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IMP
2.3.0
The Integrative Modeling Platform
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IMP
2.3.0
The Integrative Modeling Platform
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A restraint for envelope-based scoring of particles in the density map. More...
#include <IMP/em/EnvelopeFitRestraint.h>
Inheritance diagram for IMP::em::EnvelopeFitRestraint:A restraint for envelope-based scoring of particles in the density map.
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.
Public Member Functions | |
| EnvelopeFitRestraint (kernel::Particles particles, DensityMap *em_map, double density_threshold, double penetration_threshold) | |
| Constructor. More... | |
| void | apply_transformation () |
| IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| algebra::Transformation3D | get_transformation () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::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 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 (kernel::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::base::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 | |
| 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 |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint | ( | kernel::Particles | particles, |
| DensityMap * | em_map, | ||
| double | density_threshold, | ||
| double | penetration_threshold | ||
| ) |
Constructor.
| [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 |
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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::kernel::ModelObject.
Definition at line 57 of file EnvelopeFitRestraint.h.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::base::Object.
Definition at line 58 of file EnvelopeFitRestraint.h.