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IMP Reference Guide  develop.a3ebfe92e8,2023/01/27
The Integrative Modeling Platform
IMP::isd::CysteineCrossLinkRestraint Class Reference

A restraint for cysteine cross-linking data. More...

#include <IMP/isd/CysteineCrossLinkRestraint.h>

+ Inheritance diagram for IMP::isd::CysteineCrossLinkRestraint:

Detailed Description

A restraint for cysteine cross-linking data.

It models the frequency fexp derived from gel separation of cross-linked complexes. The experimental frequency fexp is derived as the fraction of dimeric versus monomeric complex, upon cysteine cross-linking. The forward model is derived from free energy calculations. The likelihood is modeled as a normal distribution function truncated over the interval [0,1]. To construct the restraint, the class CysteineCrossLinkData and CrossLinkData have to be initialized (see for instance test_CysteineCrossLinkRestraint.py). Input parameters and constructor. There are two different constructors p1 and p2 are the two cross-linked sites. \( \beta \) is the beta parameter in the distribution function. The \( \alpha \) parameter is constrained by the condition that the variance is gaussian by the formula \( \omega \) is a scale factor for the beta parameter, to allow for outlier detection. Usage: Construct the ambiguous set using CysteineCrossLinkRestraint( \( \beta \), \( \omega \), xlyield, \( f_{exp} \)) method. The model frequencies of each individual copy are summed, weighted and multiplied by the unknown crosslink yield (epsilon). Pass individual cross-linked pairs to add_contribution(p0, p1, w) command, where "w" is a state weight parameter.

Definition at line 44 of file CysteineCrossLinkRestraint.h.

Public Member Functions

 CysteineCrossLinkRestraint (Model *m, ParticleIndexAdaptor beta, ParticleIndexAdaptor sigma, ParticleIndexAdaptor epsilon, ParticleIndexAdaptor weight, CrossLinkData *data, double fexp)
 Create the restraint. More...
 
 CysteineCrossLinkRestraint (Model *m, ParticleIndexAdaptor beta, ParticleIndexAdaptor sigma, ParticleIndexAdaptor epsilon, ParticleIndexAdaptor weight, CrossLinkData *data, CysteineCrossLinkData *ccldata)
 
void add_contribution (ParticleIndexAdaptor p1, ParticleIndexAdaptor p2)
 
void add_contribution (ParticleIndexes p1, ParticleIndexes p2)
 
virtual IMP::ModelObjectsTemp do_get_inputs () const override
 
algebra::Vector3D get_CB_coordinates (const ParticleIndexes &ps) const
 
Floats get_distances () const
 
Floats get_frequencies () const
 
double get_model_frequency () const
 
double get_normal_pdf (double mean, double sigma, double x) const
 
unsigned get_number_of_contributions () const
 
double get_probability () const
 
double get_standard_error () const
 
double get_truncated_normalization (double mean, double sigma) 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...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_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 RestraintInfoget_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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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_
 

Constructor & Destructor Documentation

IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint ( Model m,
ParticleIndexAdaptor  beta,
ParticleIndexAdaptor  sigma,
ParticleIndexAdaptor  epsilon,
ParticleIndexAdaptor  weight,
CrossLinkData data,
double  fexp 
)

Create the restraint.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::isd::CysteineCrossLinkRestraint::do_get_inputs ( ) const
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.

virtual ::IMP::VersionInfo IMP::isd::CysteineCrossLinkRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 98 of file CysteineCrossLinkRestraint.h.

virtual double IMP::isd::CysteineCrossLinkRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator da) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.


The documentation for this class was generated from the following file: