-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathSLIDER_VENOM.py
executable file
·1453 lines (1257 loc) · 62.8 KB
/
SLIDER_VENOM.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
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# 15 March 2024
# Author : Rafael Borges
# Objective: Generate amino acid possibilities by residue, fit best rotamer in electron density and calculate their
# side chain and main chain real-space correlation coefficient
# USAGE: SLIDER_VENOM.py pdb_file reflections.mtz map_coeffs.mtz output TRYALL
# pdb_file should be a protein coordinate file with best possible fit against electron density
# reflections.mtz should contain intensities or amplitudes
# map_coeffs.mtz with calculated map (2FOFCWT/PH2FOFCWT)
# output should be a new path, a folder 'output' will contain all SLIDER output and files starting with output will
# summarize information:
# type_of_run (which was TRYALL in example USAGE)
#
# Type_of_run should be a string with keywords and can change how SLIDER is run:
# Amino acid possibilities can be generated in three different scenarios:
# Trying all 20 possibilities for each residue (keyword: TRYALL)
# Possibilities restricted by:
# mass spectrometry (keyword: MASSPEC)
# alignment (keyword: ALIGN)
# If the last two options are chosen, an additional file containing either mass spectrometry or alignment file should be given.
#
# The mass spectrometry file should be a file containing text of amino acids (aa) in one letter code (FASTA), each column should contain generated aa, per example, if 1st and 3rd residue should be a F and T, and 2nd residue either L,D or N, the file should be:
# -------------------------------------------------------------------------
# FLT
# D
# N
# -------------------------------------------------------------------------
#
# Keyword SKIPTEST should be given to skip RAM memory calculation;
#
# Links to the external software of Phenix and Coot should be accessible through the terminal.
#
# Output files:
# output_all.log contains information of chain and residue number, RSCC and delta contrast
# output_Resolved.log same as output_all.log, but only resolved residues
# output_Dubious.log same as output_all.log, but only dubious residues
# output_runline.log has the line used to run SLIDER_VENOM.py
# output_polder_coot_open_maps contains a script to open omit maps in coot (Go to Calculate -> Run Script -> select file)
from __future__ import print_function
from builtins import range
from builtins import bytes, str
import os,sys,time,shutil
import multiprocessing
from collections import defaultdict
import RJB_lib
import numpy
import datetime
import Bio.PDB
import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)
# from Bio import BiopythonParserWarning
# warnings.simplefilter('ignore', BiopythonParserWarning)
# from Bio import BiopythonDeprecationWarning
# warnings.simplefilter('ignore', BiopythonDeprecationWarning)
import re
import subprocess
pdb = sys.argv[1]
mtz_init = sys.argv[2]
mtz_phases = sys.argv[3]
output_folder= sys.argv[4]
typeee = sys.argv[5]
#typeee may be:
#MASSPEC: use partial MASS SPECTROMETRY DATA
#TRYALL: try all possibilities
##CONSTRUCT: add word CONSTRUCT to construct the model while it runs... Desactivated
#SINGLE: for structures composed of single protein
#ALIGN: alignment file
#MAINCHAIN: keep all atoms in residue for generating phenix.polder CC
#now default: SIDECHAIN: skip C, N, O in generating phenix.polder CC
#SELCH: do not calculate chains given in sys.argv[6] , should be A,B,C or A
#SKIPTEST: will not use RAM memory calculation / TEST
#BRAGG: use 40 cores
#ML: calculation of residue depth, number and type of side chain interactions and clashes
if 'SELCH' in typeee: RemoveChains=sys.argv[6].split(',')
else: RemoveChains=False
if 'ML' in typeee: ML=True
else: ML=False
#clashes check VDW radii (0.4 A):
#PON-SC https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1947-7
#Molprobity probe https://www.sciencedirect.com/science/article/abs/pii/S0022283698924007?via%3Dihub
#Table 1. Atomic parameters used in Reduce and Probe
#A. Bond lengths (Å)
# blCH=1.1
# blNH_OH=1.0
# blSH=1.3
# #B. Van der Waals radii (Å)
# vdwH=1.17
# vdwHarom=1.0
# vdwHpol=1.0
# vdwC=1.75
# vdwCcarbonyl=1.65
# vdwN=1.55
# vdwO=1.4
# vdwP=1.8
# vdwS=1.8
#chimera https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
#overlapij = rVDWi + rVDWj – dij – allowanceij
#For detecting clashes, cutoff values of 0.4-1.0 Å and allowance values of 0.2-0.6 Å are generally reasonable (default clash criteria 0.6 and 0.4 Å, respectively).
#hydrogen bond
# 2.2-2.5 Å as “strong, mostly covalent”,
# 2.5-3.2 Å as “moderate, mostly electrostatic”,
# 3.2-4.0 Å as “weak, electrostatic”
#http://biomodel.uah.es/en/water/hbonds.htm
#https://www.researchgate.net/post/What-are-the-standard-values-of-distance-and-angle-cutoffs-to-be-considered-for-hydrogen-bond-formation
#https://en.wikipedia.org/wiki/Van_der_Waals_force
# 4.0-6.0 Å as “weak, electrostatic”
#LigPlus
#https://www.ebi.ac.uk/thornton-srv/software/LigPlus/manual2/manual.html
# hydrogen bond 2.7 Å (H)
# hydrogen bond 3.35 Å (without H)
# non-bonded 2.9 Å (H)
# non-bonded 3.9 Å (without H)
#PLIP
#https://projects.biotec.tu-dresden.de/plip-web/plip/help
# hydrophobic distance 4.0 Å
# hydrogen bond distance 4.1 Å
# pistack distance 7.5 Å
# pi cation distance 6.0 Å
# salt bridge distance 5.5 Å
#https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full
#interaction https://www.frontiersin.org/files/Articles/164719/fmolb-02-00056-HTML/image_m/fmolb-02-00056-g001.jpg
#types of interaction: #https://www.cambridgemedchemconsulting.com/resources/molecular_interactions.html
#Typical Energies Salt Bridge ~2 kcal/mol H-Bond ~1 kcal/mol Hydrophobic ~0.7 kcal/mol Aromatic ~1-3 kcal/mol
#https://www.ncbi.nlm.nih.gov/books/NBK21726/#:~:text=There%20are%20four%20main%20types,1%20to%205%20kcal%2Fmol.
#hydrogen bonds in proteins and nucleic acids are only 1 to 2 kcal/mol
#hydrogen bond in water (≈5 kcal/mol)
#van der Waals interaction is about 1 kcal/mol
#Biomolecular Crystallography Bernhard Rupp
#S-S bond ≈62 kcal/mol
#ionic 3-10 kcal/mol
#Hydrogen 3-7 kcal/mol
#Polar 1-8 kcal/mol
#Van der Waals ≈5 kcal/mol
#Hydrophobic ~0.7 kcal/mol
# I will find only hydrophobic interaction within:
# minimum distance 2.5 Å
# maximum distance 4.0 Å
# use hbplus for hydrogen bond search https://www.ebi.ac.uk/thornton-srv/software/HBPLUS/
#Rotamers
# DicRotamers={'':}
# multiprocessing implementation of phenix.clashscore, done Mar15,2024
def phenixclashscore(clashscore_path, pdb, log):
p = subprocess.Popen([clashscore_path, pdb], stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
out, err = p.communicate()
# print (out)
with open(log, 'w') as f: f.write(out)
# multiprocessing implementation of phenix.rotalize, done Mar15,2024
def phenixrotalize(rotalyze_path, pdb, log):
p = subprocess.Popen([rotalyze_path, pdb], stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
out, err = p.communicate()
with open(log, 'w') as f: f.write(out)
print ('\n\n\n')
now = datetime.datetime.now()
date = now.isoformat()[:10] + ' ' + now.isoformat()[11:16]
print ('Initiating '+sys.argv[0]+' '+date)
RJB_lib.output_runline(output_file=output_folder+'_runline.log',printtt=True)
now = datetime.datetime.now()
date = now.isoformat()[:10] + ' ' + now.isoformat()[11:16]
print ('Running '+sys.argv[0]+' '+date)
nproc=RJB_lib.number_of_processor()
#nproc=100
#nproc=20
#nproc=24
#nproc=48
#nproc=6
if 'BRAGG' in typeee: nproc=40
####Check if files exist and if mtz_phases does not, it generates it with phenix.maps
for i in [pdb,mtz_init,mtz_phases]:
if not os.path.isfile(i):
if i==mtz_phases:
#mtz_phases=pdb[:-4] + '_map_coeffs.mtz'
print ('\nMtz file with 2Fo-Fc map and Fo-Fc not present, generating with phenix.maps with output: '+mtz_phases+'\n')
os.system('phenix.maps '+pdb+' '+mtz_init+' > '+mtz_phases[:-4]+'_run.log')
os.system('mv '+pdb[:-4] + '_map_coeffs.mtz '+mtz_phases)
if not os.path.isfile(mtz_phases):
print ('Failure to generate file. Exiting program')
exit()
else:
print (i , 'file does not exist, exiting program.')
exit()
####Checks if pdb_file contains disordered residues, if so, it removes them.
dic_disorder=RJB_lib.remove_pdb_double_occupancy_atoms_pdb (pdb , pdb[:-4]+'_removed_disordered_atoms.pdb')
#added 20181031 to remove partial occupancy atoms from dictionary
if dic_disorder!=False:
#print 'Removing residues with double occupancy using BioPython:'
#print dic_disorder
print ('The following residues with less than 1.0 occupancy atoms will be kept in model, but will be removed from SLIDER_VENOM evaluation:')
for ch in dic_disorder:
print ('in chain',ch, ' ,'.join(str(x) for x in dic_disorder[ch]))
#exit()
amino_acid_list=['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y']
amino_acid_list_3L=['ALA','CYS','ASP','GLU','PHE','GLY','HIS','ILE','LYS','LEU','MET','ASN','PRO','GLN','ARG','SER','THR','VAL','TRP','TYR']
#dfiles=defaultdict(list)
dic_res=RJB_lib.return_dic_resnumb_list (pdb)
TotResN=0
for ch,listres in dic_res.items():
TotResN+=len(listres)
if dic_disorder:
for ch,listres in dic_disorder.items():
TotResN-=len(listres)
dic_pdb=RJB_lib.return_dic_chain_resnumb_restype (pdb)
#delete empty keys (chains with ligs or waters)
deletekeys=[]
for ch,lres in dic_res.items():
#print ch,lres
if len(lres)==0 or (RemoveChains!=False and ch in RemoveChains):
deletekeys.append(ch)
for delet in deletekeys:
del dic_res[delet]
RJB_lib.mkdir(output_folder)
RJB_lib.mkdir(output_folder+'/'+'mainchain')
dic_pos_aa={}
for ch in dic_res:
dic_pos_aa[ch]=defaultdict(list)
alig=False
if 'ALIGN' in typeee:
alig=True
ali=sys.argv[6]
dic_ali=RJB_lib.generate_dict_count_alignment (ali)
##cc=0
##for resn,lmut in dic_ali.items():
## cc+=len(lmut)
##print cc
##exit()
if 'MAINCHAIN' in typeee: sidechainoption=False
else: sidechainoption=True
if 'MASSPEC' in typeee:
seq=sys.argv[6]
with open(seq) as f: lseq=f.readlines()
#print(dic_pos_aa)
#for i in dic_res['A']:
#Modification to consider multiple chains in MASSPEC input, Mar14,2024
for ch,lres in dic_res.items():
#print ('\n')
for imasspec,ires in enumerate(lres):
#print (ires)
if 'MASSPEC' in typeee:
#EvalResMASSPEC=''
for line in lseq:
if line.startswith('>'): chmasspec=line[-2]
#print (chmasspec)
elif ch==chmasspec:
if imasspec<len(line) and line[imasspec] not in [' ','-','\n']:
#print ('here',line[imasspec])
#exit()
if line[imasspec] in dic_pos_aa[ch][ires]:
print ('Repeated aminoacid',line[imasspec-1],'found in the file\n',seq)
print ('Please correct it.')
exit()
dic_pos_aa[ch][ires].append(line[imasspec])
#EvalResMASSPEC+=line[imasspec]
# if EvalResMASSPEC=='':
# for a in amino_acid_list:
# dic_pos_aa[ch][i].append(a)
elif 'TRYALL' in typeee:
for a in amino_acid_list:
dic_pos_aa[ch][ires].append(a)
#print(dic_pos_aa)
####CONVERT SINGLE CHAIN TO ALL CHAINS
##chall=''
##lch=[]
##for ch in dic_pos_aa:
## print ch
## chall+=ch
## lch.append(ch)
##dic_pos_aa[chall]=dic_pos_aa['A']
##for delet in lch:
## del dic_pos_aa[delet]
##for ch in dic_pos_aa:
## print ch
if 'MASSPEC' not in typeee and 'TRYALL' not in typeee and 'ALIGN' not in typeee:
print ('Failure. Wrong option for typeee.')
exit()
if 'SINGLE' in typeee:
newkey=''
for ch in dic_pos_aa:
newkey+=ch
newd=dic_pos_aa[ch]
dic_pos_aa={newkey:newd}
if 'ALIGN' in typeee and not 'MASSPEC' in typeee and not 'TRYALL' in typeee:
for ch in dic_pos_aa:
for i in dic_ali:
for a in dic_ali[i]:
dic_pos_aa[ch][i].append(a)
#check if coot script mutate is going to work:
##dchkcoot={}
##lseq=[]
##for ch,d1 in dic_pdb.items():
## sseq=''
## dchkcoot[ch]={}
## for resn,d2 in d1.items():
## if not d2=='A':
## dchkcoot[ch][resn]='A'
## sseq+='A'
## else:
## dchkcoot[ch][resn]='T'
## sseq+='T'
## lseq.append(sseq)
###print dchkcoot
##RJB_lib.coot_run_rotamer_sphere_refinement_multi ( input_PDB_file=pdb , input_mtz_file=mtz_phases , output_pdb='testcootmutatefn.pdb' , outputCootPy='testcootmutatefn.py' , dic=dchkcoot , radius_sph_ref=0 , coot_path=False )
###chcheckcoot,seqcheckcoot,tnrescheckcoot=RJB_lib.extract_protein_chainID_res_number('testcootmutatefn.pdb')
##seqcheckcoot=RJB_lib.return_restype_list ('testcootmutatefn.pdb')
##checkcoot=True
##print 'seqcheckcoot',seqcheckcoot
##print 'lseq ',lseq
##for i,s in enumerate (seqcheckcoot):
## for ii,aa in enumerate(s):
## if aa!=lseq[i][ii]:
## print 'COOT MUTATE FUNCTION DID NOT WORK WITH RESIDUE NUMBER',ii+1,'!!! By my testing, I would say that the residue has not all main chain atoms partially occupied, this should be the reason. Please make sure to change until coot mutate works and change PDB input file.'
## checkcoot=False
##if not checkcoot:
## print 'Exitting now'
## exit()
#all resn that only has one possibility will be first integrated into model
#if 'MASSPEC' in typeee:
dic_seq_initial=RJB_lib.return_dic_sequence(pdb)
d_imp={}
impr=False
listchains=[]
for ch,dires in dic_pos_aa.items():
listchains.append(ch)
for i,lmut in dires.items():
if len(lmut)==1 and dic_seq_initial[ch][ dic_res[ch].index(i) ]!=lmut[0]:
try:
d_imp[ch][i]=lmut[0]
impr=True
except:
d_imp[ch]={}
d_imp[ch][i]=lmut[0]
impr=True
# if impr:
# print 'Improving initial model to model residues that were given only one possibility. If the residue were already a component of that position in the initial model, then no improvement will be done in that specific residue.'
# print 'Initial PDB:',pdb,'will be saved to',output_folder+'/'+pdb[:-4]+'_imp_single_possibilities.pdb'
# if not os.path.isfile(output_folder+'/'+pdb[:-4]+'_imp_single_possibilities.pdb'):
# RJB_lib.coot_run_rotamer_sphere_refinement_multi ( input_PDB_file=pdb , input_mtz_file=mtz_phases , output_pdb=output_folder+'/'+pdb[:-4]+'_imp_single_possibilities.pdb' , outputCootPy=output_folder+'/'+pdb[:-4]+'_imp_single_possibilities.py' , dic=d_imp , radius_sph_ref=500 , removeWAT=False, coot_path=False )
# pdb=output_folder+'/'+pdb[:-4]+'_imp_single_possibilities.pdb'
# #coot_run_rotamer_sphere_refinement_multi ( input_PDB_file , input_mtz_file , output_pdb , outputCootPy , dic , radius_sph_ref=5 , coot_path=False )
####RUNNING AREAIMOL FOR SIDE CHAIN ATOMS
if not os.path.isfile (pdb[:-4]+'-areaimol.pdb'): RJB_lib.runAREAIMOLccp4_bigMolec (pdbfile=pdb,outpdb=pdb[:-4]+'-areaimol.pdb',listchains=listchains)
#added 20181031 to remove partial occupancy atoms from dictionary
if dic_disorder!=False:
for ch in dic_disorder:
for resn in dic_disorder[ch]:
if resn in dic_pos_aa[ch]: del dic_pos_aa[ch][resn]
################added 20181109 to test maximum RAM memory usage
if 'SKIPTEST' in typeee:
print ('Test of RAM memory usage for coot and polder jobs was selected to be skipped.')
NewNProcCoot=nproc
NewNProcPolder=nproc
else:
ch=list(dic_pos_aa.keys())[0]
dires=dic_pos_aa[ch]
resn=list(dic_pos_aa[ch].keys())[0]
stresn=str(resn)
#a=lmut[0]
a='A'
# print 'Chain',ch
# print 'Residue number',resn
# print 'Residue type',a
print ('\nTesting RAM Memory usage of coot & phenix.polder processes with chain',ch,'Residue number',resn,'Residue type',a)
counterr=0
ifmem=RJB_lib.GetFreeMemory()
for i in range(9):
varmem=float( RJB_lib.GetFreeMemory() )
if varmem<ifmem: ifmem=varmem
time.sleep(0.1)
print ('\nFree Memory before runnning external programs',ifmem,'Mb')
####RUNNING COOT MODELING
aa = amino_acid_list_3L[amino_acid_list.index(a)]
# COOT section
outf = output_folder + '/test-mem-coot-' + stresn + a + ''
dic = {}
for c in ch:
dic[c] = {resn: a}
# print dic
# print 'Running coot mutate, rotamer search and sphere refine in chain',ch,'and residue',stresn,'with side chain',aa,'from file:',pdb,'to save in:',outf+'.pdb'
process = multiprocessing.Process(target=RJB_lib.coot_mutate_sph_ref_correcting_files, args=(pdb, mtz_phases, outf + '.pdb', dic, dic_pdb, 5, True, False))
# coot_mutate_sph_ref_correcting_files (pdb,mtz_phases,outpdb,dic,dic_pdb radius_sph_ref=5, coot_path=False , printtt=False)
process.start()
vcootfmem=RJB_lib.GetFreeMemory()
#time.sleep(0.1)
# break
#wait coot jobs finish
while len(multiprocessing.active_children()) != 0:
varmem=float( RJB_lib.GetFreeMemory() )
if varmem<vcootfmem: vcootfmem=varmem
#print RJB_lib.GetFreeMemory()
time.sleep(0.1)
#break
print ('\nFree memory running 1 process of coot =',vcootfmem)
cootfmem=ifmem-vcootfmem
print ('Maximum RAM memory spent on coot',cootfmem,'Mb')
#print '\nNow with phenix.polder'
####RUNNING PHENIX.POLDER
#polder section
pdbinput=str(outf)+'.pdb'
outf = str ( output_folder + '/test-mem-polder' + stresn + a )
dic={ch:{resn:a}}
#print dic
#process = multiprocessing.Process(target= RJB_lib.coot_run_rotamer_sphere_refinement_multi , args= ( pdb=pdb,mtz=mtz,output=outf,ch=ch,resn=resn,rest3L_mutate=aa , coot_path=False , polder_path=False ) )
output_map=True
# while 1:
process = multiprocessing.Process(target= RJB_lib.run_phenix_polder_multiproc , args= ( pdbinput , mtz_init , dic , outf+'.log' , False , output_map , sidechainoption) )
#run_phenix_polder_multiproc ( pdb , mtz_init , dic , output , polder_path=polder_path, output_mtz=True) #dic should be dic[chain][resn]
print ('Running phenix.polder to calculate CC of refine in chain(s)',ch,'and residue',stresn,'with side chain',aa,'from file:',pdbinput,'to save in:',outf+'.log\n')
process.start()
vpolderfmem=RJB_lib.GetFreeMemory()
#wait phenix.polder jobs finish
while len(multiprocessing.active_children()) != 0:
varmem=float( RJB_lib.GetFreeMemory() )
if varmem<vpolderfmem: vpolderfmem=varmem
time.sleep(0.1)
print ('\nFree memory running 1 process of polder =',vpolderfmem)
polderfmem=ifmem-vpolderfmem
print ('Maximum RAM memory spent on polder',polderfmem,'Mb')
# '\nIt was found',nproc,'processors (counting HyperThreading if available).'
# '600 Mb will be left free as tolerance and to be free for other programs.'
if cootfmem<1.0: cootfmem=1.0
if polderfmem < 1.0: polderfmem = 1.0
NewNProcCoot= int ( (ifmem-600)/cootfmem )
NewNProcPolder= int ( (ifmem-600)/polderfmem )
print ('There is',ifmem-600,'available RAM memory')
print ('To be divided to',cootfmem,'for coot jobs')
print ('To be divided to',polderfmem,'for polder jobs')
if NewNProcCoot==0 or NewNProcPolder==0:
print ('Run requires more RAM memory than available.')
exit()
else:
if NewNProcCoot > nproc: NewNProcCoot = int(nproc)
if NewNProcPolder > nproc: NewNProcPolder = int(nproc)
print ('\nTherefore, it will be used:')
print (NewNProcCoot ,'processors for coot jobs.')
print (NewNProcPolder,'processors for polder jobs.')
