IMP::saxs::Restraint Class Reference
Calculate score based on fit to SAXS profile. More...
#include <IMP/saxs/Restraint.h>
Inheritance diagram for IMP::saxs::Restraint:Public Member Functions | |
| Restraint (const Particles &particles, const Profile &exp_profile, FormFactorType ff_type=HEAVY_ATOMS) | |
| Constructor. More... | |
| virtual void | do_show (std::ostream &out) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (Model *m, std::string name) | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| 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 |
| ContainersTemp | get_input_containers () const |
| ParticlesTemp | get_input_particles () const |
| virtual double | get_last_score () const |
| double | get_score () 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::kernel::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| 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 Member Functions | |
| void | compute_profile (Profile &model_profile) |
| Protected Member Functions inherited from IMP::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| virtual void | do_update_dependencies () |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemp | do_get_inputs () const =0 |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | update_dependencies () |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
Protected Attributes | |
| Pointer< DerivativeCalculator > | derivative_calculator_ |
| Profile | exp_profile_ |
| FormFactorType | ff_type_ |
| Particles | particles_ |
|
Pointer< ProfileFitter < ChiScore > > | profile_fitter_ |
| std::vector< Particles > | rigid_bodies_ |
| std::vector< core::RigidBody > | rigid_bodies_decorators_ |
| Profile | rigid_bodies_profile_ |
Additional Inherited Members | |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
The restraint takes rigid bodies into account, in order to speed up the calculations. Rigid body should be gived 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.
- Algorithmic details:
- The distances between the atoms of rigid body do not change, therefore their contribution to the profile is pre-computed and stored.
Definition at line 42 of file saxs/Restraint.h.
Constructor & Destructor Documentation
| IMP::saxs::Restraint::Restraint | ( | const Particles & | particles, |
| const Profile & | exp_profile, | ||
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) |
- Parameters
-
[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
The documentation for this class was generated from the following file: