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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...
 
def add_target_density_to_hierarchy
 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
densitiesThe Gaussian-decorated particles to be restrained
target_fnGMM file of the target density map (alternatively, pass the ps)
target_psList of Gaussians of the target map (alternatively, pass the filename)
cutoff_dist_model_modelDistance in model-model close pair container
cutoff_dist_model_dataDistance in model-data close pair container. Usually can set to zero because we multiply the target radii
target_mass_scaleScale 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_massSets the mass of the target density to the given value. Default is None. This will override target_mass_scale argument
target_radii_scaleScale 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_scaleScale the model density radii - only used for the close pair container
slopeLinear term added to help bring model into the density
spherical_gaussiansSet 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_containerPass 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_slopeOnly apply slope to backbone particles - only matters for atomic
scale_target_to_massSet True if you would need to scale target to EXACTLY the model mass
weightThe restraint weight
target_is_rigid_bodySet 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.
localOnly 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: