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IMP Reference Guide
2.7.0
The Integrative Modeling Platform
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A restraint for cysteine cross-linking data. More...
#include <IMP/isd/CysteineCrossLinkRestraint.h>
Inheritance diagram for IMP::isd::CysteineCrossLinkRestraint: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 |
| 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 |
| 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::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint | ( | Model * | m, |
| ParticleIndexAdaptor | beta, | ||
| ParticleIndexAdaptor | sigma, | ||
| ParticleIndexAdaptor | epsilon, | ||
| ParticleIndexAdaptor | weight, | ||
| CrossLinkData * | data, | ||
| double | fexp | ||
| ) |
Create the restraint.
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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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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 98 of file CysteineCrossLinkRestraint.h.
