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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
system_tools.py
1 from __future__ import print_function, division
2 import IMP
3 import IMP.atom
5 import IMP.pmi
6 import IMP.pmi.tools
7 from collections import defaultdict
8 from math import pi
9 import os
10 import warnings
11 
12 def resnums2str(res):
13  """Take iterable of TempResidues and return compatified string"""
14  if len(res)==0:
15  return ''
16  idxs = [r.get_index() for r in res]
17  idxs.sort()
18  all_ranges=[]
19  cur_range=[idxs[0],idxs[0]]
20  for idx in idxs[1:]:
21  if idx!=cur_range[1]+1:
22  all_ranges.append(cur_range)
23  cur_range=[idx,idx]
24  cur_range[1]=idx
25  all_ranges.append(cur_range)
26  ret = ''
27  for nr,r in enumerate(all_ranges):
28  ret+='%i-%i'%(r[0],r[1])
29  if nr<len(all_ranges)-1:
30  ret+=', '
31  return ret
32 
33 
34 def _select_ca_or_p(hiers, **kwargs):
35  """Select all CA (amino acids) or P (nucleic acids) as appropriate"""
36  sel_p = IMP.atom.Selection(hiers, atom_type=IMP.atom.AT_P, **kwargs)
37  ps = sel_p.get_selected_particles()
38  if ps:
39  # detected nucleotides. Selecting phosphorous instead of CA
40  return ps
41  else:
42  sel = IMP.atom.Selection(hiers, atom_type=IMP.atom.AT_CA, **kwargs)
43  return sel.get_selected_particles()
44 
45 
46 def get_structure(model,pdb_fn,chain_id,res_range=None,offset=0,model_num=None,ca_only=False):
47  """read a structure from a PDB file and return a list of residues
48  @param model The IMP model
49  @param pdb_fn The file to read (in traditional PDB or mmCIF format)
50  @param chain_id Chain ID to read
51  @param res_range Add only a specific set of residues.
52  res_range[0] is the starting and res_range[1] is the ending residue index
53  The ending residue can be "END", that will take everything to the end of the sequence.
54  None gets you all.
55  @param offset Apply an offset to the residue indexes of the PDB file
56  @param model_num Read multi-model PDB and return that model (0-based index)
57  @param ca_only Read only CA atoms (by default, all non-waters are read)
58  """
59  # Read file in mmCIF format if requested
60  if pdb_fn.endswith('.cif'):
61  read_file = IMP.atom.read_mmcif
62  read_multi_file = IMP.atom.read_multimodel_mmcif
63  else:
64  read_file = IMP.atom.read_pdb
65  read_multi_file = IMP.atom.read_multimodel_pdb
66  if ca_only:
68  else:
70 
71  reader = read_file if model_num is None else read_multi_file
72  mh = reader(pdb_fn, model,
74  if model_num is not None:
75  mh = mh[model_num]
76 
77  if res_range==[] or res_range is None:
78  ps = _select_ca_or_p(mh, chain=chain_id)
79  else:
80  start = res_range[0]
81  end = res_range[1]
82  if end=="END":
83  end = IMP.atom.Residue(mh.get_children()[0].get_children()[-1]).get_index()
84  ps = _select_ca_or_p(mh, chain=chain_id,
85  residue_indexes=range(start,end+1))
86  ret = []
87 
88  for p in ps:
89  res = IMP.atom.Residue(IMP.atom.Atom(p).get_parent())
90  res.set_index(res.get_index() + offset)
91  ret.append(res)
92  if len(ret) == 0:
93  warnings.warn(
94  "no residues selected from %s in range %s" % (pdb_fn, res_range),
96  return ret
97 
98 def build_bead(model,residues,input_coord=None):
99  """Generates a single bead"""
100 
101  ds_frag = (residues[0].get_index(), residues[-1].get_index())
102  prt = IMP.Particle(model)
104  ptem = IMP.core.XYZR(prt)
105  mass = IMP.atom.get_mass_from_number_of_residues(len(residues))
106 
107  if ds_frag[0] == ds_frag[-1]:
108  rt = residues[0].get_residue_type()
109  h = IMP.atom.Residue.setup_particle(prt, rt, ds_frag[0])
110  h.set_name('%i_bead' % (ds_frag[0]))
111  prt.set_name('%i_bead' % (ds_frag[0]))
112  try:
114  except IMP.ValueException:
116  IMP.atom.ResidueType("ALA"))
118  ptem.set_radius(radius)
119  else:
121  h.set_name('%i-%i_bead' % (ds_frag[0], ds_frag[-1]))
122  prt.set_name('%i-%i_bead' % (ds_frag[0], ds_frag[-1]))
123  h.set_residue_indexes(range(ds_frag[0], ds_frag[-1] + 1))
124  volume = IMP.atom.get_volume_from_mass(mass)
125  radius = 0.8 * (3.0 / 4.0 / pi * volume) ** (1.0 / 3.0)
126  ptem.set_radius(radius)
127 
129  try:
130  if tuple(input_coord) is not None:
131  ptem.set_coordinates(input_coord)
132  except TypeError:
133  pass
134  return h
135 
136 def build_necklace(model,residues, resolution, input_coord=None):
137  """Generates a string of beads with given length"""
138  out_hiers = []
139  for chunk in list(IMP.pmi.tools.list_chunks_iterator(residues, resolution)):
140  out_hiers.append(build_bead(model,chunk, input_coord=input_coord))
141  return out_hiers
142 
143 def build_ca_centers(model,residues):
144  """Create a bead on the CA position with coarsened size and mass"""
145  out_hiers = []
146  for tempres in residues:
147  residue = tempres.get_hierarchy()
148  rp1 = IMP.Particle(model)
149  rp1.set_name("Residue_%i"%residue.get_index())
150  rt = residue.get_residue_type()
151  this_res = IMP.atom.Residue.setup_particle(rp1,residue)
152  try:
154  except IMP.ValueException:
156  IMP.atom.ResidueType("ALA"))
157  try:
158  mass = IMP.atom.get_mass(rt)
159  except:
161  calpha = IMP.atom.Selection(residue,atom_type=IMP.atom.AT_CA). \
162  get_selected_particles()
163  cp=IMP.atom.Selection(residue,atom_type=IMP.atom.AT_P). \
164  get_selected_particles()
165 
166  if len(calpha)==1:
167  central_atom=calpha[0]
168  elif len(cp)==1:
169  central_atom=cp[0]
170  else:
171  raise("build_ca_centers: weird selection (no Ca, no nucleotide P or ambiguous selection found)")
173  shape = IMP.algebra.Sphere3D(IMP.core.XYZ(central_atom).get_coordinates(),radius)
176  out_hiers.append(this_res)
177  return out_hiers
178 
179 def setup_bead_as_gaussian(mh):
180  """Setup bead as spherical gaussian, using radius as variance"""
181  p = mh.get_particle()
182  center = IMP.core.XYZ(p).get_coordinates()
183  rad = IMP.core.XYZR(p).get_radius()
184  mass = IMP.atom.Mass(p).get_mass()
188 
189 
190 def show_representation(node):
191  print(node)
193  repr = IMP.atom.Representation(node)
194  resolutions = repr.get_resolutions()
195  for r in resolutions:
196  print('---- resolution %i ----' %r)
197  IMP.atom.show_molecular_hierarchy(repr.get_representation(r))
198  return True
199  else:
200  return False
201 
202 def _get_color_for_representation(rep):
203  """Return an IMP.display.Color object (or None) for the given
204  Representation."""
205  if rep.color is not None:
206  if isinstance(rep.color, float):
207  return IMP.display.get_rgb_color(rep.color)
208  elif isinstance(rep.color, str):
209  return IMP.display.Color(*IMP.pmi.tools.color2rgb(rep.color))
210  elif hasattr(rep.color,'__iter__') and len(rep.color)==3:
211  return IMP.display.Color(*rep.color)
212  elif isinstance(rep.color, IMP.display.Color):
213  return rep.color
214  else:
215  raise TypeError("Color must be Chimera color name, a hex "
216  "string, a float or (r,g,b) tuple")
217 
218 
219 def _add_fragment_provenance(fragment, first_residue, rephandler):
220  """Track the original source of a fragment's structure.
221  If the residues in the given fragment were extracted from a PDB
222  file, add suitable provenance information to the Model (the name
223  of that file, chain ID, and residue index offset)."""
224  pdb_element = rephandler.pdb_for_residue.get(first_residue.get_index())
225  if pdb_element:
226  m = fragment.get_model()
227  p = IMP.Particle(m, "input structure")
229  p, pdb_element.filename, pdb_element.chain_id, pdb_element.offset)
230  IMP.core.add_provenance(m, fragment, sp)
231 
232 
233 def build_representation(parent, rep, coord_finder, rephandler):
234  """Create requested representation.
235  For beads, identifies continuous segments and sets up as Representation.
236  If any volume-based representations (e.g.,densities) are requested,
237  will instead create a single Representation node.
238  All reps are added as children of the passed parent.
239  @param parent The Molecule to which we'll add add representations
240  @param rep What to build. An instance of pmi::topology::_Representation
241  @param coord_finder A _FindCloseStructure object to help localize beads
242  """
243  built_reps = []
244  atomic_res = 0
245  ca_res = 1
246  model = parent.hier.get_model()
247  color = _get_color_for_representation(rep)
248 
249  # first get the primary representation (currently, the smallest bead size)
250  # eventually we won't require beads to be present at all
251  primary_resolution = min(rep.bead_resolutions)
252 
253  # if collective densities, will return single node with everything
254  # below we sample or read the GMMs and add them as representation
255  single_node = False # flag indicating grouping nonlinear segments with one GMM
256  if rep.density_residues_per_component:
257  single_node = True
258  num_components = len(rep.residues)//rep.density_residues_per_component+1
259  rep_dict = defaultdict(list)
260  segp = IMP.Particle(model)
261  root_representation = IMP.atom.Representation.setup_particle(segp,
262  primary_resolution)
263  built_reps.append(root_representation)
264  res_nums = [r.get_index() for r in rep.residues]
265  IMP.atom.Fragment.setup_particle(segp,res_nums)
266  density_frag = IMP.atom.Fragment.setup_particle(IMP.Particle(model),res_nums)
267  density_frag.get_particle().set_name("Densities %i"%rep.density_residues_per_component)
268  density_ps = []
269 
270  if os.path.exists(rep.density_prefix+'.txt') and not rep.density_force_compute:
271  IMP.isd.gmm_tools.decorate_gmm_from_text(rep.density_prefix+'.txt',
272  density_ps,
273  model)
274  if len(density_ps)!=num_components or not os.path.exists(rep.density_prefix+'.txt') or rep.density_force_compute:
275  fit_coords = []
276  total_mass = 0.0
277  for r in rep.residues:
278  for p in IMP.core.get_leaves(r.hier):
279  fit_coords.append(IMP.core.XYZ(p).get_coordinates())
280  total_mass += IMP.atom.Mass(p).get_mass()
281 
282  # fit GMM
283  density_ps = []
285  num_components,
286  model,
287  density_ps,
288  min_covar=4.0,
289  mass_multiplier=total_mass)
290 
291  IMP.isd.gmm_tools.write_gmm_to_text(density_ps,rep.density_prefix+'.txt')
292  if rep.density_voxel_size>0.0:
293  IMP.isd.gmm_tools.write_gmm_to_map(density_ps,rep.density_prefix+'.mrc',
294  rep.density_voxel_size,fast=True)
295 
296  for n, d in enumerate(density_ps):
297  d.set_name('Density #%d' % n)
298  density_frag.add_child(d)
299  root_representation.add_representation(density_frag,
300  IMP.atom.DENSITIES,
301  rep.density_residues_per_component)
302 
303  # get continuous segments from residues
304  segments = []
305  rsort = sorted(list(rep.residues),key=lambda r:r.get_index())
306  prev_idx = rsort[0].get_index()-1
307  prev_structure = rsort[0].get_has_structure()
308  cur_seg = []
309  force_break = False
310  for nr,r in enumerate(rsort):
311  if r.get_index()!=prev_idx+1 or r.get_has_structure()!=prev_structure or force_break:
312  segments.append(cur_seg)
313  cur_seg = []
314  force_break = False
315  cur_seg.append(r)
316  prev_idx = r.get_index()
317  prev_structure = r.get_has_structure()
318  if r.get_index()-1 in rep.bead_extra_breaks:
319  force_break = True
320  if cur_seg!=[]:
321  segments.append(cur_seg)
322 
323  # for each segment, merge into beads
324  name_all = 'frags:'
325  name_count = 0
326  for frag_res in segments:
327  res_nums = [r.get_index() for r in frag_res]
328  rrange = "%i-%i"%(res_nums[0],res_nums[-1])
329  name = "Frag_"+rrange
330  if name_count<3:
331  name_all +=rrange+','
332  elif name_count==3:
333  name_all +='...'
334  name_count+=1
335  segp = IMP.Particle(model,name)
336  this_segment = IMP.atom.Fragment.setup_particle(segp,res_nums)
337  if not single_node:
338  this_representation = IMP.atom.Representation.setup_particle(segp,primary_resolution)
339  built_reps.append(this_representation)
340  for resolution in rep.bead_resolutions:
341  fp = IMP.Particle(model)
342  this_resolution = IMP.atom.Fragment.setup_particle(fp,res_nums)
343  this_resolution.set_name("%s: Res %i"%(name,resolution))
344  if frag_res[0].get_has_structure():
345  _add_fragment_provenance(this_resolution, frag_res[0],
346  rephandler)
347  # if structured, merge particles as needed
348  if resolution==atomic_res:
349  for residue in frag_res:
350  this_resolution.add_child(residue.get_hierarchy())
351  elif resolution==ca_res and rep.bead_ca_centers:
352  beads = build_ca_centers(model,frag_res)
353  for bead in beads:
354  this_resolution.add_child(bead)
355  else:
356  tempc = IMP.atom.Chain.setup_particle(IMP.Particle(model),"X")
357  for residue in frag_res:
358  tempc.add_child(IMP.atom.create_clone(residue.hier))
359  beads = IMP.atom.create_simplified_along_backbone(tempc,resolution)
360  for bead in beads.get_children():
361  this_resolution.add_child(bead)
362  del tempc
363  del beads
364  else:
365  # if unstructured, create necklace
366  input_coord = coord_finder.find_nearest_coord(min(r.get_index() for r in frag_res))
367  if input_coord is None:
368  input_coord = rep.bead_default_coord
369  beads = build_necklace(model,
370  frag_res,
371  resolution,
372  input_coord)
373  for bead in beads:
374  this_resolution.add_child(bead)
375 
376  # if requested, color all resolutions the same
377  if color:
378  for lv in IMP.core.get_leaves(this_resolution):
380 
381  # finally decide where to put this resolution
382  # if volumetric, collect resolutions from different segments together
383  if single_node:
384  rep_dict[resolution]+=this_resolution.get_children()
385  else:
386  if resolution==primary_resolution:
387  this_representation.add_child(this_resolution)
388  else:
389  this_representation.add_representation(this_resolution,
390  IMP.atom.BALLS,
391  resolution)
392  # if individual beads to be setup as Gaussians:
393  if rep.setup_particles_as_densities:
394  for p in IMP.core.get_leaves(this_resolution):
395  setup_bead_as_gaussian(p)
396  this_resolution.set_name(this_resolution.get_name()+' Densities %i'%resolution)
397  this_representation.add_representation(this_resolution,
398  IMP.atom.DENSITIES,
399  resolution)
400 
401  if single_node:
402  root_representation.set_name(name_all.strip(',')+": Base")
403  d = root_representation.get_representations(IMP.atom.DENSITIES)
404  d[0].set_name('%s: '%name_all + d[0].get_name())
405  for resolution in rep.bead_resolutions:
406  this_resolution = IMP.atom.Fragment.setup_particle(
407  IMP.Particle(model),
408  [r.get_index() for r in rep.residues])
409  this_resolution.set_name("%s: Res %i"%(name_all,resolution))
410  for hier in rep_dict[resolution]:
411  this_resolution.add_child(hier)
412  if resolution==primary_resolution:
413  root_representation.add_child(this_resolution)
414  else:
415  root_representation.add_representation(this_resolution,
416  IMP.atom.BALLS,
417  resolution)
418  return built_reps
def list_chunks_iterator
Yield successive length-sized chunks from a list.
