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IMP Reference Guide  develop.374319d7bb,2024/06/17
The Integrative Modeling Platform
IMP::pmi::CrossLinkRestraintSet Class Reference

A RestraintSet subclass to track cross-link metadata. More...

#include <IMP/pmi/CrossLinkRestraintSet.h>

+ Inheritance diagram for IMP::pmi::CrossLinkRestraintSet:

Detailed Description

A RestraintSet subclass to track cross-link metadata.

This is provided so that we can write information about a set of cross-links to an RMF file (e.g. the CSV file from which they were read).

Definition at line 23 of file CrossLinkRestraintSet.h.

Public Member Functions

 CrossLinkRestraintSet (Model *m, const std::string &name="CrossLinkRestraintSet %1%")
 
virtual 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...
 
void set_linker_auth_name (std::string name)
 
void set_linker_chemical_name (std::string name)
 
void set_linker_inchi (std::string name)
 
void set_linker_inchi_key (std::string name)
 
void set_linker_smiles (std::string name)
 
void set_linker_smiles_canonical (std::string name)
 
void set_metadata (std::string filename, double length, double slope)
 
- Public Member Functions inherited from IMP::RestraintSet
 RestraintSet (Model *m, double weight, const std::string &name="RestraintSet %1%")
 Create an empty set that is registered with the model. More...
 
 RestraintSet (Model *m, const std::string &name="RestraintSet %1%")
 Create an empty set that is registered with the model. More...
 
 RestraintSet (const RestraintsTemp &rs, double weight, const std::string &name="RestraintSet %1%")
 Create a set that is registered with the model. More...
 
double get_last_score () const override
 
std::pair< RestraintsTemp,
RestraintSetsTemp
get_non_sets_and_sets () const
 Divide the list of contained restraints into non-sets and sets. More...
 
double unprotected_evaluate (DerivativeAccumulator *da) const override
 Return the unweighted score for the restraint. More...
 
void remove_restraint (Restraint *d)
 
void remove_restraints (const Restraints &d)
 
void set_restraints (const Restraints &ps)
 
void set_restraints_order (const Restraints &objs)
 
unsigned int add_restraint (Restraint *obj)
 
void add_restraints (const Restraints &objs)
 
void clear_restraints ()
 
unsigned int get_number_of_restraints () const
 
bool get_has_restraints ()
 
Restraintget_restraint (unsigned int i) const
 
Restraints get_restraints () const
 
void erase_restraint (unsigned int i)
 
void reserve_restraints (unsigned int sz)
 
- 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...
 
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)
 

Additional Inherited Members

- Public Attributes inherited from IMP::RestraintSet
list restraints
 A Python list of Restraints More...
 
- 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 ModelObjectsTemp do_get_inputs () const =0
 
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_
 

Member Function Documentation

virtual RestraintInfo* IMP::pmi::CrossLinkRestraintSet::get_static_info ( ) const
overridevirtual
Returns
static key:value information about this restraint, or null.
a set of key:value pairs that contain static information about this restraint (i.e. information that doesn't change during a sampling run, such as the type of restraint or filename from which information is read). Usually this includes a "type" key with the fully qualified classname (e.g. IMP.mymodule.MyRestraint). If no such information is available, a null pointer is returned. This information is used when writing restraints to files, e.g. by the IMP.rmf module.

Reimplemented from IMP::Restraint.

virtual ::IMP::VersionInfo IMP::pmi::CrossLinkRestraintSet::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::RestraintSet.

Definition at line 61 of file CrossLinkRestraintSet.h.


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