 |
IMP
2.4.0
The Integrative Modeling Platform
|
|
IMP
2.4.0
The Integrative Modeling Platform
|
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 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.
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. More... | |
| 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 |
| 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::kernel::ModelObject | |
| ModelObject (kernel::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::base::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::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... | |
| virtual void | do_destroy () |
| IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint | ( | kernel::Particle * | beta, |
| kernel::Particle * | sigma, | ||
| kernel::Particle * | epsilon, | ||
| kernel::Particle * | weight, | ||
| CrossLinkData * | data, | ||
| double | fexp | ||
| ) |
Create the restraint.
kernel::Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.
|
virtual |
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.
|
virtual |
Get information about the module and version of the object.
Reimplemented from IMP::base::Object.
Definition at line 101 of file CysteineCrossLinkRestraint.h.
|
virtual |
This macro declares the basic needed methods: evaluate and show