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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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A restraint that uses an annotated volumetric network to score particle distances. More...
#include <IMP/bff/AVNetworkRestraint.h>
Inheritance diagram for IMP::bff::AVNetworkRestraint:A restraint that uses an annotated volumetric network to score particle distances.
The AVNetworkRestraint class represents a restraint that utilizes an annotated volumetric network to score distances between particles. It is designed to be used with the IMP library.
The restraint is initialized with a hierarchy, a filename of a fps.json file, a name, and an optional score set. The hierarchy is used to obtain the particles involved in the restraint. The fps.json file contains the annotated volumetric network data. The name parameter is used to assign a name to the restraint. The score set parameter specifies the name of the score in the fps.json file to be used for scoring. If no score set is provided, all distances are used for scoring.
Definition at line 47 of file AVNetworkRestraint.h.
Public Member Functions | |
| AVNetworkRestraint (const IMP::core::Hierarchy &hier, std::string fps_json_fn, std::string name="AVNetworkRestraint%1%", std::string score_set="", int n_samples=50000) | |
| Constructs an AVNetworkRestraint object. More... | |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const override |
| Returns the inputs required by the restraint. More... | |
| ParticleIndexes const | get_indexes () |
| Returns the particle indexes of the AVs. More... | |
| double | get_model_distance (std::string position1_name, std::string position2_name, double forster_radius, int distance_type) const |
| Returns the model distance (or FRET efficiency) between two dyes. More... | |
| double | get_probability () const |
| Returns exp(score). More... | |
| virtual std::string | get_type_name () const override |
| const IMP::bff::AVs | get_used_avs () |
| Returns the used Atom::AVs. More... | |
| const std::map< std::string, AVPairDistanceMeasurement > | get_used_distances () |
| Returns the used experimental distances. More... | |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| void | show (std::ostream &out) const |
| Prints a description of the restraint. More... | |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override |
| Evaluates 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... | |
| 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 RestraintInfo * | get_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 |
| virtual RestraintInfo * | get_static_info () 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... | |
| 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 |
| 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_ |
| IMP::bff::AVNetworkRestraint::AVNetworkRestraint | ( | const IMP::core::Hierarchy & | hier, |
| std::string | fps_json_fn, | ||
| std::string | name = "AVNetworkRestraint%1%", |
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| std::string | score_set = "", |
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| int | n_samples = 50000 |
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| ) |
Constructs an AVNetworkRestraint object.
| [in] | hier | The hierarchy used to obtain particles. |
| [in] | fps_json_fn | The filename of the fps.json file. |
| [in] | name | The name of this restraint. Default is "AVNetworkRestraint%1%". |
| [in] | score_set | The name of the score in the fps.json file. If not provided, all distances are used for scoring. |
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overridevirtual |
Returns the inputs required by the restraint.
Implements IMP::ModelObject.
| ParticleIndexes const IMP::bff::AVNetworkRestraint::get_indexes | ( | ) |
Returns the particle indexes of the AVs.
Definition at line 161 of file AVNetworkRestraint.h.
| double IMP::bff::AVNetworkRestraint::get_model_distance | ( | std::string | position1_name, |
| std::string | position2_name, | ||
| double | forster_radius, | ||
| int | distance_type | ||
| ) | const |
Returns the model distance (or FRET efficiency) between two dyes.
| [in] | position1_name | The name of the first dye position. |
| [in] | position2_name | The name of the second dye position. |
| [in] | forster_radius | The Förster radius. |
| [in] | distance_type | The type of distance calculation. |
| double IMP::bff::AVNetworkRestraint::get_probability | ( | ) | const |
Returns exp(score).
Definition at line 123 of file AVNetworkRestraint.h.
Here is the call graph for this function:| const IMP::bff::AVs IMP::bff::AVNetworkRestraint::get_used_avs | ( | ) |
Returns the used Atom::AVs.
| const std::map<std::string, AVPairDistanceMeasurement> IMP::bff::AVNetworkRestraint::get_used_distances | ( | ) |
Returns the used experimental distances.
Definition at line 137 of file AVNetworkRestraint.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 184 of file AVNetworkRestraint.h.
| void IMP::bff::AVNetworkRestraint::show | ( | std::ostream & | out | ) | const |
Prints a description of the restraint.
| [in] | out | The output stream. |
Definition at line 182 of file AVNetworkRestraint.h.
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overridevirtual |
Evaluates the restraint.
| [in] | accum | The derivative accumulator. |
Reimplemented from IMP::Restraint.