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IMP Reference Guide
2.11.0
The Integrative Modeling Platform
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Calculate score based on fit to SAXS profile. More...
#include <IMP/saxs/Restraint.h>
Inheritance diagram for IMP::saxs::Restraint:Calculate score based on fit to SAXS profile.
The restraint takes rigid bodies into account, in order to speed up the calculations. Rigid body should be given as single RigidBody Particle. Other, non-rigid body Particles can also be given.
The shape of a rigid body is assumed to be defined by the set of atom::Hierarchy leaves of the atom::Hierarchy rooted at the rigid body particle.
Definition at line 42 of file saxs/Restraint.h.
Public Member Functions | |
| Restraint (const Particles &particles, const Profile *exp_profile, FormFactorType ff_type=HEAVY_ATOMS) | |
| Constructor. More... | |
| virtual IMP::ModelObjectsTemp | do_get_inputs () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Perform the actual restraint scoring. 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 |
| virtual double | get_last_score () const |
| double | get_score () const |
| virtual RestraintInfo * | get_static_info () const |
| bool | get_was_good () 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) |
Protected Attributes | |
| Pointer< DerivativeCalculator > | derivative_calculator_ |
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Pointer < RigidBodiesProfileHandler > | handler_ |
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Pointer< ProfileFitter < ChiScore > > | profile_fitter_ |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| A restraint should override this to compute the score and derivatives. More... | |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| 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 () |
| IMP::saxs::Restraint::Restraint | ( | const Particles & | particles, |
| const Profile * | exp_profile, | ||
| FormFactorType | ff_type = HEAVY_ATOMS |
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Constructor.
| [in] | particles | The particles participating in the fitting score |
| [in] | exp_profile | The experimental profile used in the fitting score |
| [in] | ff_type | Type of the form factors for profile calculations: ALL_ATOMS - all atoms including hydrogens HEAVY_ATOMS - no hydrogens, all other atoms included CA_ATOMS - residue level, residue represented by CA |
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virtual |
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.
Reimplemented in IMP::saxs::RadiusOfGyrationRestraint.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Reimplemented in IMP::saxs::RadiusOfGyrationRestraint.
Definition at line 61 of file saxs/Restraint.h.