IMP.pmi1.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)

ote This class wraps an isd::GaussianEMRestraint

Note

This class is only available in Python.

Definition at line 21 of file lib/IMP/pmi1/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.pmi1.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 61 of file lib/IMP/pmi1/restraints/em.py.

Member Function Documentation

def IMP.pmi1.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 353 of file lib/IMP/pmi1/restraints/em.py.

def IMP.pmi1.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 231 of file lib/IMP/pmi1/restraints/em.py.

def IMP.pmi1.restraints.em.GaussianEMRestraint.write_target_gmm_to_mrc	(		self,
			fileout = None,
			voxel_size = 5.0
	)

Writes target GMM file to MRC.

Definition at line 383 of file lib/IMP/pmi1/restraints/em.py.

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

• lib/IMP/pmi1/restraints/em.py