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,
44 @param densities The Gaussian-decorated particles to be restrained
45 @param target_fn GMM file of the target density map
46 (alternatively, pass the ps)
47 @param target_ps List of Gaussians of the target map
48 (alternatively, pass the filename)
49 @param cutoff_dist_model_model Distance in model-model close
51 @param cutoff_dist_model_data Distance in model-data close pair
52 container. Usually can set to zero because we multiply the
54 @param target_mass_scale Scale up the target densities so that
56 Needed if the GMM you generated was not already scaled.
57 To make it the same as model mass, set scale_to_target_mass=True
58 @param target_mass Sets the mass of the target density to the given value. Default is None. This
59 will override target_mass_scale argument
60 @param target_radii_scale Scale the target density radii -
61 only used for the close pair container.
62 If you keep this at 3.0 or so you don't have to use cutoff dist.
63 @param model_radii_scale Scale the model density radii - only used
64 for the close pair container
65 @param slope Linear term added to help bring model into the density
66 @param spherical_gaussians Set to True for a speed bonus when
67 the model densities are spheres. (This means you don't have
68 to do a matrix multiplication if they rotate.)
69 @param close_pair_container Pass a close pair container for
70 the model if you already have one (e.g. for an excluded
71 volume restraint.) May give a speed bonus.
72 @param backbone_slope Only apply slope to backbone particles -
73 only matters for atomic
74 @param scale_target_to_mass Set True if you would need to scale
75 target to EXACTLY the model mass
76 @param weight The restraint weight
77 @param target_is_rigid_body Set True if you want to put the target density particles
78 into a rigid body that need to be sampled (e.g.,when you need to fit one density
79 against another one). Default is False.
80 @param local Only consider density particles that are within the
81 specified model-density cutoff (experimental)
86 self.sigmaissampled =
False
87 self.sigmamaxtrans = 0.3
92 self.densities = densities
93 self.em_root_hier =
None
96 self.m = self.densities[0].get_model()
98 if scale_target_to_mass:
99 def hierarchy_mass(h):
102 target_mass = sum(hierarchy_mass(h)
for h
in densities)
103 print(
'will set target mass to', target_mass)
104 print(
'will scale target mass by', target_mass_scale)
107 self._set_dataset(target_fn, representation)
113 radius_scale=target_radii_scale,
114 mass_scale=target_mass_scale)
115 elif target_ps != []:
116 self.target_ps = target_ps
118 print(
'Gaussian EM restraint: must provide target density file or properly set up target densities')
123 scale=target_mass/tmass
124 for p
in self.target_ps:
128 for p, state
in IMP.pmi.tools._all_protocol_outputs([representation],
130 p.add_em3d_restraint(state, self.target_ps, self.densities,
135 for h
in self.densities:
137 if model_radii_scale != 1.0:
138 for p
in self.model_ps:
146 if target_is_rigid_body:
154 self.sigmaglobal = IMP.pmi.tools.SetupNuisance(self.m, self.sigmainit,
155 self.sigmamin, self.sigmamax,
156 self.sigmaissampled).get_particle()
159 print(
'target num particles', len(self.target_ps), \
161 for p
in self.target_ps]))
162 print(
'model num particles', len(self.model_ps), \
164 for p
in self.model_ps]))
166 update_model=
not spherical_gaussians
172 self.sigmaglobal.get_particle().
