-
Notifications
You must be signed in to change notification settings - Fork 0
/
PDB_plugin.py
1130 lines (969 loc) · 45 KB
/
PDB_plugin.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
# Plugin for PyMol to display the images show on PDBe's website
# Author: John Berrisford
# Date: June 2018
#
# parsing the input
import json
import datetime
import socket
import re, os
import time
import sys
import random
import logging
import pymol
from pymol import cmd
from pymol import stored
from chempy.cif import *
# logging
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)
# API calls
server_root = "https://www.ebi.ac.uk/pdbe/api/"
summaryURL = server_root + "pdb/entry/summary/"
poly_seq_schemeURL = server_root + "pdb/entry/residue_listing/"
protein_mappingURL = server_root + "mappings/"
nucleic_mappingURL = server_root + "nucleic_mappings/"
# seqURL = server_root + "mappings/sequence_domains/entry/"
moleculesURL = server_root + "pdb/entry/molecules/"
validationURL = server_root + 'validation/global-percentiles/entry/'
validation_residueURL = server_root + 'validation/protein-RNA-DNA-geometry-outlier-residues/entry/'
validation_ramaURL = server_root + 'validation/protein-ramachandran-sidechain-outliers/entry/'
# ftp site
ebi_ftp = 'ftp://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/divided/mmCIF/%s/%s.cif.gz'
# clean mmcif
updated_ftp = 'https://www.ebi.ac.uk/pdbe/static/entry/%s_updated.cif.gz'
# dictionaries
stored.domain_dict = {}
stored.seq_scheme = {}
stored.molecule_dict = {}
stored.poly_count = 0
stored.residue_dict = {}
stored.ca_p_only = []
stored.assemblies = {}
stored.operators = {}
stored.cif_items = {}
stored.asym_to_chain = {}
stored.assembly_objects = {}
stored.entities = {}
sphere_scale_dict = {'sticks': '0.25',
'spheres': '0.5',
'cartoon': '',
'ribbon': ''}
pdb_id_re = re.compile(r'\d[A-z0-9]{3}')
mmCIF_file_RE = re.compile(r'mmCIF_file=(.*)')
logging_RE = re.compile(r'logging=(.*)')
# cmd.set('connect_mode', 4)
empty_cif_list = ["", ".", "?", None]
class ApiCall:
"""functions specific to API calls"""
def __init__(self, url):
self.url = url
self.data = {}
def return_data(self):
try:
import requests
except Exception as e:
logging.error(e)
return self.data
self.encode_url()
r = requests.get(url=self.url, timeout=60)
if r.status_code == 200:
json_data = r.json()
self.data = json_data
elif r.status_code == 404:
self.data = {}
else:
logging.info(r.status_code, r.reason)
self.data = {}
return self.data
def encode_url(self):
self.url = re.sub(" ", "%20", self.url)
# url handling
def url_response_urllib2(url, description):
"""try several times to get a response from the API"""
data = None
try:
import urllib2
except Exception as e:
logging.error(e)
return data
data_response = False
tries = 1
limit = 5
logging.debug(url)
date = datetime.datetime.now().strftime("%Y,%m,%d %H:%M")
while tries < limit:
try:
response = urllib2.urlopen(url, None, 60)
except urllib2.HTTPError as e:
logging.debug("##############")
logging.debug("%s HTTP API error - %s, error code - %s, try %s" % (date, description, e.code, str(tries)))
# logging.debug(e.code)
if e.code == 404:
data_response = True
data = {}
break
else:
# logging.debug(entry_url)
time.sleep(random.randint(1, 20)) # sleep 1-20 seconds
tries += 1
logging.debug(e)
data = {}
except urllib2.URLError as e:
logging.debug("##############")
logging.debug("%s URL API error - %s, try %s" % (date, e, str(tries)))
# logging.debug(entry_url)
time.sleep(random.randint(1, 20)) # sleep 1-20 seconds
tries += 1
logging.debug(e)
data = {}
except socket.timeout as e:
logging.debug("##############")
logging.debug("%s Timeout API error - %s, try %s" % (date, e, str(tries)))
# logging.debug(entry_url)
time.sleep(random.randint(1, 20)) # sleep 1-20 seconds
tries += 1
logging.debug(e)
data = {}
else:
logging.debug("received a response from the " + description + " API after " + str(tries) + " tries.")
data = json.load(response)
data_response = True
break
if not data_response:
logging.debug("No response from the %s API" % description)
# cmd.quit(1)
return data
# url handling
def url_response(url, description):
logging.debug(description)
try:
import requests
data = ApiCall(url=url).return_data()
except:
data = url_response_urllib2(url=url, description=description)
return data
def getColor(val, crange=[2, 5], inverted=1, absolute=1, buffer=32):
"""convert colour value in rgb for pymol"""
if absolute == 1: val = abs(val)
# Convert value to integer in range [0,510]
integercolor = int((val - crange[0]) / (crange[1] - crange[0]) * 510)
if integercolor < 0: integercolor = 0
if integercolor > 510: integercolor = 510
if inverted == 1: integercolor = 510 - integercolor
# first 255 values are converted in color RED --> YELLOW
if integercolor <= 255:
red = 255 - buffer
green = int(integercolor * (1 - buffer / 255))
blue = 0
# other values are converted in color YELLOW --> GREEN
elif (integercolor <= 510):
integercolor -= 255
red = int(255 + integercolor * (buffer / 255 - 1))
green = 255 - buffer
blue = 0
else:
red = 150
green = 150
blue = 150
red = float(red) / 255.0
green = float(green) / 255.0
blue = float(blue) / 255.0
# return color format used for drawing in Pymol
colour_list = []
colour_list.append(red)
colour_list.append(green)
colour_list.append(blue)
return colour_list
# return "[" + int(red) + ',' + int(green) + ',' + int(blue) + "]"
pymolcolours = [
"red", "green", "blue", "yellow", "magenta", "cyan",
"tv_red", "tv_green", "tv_blue", "tv_yellow", "lightmagenta", "palecyan",
"raspberry", "chartreuse", "marine", "paleyellow", "hotpink", "aquamarine",
"darksalmon", "splitpea", "slate", "yelloworange", "pink", "greencyan",
"salmon", "smudge", "lightblue", "limon", "lightpink", "teal",
"deepsalmon", "palegreen", "skyblue", "wheat", "dirtyviolet", "deepteal",
"warmpink", "limegreen", "purpleblue", "sand", "violet", "lightteal",
"firebrick", "lime", "deepblue", "violetpurple",
"ruby", "limon", "density", "purple",
"chocolate", "forest", "deeppurple",
"brown",
]
validation_background_colour = [0.4, 1.0, 0.4]
cmd.set_color("validation_green_background", validation_background_colour)
validation_colours = ['yellow', 'orange', 'red']
angle_bond_dict = {'angles': {'description': 'bond angles', 'colour': 'yellow', 'display': 'spheres'},
'bonds': {'description': 'bond length', 'colour': 'red', 'display': 'spheres'}}
rama_dict = {'ramachandran_outliers': {'selection': ' and name C+CA+N+O', 'colour': 'yellow', 'display': 'spheres'},
'sidechain_outliers': {'selection': ' and not name N+CA+C+O', 'colour': 'red', 'display': 'spheres'}}
def colour_return(num):
colournum = ""
factor = 1
while (num >= len(pymolcolours)):
# logging.debug(num)
num = num - (len(pymolcolours) * factor)
# logging.debug(num)
factor = factor + 1
else:
colournum = num
colour = pymolcolours[colournum]
return colour
def poly_display_type(asym, mol_type, length):
"""return either ribbon or cartoon depending on number of polymer chains"""
##start with it being cartoon - then change as needed.
display_type = "cartoon"
if stored.poly_count > 50:
display_type = "ribbon"
elif asym in stored.ca_p_only:
logging.info('set ribbon trace on')
cmd.set('ribbon_trace_atoms', 1)
display_type = "ribbon"
else:
if re.search('polypeptide', mol_type):
if length < 20:
display_type = 'sticks'
if re.search('nucleotide', mol_type):
if length < 3:
display_type = 'sticks'
if re.search('saccharide', mol_type):
display_type = 'sticks'
# logging.debug('asym: %s, mol_type: %s, length: %s, display_type: %s' %(asym, mol_type, length, display_type))
return display_type
class worker_functions():
def trans_setting(self, selection, trans_value):
cmd.set("cartoon_transparency", trans_value, selection)
cmd.set("ribbon_transparency", trans_value, selection)
cmd.set("stick_transparency", trans_value, selection)
cmd.set("sphere_transparency", trans_value, selection)
def count_poly(self, pdbid):
url = moleculesURL + pdbid
# global molecule_dict
if stored.molecule_dict == {}:
stored.molecule_dict = url_response(url, 'molecules')
if pdbid in stored.molecule_dict:
for entity in stored.molecule_dict[pdbid]:
# add ca only list
if entity['ca_p_only'] != False:
for a in entity['in_struct_asyms']:
if a not in stored.ca_p_only:
stored.ca_p_only.append(a)
if entity['molecule_type'] not in ['water', 'bound']:
stored.poly_count += 1
def poly_seq_scheme(pdbid):
"""build a dictionary like poly_seq_scheme"""
url = poly_seq_schemeURL + pdbid
data = url_response(url, 'seq_scheme')
if pdbid in data:
for entity in data[pdbid]['molecules']:
for chain in entity['chains']:
chain_id = chain['chain_id']
asym_id = chain['struct_asym_id']
for residue in chain['residues']:
CIFnum = residue['residue_number']
PDBnum = residue['author_residue_number']
PDBinsCode = residue['author_insertion_code']
residueName = residue['residue_name']
if residue['observed_ratio'] != 0:
PDBobs = True
else:
PDBobs = False
stored.seq_scheme.setdefault(asym_id, {})[CIFnum] = {'PDBnum': PDBnum, 'PDBinsCode': PDBinsCode,
'observed': PDBobs, 'residueName': residueName,
'chainID': chain_id}
def asym_from_entity(pdbid, entity_id):
url = moleculesURL + pdbid
# global molecule_dict
if stored.molecule_dict == {}:
stored.molecule_dict = url_response(url, 'molecules')
asym_id_list = []
if pdbid in stored.molecule_dict:
# logging.debug(entity_id)
for entity in stored.molecule_dict[pdbid]:
# add ca only list
if entity['ca_p_only'] != False:
for a in entity['in_struct_asyms']:
if a not in stored.ca_p_only:
stored.ca_p_only.append(a)
# logging.info(entity['entity_id'])
for a in entity['in_struct_asyms']:
if str(entity_id) == str(entity['entity_id']):
asym_id_list.append(str(a))
# logging.debug(asym_id_list)
return asym_id_list
def check_range_observed(asym_id, start, end, unobs):
range_dict = []
firstResidue = 1
lastResidue = 1
for r in stored.seq_scheme[asym_id]:
if r <= firstResidue:
firstResidue = r
if r >= lastResidue:
lastResidue = r
if end > lastResidue:
# logging.debug('ERROR: residue %s from SIFTS is greater than the lastSeqRes number %s' %(end, lastSeqRes))
end = lastResidue
# logging.debug("first residue: %s, last residue %s" %(firstResidue, lastResidue))
# logging.debug(seq_scheme[asym_id][start])
if start in stored.seq_scheme[asym_id]:
chain = stored.seq_scheme[asym_id][start]['chainID']
while stored.seq_scheme[asym_id][start]['observed'] == False:
# logging.debug("PDB start is not observed, adding 1 to residue number %s" %(start))
if start == lastResidue:
# logging.debug("domain not observed")
unobs = True
break
else:
start += 1
if start == lastResidue:
# logging.debug("domain not observed")
unobs = True
break
elif start == end:
# logging.debug("domain not observed")
unobs = True
break
if end in stored.seq_scheme[asym_id]:
while stored.seq_scheme[asym_id][end]['observed'] == False:
# logging.debug("PDB end is not observed, minusing 1 from residue number %s" %(end))
if end == firstResidue:
# logging.debug("domain not observed")
unobs = True
break
else:
end -= 1
if end == firstResidue:
# logging.debug("domain not observed")
unobs = True
break
elif start == end:
# logging.debug("domain not observed")
unobs = True
break
if unobs == False:
# logging.debug("CIF start: %s, CIF end %s" %(start, end))
# logging.debug("PDB start: %s, PDB end %s" %(PDBstart, PDBend))
# need to do something about non continuous ranges which pymol doesn't cope with.
"""find all sections where the residue number increases by one. If it jumps then store this as a separate
residue block while number is less than endbegin with number = start plus 1. see how the numbering differs
from startif its 1 then its continuous - move to the next residue
if its zero then there must be insert codes - this is ok - move to the next residue
if its greater than 1 then store the previous residues as a block.
"""
currentCIF = start
blockStartCIF = start
nextCIF = start + 1
while nextCIF < end:
currentPDB = stored.seq_scheme[asym_id][currentCIF]['PDBnum']
nextPDB = stored.seq_scheme[asym_id][nextCIF]['PDBnum']
if currentPDB not in empty_cif_list:
if nextPDB in empty_cif_list:
startPDB = stored.seq_scheme[asym_id][blockStartCIF]['PDBnum']
swap = checkOrder(startPDB, currentPDB)
startPDBins = insert_code(asym_id, blockStartCIF)
currentPDB = insert_code(asym_id, currentCIF)
if swap == False:
range_dict.append({"PDBstart": startPDBins, "PDBend": currentPDB, "chainID": chain})
else:
range_dict.append({"PDBstart": currentPDB, "PDBend": startPDBins, "chainID": chain})
# move start to next block
blockStartCIF = nextCIF
else:
currentPDB = int(stored.seq_scheme[asym_id][currentCIF]['PDBnum'])
nextPDB = int(stored.seq_scheme[asym_id][nextCIF]['PDBnum'])
if nextPDB - currentPDB > 1:
# logging.debug("numbering not continues, positive jump - store as section")
startPDB = stored.seq_scheme[asym_id][blockStartCIF]['PDBnum']
swap = checkOrder(startPDB, currentPDB)
startPDBins = insert_code(asym_id, blockStartCIF)
currentPDB = insert_code(asym_id, currentCIF)
if swap == False:
range_dict.append({"PDBstart": startPDBins, "PDBend": currentPDB, "chainID": chain})
else:
range_dict.append({"PDBstart": currentPDB, "PDBend": startPDBins, "chainID": chain})
# move start to next block
blockStartCIF = nextCIF
elif currentPDB - nextPDB > 1:
# logging.debug("numbering not continues, negative jump - store as section")
startPDB = stored.seq_scheme[asym_id][blockStartCIF]['PDBnum']
swap = checkOrder(startPDB, currentPDB)
startPDBins = insert_code(asym_id, blockStartCIF)
currentPDB = insert_code(asym_id, currentCIF)
if swap == False:
range_dict.append({"PDBstart": startPDBins, "PDBend": currentPDB, "chainID": chain})
else:
range_dict.append({"PDBstart": currentPDB, "PDBend": startPDBins, "chainID": chain})
# move start to next block
blockStartCIF = nextCIF
else:
blockStartCIF = nextCIF
nextCIF += 1
currentCIF += 1
startPDB = stored.seq_scheme[asym_id][blockStartCIF]['PDBnum']
swap = checkOrder(blockStartCIF, nextCIF)
startPDBins = insert_code(asym_id, blockStartCIF)
nextPDB = insert_code(asym_id, nextCIF)
if swap == False:
range_dict.append({"PDBstart": startPDBins, "PDBend": nextPDB, "chainID": chain})
else:
range_dict.append({"PDBstart": nextPDB, "PDBend": startPDBins, "chainID": chain})
# logging.info(range_dict)
else:
logging.info("domain unobserved")
return range_dict
def checkOrder(start, end):
swap = False
# logging.debug('PRE: start: %s, end %s, swap %s' %(start, end, swap))
if type(start) is str:
start = start.split('\\')[-1]
if type(end) is str:
end = end.split('\\')[-1]
if int(start) > int(end):
swap = True
# logging.debug('POST: start: %s, end: %s, swap %s' %(start, end, swap))
return swap
def insert_code(asym_id, CIFnum):
if stored.seq_scheme[asym_id][CIFnum]['PDBinsCode'] == None:
PDBnum = stored.seq_scheme[asym_id][CIFnum]['PDBnum']
else:
PDBnum = "%s%s" % (
stored.seq_scheme[asym_id][CIFnum]['PDBnum'], stored.seq_scheme[asym_id][CIFnum]['PDBinsCode'])
if re.search('-', str(PDBnum)):
PDBnum = re.sub('-', '\-', str(PDBnum))
return PDBnum
polymeric_types = ['']
class Validation:
def launch_validation(self, pdbid):
url = validationURL + pdbid
val_data = url_response(url, 'validation')
if val_data:
logging.info('There is validation for this entry')
url = validation_residueURL + pdbid
res_data = url_response(url, 'residue validation')
url = validation_ramaURL + pdbid
rama_data = url_response(url, 'rama validation')
self.per_residue_validation(pdbid, res_data, rama_data)
else:
logging.info("No validation for this entry")
###this takes too long for really large entries.
# Validation().per_chain_per_residue_validation(pdbid, res_data, rama_data)
"""validation of all polymeric enties"""
def validation_selection(self, selection, display_id):
# logging.debug(selection)
# uses a list so 0 means that there is one outlier for this residue.
if selection in stored.residue_dict:
colour_num = stored.residue_dict[selection] + 1
stored.residue_dict[selection] = colour_num
else:
stored.residue_dict.update({selection: 0})
colour_num = 0
if colour_num > 2:
colour_num = 2
residue_colour = validation_colours[colour_num]
# logging.debug(residue_colour)
cmd.color(residue_colour, selection)
def geometric_validation(self, pdbid, res_data, chain=False, model=1):
"""check for geometric validation outliers in res_data """
if res_data:
if pdbid in res_data:
if 'molecules' in res_data[pdbid]:
if res_data[pdbid]['molecules']:
for entity in res_data[pdbid]['molecules']:
# logging.debug(entity)
entity_id = entity['entity_id']
for chain in entity['chains']:
chain_id = chain['chain_id']
# logging.debug(chain_id)
for model in chain['models']:
model_id = int(model['model_id'])
for outlier_type in model['outlier_types']:
outliers = model['outlier_types'][outlier_type]
# logging.debug(outlier_type)
# logging.debug(outliers)
for outlier in outliers:
PDB_res_num = outlier['author_residue_number']
PDB_ins_code = outlier['author_insertion_code']
alt_code = outlier['alt_code']
if PDB_ins_code not in [None, " "]:
PDB_res_num = '%s%s' % (PDB_res_num, PDB_ins_code)
# logging.debug(PDB_res_num)
selection = "chain %s and resi %s" % (chain_id, PDB_res_num)
if model == 1 or model_id:
if chain == False or chain_id:
self.validation_selection(selection, pdbid)
else:
logging.info("no residue validation for this entry")
def ramachandran_validation(self, pdbid, rama_data, chain=False, model=1):
"""display ramachandran outliers"""
if rama_data:
if pdbid in rama_data:
for k in rama_data[pdbid]:
v = rama_data[pdbid][k]
if v:
logging.info("ramachandran %s for this entry" % k)
for outlier in rama_data[pdbid][k]:
# logging.debug(outlier)
entity_id = outlier['entity_id']
model_id = int(outlier['model_id'])
chain_id = outlier['chain_id']
PDB_res_num = outlier['author_residue_number']
PDB_ins_code = outlier['author_insertion_code']
alt_code = outlier['alt_code']
if PDB_ins_code not in [None, " "]:
PDB_res_num = '%s%s' % (PDB_res_num, PDB_ins_code)
selection = "chain %s and resi %s" % (chain_id, PDB_res_num)
if model == 1 or model_id:
if chain == False or chain_id:
self.validation_selection(selection, pdbid)
else:
logging.info("is multimodel!!!, outlier not in model 1, not shown.")
else:
logging.info("no %s" % (k))
def per_residue_validation(self, pdbid, res_data, rama_data):
"""validation of all outliers, coloured by number of outliers"""
# display only polymers
if stored.molecule_dict == {}:
url = moleculesURL + pdbid
stored.molecule_dict = url_response(url, 'molecules')
if pdbid in stored.molecule_dict:
for entity in stored.molecule_dict[pdbid]:
# logging.info(entity)
mol_type = entity['molecule_type']
ca_only_list = []
if entity['ca_p_only'] != False:
ca_only_list = entity['ca_p_only']
if mol_type not in ['Water', 'Bound']:
for a in entity['in_struct_asyms']:
if stored.seq_scheme == {}:
poly_seq_scheme(pdbid)
unobs = False
start = 1
end = entity['length']
length = entity['length']
asym_id = a
display_type = poly_display_type(asym_id, 'polypeptide', length)
# logging.debug(asym_id)
x = check_range_observed(asym_id, start, end, unobs)
if x:
for y in x:
start = y['PDBstart']
end = y['PDBend']
chain = y['chainID']
selection = "chain %s and resi %s-%s and %s" % (chain, start, end, pdbid)
# logging.debug(selection)
cmd.show(display_type, selection)
cmd.colour("validation_green_background", pdbid)
# display(pdbid, image_type)
cmd.enable(pdbid)
self.geometric_validation(pdbid, res_data)
self.ramachandran_validation(pdbid, rama_data)
# logging.info(stored.residue_dict)
def entities(pdbid):
logging.info('Display entities')
cmd.set("cartoon_transparency", 0.3, pdbid)
cmd.set("ribbon_transparency", 0.3, pdbid)
url = moleculesURL + pdbid
num = 1
if stored.molecule_dict == {}:
stored.molecule_dict = url_response(url, 'molecules')
if pdbid in stored.molecule_dict:
for entity in stored.molecule_dict[pdbid]:
entity_name = ''
if entity['molecule_name']:
if len(entity['molecule_name']) > 1:
for instance, mol in enumerate(entity['molecule_name']):
if mol != entity['molecule_name'][-1]:
mol = mol + "-"
entity_name += mol
else:
entity_name += mol
entity_name = entity_name + '_chimera'
else:
entity_name = entity['molecule_name'][0]
else:
logging.info("No name from the API")
entity_name = "entity_%s" % (entity['entity_id'])
# logging.debug('entity %s: %s' %(entity['entity_id'], entity_name))
# logging.debug(entity['entity_id'])
# see if its polymeric
mol_type = entity['molecule_type']
# entity_name = entity['molecule_name']
if entity_name:
objectName = re.sub(' ', '_', entity_name)
objectName = re.sub(r'\W+', "", objectName)
else:
objectName = "entity_%s" % (entity['entity_id'])
# logging.debug(objectName)
display_type = ""
object_selection = []
pymol_selection = ""
if mol_type != 'Water':
# use asym to find residue number and chain ID
for a in entity['in_struct_asyms']:
if stored.seq_scheme == {}:
poly_seq_scheme(pdbid)
if mol_type == 'Bound':
# bound molecules have no CIFresidue number and this is defaulted to 1 in the API
# logging.debug(entity_name)
# logging.debug(stored.seq_scheme[a])
for res in stored.seq_scheme[a]:
# logging.debug(stored.seq_scheme[a][res])
short = stored.seq_scheme[a][res]
chain = short['chainID']
res = ""
display_type = 'spheres'
# logging.debug(short)
if short['PDBinsCode'] == None:
res = str(short['PDBnum'])
else:
res = str(short['PDBnum']) + short['PDBinsCode']
selection = "chain %s and resi %s and %s" % (chain, res, pdbid)
object_selection.append(selection)
# logging.debug(selection)
else:
# find the first and last residues
unobs = False
start = 1
end = entity['length']
asym_id = a
###need to work out if cartoon is the right thing to display
length = entity['length']
display_type = poly_display_type(asym_id, mol_type, length)
# logging.debug(asym_id)
x = check_range_observed(asym_id, start, end, unobs)
# logging.debug(x)
if x:
for y in x:
start = y['PDBstart']
end = y['PDBend']
chain = y['chainID']
selection = "chain %s and resi %s-%s and %s" % (chain, start, end, pdbid)
# logging.debug(selection)
object_selection.append(selection)
for o in object_selection:
if len(object_selection) > 1:
if o == object_selection[-1]:
pymol_selection += "(%s)" % (o)
else:
pymol_selection += "(%s) or " % (o)
else:
pymol_selection += "%s" % (o)
stored.entities.setdefault(pdbid, {}) \
.setdefault('entity', {}) \
.setdefault(entity['entity_id'], {}) \
.setdefault('selection', {}).setdefault('selection_list', []).append(pymol_selection)
stored.entities[pdbid]['entity'][entity['entity_id']]['selection']['display_type'] = display_type
# logging.debug(pymol_selection)
if len(objectName) > 250:
objectName = objectName[:249]
cmd.select("test_select", pymol_selection)
cmd.create(objectName, "test_select")
# logging.debug(display_type)
cmd.show(display_type, objectName)
