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IMP Reference Guide  develop.cb6747d2d1,2024/03/28
The Integrative Modeling Platform
IMP::isd::CrossLinkMSRestraint Class Reference

A restraint for ambiguous cross-linking MS data and multiple state approach. More...

#include <IMP/isd/CrossLinkMSRestraint.h>

+ Inheritance diagram for IMP::isd::CrossLinkMSRestraint:

Detailed Description

A restraint for ambiguous cross-linking MS data and multiple state approach.

It marginalizes the false positive rate and depends on the expected fpr and an uncertainty parameter beta.

Definition at line 27 of file CrossLinkMSRestraint.h.

Public Member Functions

 CrossLinkMSRestraint (IMP::Model *m, double length, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 Create the restraint. More...
 
 CrossLinkMSRestraint (IMP::Model *m, IMP::ParticleIndexAdaptor lengthi, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 
 CrossLinkMSRestraint (IMP::Model *m, double length, double slope, bool get_log_prob=false, std::string name="CrossLinkMSRestraint%1%")
 
void add_contribution (const IMP::ParticleIndexPair &pps, const IMP::ParticleIndexPair &sigmas, IMP::ParticleIndex psi)
 
virtual IMP::ModelObjectsTemp do_get_inputs () const override
 
ParticleIndexPair get_contribution_particle_indexes (int i) const
 Get the particle indexes from a contribution. More...
 
ParticleIndex get_contribution_psi_index (int i) const
 Get the psi particle index from a contribution. More...
 
ParticleIndexPair get_contribution_sigma_indexes (int i) const
 Get the sigma particle indexes from a contribution. More...
 
bool get_has_slope () const
 Return true iff the restraint has a slope. More...
 
bool get_is_length_variable () const
 Return true iff the length is variable (stored in a Scale) More...
 
double get_length () const
 Get the length of this restraint. More...
 
bool get_log_prob () const
 
unsigned int get_number_of_contributions () const
 
double get_probability () const
 
double get_slope () const
 
RestraintInfoget_static_info () const override
 
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...
 
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
 
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)
 

Source information

These methods get or set the protein name and residue index of each end of the cross-link, as identified in the experiment (typically these will correspond to the information in a CSV file or similar). This information is not used in modeling, but is written into output RMF files and is needed to generate mmCIF files. %{

void set_source_protein1 (std::string protein1)
 Set protein name for one end of the cross-link. More...
 
std::string get_source_protein1 () const
 Get protein name for one end of the cross-link. More...
 
void set_source_protein2 (std::string protein2)
 Set protein name for one end of the cross-link. More...
 
std::string get_source_protein2 () const
 Get protein name for one end of the cross-link. More...
 
void set_source_residue1 (int residue1)
 Set residue number for one end of the cross-link. More...
 
int get_source_residue1 () const
 Get residue number for one end of the cross-link. More...
 
void set_source_residue2 (int residue2)
 Set residue number for one end of the cross-link. More...
 
int get_source_residue2 () const
 Get residue number for one end of the cross-link. More...
 

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::CrossLinkMSRestraint::CrossLinkMSRestraint ( IMP::Model m,
double  length,
bool  get_log_prob = false,
std::string  name = "CrossLinkMSRestraint%1%" 
)

Create the restraint.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::isd::CrossLinkMSRestraint::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.

ParticleIndexPair IMP::isd::CrossLinkMSRestraint::get_contribution_particle_indexes ( int  i) const

Get the particle indexes from a contribution.

Definition at line 148 of file CrossLinkMSRestraint.h.

ParticleIndex IMP::isd::CrossLinkMSRestraint::get_contribution_psi_index ( int  i) const

Get the psi particle index from a contribution.

Definition at line 143 of file CrossLinkMSRestraint.h.

ParticleIndexPair IMP::isd::CrossLinkMSRestraint::get_contribution_sigma_indexes ( int  i) const

Get the sigma particle indexes from a contribution.

Definition at line 138 of file CrossLinkMSRestraint.h.

bool IMP::isd::CrossLinkMSRestraint::get_has_slope ( ) const

Return true iff the restraint has a slope.

Definition at line 129 of file CrossLinkMSRestraint.h.

bool IMP::isd::CrossLinkMSRestraint::get_is_length_variable ( ) const

Return true iff the length is variable (stored in a Scale)

Definition at line 124 of file CrossLinkMSRestraint.h.

double IMP::isd::CrossLinkMSRestraint::get_length ( ) const

Get the length of this restraint.

Note that if the restraint was constructed with a length Scale, this can change during sampling.

Definition at line 115 of file CrossLinkMSRestraint.h.

std::string IMP::isd::CrossLinkMSRestraint::get_source_protein1 ( ) const

Get protein name for one end of the cross-link.

Definition at line 81 of file CrossLinkMSRestraint.h.

std::string IMP::isd::CrossLinkMSRestraint::get_source_protein2 ( ) const

Get protein name for one end of the cross-link.

Definition at line 87 of file CrossLinkMSRestraint.h.

int IMP::isd::CrossLinkMSRestraint::get_source_residue1 ( ) const

Get residue number for one end of the cross-link.

Definition at line 93 of file CrossLinkMSRestraint.h.

int IMP::isd::CrossLinkMSRestraint::get_source_residue2 ( ) const

Get residue number for one end of the cross-link.

Definition at line 99 of file CrossLinkMSRestraint.h.

RestraintInfo* IMP::isd::CrossLinkMSRestraint::get_static_info ( ) const
overridevirtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

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

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 161 of file CrossLinkMSRestraint.h.

void IMP::isd::CrossLinkMSRestraint::set_source_protein1 ( std::string  protein1)

Set protein name for one end of the cross-link.

Definition at line 78 of file CrossLinkMSRestraint.h.

void IMP::isd::CrossLinkMSRestraint::set_source_protein2 ( std::string  protein2)

Set protein name for one end of the cross-link.

Definition at line 84 of file CrossLinkMSRestraint.h.

void IMP::isd::CrossLinkMSRestraint::set_source_residue1 ( int  residue1)

Set residue number for one end of the cross-link.

Definition at line 90 of file CrossLinkMSRestraint.h.

void IMP::isd::CrossLinkMSRestraint::set_source_residue2 ( int  residue2)

Set residue number for one end of the cross-link.

Definition at line 96 of file CrossLinkMSRestraint.h.

virtual double IMP::isd::CrossLinkMSRestraint::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: