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IMP
2.1.0
The Integrative Modeling Platform
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IMP
2.1.0
The Integrative Modeling Platform
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Calculate score based on fit to EM map.
#include <IMP/em/PCAFitRestraint.h>
Inheritance diagram for IMP::em::PCAFitRestraint:Public Member Functions | |
| PCAFitRestraint (kernel::ParticlesTemp ps, DensityMap *em_map, float threahold, float max_pca_size_diff, float max_angle_diff, float max_centroid_diff, FloatKey weight_key=atom::Mass::get_mass_key()) | |
| Constructor. More... | |
| unsigned int | add_particle (kernel::Particle *obj) |
| void | add_particles (const kernel::Particles &objs) |
| void | clear_particles () |
| virtual IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| bool | get_has_particles () |
| unsigned int | get_number_of_particles () const |
| kernel::Particle * | get_particle (unsigned int i) const |
| kernel::Particles | get_particles () 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. | |
| void | remove_particle (kernel::Particle *d) |
| void | remove_particles (const kernel::Particles &d) |
| void | reserve_particles (unsigned int sz) |
| void | set_particles (const kernel::Particles &ps) |
| void | set_particles_order (const kernel::Particles &objs) |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::Model *m, std::string name) | |
| Restraint (std::string name="Restraint %1%") | |
| 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 (kernel::Model *m, std::string name) | |
| ModelObject (std::string name) | |
| virtual void | do_set_model (kernel::Model *) |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. | |
| bool | get_has_required_score_states () const |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| bool | get_is_part_of_model () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| void | set_has_dependencies (bool tf) |
| void | set_has_required_score_states (bool tf) |
| virtual void | set_model (kernel::Model *m) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| 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) |
Public Attributes | |
| virtual double | const |
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... | |
| Object () | |
Definition at line 32 of file PCAFitRestraint.h.
| IMP::em::PCAFitRestraint::PCAFitRestraint | ( | kernel::ParticlesTemp | ps, |
| DensityMap * | em_map, | ||
| float | threahold, | ||
| float | max_pca_size_diff, | ||
| float | max_angle_diff, | ||
| float | max_centroid_diff, | ||
| FloatKey | weight_key = atom::Mass::get_mass_key() |
||
| ) |
| [in] | ps | The particles participating in the fitting score |
| [in] | em_map | The density map used in the fitting score |
| [in] | threahold | consider all voxels above this value for PCA calculation |
| [in] | weight_key | the name of the weight attribute of the particles |
| [in] | max_pca_size_diff | |
| [in] | max_angle_diff | |
| [in] | max_centroid_diff |
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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.