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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
pmi/restraints/proteomics.py
1 """@namespace IMP.pmi.restraints.proteomics
2 Restraints for handling various kinds of proteomics data.
3 """
4 
5 from __future__ import print_function
6 import IMP
7 import IMP.core
8 import IMP.algebra
9 import IMP.atom
10 import IMP.container
11 import IMP.pmi.tools
12 
13 class ConnectivityRestraint(object):
14 
15  '''
16  generate a connectivity restraint between domains
17  setting up the restraint
18  example:
19  cr=restraints.ConnectivityRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")])
20  cr.add_to_model()
21  cr.set_label("CR1")
22  Multistate support =No
23  Selection type=selection tuple
24  Resolution=Yes
25  '''
26 
27  def __init__(
28  self,
29  representation,
30  selection_tuples,
31  kappa=10.0,
32  resolution=None,
33  label="None"):
34 
35  self.weight = 1.0
36  self.kappa = kappa
37  self.label = label
38  if self.label == "None":
39  self.label = str(selection_tuples)
40  self.m = representation.prot.get_model()
41  self.rs = IMP.RestraintSet(self.m, label)
42 
43  sels = []
44 
45  for s in selection_tuples:
46  particles = IMP.pmi.tools.select_by_tuple(representation, s,
47  resolution=resolution, name_is_ambiguous=True)
48  sel = IMP.atom.Selection(particles)
49  sels.append(sel)
50 
52  sels,
53  self.kappa,
54  self.label)
55  self.rs.add_restraint(cr)
56 
57  def set_label(self, label):
58  self.label = label
59  self.rs.set_name(label)
60  for r in self.rs.get_restraints():
61  r.set_name(label)
62 
63  def add_to_model(self):
65 
66  def get_restraint(self):
67  return self.rs
68 
69  def get_restraints(self):
70  rlist = []
71  for r in self.rs.get_restraints():
72  rlist.append(IMP.core.PairRestraint.get_from(r))
73  return rlist
74 
75  def set_weight(self, weight):
76  self.weight = weight
77  self.rs.set_weight(weight)
78 
79  def get_output(self):
80  self.m.update()
81  output = {}
82  score = self.weight * self.rs.unprotected_evaluate(None)
83  output["_TotalScore"] = str(score)
84  output["ConnectivityRestraint_" + self.label] = str(score)
85  return output
86 
87 #
88 class CompositeRestraint(object):
89 
90  '''
91  handleparticles is a selection tuple
92  compositeparticles is a list of selection tuples
93  '''
94  import IMP.pmi
95 
96  def __init__(
97  self,
98  representation,
99  handleparticles_tuples,
100  compositeparticles_tuple_list,
101  cut_off=5.0,
102  lam=1.0,
103  plateau=0.0,
104  resolution=None,
105  label="None"):
106 
107  # composite particles: all particles beside the handle
108  self.label = label
109  self.m = representation.prot.get_model()
110  self.rs = IMP.RestraintSet(self.m, 'cr')
111 
112  self.handleparticles = []
113  for s in handleparticles_tuples:
114  self.handleparticles += IMP.pmi.tools.select_by_tuple(representation, s,
115  resolution=resolution, name_is_ambiguous=True)
116  self.compositeparticles=[]
117  compositeparticle_list = []
118  for list in compositeparticles_tuple_list:
119  tmplist = []
120  for s in list:
121  tmplist += IMP.pmi.tools.select_by_tuple(
122  representation, s,
123  resolution=resolution, name_is_ambiguous=True)
124  compositeparticle_list.append(tmplist)
125  self.compositeparticles+=tmplist
126 
127 
129  self.m,
130  self.handleparticles,
131  cut_off,
132  lam,
133  True,
134  plateau)
135 
136  for ps in compositeparticle_list:
137  # composite particles is a list of list of particles
138  ln.add_composite_particle(ps)
139 
140  self.rs.add_restraint(ln)
141 
142  def set_label(self, label):
143  self.label = label
144 
145  def get_handle_particles(self):
146  return self.handleparticles
147 
148  def get_composite_particles(self):
149  return self.compositeparticles
150 
151  def get_restraint(self):
152  return self.rs
153 
154  def add_to_model(self):
155  IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
156 
157  def get_output(self):
158  self.m.update()
159  output = {}
160  score = self.rs.unprotected_evaluate(None)
161  output["_TotalScore"] = str(score)
162  output["CompositeRestraint_" + self.label] = str(score)
163  return output
164 
165 
166 #
168 
169  '''
170  this restraint allows ambiguous crosslinking between multiple copies
171  excluding between symmetric copies
172  It allows name ambiguity
173  '''
174 
175  def __init__(
176  self,
177  representation,
178  restraints_file,
179  cut_off=5.0,
180  lam=1.0,
181  plateau=0.01,
182  resolution=None,
183  label="None"):
184 
185  self.weight = 1.0
186  self.m = representation.prot.get_model()
187  self.rs = IMP.RestraintSet(self.m, 'data')
188  self.label = "None"
189  self.pairs = []
190 
191  self.outputlevel = "low"
192  self.cut_off = cut_off
193  self.lam = lam
194  self.plateau = plateau
195 
196  fl = IMP.pmi.tools.open_file_or_inline_text(restraints_file)
197 
198  for line in fl:
199 
200  tokens = line.split()
201  # skip character
202  if (tokens[0] == "#"):
203  continue
204  r1 = int(tokens[2])
205  c1 = tokens[0]
206  r2 = int(tokens[3])
207  c2 = tokens[1]
208 
209  ps1 = IMP.pmi.tools.select(
210  representation,
211  resolution=resolution,
212  name=c1,
213  name_is_ambiguous=True,
214  residue=r1)
215  hrc1 = [representation.hier_db.particle_to_name[p] for p in ps1]
216  ps1nosym = [
217  p for p in ps1 if IMP.pmi.Symmetric(
218  p).get_symmetric(
219  ) == 0]
220  hrc1nosym = [representation.hier_db.particle_to_name[p]
221  for p in ps1nosym]
222 
223  if len(ps1) == 0:
224  print("AmbiguousCompositeRestraint: WARNING> residue %d of chain %s is not there" % (r1, c1))
225  continue
226 
227  ps2 = IMP.pmi.tools.select(
228  representation,
229  resolution=resolution,
230  name=c2,
231  name_is_ambiguous=True,
232  residue=r2)
233  hrc2 = [representation.hier_db.particle_to_name[p] for p in ps2]
234  ps2nosym = [
235  p for p in ps2 if IMP.pmi.Symmetric(
236  p).get_symmetric(
237  ) == 0]
238  hrc2nosym = [representation.hier_db.particle_to_name[p]
239  for p in ps2nosym]
240 
241  if len(ps2) == 0:
242  print("AmbiguousCompositeRestraint: WARNING> residue %d of chain %s is not there" % (r2, c2))
243  continue
244 
246  self.m,
247  ps1nosym,
248  self.cut_off,
249  self.lam,
250  True,
251  self.plateau)
252  cr.add_composite_particle(ps2)
253 
254  self.rs.add_restraint(cr)
255  self.pairs.append(
256  (ps1nosym,
257  hrc1nosym,
258  c1,
259  r1,
260  ps2,
261  hrc2,
262  c2,
263  r2,
264  cr))
265 
267  self.m,
268  ps1,
269  self.cut_off,
270  self.lam,
271  True,
272  self.plateau)
273  cr.add_composite_particle(ps2nosym)
274 
275  self.rs.add_restraint(cr)
276  self.pairs.append(
277  (ps1,
278  hrc1,
279  c1,
280  r1,
281  ps2nosym,
282  hrc2nosym,
283  c2,
284  r2,
285  cr))
286 
287  def plot_restraint(
288  self,
289  maxdist=100,
290  npoints=100):
291  import IMP.pmi.output as output
292 
293  p1 = IMP.Particle(self.m)
294  p2 = IMP.Particle(self.m)
298  self.m,
299  [p1],
300  self.cut_off,
301  self.lam,
302  True,
303  self.plateau)
304  cr.add_composite_particle([p2])
305  dists = []
306  scores = []
307  for i in range(npoints):
308  d2.set_coordinates(
309  IMP.algebra.Vector3D(maxdist / npoints * float(i), 0, 0))
310  dists.append(IMP.core.get_distance(d1, d2))
311  scores.append(cr.unprotected_evaluate(None))
312  output.plot_xy_data(dists, scores)
313 
314  def set_label(self, label):
315  self.label = label
316  self.rs.set_name(label)
317  for r in self.rs.get_restraints():
318  r.set_name(label)
319 
320  def add_to_model(self):
321  IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
322 
323  def get_hierarchies(self):
324  return self.prot
325 
326  def get_restraint_sets(self):
327  return self.rs
328 
329  def get_restraint(self):
330  return self.rs
331 
332  def set_output_level(self, level="low"):
333  # this might be "low" or "high"
334  self.outputlevel = level
335 
336  def set_weight(self, weight):
337  self.weight = weight
338  self.rs.set_weight(weight)
339 
340  def get_output(self):
341  # content of the crosslink database pairs
342  # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
343  self.m.update()
344 
345  output = {}
346  score = self.weight * self.rs.unprotected_evaluate(None)
347  output["_TotalScore"] = str(score)
348  output["AmbiguousCompositeRestraint_Score_" + self.label] = str(score)
349  for n, p in enumerate(self.pairs):
350 
351  ps1 = p[0]
352  hrc1 = p[1]
353  c1 = p[2]
354  r1 = p[3]
355  ps2 = p[4]
356  hrc2 = p[5]
357  c2 = p[6]
358  r2 = p[7]
359  cr = p[8]
360  for n1, p1 in enumerate(ps1):
361  name1 = hrc1[n1]
362 
363  for n2, p2 in enumerate(ps2):
364  name2 = hrc2[n2]
365  d1 = IMP.core.XYZR(p1)
366  d2 = IMP.core.XYZR(p2)
367  label = str(r1) + ":" + name1 + "_" + str(r2) + ":" + name2
368  output["AmbiguousCompositeRestraint_Distance_" +
369  label] = str(IMP.core.get_distance(d1, d2))
370 
371  label = str(r1) + ":" + c1 + "_" + str(r2) + ":" + c2
372  output["AmbiguousCompositeRestraint_Score_" +
373  label] = str(self.weight * cr.unprotected_evaluate(None))
374 
375  return output
376 
377 
378 #
379 class SimplifiedPEMAP(object):
380 
381  def __init__(
382  self,
383  representation,
384  restraints_file,
385  expdistance,
386  strength,
387  resolution=None):
388 
389  self.m = representation.prot.get_model()
390  self.rs = IMP.RestraintSet(self.m, 'data')
391  self.label = "None"
392  self.pairs = []
393 
394  self.outputlevel = "low"
395  self.expdistance = expdistance
396  self.strength = strength
397 
398  fl = IMP.pmi.tools.open_file_or_inline_text(restraints_file)
399 
400  for line in fl:
401 
402  tokens = line.split()
403  # skip character
404  if (tokens[0] == "#"):
405  continue
406  r1 = int(tokens[2])
407  c1 = tokens[0]
408  r2 = int(tokens[3])
409  c2 = tokens[1]
410  pcc = float(tokens[4])
411 
412  ps1 = IMP.pmi.tools.select(
413  representation,
414  resolution=resolution,
415  name=c1,
416  name_is_ambiguous=False,
417  residue=r1)
418  if len(ps1) == 0:
419  print("SimplifiedPEMAP: WARNING> residue %d of chain %s is not there (w/ %d %s)" % (r1, c1, r2, c2))
420  continue
421  if len(ps1) > 1:
422  print("SimplifiedPEMAP: WARNING> residue %d of chain %s selected multiple particles" % (r1, c1))
423  continue
424 
425  ps2 = IMP.pmi.tools.select(
426  representation,
427  resolution=resolution,
428  name=c2,
429  name_is_ambiguous=False,
430  residue=r2)
431  if len(ps2) == 0:
432  print("SimplifiedPEMAP: WARNING> residue %d of chain %s is not there (w/ %d %s)" % (r1, c1, r2, c2))
433  continue
434  if len(ps2) > 1:
435  print("SimplifiedPEMAP: WARNING> residue %d of chain %s selected multiple particles" % (r2, c2))
436  continue
437 
438  p1 = ps1[0]
439  p2 = ps2[0]
440 
441  # This is harmonic potential for the pE-MAP data
442  upperdist = self.get_upper_bond(pcc)
443  limit = self.strength * (upperdist + 15) ** 2 + 10.0
445  upperdist,
446  self.strength,
447  upperdist +
448  15,
449  limit)
450 
451  # This is harmonic for the X-link
452  #hub= IMP.core.TruncatedHarmonicBound(17.0,self.strength,upperdist+15,limit)
453 
455  dr = IMP.core.PairRestraint(df, (p1, p2))
456  self.rs.add_restraint(dr)
457  self.pairs.append((p1, p2, dr, r1, c1, r2, c2))
458 
459  # Lower-bound restraint
460  lowerdist = self.get_lower_bond(pcc)
461  limit = self.strength * (lowerdist - 15) ** 2 + 10.0
463  lowerdist,
464  self.strength,
465  lowerdist +
466  15,
467  limit)
468 
469  # This is harmonic for the X-link
470  #hub2= IMP.core.TruncatedHarmonicBound(17.0,self.strength,upperdist+15,limit)
471 
473  dr2 = IMP.core.PairRestraint(df2, (p1, p2))
474  self.rs.add_restraint(dr2)
475  self.pairs.append((p1, p2, dr2, r1, c1, r2, c2))
476 
477  def get_upper_bond(self, pearsoncc):
478  # return (pearsoncc-1.)/-0.0075
479  return (pearsoncc - .5) / (-0.005415)
480 
481  def get_lower_bond(self, pearsoncc):
482  return (pearsoncc - 1.) / -0.0551
483 
484  def set_label(self, label):
485  self.label = label
486 
487  def add_to_model(self):
488  IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
489 
490  def get_hierarchies(self):
491  return self.prot
492 
493  def get_restraint_sets(self):
494  return self.rs
495 
496  def set_output_level(self, level="low"):
497  # this might be "low" or "high"
498  self.outputlevel = level
499 
500  def get_output(self):
501  # content of the crosslink database pairs
502  # self.pairs.append((p1,p2,dr,r1,c1,r2,c2))
503  self.m.update()
504 
505  output = {}
506  score = self.rs.unprotected_evaluate(None)
507  output["_TotalScore"] = str(score)
508  output["SimplifiedPEMAP_Score_" + self.label] = str(score)
509  for i in range(len(self.pairs)):
510 
511  p0 = self.pairs[i][0]
512  p1 = self.pairs[i][1]
513  crosslinker = 'standard'
514  ln = self.pairs[i][2]
515  resid1 = self.pairs[i][3]
516  chain1 = self.pairs[i][4]
517  resid2 = self.pairs[i][5]
518  chain2 = self.pairs[i][6]
519 
520  label = str(resid1) + ":" + chain1 + "_" + \
521  str(resid2) + ":" + chain2
522  output["SimplifiedPEMAP_Score_" + crosslinker + "_" +
523  label] = str(ln.unprotected_evaluate(None))
524 
525  d0 = IMP.core.XYZ(p0)
526  d1 = IMP.core.XYZ(p1)
527  output["SimplifiedPEMAP_Distance_" +
528  label] = str(IMP.core.get_distance(d0, d1))
529 
530  return output
531 
532 
534 
535  '''
536  generates and wraps a IMP.pmi.ConnectivityRestraint between domains
537  example:
538  cr=restraints.ConnectivityNetworkRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")])
539  cr.add_to_model()
540  cr.set_label("CR1")
541 
542  Multistate support =No
543  Selection type=selection tuple
544  Resolution=Yes
545  '''
546 
547  def __init__(
548  self,
549  representation,
550  selection_tuples,
551  kappa=10.0,
552  resolution=1.0,
553  label="None"):
554 
555  self.weight = 1.0
556  self.kappa = kappa
557  self.label = label
558  if self.label == "None":
559  self.label = str(selection_tuples)
560 
561  self.m = representation.m
562  self.rs = IMP.RestraintSet(self.m, label)
563 
565 
566  for s in selection_tuples:
567  particles = IMP.pmi.tools.select_by_tuple(representation, s,
568  resolution=resolution,
569  name_is_ambiguous=False)
570 
571  cr.add_particles([p.get_particle() for p in particles])
572 
573  self.rs.add_restraint(cr)
574 
575  def set_label(self, label):
576  self.label = label
577  self.rs.set_name(label)
578  for r in self.rs.get_restraints():
579  r.set_name(label)
580 
581  def add_to_model(self):
582  IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
583 
584  def get_restraint(self):
585  return self.rs
586 
587  def get_restraints(self):
588  rlist = []
589  for r in self.rs.get_restraints():
590  rlist.append(IMP.core.PairRestraint.get_from(r))
591  return rlist
592 
593  def set_weight(self, weight):
594  self.weight = weight
595  self.rs.set_weight(weight)
596 
597  def get_output(self):
598  self.m.update()
599  output = {}
600  score = self.weight * self.rs.unprotected_evaluate(None)
601  output["_TotalScore"] = str(score)
602  output["ConnectivityNetworkRestraint_" + self.label] = str(score)
603  return output
604 
605 
606 
608  '''
609  a python restraint that computes the score for a composite of proteins
610  Authors: G. Bouvier, R. Pellarin. Pasteur Institute.
611  '''
612 
613  import numpy
614  import math
615 
616  def __init__(self,m,slope=1.0,theta=0.0,plateau=0.0000000001,linear_slope=0.015):
617  '''
618  input a list of particles, the slope and theta of the sigmoid potential
619  theta is the cutoff distance for a protein-protein contact
620  '''
621  IMP.Restraint.__init__(self, m, "ConnectivityNetworkRestraint %1%")
622  self.slope=slope
623  self.theta=theta
624  self.linear_slope=linear_slope
625  self.plateau=plateau
626  self.particles_blocks=[]
627  self.particle_list=[]
628 
629  def get_number_of_particle_blocks(self):
630  return len(self.particles_blocks)
631 
632  def get_number_of_particles_for_block(self,block_index):
633  return len(self.particles_blocks[block_index])
634 
635  def add_particles(self,particles):
636  self.particles_blocks.append(particles)
637  self.particle_list+=particles
638 
639  def get_full_graph(self):
640  '''
641  get the full graph of distances between every particle pair
642  '''
643  import networkx
644  import scipy.spatial
645 
646  pdist_array = self.numpy.array(IMP.pmi.get_list_of_bipartite_minimum_sphere_distance(self.particles_blocks))
647  pdist_mat=scipy.spatial.distance.squareform(pdist_array)
648  pdist_mat[pdist_mat < 0] = 0
649  graph = networkx.Graph(pdist_mat)
650  return graph
651 
653  """
654  return the minimum spanning tree
655  """
656  import networkx
657  graph = self.get_full_graph()
658  graph = networkx.minimum_spanning_tree(graph)
659  return graph
660 
661  def sigmoid(self,x):
662  '''
663  a sigmoid function that scores the probability of a contact
664  between two proteins
665  '''
666  #return 1 - (x)**self.slope/ float(((x)**self.slope + self.theta**self.slope))
667  argvalue=(x-self.theta)/self.slope
668  return 1.0-(1.0-self.plateau)/(1.0+self.math.exp(-argvalue))
669 
670  def unprotected_evaluate(self,da):
671  graph = self.get_minimum_spanning_tree()
672  score = 0.0
673  for e in graph.edges():
674  dist=graph.get_edge_data(*e)['weight']
675  prob=self.sigmoid(dist)
676  score+=-self.numpy.log(prob)
677  score+=self.linear_slope*dist
678  return score
679 
680  def do_get_inputs(self):
681  return self.particle_list
682 
683 
685 
686  '''
687 
688  '''
689 
690 
691  def __init__(
692  self,
693  representation,
694  selection_tuples_above=None,
695  selection_tuples_inside=None,
696  selection_tuples_below=None,
697  z_init=0.0,
698  z_min=0.0,
699  z_max=0.0,
700  thickness=30,
701  resolution=1,
702  label="None"):
703 
704  self.weight = 1.0
705  self.label = label
706  self.m = representation.prot.get_model()
707  self.rs = IMP.RestraintSet(self.m, label)
708  self.representation=representation
709  self.thickness=thickness
710 
711  self.z_center=IMP.pmi.tools.SetupNuisance(self.m, z_init, z_min, z_max, isoptimized=True).get_particle()
712 
713  softness=3.0
714  plateau=1e-10
715  linear=0.02
716  mr = IMP.pmi.MembraneRestraint(self.m,self.z_center.get_particle_index(),self.thickness, softness, plateau, linear)
717 
718  if selection_tuples_above is not None:
719  particles_above = []
720  for s in selection_tuples_above:
721  particles = IMP.pmi.tools.select_by_tuple(self.representation, s,
722  resolution=resolution, name_is_ambiguous=True)
723  particles_above+=particles
724 
725  mr.add_particles_above([h.get_particle().get_index() for h in particles_above])
726 
727  if selection_tuples_below is not None:
728  particles_below = []
729  for s in selection_tuples_below:
730  particles = IMP.pmi.tools.select_by_tuple(self.representation, s,
731  resolution=resolution, name_is_ambiguous=True)
732  particles_below+=particles
733  mr.add_particles_below([h.get_particle().get_index() for h in particles_below])
734 
735  if selection_tuples_inside is not None:
736  particles_inside = []
737  for s in selection_tuples_inside:
738  particles = IMP.pmi.tools.select_by_tuple(self.representation, s,
739  resolution=resolution, name_is_ambiguous=True)
740  particles_inside+=particles
741  mr.add_particles_inside([h.get_particle().get_index() for h in particles_inside])
742 
743  self.rs.add_restraint(mr)
744 
745  def create_box(self, x_center, y_center):
746 
747  z=self.z_center.get_nuisance()
748  p=IMP.Particle(self.m)
750  h.set_name("Membrane_"+self.label)
751  self.representation.prot.add_child(h)
752 
753  particles_box=[]
754  p_origin=IMP.Particle(self.m)
755 
756  IMP.atom.Mass.setup_particle(p_origin,100)
757  d=IMP.core.XYZR.setup_particle(p_origin)
758  d.set_coordinates((x_center,y_center,0))
759  d.set_radius(1)
760  h_origin=IMP.atom.Hierarchy.setup_particle(p_origin)
761  h.add_child(h_origin)
762  particles_box.append(p_origin)
763 
764  p1=IMP.Particle(self.m)
767  d.set_coordinates((x_center,y_center,z+100))
768  d.set_radius(1)
770  h.add_child(h1)
771  particles_box.append(p1)
772 
773  p2=IMP.Particle(self.m)
776  d.set_coordinates((x_center,y_center,z-100))
777  d.set_radius(1)
779  h.add_child(h2)
780  particles_box.append(p2)
781 
784 
786 
787  p1.set_name("z_positive")
788  p2.set_name("z_negative")
789 
790  # to display the membrane in the rmf file
791  for offs in [self.thickness/2,-self.thickness/2]:
792  p1=IMP.Particle(self.m)
795  d.set_coordinates((-100+x_center,-100+y_center,z+offs))
796  d.set_radius(1)
798  h.add_child(h1)
799  particles_box.append(p1)
800 
801  p2=IMP.Particle(self.m)
804  d.set_coordinates((-100+x_center,100+y_center,z+offs))
805  d.set_radius(1)
807  h.add_child(h2)
808  particles_box.append(p2)
809 
810  p3=IMP.Particle(self.m)
813  d.set_coordinates((100+x_center,-100+y_center,z+offs))
814  d.set_radius(1)
816  h.add_child(h3)
817  particles_box.append(p3)
818 
819  p4=IMP.Particle(self.m)
822  d.set_coordinates((100+x_center,100+y_center,z+offs))
823  d.set_radius(1)
825  h.add_child(h4)
826  particles_box.append(p4)
827 
832 
837 
838  sm = self._MembraneSingletonModifier(p_origin,self.z_center)
840  for p in particles_box:
841  IMP.core.XYZ(p).set_coordinates_are_optimized(True)
842  lc.add(p.get_index())
843  print(p)
844  c = IMP.container.SingletonsConstraint(sm, None, lc)
845  self.m.add_score_state(c)
846  self.m.update()
847 
848  class _MembraneSingletonModifier(IMP.SingletonModifier):
849  """A class that updates the membrane particles
850  """
851 
852  def __init__(self, p_origin,z_nuisance):
853  IMP.SingletonModifier.__init__(self, "MembraneSingletonModifier%1%")
854  self.p_origin_index=p_origin.get_index()
855  self.z_nuisance=z_nuisance
856 
857  def apply_index(self, m, pi):
858  z_center=IMP.core.XYZ(m,self.p_origin_index).get_z()
859  new_z=self.z_nuisance.get_nuisance()
860  d = IMP.core.XYZ(m, pi)
861  current_z=d.get_z()
862  d.set_z(current_z+new_z-z_center)
863 
864  def do_get_inputs(self, m, pis):
865  return IMP.get_particles(m, pis)
866 
867  def do_get_outputs(self, m, pis):
868  return self.do_get_inputs(m, pis)
869 
870  def set_label(self, label):
871  self.label = label
872  self.rs.set_name(label)
873  for r in self.rs.get_restraints():
874  r.set_name(label)
875 
876  def add_to_model(self):
877  IMP.pmi.tools.add_restraint_to_model(self.m, self.rs)
878 
879  def get_restraint(self):
880  return self.rs
881 
882  def set_weight(self, weight):
883  self.weight = weight
884  self.rs.set_weight(weight)
885 
886  def get_particles_to_sample(self):
887  ps = {}
888 
889  ps["Nuisances_MembraneRestraint_Z_" + self.label] =([self.z_center],2.0)
890  return ps
891 
892  def get_output(self):
893  self.m.update()
894  output = {}
895  score = self.weight * self.rs.unprotected_evaluate(None)
896  output["_TotalScore"] = str(score)
897  output["MembraneRestraint_" + self.label] = str(score)
898  output["MembraneRestraint_Z_"+ self.label] = str(self.z_center.get_nuisance())
899  return output
900 
901 
902 
903 class FuzzyBoolean(object):
904  '''
905  Fully Ambiguous Restraint that can be built using boolean logic
906  R. Pellarin. Pasteur Institute.
907  '''
908 
909  def __init__(self,p1,operator=None,p2=None):
910  '''
911  input a list of particles, the slope and theta of the sigmoid potential
912  theta is the cutoff distance for a protein-protein contact
913  '''
914  if isinstance(p1, FuzzyBoolean) and isinstance(p2, FuzzyBoolean):
915  self.operations = [p1, operator, p2]
916  self.value = None
917  else:
918  self.operations = []
919  self.value = p1
920 
921  def __or__(self, FuzzyBoolean2):
922  return FuzzyBoolean(self, self.or_, FuzzyBoolean2)
923 
924  def __and__(self, FuzzyBoolean2):
925  return FuzzyBoolean(self, self.and_, FuzzyBoolean2)
926 
927  def and_(self,a,b):
928  return a*b
929 
930  def or_(self,a,b):
931  return 1.0-(1.0-a)*(1.0-b)
932 
933  def evaluate(self):
934 
935  if len(self.operations) == 0:
936  return self.value
937  FuzzyBoolean1, op, FuzzyBoolean2 = self.operations
938 
939  return op(FuzzyBoolean1.evaluate(),FuzzyBoolean2.evaluate())
940 
942  '''
943  Fully Ambiguous Restraint that can be built using boolean logic
944  R. Pellarin. Pasteur Institute.
945  '''
946  import math
947  plateau=0.00000000000001
948  theta=5.0
949  slope=2.0
950  innerslope=0.01
951  import sys
952 
953  def __init__(self,m,p1,p2,operator=None):
954  '''
955  input a list of particles, the slope and theta of the sigmoid potential
956  theta is the cutoff distance for a protein-protein contact
957  '''
958  IMP.Restraint.__init__(self, m, "FuzzyRestraint %1%")
959  self.m=m
960  self.min=self.sys.float_info.min
961  if isinstance(p1, FuzzyRestraint) and isinstance(p2, FuzzyRestraint):
962  self.operations = [p1, operator, p2]
963  self.particle_pair = None
964  elif isinstance(p1, FuzzyRestraint) and p2 is None:
965  self.operations = [p1, operator, None]
966  self.particle_pair = None
967  else:
968  self.operations = []
969  self.particle_pair = (p1,p2)
970 
971  def __or__(self, FuzzyRestraint2):
972  return FuzzyRestraint(self.m, self, FuzzyRestraint2, self.or_)
973 
974  def __and__(self, FuzzyRestraint2):
975  return FuzzyRestraint(self.m, self, FuzzyRestraint2, self.and_)
976 
977  def __invert__(self):
978  return FuzzyRestraint(self.m, self, None, self.invert_)
979 
980  def and_(self,a,b):
981  c=a+b
982  return c
983 
984  def or_(self,a,b):
985  c=self.math.exp(-a)+self.math.exp(-b)-self.math.exp(-a-b)
986  return -self.math.log(c)
987 
988  def invert_(self,a):
989  c=1.0-self.math.exp(-a)
990  return -self.math.log(c)
991 
992  def evaluate(self):
993  if len(self.operations) == 0:
994  return self.distance()
995  FuzzyRestraint1, op, FuzzyRestraint2 = self.operations
996 
997  if FuzzyRestraint2 is not None:
998  return op(FuzzyRestraint1.evaluate(),FuzzyRestraint2.evaluate())
999  else:
1000  return op(FuzzyRestraint1.evaluate())
1001 
1002  def distance(self):
1003  d1=IMP.core.XYZ(self.particle_pair[0])
1004  d2=IMP.core.XYZ(self.particle_pair[1])
1005  d=IMP.core.get_distance(d1,d2)
1006  argvalue=(d-self.theta)/self.slope
1007  return -self.math.log(1.0-(1.0-self.plateau)/(1.0+self.math.exp(-argvalue)))+self.innerslope*d
1008 
1009  def add_to_model(self):
1011 
1012  def unprotected_evaluate(self,da):
1013  return self.evaluate()
1014 
1015  def __str__(self):
1016  if len(self.operations) == 0:
1017  return str(self.particle_pair)
1018  FuzzyRestraint1, op, FuzzyRestraint2 = self.operations
1019  if FuzzyRestraint2 is not None:
1020  return str(FuzzyRestraint1)+str(op)+str(FuzzyRestraint2)
1021  else:
1022  return str(FuzzyRestraint1)+str(op)
1023 
1024  def do_get_inputs(self):
1025  if len(self.operations) == 0:
1026  return list(self.particle_pair)
1027  FuzzyRestraint1, op, FuzzyRestraint2 = self.operations
1028  if FuzzyRestraint2 is not None:
1029  return list(set(FuzzyRestraint1.do_get_inputs()+FuzzyRestraint2.do_get_inputs()))
1030  else:
1031  return list(set(FuzzyRestraint1.do_get_inputs()))
A base class for modifiers of ParticlesTemp.
A function that is harmonic over an interval.
Apply a SingletonFunction to a SingletonContainer to maintain an invariant.
this restraint allows ambiguous crosslinking between multiple copies excluding between symmetric copi...
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
A decorator for a particle which has bonds.
def get_full_graph
get the full graph of distances between every particle pair
Miscellaneous utilities.
Definition: tools.py:1
Add symmetric attribute to a particle.
Definition: Symmetric.h:23
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
A score on the distance between the surfaces of two spheres.
double get_distance(XYZR a, XYZR b)
Compute the sphere distance between a and b.
Definition: XYZR.h:87
generates and wraps a IMP.pmi.ConnectivityRestraint between domains example: cr=restraints.ConnectivityNetworkRestraint(simo,["CCC",(1,100,"TTT"),(100,150,"AAA")]) cr.add_to_model() cr.set_label("CR1")
Bond create_bond(Bonded a, Bonded b, Bond o)
Connect the two wrapped particles by a custom bond.
Object used to hold a set of restraints.
Definition: RestraintSet.h:36
a python restraint that computes the score for a composite of proteins Authors: G.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
def __init__
input a list of particles, the slope and theta of the sigmoid potential theta is the cutoff distance ...
Store a list of ParticleIndexes.
static Mass setup_particle(Model *m, ParticleIndex pi, Float mass)
Definition: Mass.h:44
def add_restraint_to_model
Add a PMI restraint to the model.
Definition: tools.py:37
static Bonded setup_particle(Model *m, ParticleIndex pi)
A restraint for ambiguous cross-linking MS data and multiple state approach.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
handleparticles is a selection tuple compositeparticles is a list of selection tuples ...
Classes for writing output files and processing them.
Definition: output.py:1
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...
Fully Ambiguous Restraint that can be built using boolean logic R.
def __init__
input a list of particles, the slope and theta of the sigmoid potential theta is the cutoff distance ...
VectorD< 3 > Vector3D
Definition: VectorD.h:395
Class to handle individual model particles.
Definition: Particle.h:37
Floats get_list_of_bipartite_minimum_sphere_distance(const ParticlesTemps &pss)
Definition: utilities.h:61
def sigmoid
a sigmoid function that scores the probability of a contact between two proteins
Restraint * create_connectivity_restraint(const Selections &s, double x0, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
Applies a PairScore to a Pair.
Definition: PairRestraint.h:29
def select
this function uses representation=SimplifiedModel it returns the corresponding selected particles rep...
Definition: tools.py:702
Python classes to represent, score, sample and analyze models.
Functionality for loading, creating, manipulating and scoring atomic structures.
Select hierarchy particles identified by the biological name.
Definition: Selection.h:66
Fully Ambiguous Restraint that can be built using boolean logic R.
def __init__
input a list of particles, the slope and theta of the sigmoid potential theta is the cutoff distance ...
virtual ModelObjectsTemp do_get_inputs() const =0
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52
A decorator for a particle with x,y,z coordinates and a radius.
Definition: XYZR.h:27