IMP Reference Guide  develop.716bca0a46,2020/04/04 The Integrative Modeling Platform
IMP.pmi.restraints.em.GaussianEMRestraint Class Reference

Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) More...

Inherits object.

## Detailed Description

Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians)

Note
This class wraps an isd::GaussianEMRestraint
This class is only available in Python.

Definition at line 20 of file lib/IMP/pmi/restraints/em.py.

## Public Member Functions

def __init__
Constructor. More...

Can add a target GMM to a Hierarchy. More...

def get_center_of_mass
Returns the geometric center of the GMM particles. More...

def write_target_gmm_to_mrc
Writes target GMM file to MRC. More...

## Constructor & Destructor Documentation

 def IMP.pmi.restraints.em.GaussianEMRestraint.__init__ ( self, densities, target_fn = '', target_ps = [], cutoff_dist_model_model = 0.0, cutoff_dist_model_data = 0.0, target_mass_scale = 1.0, target_mass = None, target_radii_scale = 3.0, model_radii_scale = 1.0, slope = 0.0, spherical_gaussians = False, close_pair_container = None, backbone_slope = False, scale_target_to_mass = False, weight = 1.0, target_is_rigid_body = False, local = False, representation = None )

Constructor.

Parameters
 densities The Gaussian-decorated particles to be restrained target_fn GMM file of the target density map (alternatively, pass the ps) target_ps List of Gaussians of the target map (alternatively, pass the filename) cutoff_dist_model_model Distance in model-model close pair container cutoff_dist_model_data Distance in model-data close pair container. Usually can set to zero because we multiply the target radii target_mass_scale Scale up the target densities so that the mass is accurate. Needed if the GMM you generated was not already scaled. To make it the same as model mass, set scale_to_target_mass=True target_mass Sets the mass of the target density to the given value. Default is None. This will override target_mass_scale argument target_radii_scale Scale the target density radii - only used for the close pair container. If you keep this at 3.0 or so you don't have to use cutoff dist. model_radii_scale Scale the model density radii - only used for the close pair container slope Linear term added to help bring model into the density spherical_gaussians Set to True for a speed bonus when the model densities are spheres. (This means you don't have to do a matrix multiplication if they rotate.) close_pair_container Pass a close pair container for the model if you already have one (e.g. for an excluded volume restraint.) May give a speed bonus. backbone_slope Only apply slope to backbone particles - only matters for atomic scale_target_to_mass Set True if you would need to scale target to EXACTLY the model mass weight The restraint weight target_is_rigid_body Set True if you want to put the target density particles into a rigid body that need to be sampled (e.g.,when you need to fit one density against another one). Default is False. local Only consider density particles that are within the specified model-density cutoff (experimental)

Definition at line 60 of file lib/IMP/pmi/restraints/em.py.

## Member Function Documentation

 def IMP.pmi.restraints.em.GaussianEMRestraint.add_target_density_to_hierarchy ( self, inp )

Can add a target GMM to a Hierarchy.

For PMI2 a state object may also be passed

Definition at line 336 of file lib/IMP/pmi/restraints/em.py.

 def IMP.pmi.restraints.em.GaussianEMRestraint.get_center_of_mass ( self, target = True )

Returns the geometric center of the GMM particles.

Parameters
 target = True - returns target map gmm COM target = False - returns model gmm COM

Definition at line 217 of file lib/IMP/pmi/restraints/em.py.

 def IMP.pmi.restraints.em.GaussianEMRestraint.write_target_gmm_to_mrc ( self, fileout = None, voxel_size = 5.0 )

Writes target GMM file to MRC.

Definition at line 368 of file lib/IMP/pmi/restraints/em.py.

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