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IMP
2.2.1
The Integrative Modeling Platform
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IMP
2.2.1
The Integrative Modeling Platform
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#include <IMP/isd/CysteineCrossLinkRestraint.h>
Inheritance diagram for IMP::isd::CysteineCrossLinkRestraint:Public Member Functions | |
| CysteineCrossLinkRestraint (kernel::Particle *beta, kernel::Particle *sigma, kernel::Particle *epsilon, kernel::Particle *weight, CrossLinkData *data, double fexp) | |
| Create the restraint. More... | |
| CysteineCrossLinkRestraint (kernel::Particle *beta, kernel::Particle *sigma, kernel::Particle *epsilon, kernel::Particle *weight, CrossLinkData *data, CysteineCrossLinkData *ccldata) | |
| void | add_contribution (kernel::Particle *p1, kernel::Particle *p2) |
| void | add_contribution (kernel::Particles p1, kernel::Particles p2) |
| virtual IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| algebra::Vector3D | get_CB_coordinates (const kernel::Particles &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::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. | |
| virtual double | unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| 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 |
| 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::kernel::ModelObject | |
| ModelObject (kernel::Model *m, std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. | |
| bool | get_has_required_score_states () const |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| void | set_has_dependencies (bool tf) |
| void | set_has_required_score_states (bool tf) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| 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::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
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 likelyhood is modeled as a normal distribution function truncated over the interval [0,1]. To contruct 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.
| IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint | ( | kernel::Particle * | beta, |
| kernel::Particle * | sigma, | ||
| kernel::Particle * | epsilon, | ||
| kernel::Particle * | weight, | ||
| CrossLinkData * | data, | ||
| double | fexp | ||
| ) |
kernel::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::kernel::ModelObject.
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This macro declares the basic needed methods: evaluate and show