1 """@namespace IMP.pmi.restraints.em
2 Restraints for handling electron microscopy maps.
5 from __future__
import print_function
21 """Fit Gaussian-decorated particles to an EM map
22 (also represented with a set of Gaussians)
23 @note This class wraps an isd::GaussianEMRestraint
28 cutoff_dist_model_model=0.0,
29 cutoff_dist_model_data=0.0,
30 target_mass_scale=1.0,
32 target_radii_scale=3.0,
33 model_radii_scale=1.0,
35 spherical_gaussians=
False,
36 close_pair_container=
None,
38 scale_target_to_mass=
False,
40 target_is_rigid_body=
False,
43 @param densities The Gaussian-decorated particles to be restrained
44 @param target_fn GMM file of the target density map
45 (alternatively, pass the ps)
46 @param target_ps List of Gaussians of the target map
47 (alternatively, pass the filename)
48 @param cutoff_dist_model_model Distance in model-model close
50 @param cutoff_dist_model_data Distance in model-data close pair
51 container. Usually can set to zero because we multiply the
53 @param target_mass_scale Scale up the target densities so that
55 Needed if the GMM you generated was not already scaled.
56 To make it the same as model mass, set scale_to_target_mass=True
57 @param target_mass Sets the mass of the target density to the given value. Default is None. This
58 will override target_mass_scale argument
59 @param target_radii_scale Scale the target density radii -
60 only used for the close pair container.
61 If you keep this at 3.0 or so you don't have to use cutoff dist.
62 @param model_radii_scale Scale the model density radii - only used
63 for the close pair container
64 @param slope Linear term added to help bring model into the density
65 @param spherical_gaussians Set to True for a speed bonus when
66 the model densities are spheres. (This means you don't have
67 to do a matrix multiplication if they rotate.)
68 @param close_pair_container Pass a close pair container for
69 the model if you already have one (e.g. for an excluded
70 volume restraint.) May give a speed bonus.
71 @param backbone_slope Only apply slope to backbone particles -
72 only matters for atomic
73 @param scale_target_to_mass Set True if you would need to scale
74 target to EXACTLY the model mass
75 @param weight The restraint weight
76 @param target_is_rigid_body Set True if you want to put the target density particles
77 into a rigid body that need to be sampled (e.g.,when you need to fit one density
78 against another one). Default is False.
79 @param local Only consider density particles that are within the
80 specified model-density cutoff (experimental)
85 self.sigmaissampled =
False
86 self.sigmamaxtrans = 0.3
91 self.densities = densities
92 self.em_root_hier =
None
95 self.m = self.densities[0].get_model()
97 if scale_target_to_mass:
98 def hierarchy_mass(h):
101 target_mass = sum(hierarchy_mass(h)
for h
in densities)
102 print(
'will set target mass to', target_mass)
103 print(
'will scale target mass by', target_mass_scale)
106 self._set_dataset(target_fn)
112 radius_scale=target_radii_scale,
113 mass_scale=target_mass_scale)
114 elif target_ps != []:
115 self.target_ps = target_ps
117 print(
'Gaussian EM restraint: must provide target density file or properly set up target densities')
122 scale=target_mass/tmass
123 for p
in self.target_ps:
127 for p, state
in IMP.pmi.tools._all_protocol_outputs(densities[0]):
128 p.add_em3d_restraint(state, self.target_ps, self.densities,
133 for h
in self.densities:
135 if model_radii_scale != 1.0:
136 for p
in self.model_ps:
144 if target_is_rigid_body:
152 self.sigmaglobal = IMP.pmi.tools.SetupNuisance(self.m, self.sigmainit,
153 self.sigmamin, self.sigmamax,
154 self.sigmaissampled).get_particle()
157 print(
'target num particles', len(self.target_ps), \
159 for p
in self.target_ps]))
160 print(
'model num particles', len(self.model_ps), \
162 for p
in self.model_ps]))
164 update_model=
not spherical_gaussians
170 self.sigmaglobal.get_particle().
get_index(),
171 cutoff_dist_model_model,
172 cutoff_dist_model_data,
174 update_model, backbone_slope, local)
176 self.gaussianEM_restraint.set_density_filename(target_fn)
178 print(
'done EM setup')
180 self.rs.add_restraint(self.gaussianEM_restraint)
181 self.set_weight(weight)
183 def _set_dataset(self, target_fn):
184 """Set the dataset to point to the input file"""
186 self.dataset = p.parse_file(target_fn)[
'dataset']
188 def center_target_density_on_model(self):
191 for p
in self.target_ps:
194 target_com += pos * mass
196 target_com /= target_mass
197 print(
'target com', target_com)
200 for p
in self.model_ps:
203 model_com += pos * mass
205 model_com /= model_mass
206 print(
'model com', model_com)
208 v = target_com - model_com
209 print(
'translating with', -v)
211 for p
in self.target_ps:
216 '''Returns the geometric center of the GMM particles
217 @param target = True - returns target map gmm COM
218 @param target = False - returns model gmm COM'''
233 def center_target_density_on_origin(self):
235 print(
'target com', target_com)
237 print(
'model com', model_com)
238 v = target_com - model_com
239 print(
'translating with', -v)
241 for p
in self.target_ps:
245 def center_model_on_target_density(self, input_object):
246 hier = input_object.get_hierarchy()
248 print(
'target com', target_com)
250 print(
'model com', model_com)
251 v = target_com - model_com
252 print(
'translating with', v)
265 for rb
in list(rigid_bodies):
268 for p
in list(XYZRs):
271 def center_on_target_density(self):
273 print(
'target com', target_com)
275 print(
'model com', model_com)
276 v = target_com - model_com
277 print(
'translating with', v)
283 for p
in self.model_ps:
290 for rb
in list(rigid_bodies):
293 for p
in list(XYZRs):
299 def set_weight(self,weight):
301 self.rs.set_weight(weight)
303 def set_label(self, label):
306 def add_to_model(self):
309 def get_particles_to_sample(self):
311 if self.sigmaissampled:
312 ps[
"Nuisances_GaussianEMRestraint_sigma_" +
313 self.label] = ([self.sigmaglobal], self.sigmamaxtrans)
315 ps[
"Rigid_Bodies_GaussianEMRestraint"] = (
321 def get_rigid_body(self):
323 raise Exception(
"No rigid body created for GMM particles. Ensure target_is_rigid_body is set to True")
326 def get_density_as_hierarchy(self):
327 if self.em_root_hier
is None:
329 self.em_root_hier.set_name(
"GaussianEMRestraint_density_"+self.label)
330 for p
in self.target_ps:
331 self.em_root_hier.add_child(p)
332 return self.em_root_hier
335 ''' Can add a target GMM to a Hierarchy.
336 For PMI2 a state object may also be passed'''
338 inp.get_hierarchy().add_child(self.get_density_as_hierarchy())
340 inp.add_child(self.get_density_as_hierarchy())
342 raise Exception(
"Can only add a density to a PMI State object or IMP.atom.Hierarchy. You passed a", type(inp))
344 def get_restraint(self):
347 def get_restraint_set(self):
350 def get_output(self):
352 score = self.weight * self.rs.unprotected_evaluate(
None)
353 ccc = self.gaussianEM_restraint.get_cross_correlation_coefficient()
355 output[
"_TotalScore"] = str(score)
356 output[
"GaussianEMRestraint_" +
357 self.label] = str(score)
358 output[
"GaussianEMRestraint_%s_CCC" % self.label] = ccc
359 output[
"GaussianEMRestraint_sigma_" +
360 self.label] = str(self.sigmaglobal.get_scale())
364 return self.weight * self.rs.unprotected_evaluate(
None)
367 '''Writes target GMM file to MRC'''
369 fileout=
"Gaussian_map_" + self.label +
".mrc"
377 "If you use this class please let the PMI developers know.")
379 """Fit particles to an EM map. This creates a simulate density map and updates them every eval.
380 @note Wraps an em::FitRestraint
391 @param ps The particles to restrain. Currently these must be atomic particles.
392 @param map_fn The EM density map to fit to
393 @param resolution Map resolution
394 @param origin In case you need to tell IMP the correct origin
395 @param voxel_size In case you need to tell IMP the angstroms per pixel
396 @param weight The data weight
397 @param label Extra PMI label
399 print(
'FitRestraint: setup')
401 print(
'\tresolution',resolution)
402 print(
'\tvoxel_size',voxel_size)
403 print(
'\torigin',origin)
404 print(
'\tweight',weight)
407 self.mdl = ps[0].get_model()
413 self.dmap.update_voxel_size(voxel_size)
414 if origin
is not None:
415 if isinstance(origin, IMP.algebra.Vector3D):
416 self.dmap.set_origin(origin)
417 elif isinstance(origin, list):
418 self.dmap.set_origin(*origin)
420 print(
'FitRestraint did not recognize format of origin')
424 self.rs.add_restraint(fr)
425 self.set_weight(weight)
427 def set_weight(self,weight):
429 self.rs.set_weight(weight)
431 def set_label(self, label):
434 def add_to_model(self):
437 def get_restraint_set(self):
440 def get_output(self):
442 score = self.weight * self.rs.unprotected_evaluate(
None)
443 output[
"_TotalScore"] = str(score)
444 output[
"EMRestraint_" + self.label] = str(score)
448 return self.weight * self.rs.unprotected_evaluate(
None)
454 class ElectronMicroscopy2D(object):
463 self.m = representation.prot.get_model()
468 particles = IMP.pmi.tools.select(
470 resolution=resolution)
473 self.rs.add_restraint(em2d)
475 def set_label(self, label):
478 def add_to_model(self):
481 def get_restraint(self):
484 def set_weight(self,weight):
486 self.rs.set_weigth(self.weight)
488 def get_output(self):
490 score = self.weight*self.rs.unprotected_evaluate(
None)
491 output[
"_TotalScore"] = str(score)
492 output[
"ElectronMicroscopy2D_" + self.label] = str(score)
Support for the mmCIF file format.
Fit Gaussian-decorated particles to an EM map (also represented with a set of Gaussians) ...
A member of a rigid body, it has internal (local) coordinates.
static bool get_is_setup(const IMP::ParticleAdaptor &p)
def write_target_gmm_to_mrc
Writes target GMM file to MRC.
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
double get_mass(ResidueType c)
Get the mass from the residue type.
Extract metadata from an EM density GMM file.
def add_target_density_to_hierarchy
Can add a target GMM to a Hierarchy.
static bool get_is_setup(const IMP::ParticleAdaptor &p)
Object used to hold a set of restraints.
ParticleIndexPairs get_indexes(const ParticlePairsTemp &ps)
The standard decorator for manipulating molecular structures.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
void transform(XYZ a, const algebra::Transformation3D &tr)
Apply a transformation to the particle.
Restraint between two Gaussian Mixture Models, "model" and "density".
A decorator for a particle with x,y,z coordinates.
def get_center_of_mass
Returns the geometric center of the GMM particles.
static Copy setup_particle(Model *m, ParticleIndex pi, Int number)
def deprecated_object
Python decorator to mark a class as deprecated.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Calculate score based on fit to EM map.
The general base class for IMP exceptions.
IMP::core::RigidBody create_rigid_body(Hierarchy h)
Class to handle individual particles of a Model object.
Stores a list of Molecules all with the same State index.
A decorator for a rigid body.
Functionality for loading, creating, manipulating and scoring atomic structures.
Hierarchies get_leaves(const Selection &h)
Fit particles to an EM map.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A decorator for a particle with x,y,z coordinates and a radius.