# colour by entity.
colour = colour_return(int(entity['entity_id']))
# logging.debug(colour)
cmd.color(colour, objectName)
cmd.delete("test_select")
# cmd.show("cartoon", pdbid)
def show_assemblies(pdbid, mmCIF_file):
"""iterate through the assemblies and output images"""
logging.info('Generating assemblies')
# cmd.hide('everything')
worker_functions().trans_setting('all', 0.0)
try:
assemblies = cmd.get_assembly_ids(pdbid) # list or None
logging.info(assemblies)
if assemblies:
for a_id in assemblies:
logging.info("Assembly: %s" % (a_id))
assembly_name = pdbid + '_assem_' + a_id
logging.info(assembly_name)
cmd.set('assembly', a_id)
cmd.load(mmCIF_file, assembly_name, format='cif')
logging.info('finished Assembly: %s' % (a_id))
except:
logging.info('pymol version does not support assemblies')
def mapping(pdbid):
"""make domain objects"""
if not stored.seq_scheme:
poly_seq_scheme(pdbid)
domain_to_make = ['CATH', 'SCOP', 'Pfam', 'Rfam']
segment_identifier = {'CATH': 'domain', 'SCOP': 'scop_id', 'Pfam': '', 'Rfam': ''}
protein_url = protein_mappingURL + pdbid
nucleic_url = nucleic_mappingURL + pdbid
protein_domains = url_response(protein_url, "protein_domains")
nucleic_domains = url_response(nucleic_url, "nucleic_domains")
for data in [protein_domains, nucleic_domains]:
if data == {}:
logging.info("no domain information for this entry")
else:
for domain_type in data[pdbid]:
if domain_type in domain_to_make:
for domain in data[pdbid][domain_type]:
if data[pdbid][domain_type][domain]['mappings']:
identifier = data[pdbid][domain_type][domain]['identifier']
# logging.debug(domain_type)
# logging.debug(domain)
for mapping in data[pdbid][domain_type][domain]['mappings']:
unobs = False
domain_name = ""
# check segment id
if 'segment_id' in mapping:
domain_segment_id = mapping['segment_id']
else:
# force it to be one if its missing
domain_segment_id = 1
if segment_identifier[domain_type] in mapping:
domain_name = str(mapping[segment_identifier[domain_type]])
# logging.debug("%s: %s" %(domain_name, domain_segment_id))
# then check it exits
start = mapping['start']['residue_number']
end = mapping['end']['residue_number']
chain = mapping['chain_id']
entity_id = mapping['entity_id']
asym_id = mapping['struct_asym_id']
if asym_id in stored.seq_scheme:
x = check_range_observed(asym_id, start, end, unobs)
if x:
for y in x:
start = y['PDBstart']
end = y['PDBend']
stored.domain_dict.setdefault(domain_type, {}) \
.setdefault(domain, {}) \
.setdefault(domain_name, []).append(
{'asym_id': asym_id, 'chain': chain, 'start': start, 'end': end,
'entity_id': entity_id})
def domains(pdbid):
mapping(pdbid)
obj_dict = {}
chain_dict = {}
if stored.domain_dict:
# logging.info(domain_dict)
for domain_type in stored.domain_dict:
for domain in stored.domain_dict[domain_type]:
# logging.debug(domain)
for instance in stored.domain_dict[domain_type][domain]:
asym_list = []
entity_list = []
# logging.debug(instance)
object_selection = []
pymol_selection = ""
for segment in stored.domain_dict[domain_type][domain][instance]:
PDBstart = segment['start']
PDBend = segment['end']
chain = segment['chain']
asym_id = segment['asym_id']
entity_id = segment['entity_id']
asym_list.append(asym_id)
entity_list.append(entity_id)
# chain_dict.update({asym_id: {'chain': chain, 'entity_id': entity_id}})
selection = "chain %s and resi %s-%s and %s" % (chain, PDBstart, PDBend, pdbid)
