IMP Reference Guide
develop.7cb8855c60,2024/10/08
The Integrative Modeling Platform
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A RestraintSet subclass to track cross-link metadata. More...
#include <IMP/pmi/CrossLinkRestraintSet.h>
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.