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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) More...
Inherits object.
Fit Gaussian-decorated 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 = '', |
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target_ps = [], |
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cutoff_dist_model_model = 10.0, |
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cutoff_dist_model_data = 10.0, |
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target_mass_scale = 1.0, |
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target_mass = None, |
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target_radii_scale = 3.0, |
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model_radii_scale = 1.0, |
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slope = 0.0, |
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spherical_gaussians = False, |
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close_pair_container = None, |
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backbone_slope = False, |
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scale_target_to_mass = False, |
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weight = 1.0, |
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target_is_rigid_body = False |
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| ) |
Constructor.
| 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. |
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 |
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| ) |
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, |
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voxel_size = 5.0 |
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| ) |
Writes target GMM file to MRC.
Definition at line 393 of file bayesianem/restraint.py.