IMP
2.0.0
The Integrative Modeling Platform
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#include <IMP/em2d/Em2DRestraint.h>
Public Member Functions | |
Em2DRestraint () | |
virtual void | do_show (std::ostream &out) const |
RegistrationResults | get_registration_results () const |
void | set_coarse_registration_mode (bool opt) |
void | set_fast_mode (unsigned int n) |
void | set_images (const em2d::Images em_images) |
void | set_particles (SingletonContainer *particles_container) |
void | set_variance_images (const em2d::Images variance_images) |
void | setup (ScoreFunction *score_function, const Em2DRestraintParameters ¶ms) |
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) |
Related Functions | |
(Note that these are not member functions.) | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Em2DRestraint > > | Em2DRestraintsTemp |
Related Functions inherited from IMP::kernel::Restraint | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Related Functions inherited from IMP::kernel::ModelObject | |
typedef IMP::base::Vector < IMP::base::WeakPointer < ModelObject > > | ModelObjectsTemp |
Related Functions inherited from IMP::base::Object | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
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 () |
This restraint ensures that a set of particles are similar to a set of EM images. The restraint generates projections of the model that are then compared with the EM images. The projections are generated from the radius of its particles. In the case of atoms, the radius is generated automatically. For other particles the radius has to be provided.
Definition at line 32 of file Em2DRestraint.h.
IMP::em2d::Em2DRestraint::Em2DRestraint | ( | ) |
Creates the restraint. You are not done yet by creating the restraint. After creating it, you need to call the setup() function
Definition at line 53 of file Em2DRestraint.h.
RegistrationResults IMP::em2d::Em2DRestraint::get_registration_results | ( | ) | const |
Get the registration results for each of the images after finishing the optimization. Obviously, requesting the results before optimizing is an error
Definition at line 132 of file Em2DRestraint.h.
void IMP::em2d::Em2DRestraint::set_coarse_registration_mode | ( | bool | opt | ) |
If the value provided to this function is true, restraint operates only using a coarse registration scheme (maximizing the cross correlation coefficient). This option (which is set to false by default) can speed the evaluation of the restraint by a order of magnitude, but the values obtained are not going to be less accurate. You could want to activate it at the beginning of an optimization.
opt | true if you want to use the coarse mode |
Definition at line 122 of file Em2DRestraint.h.
void IMP::em2d::Em2DRestraint::set_fast_mode | ( | unsigned int | n | ) |
Sets fast mode for computing the restraint. This mode only makes sense it the set_coarse_registration_mode option is false. This option only optimizes some coarse results (those given by the argument) to get the refined value. This option is very fast compared to a full optimization, and almost always is a good idea to use it with 1-5 results. This mode is still significantly slow compared to set_coarse_registration_mode(), but the values optimized are optimum.
n | The number of images to optimize |
void IMP::em2d::Em2DRestraint::set_images | ( | const em2d::Images | em_images | ) |
Sets the EM images to use as restraints
em_images | The images |
void IMP::em2d::Em2DRestraint::set_particles | ( | SingletonContainer * | particles_container | ) |
Sets the particles used to compute projections.
particles_container | All the particles must be in the container |
void IMP::em2d::Em2DRestraint::set_variance_images | ( | const em2d::Images | variance_images | ) |
Sets the variance images of EM images. This is useful if the image is a class average Note: Not all the scoring function use this data Sets the variance images for class averages. If class averages are used as restraints, it is possible to use the variance images to assign a standard deviation (error) for each of the pixels in a class average.
variance_images |
void IMP::em2d::Em2DRestraint::setup | ( | ScoreFunction * | score_function, |
const Em2DRestraintParameters & | params | ||
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Initializes the restraint
score_function | Scoring function to use to evalute the similarity between particles and projections |
params | All the parameters required for the restraint |
Definition at line 61 of file Em2DRestraint.h.
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related |
Pass a set of objects.
Definition at line 139 of file Em2DRestraint.h.