################added 20181109 to test maximum RAM memory usage END
#As coot now uses multiple CPUs, I am reducing by 4 the #CPU processors running coot.
NewNProcCoot=int(NewNProcCoot/4)
print ('As coot now uses multiple CPUs, I am reducing by 4 the #CPU processors running coot.')
print (NewNProcCoot ,'processors for coot jobs.')
#Run Residue Depth from https://biopython.org/docs/1.75/api/Bio.PDB.ResidueDepth.html
if ML:
if not os.path.isfile(output_folder+'_ResDepth.log'):
parser = Bio.PDB.PDBParser()
structure = parser.get_structure("ResDepth", pdb)
model = structure[0]
rd = Bio.PDB.ResidueDepth(model)
resdepth=open(output_folder+'_ResDepth.log','w')
resdepth.write('Ch\tResN\tResDepth')
for ch,dires in dic_pos_aa.items():
for resn,lmut in dires.items():
#print(ch,resn,lmut)
resdepthvar=rd[ch, (' ', resn, ' ')]
resdepthvar='%.1f'%(resdepthvar[1])
resdepth.write('\n'+ch+'\t'+str(resn)+'\t'+resdepthvar)
RJB_lib.mkdir(output_folder+'/eval')
for ch,dires in dic_pos_aa.items():
#print ch
RJB_lib.mkdir(output_folder+'/'+ch)
RJB_lib.mkdir(output_folder + '/eval/'+ch)
for resn,lmut in dires.items():
print ('\nEvaluating chain',ch,'and residue',resn,' with: ',', '.join(lmut),' (total: ',str(len(lmut))+')')
print ('Running coot mutate, rotamer search and sphere refine')
#print lmut
#print resn
stresn=str(resn)
outfold=output_folder+'/'+ch+'/'+stresn+'/'
RJB_lib.mkdir(outfold)
if (not os.path.isfile(outfold+ch+'_'+stresn+'_polder.log')):
####RUNNING COOT MODELING
#print (lmut)
for a in lmut:
#print a
aa=amino_acid_list_3L[amino_acid_list.index(a)]
#COOT section
outf=outfold+stresn+a+''
dic={}
for c in ch:
dic[c]={resn:a}
#print dic
if not os.path.isfile( outf+'.pdb' ):
if NewNProcCoot > -1: #NOTE: PROCESSES es el numero de cores que quieres lanzar, default == numero de cores-1
# print "I found ", sym.REALPROCESSES, "CPUs." #NOTE: REALPROCESSES es el numero de cores de tu ordenador
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) < NewNProcCoot:
#print 'Running coot mutate, rotamer search and sphere refine in chain',ch,'and residue',stresn,'with side chain',aa,'from file:',pdb,'to save in:',outf+'.pdb'
process = multiprocessing.Process(target= RJB_lib.coot_mutate_sph_ref_correcting_files , args= ( pdb , mtz_phases , outf+'.pdb' , dic ,dic_pdb, 5, False , False ) )
#coot_mutate_sph_ref_correcting_files (pdb,mtz_phases,outpdb,dic,dic_pdb=False, radius_sph_ref=5, removeWAT=False , coot_path=False , printtt=False)
process.start()
time.sleep(0.1)
break
else:
print ("FATAL ERROR: I cannot load correctly information of CPUs.")
exit()
# wait coot jobs finish
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) == 0:
break
if ML:
for ch,dires in dic_pos_aa.items():
for resn,lmut in dires.items():
#Evaluation of clashes and interactions (hydrogen / SS-bond / hydrophobic) and their energy
stresn = str(resn)
outfold = output_folder + '/' + ch + '/' + stresn + '/'
outfold2=output_folder + '/eval/'+ch+'/'+stresn
#print ('Generating files in',outfold2)
RJB_lib.mkdir(outfold2)
# fwclashes.write(str(resn))
#if not os.path.isfile(outfold2+'/'+ch+'_'+stresn+'_clash.log') and not os.path.isfile(outfold2+'/'+ch+'_'+stresn+'_nInt.log'):
if True:
print ('Calculating clashes and interactions in folder',outfold2)
# Found a water molecule (from symmetry) laying in top of 2B04/A1E, need to remove waters
for a in lmut:
#print(ch, stresn,a)
outi = output_folder+'/'+ch+'/'+stresn+'/'+stresn+a+'.pdb'
outf = outfold2 +'/'+ stresn + a + '.pdb'
# t1 = time.time()
if not os.path.isfile(outf):
#RJB_lib.GenerateSym(pdbin=outi,pdbout=outf,dist=5.5)
RJB_lib.GenerateSymKeepNearRes(pdbin=outi,pdbout=outf, ch=ch, NRes=stresn, dist=5.5, pymolpath='pymol', pymolins='')
# t2 = time.time()
#print (a)
LRemoveWatChResnVar=RJB_lib.CheckWatersFromSymmetry(pdbin=outi,pdbsym=outf,chf=ch,resnf=resn,dist=2.5)
RJB_lib.RemoveWat(LChResnWat=LRemoveWatChResnVar,pdbin=outf,pdbout=outf)
#print (a,LRemoveWatChResnVar)
#ldiff=RJB_lib.CheckWatPDBs(pdb1=output_folder+'/'+ch+'/'+stresn+'/'+stresn+a+'.pdb2',pdb2=output_folder+'/'+ch+'/'+stresn+'/'+stresn+a+'.pdb')
#if ldiff!=[]: print (resn,a,ldiff)
#exit()
#t2 = time.time()
for a in lmut:
outi = output_folder+'/'+ch+'/'+stresn+'/'+stresn+a+'.pdb'
outf = outfold2 +'/'+ stresn + a + '.pdb'
RJB_lib.ChangeChSym(pdbin=outf,pdbout=outf)
outfhbplus=outf[:-4]+'_4hbplus.pdb'
loghbplus=outfhbplus[:-3]+'hb2'
outfphenixclash=outf[:-4]+'_4phenix.clash.pdb'
logfphenixclash=outfphenixclash[:-3]+'log'
logfclash=outf[:-4]+'_clash.log'
#print('checking files ' + outfhbplus + ' ' + outfphenixclash + ' ' + outf[:-4] + '_dist.log ' + logfclash)
if not os.path.isfile(outfhbplus) and not os.path.isfile(outfphenixclash) and not os.path.isfile(outf[:-4]+'_dist.log') and not os.path.isfile(logfclash):
#print('checking files '+outfhbplus+' '+outfphenixclash+' '+outf[:-4]+'_dist.log'+logfclash)
RJB_lib.RemoveCheckResAboveDist(pdbin=outf,chf=ch,resnf=resn,pdboutshort=outfhbplus,pdboutlarge=outfphenixclash,distout=outf[:-4]+'_dist.log',clashout=logfclash,distint=4.0,distclash=2.4)
# Single processor
# if not os.path.isfile(logfphenixclash): # os.system('phenix.rotalyze '+outfold2+res+'.pdb > '+outfold2+res+'.log')
# os.system('phenix.clashscore ' + outfphenixclash + ' > ' + logfphenixclash)
#Multiprocessing
# print('Checking files ' + outfphenixclash + ' ' + logfphenixclash)
# print('Checking file1 '+outfphenixclash , os.path.isfile(outfphenixclash))
# print('Checking file2 ' + logfphenixclash , os.path.isfile(logfphenixclash))
if not os.path.isfile(logfphenixclash):
# print('Checking file2.2 ' + logfphenixclash, os.path.isfile(logfphenixclash))
if nproc > -1: # NOTE: PROCESSES es el numero de cores que quieres lanzar, default == numero de cores-1
# print "I found ", sym.REALPROCESSES, "CPUs." #NOTE: REALPROCESSES es el numero de cores de tu ordenador
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) < nproc:
#print('Running phenix.clashscore', outfphenixclash,logfphenixclash)
process = multiprocessing.Process(target=phenixclashscore, args=(
'phenix.clashscore', outfphenixclash,logfphenixclash))
process.start()
time.sleep(0.1)
break
else:
print("FATAL ERROR: I cannot load correctly information of CPUs.")
