IMP Reference Guide
2.20.2
The Integrative Modeling Platform
|
#include <IMP/isd/LognormalAmbiguousRestraint.h>
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 override |
void | draw_k_from_posterior (double kt) |
unsigned | get_number_of_contributions () const |
double | get_probability () const |
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 |
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::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.
|
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.
|
overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 79 of file LognormalAmbiguousRestraint.h.
|
overridevirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.