1}{\lambda_0+\sigma(\sqrt(\pi/2)-1)} [1+\theta(r_k-\lambda_0+\sigma)[exp(-\frac{(r_k- \lambda_0+\sigma)^2}{2\sigma^2})]] \]
where \( \sigma=z_i\sigma_G+(1-z_i)\sigma_B \) and \( r_k \) is the distance between part0 and part1.
Definition at line 45 of file LognormalAmbiguousRestraint.h.
Public Member Functions | |
| LognormalAmbiguousRestraint (Particle *p1, Particle *p2, Particle *ki, Particle *sigmaG) | |
| Create the restraint. More... | |
| void | add_contribution (double lexp, Particle *omega) |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const |
| void | draw_k_from_posterior (double kt) |
| unsigned | get_number_of_contributions () const |
| double | get_probability () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (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::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 |
| A restraint should override this to compute the score and derivatives. More... | |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| 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 () |
| IMP::isd::LognormalAmbiguousRestraint::LognormalAmbiguousRestraint | ( | Particle * | p1, |
| Particle * | p2, | ||
| Particle * | ki, | ||
| Particle * | sigmaG | ||
| ) |
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::ModelObject.
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Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 79 of file LognormalAmbiguousRestraint.h.
