IMP Reference Guide
develop.4390929e3e,2024/11/12
The Integrative Modeling Platform

Fit Gaussiandecorated particles to an EM map (also represented with a set of Gaussians) More...
Inherits object.
Fit Gaussiandecorated particles to an EM map (also represented with a set of Gaussians)
ote This class wraps an IMP::bayesianem::GaussianEMRestraint
Definition at line 19 of file bayesianem/restraint.py.
Public Member Functions  
def  __init__ 
Constructor. More...  
def  add_target_density_to_hierarchy 
Can add a target GMM to a Hierarchy. More...  
def  center_model_on_target_density 
aligns the model on the target density More...  
def  center_on_target_density 
align the model on target GMM More...  
def  center_target_density_on_model 
aligns the center of mass of the target GMM on the center of mass of the model More...  
def  center_target_density_on_origin 
aligns the center of mass of the target GMM on the origin More...  
def  get_center_of_mass 
Returns the geometric center of the GMM particles. More...  
def  get_density_as_hierarchy 
returns a hierarchy whose leaves are the gaussian particles of the target GMM More...  
def  set_weight 
set the weight of the restraint More...  
def  write_target_gmm_to_mrc 
Writes target GMM file to MRC. More...  
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.__init__  (  self,  
densities,  
target_fn = '' , 

target_ps = [] , 

cutoff_dist_model_model = 10.0 , 

cutoff_dist_model_data = 10.0 , 

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 

) 
Constructor.
densities  The Gaussiandecorated 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 modelmodel close pair container 
cutoff_dist_model_data  Distance in modeldata 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. 
Definition at line 57 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.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 366 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.center_model_on_target_density  (  self,  
input_object  
) 
aligns the model on the target density
input_objects  IMP.pmi.representation.Representation or IMP.pmi.topology.State 
Definition at line 260 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.center_on_target_density  (  self  ) 
align the model on target GMM
Definition at line 295 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.center_target_density_on_model  (  self  ) 
aligns the center of mass of the target GMM on the center of mass of the model
Definition at line 197 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.center_target_density_on_origin  (  self  ) 
aligns the center of mass of the target GMM on the origin
Definition at line 245 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.get_center_of_mass  (  self,  
target = True 

) 
Returns the geometric center of the GMM particles.
target  = True  returns target map gmm COM 
target  = False  returns model gmm COM 
Definition at line 227 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.get_density_as_hierarchy  (  self  ) 
returns a hierarchy whose leaves are the gaussian particles of the target GMM
Definition at line 355 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.set_weight  (  self,  
weight  
) 
set the weight of the restraint
weight 
Definition at line 324 of file bayesianem/restraint.py.
def IMP.bayesianem.restraint.GaussianEMRestraintWrapper.write_target_gmm_to_mrc  (  self,  
fileout = None , 

voxel_size = 5.0 

) 
Writes target GMM file to MRC.
Definition at line 393 of file bayesianem/restraint.py.