object_selection.append(selection)
for o in object_selection:
if len(object_selection) > 1:
if o == object_selection[-1]:
pymol_selection += "(%s)" % (o)
else:
pymol_selection += "(%s) or " % (o)
else:
pymol_selection += "%s" % (o)
# logging.debug(pymol_selection)
objectName = "%s_%s_%s" % (domain_type, domain, instance)
obj_dict.update({objectName: {'asym_list': asym_list, 'entity_list': entity_list}})
cmd.select("test_select", pymol_selection)
cmd.create(objectName, "test_select")
num = 1
# logging.debug(obj_dict)
for obj in obj_dict:
# logging.debug(obj)
cmd.enable(obj)
# domain can span multiple asym_id's, could be different type
for i, a in enumerate(obj_dict[obj]['asym_list']):
entity_id = obj_dict[obj]['entity_list'][i]
length = None
for entity in stored.molecule_dict[pdbid]:
if entity_id == entity['entity_id']:
length = entity['length']
display_type = poly_display_type(a, 'polypeptide', length)
cmd.show(display_type, obj)
colour = colour_return(num)
# logging.debug(colour)
cmd.color(colour, obj)
num += 1
cmd.delete("test_select")
def PDBe_startup(pdbid, method, mmCIF_file=None, file_path=None):
if pdbid:
pdbid = pdbid.lower()
if mmCIF_file:
filename = os.path.basename(mmCIF_file)
if re.search('_', filename):
pdbid = re.split('_', filename)[0].lower()
else:
pdbid = re.split('\.', filename)[0].lower()
try:
cmd.set('cif_keepinmemory')
except:
logging.info('version of pymol does not support keeping all cif items')
# check the PDB code actually exists.
url = summaryURL + pdbid
summary = url_response(url, "summary")
if summary:
# clear the dictionaries
stored.domain_dict = {}
stored.seq_scheme = {}
stored.molecule_dict = {}
stored.residue_dict = {}
logging.info('pdbid: %s' % (pdbid))
mid_pdb = pdbid[1:3]
obj_list = cmd.get_object_list('all')
if pdbid not in obj_list:
if mmCIF_file:
file_path = mmCIF_file
else:
# if local file exists then use it
if os.path.exists("%s.cif" % (pdbid)):
logging.info("CIF found in current directory")
file_path = "%s.cif" % (pdbid)
else:
logging.info("fetching %s" % (pdbid))
try:
# connect mode 4 works only with version 1.7 of pymol
cmd.set('assembly', '')
file_path = updated_ftp % pdbid
logging.info('setting connect mode to mode 4')
cmd.set('connect_mode', 4)
except:
logging.info('pymol version does not support assemblies or connect mode 4')
file_path = ebi_ftp % (mid_pdb, pdbid)
logging.info('File to load: %s' % file_path)
cmd.load(file_path, pdbid, format="cif")
cmd.hide("everything", pdbid)
worker_functions().count_poly(pdbid)
if method == "entity":
entities(pdbid)
if method == "domains":
entities(pdbid)
domains(pdbid)
elif method == "validation":
Validation().launch_validation(pdbid)
elif method == 'assemblies':
entities(pdbid)
show_assemblies(pdbid, file_path)
elif method == 'show_assembly':
show_assemblies(pdbid, file_path)
elif method == 'all':
entities(pdbid)
domains(pdbid)
show_assemblies(pdbid, file_path)
Validation().launch_validation(pdbid)
else:
logging.info("provide a method")
cmd.zoom(pdbid, complete=1)
elif mmCIF_file:
logging.info('no PDB ID, show assemblies from mmCIF file')
cmd.load(mmCIF_file, pdbid, format="cif")
# worker_functions().count_poly(pdbid)
show_assemblies(pdbid, mmCIF_file)
else:
logging.info("please provide a 4 letter PDB code")
def __init__(self):
try:
# Simply add the menu entry and callback