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IMP Reference Guide  develop.731656d855,2020/02/17
The Integrative Modeling Platform
IMP::isd::GaussianEMRestraint Class Reference

Restraint between two Gaussian Mixture Models, "model" and "density". More...

#include <IMP/isd/GaussianEMRestraint.h>

+ Inheritance diagram for IMP::isd::GaussianEMRestraint:

Detailed Description

Restraint between two Gaussian Mixture Models, "model" and "density".

This restrains two sets of GMMs with a density overlap function. The function is correlation of the two GMMs \(f_M\) and \(f_D\):

\[ \frac{2\int{f_M(x)f_D(x)dx}}{\int{f_M^2(x)+f_D^2(x)dx}} \]

Where the integral is the "overlap function" given by:

\[ ov(f_M,f_D) = \sum_{i=1}^{N_M} \sum_{j=1}^{N_D} \frac{1}{(2 \pi)^{3/2}|\Sigma_{Mi}+\Sigma_{Dj}|^{1/2}}\exp\left [-\frac{1}{2}(\boldsymbol\mu_{Mi} - \boldsymbol\mu_{Dj})^\top (\Sigma_{Mi}+\Sigma_{Dj})^{-1} (\boldsymbol\mu_{Mi} - \boldsymbol \mu_{Dj})\right ] \]

Note
Source: Greenberg, Pellarin, Sali. In preparation.

Definition at line 41 of file isd/GaussianEMRestraint.h.

Public Member Functions

 GaussianEMRestraint (Model *mdl, ParticleIndexes model_ps, ParticleIndexes density_ps, ParticleIndex global_sigma, Float model_cutoff_dist, Float density_cutoff_dist, Float slope, bool update_model=true, bool backbone_slope=false, bool local=false, std::string name="GaussianEMRestraint%1%")
 Setup the GaussianEMRestraint. More...
 
void compute_initial_scores ()
 Pre-calculate the density-density and model-model scores. More...
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
double get_cross_correlation_coefficient () const
 Get cross correlation between the model and the map. More...
 
RestraintInfoget_dynamic_info () const
 
double get_probability () const
 Returns exp(score) More...
 
Float get_slope ()
 Get restraint slope. More...
 
RestraintInfoget_static_info () const
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
void set_density_filename (std::string density_fn)
 Set the filename corresponding to the density GMM particles. More...
 
void set_slope (Float s)
 Set restraint slope. More...
 
void show (std::ostream &out) const
 
virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_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::ModelObject
 ModelObject (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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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::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::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Constructor & Destructor Documentation

IMP::isd::GaussianEMRestraint::GaussianEMRestraint ( Model mdl,
ParticleIndexes  model_ps,
ParticleIndexes  density_ps,
ParticleIndex  global_sigma,
Float  model_cutoff_dist,
Float  density_cutoff_dist,
Float  slope,
bool  update_model = true,
bool  backbone_slope = false,
bool  local = false,
std::string  name = "GaussianEMRestraint%1%" 
)

Setup the GaussianEMRestraint.

Parameters
[in]mdlthe Model object to operate on
[in]model_psparticles for the model GMM
[in]density_psparticles for the density GMM
[in]global_sigmaParticle to modulate the uncertainty
[in]model_cutoff_distCutoff for the model-model interactions
[in]density_cutoff_distCutoff for model-density interactions
[in]slopeGentle term to move all particles to the density
[in]update_model(DEPRECATED) update model each cycle
[in]backbone_slopeLimit the slope only to backbone particles
[in]localOnly consider density particles that are within the specified cutoff of the model particles (experimental)
[in]nameName of this restraint
Note
the model and density particles must be set up as Gaussian

Member Function Documentation

void IMP::isd::GaussianEMRestraint::compute_initial_scores ( )

Pre-calculate the density-density and model-model scores.

This is automatically called by the constructor. You only need to call it manually if you change Gaussian variances.

virtual IMP::ModelObjectsTemp IMP::isd::GaussianEMRestraint::do_get_inputs ( ) const
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::ModelObject.

double IMP::isd::GaussianEMRestraint::get_cross_correlation_coefficient ( ) const

Get cross correlation between the model and the map.

This CCC is that calculated from the last scoring function evaluation; calling this function before the score is calculated results in undefined behavior.

Definition at line 80 of file isd/GaussianEMRestraint.h.

RestraintInfo* IMP::isd::GaussianEMRestraint::get_dynamic_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

double IMP::isd::GaussianEMRestraint::get_probability ( ) const

Returns exp(score)

Definition at line 71 of file isd/GaussianEMRestraint.h.

Float IMP::isd::GaussianEMRestraint::get_slope ( )

Get restraint slope.

Definition at line 103 of file isd/GaussianEMRestraint.h.

RestraintInfo* IMP::isd::GaussianEMRestraint::get_static_info ( ) const
virtual
Returns
Information for writing to RMF files

Reimplemented from IMP::Restraint.

virtual ::IMP::VersionInfo IMP::isd::GaussianEMRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 115 of file isd/GaussianEMRestraint.h.

void IMP::isd::GaussianEMRestraint::set_density_filename ( std::string  density_fn)

Set the filename corresponding to the density GMM particles.

If the density GMM particles were read from a file, this method can be used to tell the restraint so that it can track this information back to the original EM density file, which is useful for deposition.

Definition at line 89 of file isd/GaussianEMRestraint.h.

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void IMP::isd::GaussianEMRestraint::set_slope ( Float  s)

Set restraint slope.

Definition at line 100 of file isd/GaussianEMRestraint.h.


The documentation for this class was generated from the following file: