IMP::em::EnvelopeFitRestraint Class Reference
A restraint for envelope-based scoring of particles in the density map. More...
#include <IMP/em/EnvelopeFitRestraint.h>
Inheritance diagram for IMP::em::EnvelopeFitRestraint:Public Member Functions | |
| EnvelopeFitRestraint (Particles particles, DensityMap *em_map, double density_threshold, double penetration_threshold) | |
| Constructor. More... | |
| void | apply_transformation () |
| IMP::ModelObjectsTemp | do_get_inputs () const |
| algebra::Transformation3D | get_transformation () const |
| double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) 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) |
Additional Inherited Members | |
| 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 () |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
The restraint fits the particles into the density map by alignment of principal components of the particles with principal components of the map. Therefore, the particle set should comprise all subunits that fill the map. The aligned particles are scored using EnvelopeScore. This is a fast alignment and scoring that works well for low resolution density maps.
Definition at line 32 of file EnvelopeFitRestraint.h.
Constructor & Destructor Documentation
| IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint | ( | Particles | particles, |
| DensityMap * | em_map, | ||
| double | density_threshold, | ||
| double | penetration_threshold | ||
| ) |
- Parameters
-
[in] particles The particles participating in the score [in] em_map The density map used in the fitting score [in] density_threshold Density map threshold [in] penetration_threshold A distance for which penetration of particles out of the map envelope (as defined by density_threshold) is allowed. Recommended value is approximately map resolution
Member Function Documentation
|
virtual |
Override if this reads other objects during evaluate.
Implements IMP::kernel::ModelObject.
Definition at line 59 of file EnvelopeFitRestraint.h.
The documentation for this class was generated from the following file: