forked from amirbarati/conformation
-
Notifications
You must be signed in to change notification settings - Fork 0
/
analysis.py
1145 lines (951 loc) · 39.4 KB
/
analysis.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
from io_functions import *
import numpy as np
import copy
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
from matplotlib.colors import LogNorm
from matplotlib.backends.backend_pdf import PdfPages
from functools import partial
import multiprocessing as mp
import mdtraj as md
import csv
import operator
from msmbuilder.utils import verbosedump, verboseload
from sklearn.metrics import mutual_info_score
from scipy.stats import pearsonr
from scipy import stats
import pandas as pd
def function_mapper(fxn, worker_pool, parallel, var_list):
if worker_pool is not None:
results = worker_pool.map_sync(fxn, var_list)
elif parallel:
pool = mp.Pool(mp.cpu_count())
results = pool.map(fxn, var_list)
pool.terminate
else:
results = [fxn(var) for var in var_list]
return(results)
def calc_mean_and_stdev(rmsd_map):
stats_map = {}
for key in list(rmsd_map.keys()):
rmsds = np.array(rmsd_map[key])
mean = np.mean(rmsds, axis = 0)
stdev = np.std(rmsds, axis = 0)
stats_map[key] = (mean, stdev)
return stats_map
def calc_mean(rmsd_map):
stats_map = {}
for key in list(rmsd_map.keys()):
rmsds = np.array(rmsd_map[key])
mean = np.mean(rmsds, axis = 0)
stats_map[key] = [mean]
return stats_map
def find_cos(index, k_mean, features):
traj = index[0]
frame = index[1]
conformation = features[traj][frame]
a = conformation
b = k_mean
return (traj, frame, np.dot(a,b) / (np.linalg.norm(a) * np.linalg.norm(b)))
def rmsd_connector(traj, inactive, residues=[], residues_map = None):
if residues_map is not None:
residues = map_residues(residues_map, residues)
nonsymmetric = ["CG2", "CG1", "CD1", "CD2", "CE1", "CE2"]
connector_atoms = []
for residue in residues:
connector_atoms += [(a.index, str(a)) for a in traj.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and "hydrogen" not in a.element and not any(substring in str(a) for substring in nonsymmetric)]
connector_atoms = sorted(connector_atoms, key=operator.itemgetter(1), reverse = True)
connector_atoms = [a[0] for a in connector_atoms]
traj_stripped = traj.atom_slice(connector_atoms)
connector_atoms_target = []
for residue in residues:
connector_atoms_target += [(a.index, str(a)) for a in inactive.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and "hydrogen" not in a.element and not any(substring in str(a) for substring in nonsymmetric)]
connector_atoms_target = sorted(connector_atoms_target, key=operator.itemgetter(1), reverse = True)
connector_atoms_target = [a[0] for a in connector_atoms_target]
inactive_stripped = inactive.atom_slice(connector_atoms_target)
try:
traj_stripped_aligned = traj_stripped.superpose(inactive_stripped)
rmsds = md.rmsd(traj_stripped, inactive_stripped) * 10.0
except:
rmsds = np.empty(traj_stripped.n_frames)
return rmsds
def rmsd_npxxy(traj, inactive, residues=[], residues_map = None):
if residues_map is not None:
residues = map_residues(residues_map, residues)
npxxy_atoms = []
for residue in residues:
npxxy_atoms += [(a.index,str(a)) for a in traj.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and a.is_backbone and a.residue.is_protein]
npxxy_atoms = sorted(npxxy_atoms, key=operator.itemgetter(1), reverse = True)
npxxy_atoms = [a[0] for a in npxxy_atoms]
#print npxxy_atoms
traj_stripped = traj.atom_slice(npxxy_atoms)
npxxy_atoms_target = []
for residue in residues:
npxxy_atoms_target += [(a.index,str(a)) for a in inactive.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and a.is_backbone and a.residue.is_protein]
npxxy_atoms_target = sorted(npxxy_atoms_target, key=operator.itemgetter(1), reverse = True)
npxxy_atoms_target = [a[0] for a in npxxy_atoms_target]
#print npxxy_atoms_target
inactive_stripped = inactive.atom_slice(npxxy_atoms_target)
try:
traj_stripped_aligned = traj_stripped.superpose(inactive_stripped)
rmsds = md.rmsd(traj_stripped, inactive_stripped) * 10.0
except:
rmsds = np.empty(traj_stripped.n_frames)
return rmsds
def compute_distance(traj, inactive, residues=[], residues_map = None):
if residues_map is not None:
residues = map_residues(residues_map, residues)
motif_atoms = []
for residue in residues:
motif_atoms += [(a.index,str(a)) for a in traj.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and "H" not in a.name]
motif_atoms = sorted(motif_atoms, key=operator.itemgetter(1), reverse = True)
motif_atoms = [a[0] for a in motif_atoms]
#print motif_atoms
traj_stripped = traj.atom_slice(motif_atoms)
motif_atoms_target = []
for residue in residues:
motif_atoms_target += [(a.index,str(a)) for a in inactive.topology.atoms if residue.is_mdtraj_res_equivalent(a.residue) and "H" not in a.name]
motif_atoms_target = sorted(motif_atoms_target, key=operator.itemgetter(1), reverse = True)
motif_atoms_target = [a[0] for a in motif_atoms_target]
#print motif_atoms_target
inactive_stripped = inactive.atom_slice(motif_atoms_target)
traj_stripped_aligned = traj_stripped.superpose(inactive_stripped)
rmsds = md.rmsd(traj_stripped, inactive_stripped) * 10.0
return rmsds
def helix6_helix3_dist(traj, residues=[], residues_map = None):
if residues_map is not None:
residues = map_residues(residues_map, residues)
atom_3 = [a.index for a in traj.topology.atoms if residues[0].is_mdtraj_res_equivalent(a.residue) and a.name == "CA"][0]
atom_6 = [a.index for a in traj.topology.atoms if residues[1].is_mdtraj_res_equivalent(a.residue) and a.name == "CA"][0]
indices = np.empty([1,2])
indices[0] = [atom_3, atom_6]
dist = md.compute_distances(traj, indices) * 10.0
return np.concatenate(dist)
def compute_closest_heavy(traj, residues=[], residues_map = None):
if residues_map is not None:
residues = map_residues(residues_map, residues)
atoms_i = [a.index for a in traj.topology.atoms if residues[0].is_mdtraj_res_equivalent(a.residue) and "H" not in a.name]
atoms_j = [a.index for a in traj.topology.atoms if residues[1].is_mdtraj_res_equivalent(a.residue) and "H" not in a.name]
pairs = []
for i in range(0, len(atoms_i)):
for j in range(i, len(atoms_j)):
pairs.append([atoms_i[i], atoms_j[j]])
pairs = np.array(pairs)
dist = md.compute_distances(traj, pairs) * 10.0
dist = np.amin(dist, axis=1)
return dist
def plot_pnas_vs_docking(docking_dir, pnas_dir, save_dir, selected = False):
dock_scores = convert_csv_to_map_nocombine(docking_dir)
pnas_vectors = convert_csv_to_map_nocombine(pnas_dir)
x = []
y = []
c = []
for key in list(dock_scores.keys()):
if selected is not False:
if key not in selected: continue
#print "PNAS"
#print key
#print pnas_vectors[key]
if key in list(pnas_vectors.keys()):
#print pnas_vectors[key]
x.append(pnas_vectors[key][0])
y.append(pnas_vectors[key][1])
c.append(abs(dock_scores[key][0]))
#plt.annotate("%s" %key, xy=(pnas_vectors[key][0], pnas_vectors[key][1]), xytext=(pnas_vectors[key][0], pnas_vectors[key][1]),size=6)
#print dock_scores.keys()
plt.scatter(x, y, c=c, s=50, cmap = mpl.cm.RdYlBu_r)
pp = PdfPages(save_dir)
pp.savefig()
pp.close()
def pnas_distance(traj_file, inactive_file, active_file):
traj = md.load(traj_file)
inactive = md.load(inactive_file)
active = md.load(active_file)
scale = 7.14
inactive_tuple = np.array([helix6_helix3_dist(inactive) / scale, rmsd_npxxy(inactive, inactive)])
active_tuple = np.array([helix6_helix3_dist(active) / scale, rmsd_npxxy(active, inactive)])
traj_coords = [helix6_helix3_dist(traj, traj_file = traj_file) / scale, rmsd_npxxy(traj, inactive, traj_file = traj_file)]
traj_tuple = np.array(traj_coords)
active_dist = np.linalg.norm(traj_tuple - active_tuple)
inactive_dist = np.linalg.norm(traj_tuple - inactive_tuple)
distances = [inactive_dist, active_dist]
print(distances[1])
return [traj_coords, distances]
def pnas_distances(traj_dir, inactive_file, active_file):
scale = 7.14
save_file_i = "%s/inactive_pnas_distances.csv" %traj_dir
save_file_a = "%s/active_pnas_distances.csv" %traj_dir
coord_file = "%s/pnas_coords.csv" %traj_dir
distances_i = open(save_file_i, "wb")
distances_i.write("conformation, inactive_pnas_distance, a \n")
distances_a = open(save_file_a, "wb")
distances_a.write("conformation, active_pnas_distance, a \n")
coordinates = open(coord_file, "wb")
coordinates.write("cluster, tm6_tm3_dist, npxxy_rmsd_inactive \n")
pnas_partial = partial(pnas_distance, inactive_file = inactive_file, active_file = active_file)
trajs = get_trajectory_files(traj_dir, ext = ".pdb")
pool = mp.Pool(mp.cpu_count())
distances = pool.map(pnas_partial, trajs)
pool.terminate()
for i in range(0, len(trajs)):
traj = trajs[i]
pnas_coord = distances[i][0]
pnas_dist = distances[i][1]
traj_name = traj.split("/")[len(traj.split("/"))-1].split(".")[0]
distances_i.write("%s, %f \n" %(traj_name, pnas_dist[0]))
distances_a.write("%s, %f \n" %(traj_name, pnas_dist[1]))
coordinates.write("%s, %f, %f \n" %(traj_name, (pnas_coord[0]*scale), pnas_coord[1]))
distances_i.close()
distances_a.close()
coordinates.close()
return [save_file_i, save_file_a]
def plot_pnas_vs_tics(pnas_dir, tic_dir, pnas_names, directory, scale = 7.14, refcoords_file = None):
pnas = np.concatenate(load_file(pnas_dir))
pnas[:,0] *= scale
print((np.shape(pnas)))
print((len(pnas_names)))
if("ktICA" in tic_dir):
tics = load_dataset(tic_dir)
else:
tics = verboseload(tic_dir)
print((np.shape(tics)))
tics = np.concatenate(tics)
print((np.shape(tics)))
if len(pnas_names) != np.shape(pnas)[1]:
print("Invalid pnas names")
return
for i in range(0,np.shape(pnas)[1]):
for j in range(0,np.shape(tics)[1]):
tic = tics[:,j]
pnas_coord = pnas[:,i]
plt.hexbin(tic, pnas_coord, bins = 'log', mincnt=1, cmap=plt.cm.RdYlBu_r)
coord_name = pnas_names[i]
tic_name = "tIC.%d" %(j+1)
plt.xlabel(tic_name)
plt.ylabel(coord_name)
pp = PdfPages("%s/%s_%s_hexbin.pdf" %(directory, tic_name, coord_name))
pp.savefig()
pp.close()
plt.clf()
return
def plot_hex(transformed_data_file, figure_directory, colors = None, scale = 1.0):
transformed_data = verboseload(transformed_data_file)
trajs = np.concatenate(transformed_data)
print(trajs)
plt.hexbin(trajs[:,0] * scale, trajs[:,1], bins='log', mincnt=1, cmap=plt.cm.RdYlBu_r)
pp = PdfPages(figure_directory)
pp.savefig()
pp.close()
return
def plot_col(transformed_data_file, figure_directory, colors_file):
transformed_data = verboseload(transformed_data_file)
trajs = np.concatenate(transformed_data)
colors = np.concatenate(verboseload(colors_file))
sc = plt.scatter(trajs[:,0], trajs[:,1], c=colors, s=50, cmap = mpl.cm.RdYlBu_r)
plt.colorbar(sc)
plt.show()
pp = PdfPages(figure_directory)
pp.savefig()
pp.close()
return
def save_pdb(traj_dir, clusterer, i):
location = clusterer.cluster_ids_[i,:]
traj = get_trajectory_files(traj_dir)[location[0]]
print(("traj = %s, frame = %d" %(traj, location[1])))
conformation = md.load_frame(traj, location[1])
conformation.save_pdb("/scratch/users/enf/b2ar_analysis/clusters_1000_allprot/%d.pdb" %i)
return None
def get_cluster_centers(clusterer_dir, traj_dir):
clusterer = verboseload(clusterer_dir)
centers = clusterer.cluster_centers_
save_pdb_partial = partial(save_pdb, traj_dir = traj_dir, clusterer = clusterer)
indices = list(range(0, np.shape(centers)[0]))
pool = mp.Pool(mp.cpu_count())
pool.map(save_pdb_partial, indices)
pool.terminate()
return
def plot_tica(transformed_data_dir, lag_time):
transformed_data = verboseload(transformed_data_dir)
trajs = np.concatenate(transformed_data)
plt.hexbin(trajs[:,0], trajs[:,1], bins='log', mincnt=1, cmap=plt.cm.RdYlBu_r)
pp = PdfPages("/scratch/users/enf/b2ar_analysis/tica_phi_psi_chi2_t%d.pdf" %lag_time)
pp.savefig()
pp.close()
def plot_tica_and_clusters(component_j, transformed_data, lag_time, component_i, n_clusters, main="", label = "dot", active_cluster_ids = [], intermediate_cluster_ids = [], inactive_cluster_ids = [], inactive_subsample=5, intermediate_subsample=5, tica_dir = "", center_i=None, center_j=None, centers=None, concatenate=True, axes=None):
print((component_i, component_j))
if concatenate:
trajs = np.concatenate(transformed_data)
else:
trajs = transformed_data
plt.hexbin(trajs[:,component_i], trajs[:,component_j], bins='log', mincnt=1, cmap=plt.cm.RdYlBu_r)
if axes is not None:
plt.axis((axes[component_i][0], axes[component_i][1], axes[component_j][0], axes[component_j][1]))
plt.xlabel("tIC %d" %(component_i + 1))
plt.ylabel('tIC %d' %(component_j+1))
indices = [j for j in range(0,len(active_cluster_ids),1)]
if center_i is None:
center_i = component_i
if center_j is None:
center_j = component_j
for i in [active_cluster_ids[j] for j in indices]:
center = centers[int(i),:]
if label == "dot":
plt.scatter([center[center_i]],[center[center_j]], marker='v', c='k', s=10)
else:
plt.annotate('%d' %i, xy=(center[center_i],center[center_j]), xytext=(center[center_i], center[center_j]),size=6)
indices = [j for j in range(0,len(intermediate_cluster_ids),intermediate_subsample)]
for i in [intermediate_cluster_ids[j] for j in indices]:
center = centers[int(i),:]
if label == "dot":
plt.scatter([center[center_i]],[center[center_j]], marker='8', c='m', s=10)
else:
plt.annotate('%d' %i, xy=(center[center_i],center[center_j]), xytext=(center[center_i], center[center_j]),size=6)
indices = [j for j in range(0,len(inactive_cluster_ids),inactive_subsample)]
for i in [inactive_cluster_ids[j] for j in indices]:
center = centers[int(i),:]
if label == "dot":
plt.scatter([center[center_i]],[center[center_j]], marker='s', c='w', s=10)
else:
plt.annotate('%d' %i, xy=(center[center_i],center[center_j]), xytext=(center[center_i], center[center_j]),size=6)
pp = PdfPages("%s/%s_c%d_c%d_clusters%d.pdf" %(tica_dir, main, (component_i+1), (component_j+1), n_clusters))
pp.savefig()
pp.close()
plt.clf()
def plot_all_tics_and_clusters(tica_dir, transformed_data_dir, clusterer_dir, lag_time, tic_range=None, main="", label = "dot", active_cluster_ids = [], intermediate_cluster_ids = [], inactive_cluster_ids = [], inactive_subsample=5, intermediate_subsample=5, custom_cluster_centers=None, concatenate=True, axes=None):
try:
transformed_data = verboseload(transformed_data_dir)
except:
transformed_data = load_dataset(transformed_data_dir)
if custom_cluster_centers is None:
clusterer = verboseload(clusterer_dir)
centers = clusterer.cluster_centers_
#print centers
if not concatenate:
num_tics = np.shape(transformed_data)[1]
else:
num_tics = np.shape(transformed_data[0])[1]
if tic_range == None:
tic_range = range(0,num_tics)
for i in tic_range:
js = [j for j in tic_range if j > i]
plot_partial = partial(plot_tica_and_clusters, n_clusters = len(centers), tica_dir = tica_dir, main=main, transformed_data = transformed_data, lag_time = lag_time, label = label, active_cluster_ids = active_cluster_ids, intermediate_cluster_ids = intermediate_cluster_ids, inactive_cluster_ids = inactive_cluster_ids, inactive_subsample=inactive_subsample, intermediate_subsample=intermediate_subsample, component_i = i, centers=centers, concatenate=concatenate, axes=axes)
#for j in js:
# plot_partial(j)
pool = mp.Pool(mp.cpu_count())
pool.map(plot_partial, js)
pool.terminate()
#plot_tica_and_clusters(tica_dir = tica_dir, transformed_data = transformed_data, clusterer = clusterer, lag_time = lag_time, label = "dot", active_cluster_ids = active_cluster_ids, intermediate_cluster_ids = intermediate_cluster_ids, inactive_cluster_ids = inactive_cluster_ids, component_i = i, component_j = j)
print("Printed all tICA coords and all requested clusters")
def plot_tica_component_i_j(tica_dir, transformed_data_dir, lag_time, component_i = 0, component_j = 1):
transformed_data = verboseload(transformed_data_dir)
trajs = np.concatenate(transformed_data)
plt.hexbin(trajs[:,component_i], trajs[:,component_j], bins='log', mincnt=1)
pp = PdfPages("%s/c%d_c%d.pdf" %(tica_dir, component_i, component_j))
pp.savefig()
pp.close()
plt.clf()
def plot_column_pair(i, num_columns, save_dir, titles, data, refcoords, main, axes=None):
for j in range(i+1, num_columns):
plt.hexbin(data[:,i], data[:,j], bins = 'log', mincnt=1,cmap=plt.cm.RdYlBu_r)
if axes is not None:
x1 = axes[i][0]
x2 = axes[i][1]
y1 = axes[j][0]
y2 = axes[j][1]
plt.axis((x1, x2, y1, y2))
if refcoords is not None:
print([refcoords[0,i], refcoords[0,j]])
plt.scatter([refcoords[0,i]], [refcoords[0,j]], marker = 's', c='g',s=15)
plt.scatter([refcoords[1,i]], [refcoords[1,j]], marker = 'v', c='k',s=15)
if titles is not None:
pp = PdfPages("%s/%s_%s_%s.pdf" %(save_dir, main, titles[i], titles[j]))
plt.xlabel(titles[i])
plt.ylabel(titles[j])
plt.title(main)
pp.savefig()
pp.close()
plt.clf()
else:
pp = PdfPages("%s/tIC.%d_tIC.%d.pdf" %(save_dir, i+1, j+1))
plt.xlabel("tIC.%d" %(i+1))
plt.ylabel("tIC.%d" %(j+1))
pp.savefig()
pp.close()
plt.clf()
def plot_columns(save_dir, data_file, titles = None, main = "", tICA = False, scale = 1.0, refcoords_file = None, axes=None, concatenate=True, reshape=True):
data = verboseload(data_file)
if concatenate:
data = np.concatenate(data)
data[:,0] *= scale
if(refcoords_file is not None):
refcoords = load_file(refcoords_file)
if reshape:
refcoords = np.transpose(np.vstack(refcoords))
else:
refcoords = None
print((np.shape(refcoords)))
print(refcoords)
num_columns = np.shape(data)[1]
plot_column_pair_partial = partial(plot_column_pair, main = main, num_columns = num_columns, save_dir = save_dir, titles = titles, data = data, refcoords = refcoords, axes=axes)
pool = mp.Pool(mp.cpu_count())
pool.map(plot_column_pair_partial, range(0,num_columns))
pool.terminate()
#for i in range(0,num_columns):
# plot_column_pair_partial(i)
print("Done plotting columns")
return
def calc_kde(data, kde):
return kde(data.T)
def plot_all_tics(tica_dir, transformed_data_dir, lag_time):
transformed_data = verboseload(transformed_data_dir)
num_tics = np.shape(transformed_data[0])[1]
print("Looking at %d tICS" %num_tics)
for i in range(0,num_tics):
for j in range(i+1,num_tics):
plot_tica_component_i_j(tica_dir, transformed_data_dir, lag_time, component_i = i, component_j = j)
print("Printed all tICA coords")
#Add way to plot location of specific clusters as well
def plot_all_tics_samples(tica_coords_csv, save_dir, docking_csv = False, specific_clusters = False):
tica_coords_map = convert_csv_to_map_nocombine(tica_coords_csv)
n_samples = len(list(tica_coords_map.keys()))
if docking_csv is not False: docking_map = convert_csv_to_map_nocombine(docking_csv)
num_tics = len(tica_coords_map[list(tica_coords_map.keys())[0]])
for i in range(0, 1):
for j in range(i + 1, num_tics):
print(("plotting tICS %d %d" %(i, j)))
x = []
y = []
if docking_csv is not False: c = []
for sample in list(tica_coords_map.keys()):
x.append(tica_coords_map[sample][i])
y.append(tica_coords_map[sample][j])
if docking_csv is not False:
sample_id = "cluster%s" %sample
print(docking_map[sample_id])
c.append(abs(docking_map[sample_id][0]))
if docking_csv is not False:
plt.scatter(x, y, c=c, s=50, cmap = mpl.cm.RdYlBu_r)
else:
plt.scatter(x, y, s=50, color = 'red')
if specific_clusters is not False:
for cluster in specific_clusters:
cluster = str(cluster)
cluster_x = float(tica_coords_map[cluster][i])
cluster_y = float(tica_coords_map[cluster][j])
plt.annotate('%s' %cluster, xy=(cluster_x,cluster_y), xytext=(cluster_x, cluster_y),size=15)
plot_dir = "%s/samples_%d_tICS_%d_%d.pdf" %(save_dir, n_samples, i, j)
pp = PdfPages(plot_dir)
pp.savefig()
pp.close()
plt.clf()
def plot_timescales(clusterer_dir, n_clusters, lag_time):
clusterer = verboseload(clusterer_dir)
sequences = clusterer.labels_
lag_times = list(np.arange(1,150,5))
n_timescales = 5
msm_timescales = implied_timescales(sequences, lag_times, n_timescales=n_timescales, msm=MarkovStateModel(verbose=False))
print(msm_timescales)
for i in range(n_timescales):
plt.plot(lag_times, msm_timescales[:,i])
plt.semilogy()
pp = PdfPages("/scratch/users/enf/b2ar_analysis/kmeans_%d_%d_implied_timescales.pdf" %(n_clusters, lag_time))
pp.savefig()
pp.close()
plt.clf()
def rmsd_to_structure(clusters_dir, ref_dir, text):
pdbs = get_trajectory_files(clusters_dir)
ref = md.load_frame(ref_dir, index=0)
rmsds = np.zeros(shape=(len(pdbs),2))
for i in range(0,len(pdbs)):
print(i)
pdb_file = pdbs[i]
pdb = md.load_frame(pdb_file, index=0)
rmsd = md.rmsd(pdb, ref, 0)
rmsds[i,0] = i
rmsds[i,1] = rmsd[0]
rmsd_file = "%s/%s_rmsds.csv" %(clusters_dir, text)
np.savetxt(rmsd_file, rmsds, delimiter=",")
def rmsd_pymol(pdb_dir, ref_dir, script_dir, rmsd_dir):
script = open(script_dir, "rb")
lines = script.readlines()
new_script = open(script_dir, "wb")
for line in lines:
if line[0:7] == "pdb_dir":
#print ("found pdb line")
line = "pdb_dir = '%s'\n" %pdb_dir
elif line[0:7] == "ref_dir": line = "ref_dir = '%s'\n" %ref_dir
elif line[0:8] == "rmsd_dir": line = "rmsd_dir = '%s'\n" %rmsd_dir
new_script.write(line)
new_script.close()
command = "/scratch/users/enf/pymol/pymol %s" %script_dir
print(command)
os.system(command)
def analyze_rmsds(inactive_rmsd_file, active_rmsd_file, pnas_i, pnas_a, combined_file, analysis_file):
inactive_rmsd_map = convert_csv_to_map(inactive_rmsd_file)
inactive_stats_map = calc_mean_and_stdev(inactive_rmsd_map)
active_rmsd_map = convert_csv_to_map(active_rmsd_file)
active_stats_map = calc_mean_and_stdev(active_rmsd_map)
pnas_map_i = convert_csv_to_map(pnas_i)
pnas_stats_i = calc_mean_and_stdev(pnas_map_i)
pnas_map_a = convert_csv_to_map(pnas_a)
pnas_stats_a = calc_mean_and_stdev(pnas_map_a)
rmsd_i_map = convert_csv_to_map_nocombine(inactive_rmsd_file)
rmsd_a_map = convert_csv_to_map_nocombine(active_rmsd_file)
dist_i_map = convert_csv_to_map_nocombine(pnas_i)
dist_a_map = convert_csv_to_map_nocombine(pnas_a)
new_file = open(analysis_file, "wb")
new_file.write("cluster, inactive_rmsd, inactive_stdev, inactive_pnas_dist, inactive_pnas_stdev, active_rmsd, active_stdev, active_pnas_dist, active_pnas_stdev \n")
combined = open(combined_file, "wb")
combined.write("cluster, inactive_rmsd, inactive_pnas_dist, active_rmsd, active_pnas_dist \n")
for key in sorted(inactive_rmsd_map.keys()):
new_file.write("%s, %f, %f, %f, %f, %f, %f, %f, %f \n" %(key, inactive_stats_map[key][0], inactive_stats_map[key][1], pnas_stats_i[key][0], pnas_stats_i[key][1], active_stats_map[key][0], active_stats_map[key][1], pnas_stats_a[key][0], pnas_stats_a[key][1]))
for key in sorted(rmsd_i_map.keys()):
combined.write("%s, %f, %f, %f, %f \n" %(key, rmsd_i_map[key][0], dist_i_map[key][0], rmsd_a_map[key][0], dist_a_map[key][0]))
new_file.close()
combined.close()
return [inactive_stats_map, active_stats_map]
def merge_samples(results_map):
merged_results = {}
for key in list(results_map.keys()):
cluster = key.split("_")[0]
if cluster not in list(merged_results.keys()):
merged_results[cluster] = [results_map[key]]
else:
merged_results[cluster].append(results_map[key])
stats_map = calc_mean_and_stdev(merged_results)
return stats_map
def print_stats_map(merged_results, directory):
mapfile = "%s/stats_map.csv" %directory
mapcsv = open(mapfile, "wb")
mapcsv.write("cluster, mean_score, stdev \n")
for key in sorted(merged_results.keys()):
mapcsv.write("%s, %f, %f \n" %(key, merged_results[key][0], merged_results[key][1]))
mapcsv.close()
return
def analyze_log_file(log_file):
log = open(log_file, "rb")
conformation = log_file.rsplit(".", 1)[0]
conformation = conformation.split("/")[len(conformation.split("/"))-1 ]
score = 0.0
xp_score = None
lines = log.readlines()
current_pose = 0
best_pose = 0
for line in lines:
line = [w.decode("utf-8") for w in line.split()]
if len(line) >= 3:
if (line[0] == "Best" and line[1] == "XP" and line[2] == "pose:"):
current_pose += 1
xp_score = float(line[6])
#print "%f, %f" %(xp_score, score)
if xp_score < score:
score = xp_score
best_pose = current_pose
elif (line[0] == "Best" and line[1] == "Emodel="):
current_pose += 1
xp_score = float(line[8])
#print("%f, %f" %(xp_score, score))
if xp_score < score:
score = xp_score
best_pose = current_pose
score = -1.0*score
log.close()
return (conformation, score, best_pose)
def analyze_docking_results(docking_dir, ligand, precision, docking_summary, reread=True, write_to_disk=False):
try:
results_file = docking_summary
n_clusters = len(get_trajectory_files(docking_dir, ext = ".in"))
if os.path.exists(results_file):
if reread:
df = pd.read_csv(results_file)
if df.shape[0] >= n_clusters:
return (ligand, df)
logs = get_trajectory_files(docking_dir, ext = ".log")
scores_list = []
for log in logs:
scores_list.append(analyze_log_file(log))
scores_df = pd.DataFrame(scores_list, columns=["sample", "%s" %("%s_%s_score" %(ligand, precision)), "best_pose_id"])
if write_to_disk:
scores_df.to_csv(results_file)
#scores_map = {score[0] : score[1] for score in scores_list}
#titles = ["sample", "%s" %("%s_%s_score" %(ligand, precision))]
#write_map_to_csv(results_file, scores_map, titles)
#merged_results = merge_samples(scores_map)
return (ligand, scores_df)
except:
return None
def analyze_docking_results_wrapper(args):
return analyze_docking_results(*args)
def get_lig_names(docking_dir):
subdirs = [x[0] for x in os.walk(docking_dir)]
lig_names = []
for subdir in subdirs:
lig_name = subdir.split("/")[len(subdir.split("/"))-1]
lig_names.append(lig_name)
return lig_names
def listdirs(folder):
#return [
# d for d in (os.path.join(folder, d1) for d1 in os.listdir(folder))
# if os.path.isdir(d)
#]
#from glob import glob
return(["%s/%s" %(folder, f) for f in os.listdir(folder)])
#return([d.path for d in os.scandir(folder) if d.is_dir()])
def parse_log_file(result):
ligand, result = result
keep_columns = [c for c in result.columns.values.tolist() if "score" in c]
result.index = result['sample'].values
docking_pose = result["best_pose_id"]
result = result[keep_columns]
return (ligand, docking_pose, result)
def get_arg_tuple(subdir, ligands=None, precision="SP", redo=False, reread=True, write_to_disk=False):
lig_name = subdir.split("/")[len(subdir.split("/"))-1]
if ligands is not None:
if lig_name not in ligands:
return None
docking_summary = "%s/docking_summary.csv" %subdir
return([subdir, lig_name, precision, docking_summary, reread, write_to_disk])
import time
def analyze_docking_results_multiple(docking_dir, precision, summary,
ligands=None, poses_summary=None, redo=False, reread=True,
write_to_disk=False, parallel=False, worker_pool=None):
if os.path.exists(summary) and not redo:
with open(summary, "rb") as f:
df = pickle.load(f)
return(df, None)
#df = pd.read_csv(summary, index_col=0).transpose()
return df, None
print("Analyzing docking results")
print(docking_dir)
subdirs = listdirs(docking_dir)
#print subdirs
results_list = []
lig_names = []
arg_tuples = []
print("Obtaining docking scores now...")
get_arg_tuple_partial = partial(get_arg_tuple,
ligands=ligands,
precision=precision,
redo=redo, reread=reread,
write_to_disk=write_to_disk)
pool = mp.Pool(mp.cpu_count()-1)
arg_tuples = pool.map_async(get_arg_tuple_partial,
subdirs)
arg_tuples.wait()
arg_tuples = arg_tuples.get()
arg_tuples = [t for t in arg_tuples if t is not None]
pool.terminate()
#arg_tuples = function_mapper(get_arg_tuple_partial,
# worker_pool,
# parallel, subdirs)
print("Obtained ligand arguments.")
#results_list = function_mapper(analyze_docking_results_wrapper, worker_pool, parallel, arg_tuples)
a = time.time()
pool = mp.Pool(mp.cpu_count()-1)
results_list = pool.map_async(analyze_docking_results_wrapper, arg_tuples)
results_list.wait()
results_list = results_list.get()
pool.terminate()
results_list = [r for r in results_list if r is not None]
print(time.time()-a)
print("Examined all ligands.")
a = time.time()
pool = mp.Pool(mp.cpu_count()-1)
results = pool.map_async(parse_log_file, results_list)
results.wait()
results = results.get()
pool.terminate()
all_docking_results = [t[2] for t in results]
all_docking_poses = [t[1] for t in results]
lig_names = [t[0] for t in results]
print(time.time()-a)
print("Parsed all log files.")
all_docking_poses = pd.concat(all_docking_poses, axis=1)
all_docking_poses.columns = lig_names
if poses_summary is not None:
all_docking_poses.to_csv(poses_summary)
all_docking_results = pd.concat(all_docking_results, axis=1)
all_docking_results.columns = lig_names
all_docking_results = all_docking_results.transpose()
with open(summary, "wb") as f:
pickle.dump(all_docking_results, f, protocol=2)
#all_docking_results.to_csv(summary)
return all_docking_results, all_docking_poses
#combined_map = combine_maps(results_list)
#combined_filename = summary
#write_map_to_csv(combined_filename, combined_map, ["sample"] + lig_names)
def compute_means(docking_csv, joined_csv, means_csv):
print("analyzing %s" %docking_csv)
titles = get_titles(docking_csv)
docking_scores = convert_csv_to_joined_map(docking_csv, joined_csv)[0]
docking_averages = calc_mean(docking_scores)
write_map_to_csv(means_csv, docking_averages, titles)
return docking_averages
def compute_means_ligands(docking_dir, pnas_means, ligands):
subdirs = [x[0] for x in os.walk(docking_dir)]
subdirs = subdirs[1:len(subdirs)]
docking_csv_files = []
docking_means_files = []
docking_joined_files = []
for subdir in subdirs:
lig = subdir.split("/")[len(subdir.split("/"))-1]
if lig not in ligands: continue
docking_csv = "%s/docking_summary.csv" %subdir
docking_means = "%s/docking_means.csv" %subdir
docking_joined = "%s/docking_joined.csv" %subdir
compute_means(docking_csv, docking_joined, docking_means)
pnas_joined_csv = "%s/docking_means_pnas_means.csv" %subdir
combine_csv_list([docking_means, pnas_means], pnas_joined_csv)
return
def compute_z(value, mean, stdev):
return (value - mean) / stdev
def compute_aggregate_scores(docking_csv, inverse_agonists = [], summary = "", z_scores_csv = ""):
scores_map = convert_csv_to_map_nocombine(docking_csv)
docking_titles = get_titles(docking_csv)
lig_names = docking_titles[1:len(docking_titles)]
scores_per_ligand = {}
for lig_name in lig_names:
scores_per_ligand[lig_name] = []
for receptor in list(scores_map.keys()):
receptor_scores = scores_map[receptor]
for i in range(0, len(receptor_scores)):
lig_name = lig_names[i]
lig_score = receptor_scores[i]
scores_per_ligand[lig_name].append(lig_score)
ligand_stats = calc_mean_and_stdev(scores_per_ligand)
z_scores_per_receptor = {}
for receptor in list(scores_map.keys()):
receptor_scores = scores_map[receptor]
z_scores_per_receptor[receptor] = []
for i in range(0, len(receptor_scores)):
lig_score = receptor_scores[i]
lig_name = lig_names[i]
lig_mean = ligand_stats[lig_name][0]
lig_stdev = ligand_stats[lig_name][1]
z_score = compute_z(lig_score, lig_mean, lig_stdev)
if abs(lig_score - 0.0) < 0.001: z_score = -3.0
if lig_name in inverse_agonists:
#print lig_name
z_score = -1.0 * z_score
z_scores_per_receptor[receptor].append(z_score)
aggregate_scores = calc_mean(z_scores_per_receptor)
titles = ["sample", "average_z_score"]
write_map_to_csv(z_scores_csv, z_scores_per_receptor, docking_titles)
write_map_to_csv(summary, aggregate_scores, titles)
def combine_docking_distances(docking_csv, distances_csv, docking_dir):
docking_map = convert_csv_to_map_nocombine(docking_csv)
distances_map = convert_csv_to_map_nocombine(distances_csv)
combined_map = copy.deepcopy(distances_map)
for key in list(distances_map.keys()):
if key in list(docking_map.keys()):
combined_map[key].append(-1.0 * docking_map[key][0])
else:
combined_map.pop(key, None)
firstline = "cluster, inactive_rmsd, inactive_pnas, active_rmsd, active_pnas, docking \n"
filename = "%s/distances_docking.csv" %docking_dir
write_map_to_csv(filename, combined_map, firstline)
def top_n_scoring_clusters(docking_csv, score_type = 1, n = 50):
docking_list = convert_csv_to_list(docking_csv)
docking_list_sorted = sorted(docking_list, key=operator.itemgetter(score_type), reverse = True)
top_n = []
for i in range(0, n):
top_n.append(docking_list_sorted[i][0])
return top_n
def top_n_scoring_samples(docking_csv, score_type = "mean_docking_score", n = 100, n_samples = 10):
docking_list = convert_csv_to_list(docking_csv)
titles = docking_list[0]
for i in range(0, len(titles)):
if titles[i] == score_type: break
#print i
#print titles[i]
docking_list_sorted = sorted(docking_list, key=operator.itemgetter(i), reverse = True)
#print docking_list_sorted
top_n = []
for i in range(0, n):
top_n.append(docking_list_sorted[i][0])
if "sample" not in top_n[0]:
top_n_new = []
for cluster in top_n:
for i in range(0,n_samples):
top_n_new.append("%s_sample%d" %(cluster, i))
top_n = top_n_new
return top_n
def combine_docking_mmgbsa(combined_csv, mmgbsa_csv, mmgbsa_dir, filename):
combined_map = convert_csv_to_map_nocombine(combined_csv)
mmgbsa_map = convert_csv_to_map_nocombine(mmgbsa_csv)
new_map = copy.deepcopy(combined_map)
for key in list(mmgbsa_map.keys()):
if key in list(combined_map.keys()):
new_map[key].append(-1.0 * mmgbsa_map[key][0])
else:
new_map.pop(key, None)
firstline = "sample, inactive_rmsd, inactive_pnas, active_rmsd, active_pnas, docking, mmgbsa \n"
write_map_to_csv(filename, new_map, firstline)
def analyze_mmgbsa_results(mmgbsa_dir, ligand, chosen_receptors):
analysis_csv = "%s/mmgbsa_summary.csv" %mmgbsa_dir
csvfile = open(analysis_csv, "wb")
csvfile.write("sample, %s_mmgbsa \n" %ligand)
outputs = get_trajectory_files(mmgbsa_dir, ".csv")
analyzed_samples = set()
for output in outputs:
output_name = output.split("/")[len(output.split("/"))-1]
sample = output_name.split("-out.csv")[0]
if chosen_receptors is not False:
if sample not in chosen_receptors: continue
analyzed_samples.add(sample)
results = open(output, "rt")
reader = csv.reader(results)
score = 10000.0
i = 0
for row in reader:
if i == 0:
i += 1
continue
print(row[0])
temp = float(row[1])
if temp < score:
score = temp
score = -1.0 * score
csvfile.write("%s, %f \n" %(sample, score))
results.close()
not_analyzed_samples = set(chosen_receptors) - analyzed_samples
for sample in not_analyzed_samples:
if sample not in analyzed_samples:
csvfile.write("%s, %f \n" %(sample, 0.00))
csvfile.close()
results_map = convert_csv_to_map_nocombine(analysis_csv)
return results_map
def analyze_mmgbsa_results_multiple(mmgbsa_dir, summary, ligands, chosen_receptors):
subdirs = [x[0] for x in os.walk(mmgbsa_dir)]
subdirs = subdirs[1:len(subdirs)]
#print subdirs
results_list = []
lig_names = []
for subdir in subdirs:
lig_name = subdir.split("/")[len(subdir.split("/"))-1]
if lig_name not in ligands: continue
lig_names.append(lig_name)
mmgbsa_summary = "%s/mmgbsa_summary.csv" %subdir