IMP
2.0.0
The Integrative Modeling Platform
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Calculate score based on fit to EM map.
#include <IMP/em/FitRestraint.h>
Public Member Functions | |
FitRestraint (ParticlesTemp ps, DensityMap *em_map, FloatPair norm_factors=FloatPair(0., 0.), FloatKey weight_key=atom::Mass::get_mass_key(), float scale=1, bool use_rigid_bodies=true, KernelType kt=GAUSSIAN) | |
Constructor. More... | |
unsigned int | add_particle (Particle *obj) |
void | add_particles (const Particles &objs) |
void | clear_particles () |
virtual void | do_show (std::ostream &out) const |
bool | get_has_particles () |
SampledDensityMap * | get_model_dens_map () const |
unsigned int | get_number_of_particles () const |
Particle * | get_particle (unsigned int i) const |
Particles | get_particles () const |
float | get_scale_factor () const |
void | remove_particle (Particle *d) |
void | remove_particles (const Particles &d) |
void | reserve_particles (unsigned int sz) |
void | set_particles (const Particles &ps) |
void | set_particles_order (const Particles &objs) |
void | set_scale_factor (float scale) |
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 |
Definition at line 32 of file FitRestraint.h.
IMP::em::FitRestraint::FitRestraint | ( | ParticlesTemp | ps, |
DensityMap * | em_map, | ||
FloatPair | norm_factors = FloatPair(0., 0.) , |
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FloatKey | weight_key = atom::Mass::get_mass_key() , |
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float | scale = 1 , |
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bool | use_rigid_bodies = true , |
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KernelType | kt = GAUSSIAN |
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[in] | ps | The particles participating in the fitting score |
[in] | em_map | The density map used in the fitting score |
[in] | norm_factors | if set, they are used as normalization factors for the cross correlation calculations. This is relevant when the cross-correlation score of the entire system is decomposed. |
[in] | weight_key | the name of the weight attribute of the particles |
[in] | scale | multiply the fitting restraint score and derivatives by this value |
[in] | use_rigid_bodies | if some of the particles are part of a rigid body, use the rigid body for faster calculations |
[in] | kt | KernelType to use for simulating density from particles |
SampledDensityMap* IMP::em::FitRestraint::get_model_dens_map | ( | ) | const |
Definition at line 63 of file FitRestraint.h.