IMP
2.4.0
The Integrative Modeling Platform
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Tools for handling Gaussian Mixture Models. More...
Tools for handling Gaussian Mixture Models.
Functions | |
def | decorate_gmm_from_text |
read the output from write_gmm_to_text, decorate as Gaussian and Mass More... | |
def | draw_points |
given some points (and optional transform), write them to chimera 'bild' format colors flag only applies to ellipses, otherwise it'll be weird More... | |
def | fit_dirichlet_gmm_to_points |
fit a GMM to some points. More... | |
def | fit_gmm_to_points |
fit a GMM to some points. More... | |
def | write_gmm_to_map |
write density map from GMM. More... | |
def | write_gmm_to_text |
write a list of gaussians to text. More... | |
def | write_sklearn_gmm_to_map |
write density map directly from sklearn GMM (kinda slow) More... | |
def IMP.isd.gmm_tools.decorate_gmm_from_text | ( | in_fn, | |
ps, | |||
mdl, | |||
transform = None , |
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radius_scale = 1.0 , |
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mass_scale = 1.0 |
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) |
read the output from write_gmm_to_text, decorate as Gaussian and Mass
Definition at line 22 of file gmm_tools.py.
def IMP.isd.gmm_tools.draw_points | ( | pts, | |
out_fn, | |||
trans = IMP.algebra.get_identity_transformation_3d() , |
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use_colors = False |
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) |
given some points (and optional transform), write them to chimera 'bild' format colors flag only applies to ellipses, otherwise it'll be weird
Definition at line 115 of file gmm_tools.py.
def IMP.isd.gmm_tools.fit_dirichlet_gmm_to_points | ( | points, | |
n_components, | |||
mdl, | |||
ps = [] , |
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num_iter = 100 , |
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covariance_type = 'full' , |
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mass_multiplier = 1.0 |
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) |
fit a GMM to some points.
Will return core::Gaussians. if no particles are provided, they will be created
points: list of coordinates (python) n_components: number of gaussians to create mdl: IMP Model ps: list of particles to be decorated. if empty, will add num_iter: number of EM iterations covariance_type: covar type for the gaussians. options: 'full', 'diagonal', 'sphereical' init_centers: initial coordinates of the GMM force_radii: fix the radii (spheres only) force_weight: fix the weights mass_multiplier: multiply the weights of all the gaussians by this value
Definition at line 282 of file gmm_tools.py.
def IMP.isd.gmm_tools.fit_gmm_to_points | ( | points, | |
n_components, | |||
mdl, | |||
ps = [] , |
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num_iter = 100 , |
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covariance_type = 'full' , |
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init_centers = [] , |
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force_radii = -1.0 , |
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force_weight = -1.0 , |
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mass_multiplier = 1.0 |
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) |
fit a GMM to some points.
Will return core::Gaussians. if no particles are provided, they will be created
points: list of coordinates (python) n_components: number of gaussians to create mdl: IMP Model ps: list of particles to be decorated. if empty, will add num_iter: number of EM iterations covariance_type: covar type for the gaussians. options: 'full', 'diagonal', 'sphereical' init_centers: initial coordinates of the GMM force_radii: fix the radii (spheres only) force_weight: fix the weights mass_multiplier: multiply the weights of all the gaussians by this value dirichlet: use the DGMM fitting (can reduce number of components, takes longer)
Definition at line 204 of file gmm_tools.py.
def IMP.isd.gmm_tools.write_gmm_to_map | ( | to_draw, | |
out_fn, | |||
voxel_size, | |||
bounding_box = None |
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) |
write density map from GMM.
input can be either particles or gaussians
Definition at line 62 of file gmm_tools.py.
def IMP.isd.gmm_tools.write_gmm_to_text | ( | ps, | |
out_fn | |||
) |
write a list of gaussians to text.
must be decorated as Gaussian and Mass
Definition at line 43 of file gmm_tools.py.
def IMP.isd.gmm_tools.write_sklearn_gmm_to_map | ( | gmm, | |
out_fn, | |||
apix = 0 , |
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bbox = None , |
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dmap_model = None |
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) |
write density map directly from sklearn GMM (kinda slow)
Definition at line 93 of file gmm_tools.py.