get_index(),
173 cutoff_dist_model_model,
174 cutoff_dist_model_data,
176 update_model, backbone_slope, local)
178 self.gaussianEM_restraint.set_density_filename(target_fn)
180 print(
'done EM setup')
182 self.rs.add_restraint(self.gaussianEM_restraint)
183 self.set_weight(weight)
185 def _set_dataset(self, target_fn, representation):
186 """Set the dataset to point to the input file"""
188 self.dataset = p.parse_file(target_fn)[
'dataset']
190 def center_target_density_on_model(self):
193 for p
in self.target_ps:
196 target_com += pos * mass
198 target_com /= target_mass
199 print(
'target com', target_com)
202 for p
in self.model_ps:
205 model_com += pos * mass
207 model_com /= model_mass
208 print(
'model com', model_com)
210 v = target_com - model_com
211 print(
'translating with', -v)
213 for p
in self.target_ps:
218 '''Returns the geometric center of the GMM particles
219 @param target = True - returns target map gmm COM
220 @param target = False - returns model gmm COM'''
235 def center_target_density_on_origin(self):
237 print(
'target com', target_com)
239 print(
'model com', model_com)
240 v = target_com - model_com
241 print(
'translating with', -v)
243 for p
in self.target_ps:
247 def center_model_on_target_density(self, input_object):
249 hier = input_object.prot
251 hier = input_object.get_hierarchy()
253 raise Exception(
"Input must be a Representation or topology.State object")
255 print(
'target com', target_com)
257 print(
'model com', model_com)
258 v = target_com - model_com
259 print(
'translating with', v)
272 for rb
in list(rigid_bodies):
275 for p
in list(XYZRs):
278 def center_on_target_density(self):
280 print(
'target com', target_com)
282 print(
'model com', model_com)
283 v = target_com - model_com
284 print(
'translating with', v)
290 for p
in self.model_ps:
297 for rb
in list(rigid_bodies):
300 for p
in list(XYZRs):
306 def set_weight(self,weight):
308 self.rs.set_weight(weight)
310 def set_label(self, label):
313 def add_to_model(self):
316 def get_particles_to_sample(self):
318 if self.sigmaissampled:
319 ps[
"Nuisances_GaussianEMRestraint_sigma_" +
320 self.label] = ([self.sigmaglobal], self.sigmamaxtrans)
322 ps[
"Rigid_Bodies_GaussianEMRestraint"] = (
328 def get_rigid_body(self):
330 raise Exception(
"No rigid body created for GMM particles. Ensure target_is_rigid_body is set to True")
333 def get_density_as_hierarchy(self):
334 if self.em_root_hier
is None:
336 self.em_root_hier.set_name(
"GaussianEMRestraint_density_"+self.label)
337 for p
in self.target_ps:
338 self.em_root_hier.add_child(p)
339 return self.em_root_hier
342 ''' Can add a target GMM to a Hierarchy.
343 For PMI2 a state object may also be passed'''
345 inp.get_hierarchy().add_child(self.get_density_as_hierarchy())
347 inp.add_child(self.get_density_as_hierarchy())
349 raise Exception(
"Can only add a density to a PMI State object or IMP.atom.Hierarchy. You passed a", type(inp))
351 def get_restraint(self):
354 def get_restraint_set(self):
357 def get_output(self):
359 score = self.weight * self.rs.unprotected_evaluate(
None)
360 ccc = self.gaussianEM_restraint.get_cross_correlation_coefficient()
362 output[
"_TotalScore"] = str(score)
363 output[
"GaussianEMRestraint_" +
364 self.label] = str(score)
365 output[
"GaussianEMRestraint_%s_CCC" % self.label] = ccc
366 output[
"GaussianEMRestraint_sigma_" +
367 self.label] = str(self.sigmaglobal.get_scale())
371 return self.weight * self.rs.unprotected_evaluate(
None)
374 '''Writes target GMM file to MRC'''
376 fileout=
"Gaussian_map_" + self.label +
".mrc"
384 """Fit particles to an EM map. This creates a simulate density map and updates them every eval.
385 @note Wraps an em::FitRestraint
396 @param ps The particles to restrain. Currently these must be atomic particles.
397 @param map_fn The EM density map to fit to
398 @param resolution Map resolution
399 @param origin In case you need to tell IMP the correct origin
400 @param voxel_size In case you need to tell IMP the angstroms per pixel
401 @param weight The data weight
402 @param label Extra PMI label
404 print(
'FitRestraint: setup')
406 print(
'\tresolution',resolution)
407 print(
'\tvoxel_size',voxel_size)
408 print(
'\torigin',origin)
409 print(
'\tweight',weight)
412 self.mdl = ps[0].get_model()
418 self.dmap.update_voxel_size(voxel_size)
419 if origin
is not None:
420 if isinstance(origin, IMP.algebra.Vector3D):
421 self.dmap.set_origin(origin)
422 elif isinstance(origin, list):
423 self.dmap.set_origin(*origin)
425 print(
'FitRestraint did not recognize format of origin')
429 self.rs.add_restraint(fr)
430 self.set_weight(weight)
432 def set_weight(self,weight):
434 self.rs.set_weight(weight)
436 def set_label(self, label):
439 def add_to_model(self):
442 def get_restraint_set(self):
445 def get_output(self):
447 score = self.weight * self.rs.unprotected_evaluate(
None)
448 output[
"_TotalScore"] = str(score)
449 output[
"EMRestraint_" + self.label] = str(score)
453 return self.weight * self.rs.unprotected_evaluate(
None)
458 class ElectronMicroscopy2D(object):
467 self.m = representation.prot.get_model()
474 resolution=resolution)
477 self.rs.add_restraint(em2d)
479 def set_label(self, label):
482 def add_to_model(self):
485 def get_restraint(self):
488 def set_weight(self,weight):
490 self.rs.set_weigth(self.weight)
492 def get_output(self):
494 score = self.weight*self.rs.unprotected_evaluate(
None)
495 output[
"_TotalScore"] = str(score)
496 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)
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.
Set up the representation of all proteins and nucleic acid macromolecules.
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.