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IMP Reference Guide
develop.5128fd965d,2024/12/03
The Integrative Modeling Platform
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A RestraintSet subclass to track cross-link metadata. More...
#include <IMP/pmi/CrossLinkRestraintSet.h>
Inheritance diagram for IMP::pmi::CrossLinkRestraintSet: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 RestraintInfo * | get_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 () |
| Restraint * | get_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... | |
| 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... | |
| 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... | |
| 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 | |
| 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_ |
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overridevirtual |
Reimplemented from IMP::Restraint.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::RestraintSet.
Definition at line 61 of file CrossLinkRestraintSet.h.