Definition: tools.py:645
Tools for handling Gaussian Mixture Models.
Definition: gmm_tools.py:1
Add mass to a particle.
Definition: Mass.h:23
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Simple 3D transformation class.
Represent an RGB color.
Definition: Color.h:24
static Gaussian setup_particle(Model *m, ParticleIndex pi)
Definition: core/Gaussian.h:48
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
static Fragment setup_particle(Model *m, ParticleIndex pi)
Definition: Fragment.h:63
double get_mass(const Selection &s)
Get the total mass of a hierarchy, in Daltons.
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
Select atoms which are selected by both selectors.
Definition: pdb.h:348
double get_mass(ResidueType c)
Get the mass from the residue type.
static StructureProvenance setup_particle(Model *m, ParticleIndex pi, std::string filename, std::string chain_id, int residue_offset)
Definition: provenance.h:157
Color get_rgb_color(double f)
Return the color for f from the RGB color map.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Miscellaneous utilities.
Definition: tools.py:1
double get_ball_radius_from_volume_3d(double volume)
Return the radius of a sphere with a given volume.
Definition: Sphere3D.h:35
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
Definition: Residue.h:158
static Representation setup_particle(Model *m, ParticleIndex pi)
GenericHierarchies get_leaves(Hierarchy mhd)
Get all the leaves of the bit of hierarchy.
A reference frame in 3D.
def color2rgb
Given a Chimera color name or hex color value, return RGB.
Definition: tools.py:1570
Warning related to handling of structures.
A Gaussian distribution in 3D.
Definition: Gaussian3D.h:24
def fit_gmm_to_points
fit a GMM to some points.
Definition: gmm_tools.py:233
A decorator for a representation.
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
A decorator for a particle representing an atom.
Definition: atom/Atom.h:234
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:48
The type for a residue.
PDBSelector * get_default_pdb_selector()
Definition: pdb.h:473
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
static Colored setup_particle(Model *m, ParticleIndex pi, Color color)
Definition: Colored.h:62
def write_gmm_to_map
write density map from GMM.
Definition: gmm_tools.py:115
A decorator for a residue.
Definition: Residue.h:135
static bool get_is_setup(const IMP::ParticleAdaptor &p)
Hierarchy create_simplified_along_backbone(Chain input, const IntRanges &residue_segments, bool keep_detailed=false)
Rotation3D get_identity_rotation_3d()
Return a rotation that does not do anything.
Definition: Rotation3D.h:356
Class to handle individual particles of a Model object.
Definition: Particle.h:41
Select all CA ATOM records.
Definition: pdb.h:77
Python classes to represent, score, sample and analyze models.
def write_gmm_to_text
write a list of gaussians to text.
Definition: gmm_tools.py:64
Functionality for loading, creating, manipulating and scoring atomic structures.
void add_provenance(Model *m, ParticleIndex pi, Provenance p)
Add provenance to part of the model.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Definition: Chain.h:81
An exception for an invalid value being passed to IMP.
Definition: exception.h:137
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66
Select all ATOM and HETATM records with the given chain ids.
Definition: pdb.h:189
def decorate_gmm_from_text
read the output from write_gmm_to_text, decorate as Gaussian and Mass
Definition: gmm_tools.py:23
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27