exit()
# exit()
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) == 0:
break
#t3 = time.time()
# for a in lmut:
# outfphenixclash=outf[:-4]+'_4phenix.clash.pdb'
# logfphenixclash=outfphenixclash[:-3]+'log'
#
# if not os.path.isfile(logfphenixclash):
# os.system('phenix.clashscore ' + outfphenixclash + ' > '+logfphenixclash)
# for a in lmut: fwclash.write()
for ch, dires in dic_pos_aa.items():
for resn,lmut in dires.items():
stresn=str(resn)
if ML:
outfold2=output_folder + '/eval/'+ch+'/'+stresn
fwclash = open(outfold2 + '/' + ch + '_' + stresn + '_clash.log', 'w')
fwclash.write('Aa\tSClDist\tPhClSum\tPhClSc')
fwInt = open(outfold2 + '/' + ch + '_' + stresn + '_nInt.log', 'w')
fwInt.write('Aa\tnSSb\tnHb\tnSalt\tnHydInt\tEnergy')
for a in lmut:
outi = output_folder+'/'+ch+'/'+stresn+'/'+stresn+a+'.pdb'
outf = outfold2 +'/'+ stresn + a + '.pdb'
# t2 = time.time()
RJB_lib.ChangeChSym(pdbin=outf,pdbout=outf)
# t3 = time.time()
outfhbplus=outf[:-4]+'_4hbplus.pdb'
loghbplus=outfhbplus[:-3]+'hb2'
outfphenixclash=outf[:-4]+'_4phenix.clash.pdb'
logfphenixclash=outfphenixclash[:-3]+'log'
logfclash=outf[:-4]+'_clash.log'
# if not os.path.isfile(outfhbplus) and not os.path.isfile(outfphenixclash) and not os.path.isfile(outf[:-4]+'_dist.log') and not os.path.isfile(logfclash):
# RJB_lib.RemoveCheckResAboveDist(pdbin=outf,chf=ch,resnf=resn,pdboutshort=outfhbplus,pdboutlarge=outfphenixclash,distout=outf[:-4]+'_dist.log',clashout=logfclash,distint=4.0,distclash=2.4)
SumClashDist,nSSb=RJB_lib.RetrieveSumClashSSbond(clashin=logfclash,maxdist=2.5)
# if not os.path.isfile(logfphenixclash):
# os.system('phenix.clashscore ' + outfphenixclash + ' > '+logfphenixclash)
#print (logfphenixclash)
clashscore,clashscoresum=RJB_lib.readPhenixClashscore(log=logfphenixclash,chf=ch,resnf=resn)
SumClashDist,clashscoresum,clashscore='%.1f'%(SumClashDist),'%.1f'%(clashscoresum),'%.1f'%(clashscore)
#print (a,SumClashDist,clashscoresum,clashscore )
fwclash.write('\n'+a+'\t'+SumClashDist+'\t'+clashscoresum+'\t'+clashscore)
# print (clashscore,clashscoresum)
#os.remove(outf)
# t4 = time.time()
# print('t of GenerateSym = ',t2-t1)
# print('t of ChangeChSym = ', t3 - t2)
# print('t of RemoveCheckResAboveDist = ', t4 - t3)
if not os.path.isfile(loghbplus):
os.system('hbplus '+outfhbplus+' > /dev/null')
# print (loghbplus[loghbplus.rindex('/')+1:],loghbplus)
shutil.move(loghbplus[loghbplus.rindex('/')+1:],loghbplus)
nH,nSalt=RJB_lib.ReturnHSaltbonds(login=loghbplus,chf=ch,resnf=resn)
#print (loghbplus,nH)
nHydInt=RJB_lib.ReturnHydInt(login=outf[:-4]+'_dist.log')
energySC=62*nSSb+(nH+nSalt)*3+nHydInt*0.7
senergySC='%.1f'%(energySC)
fwInt.write('\n'+a+'\t'+str(nSSb)+'\t'+str(nH)+'\t'+str(nSalt)+'\t'+str(nHydInt)+'\t'+senergySC) #'Aa\tnSSb\tnHb\tnSalt\tnHydInt\tEnergy')
#exit()
#RJB_lib.Run_hbplus(pdbin=outi,hbplus='/home/rborges/LigPlus/lib/exe_linux64/hbplus')
# print (outf)
# exit()
#exit()
fwclash.close()
fwInt.close()
#t4 = time.time()
# print('running All evalutation clashscore', t3 - t2)
# print('running Post evalutation clashscore', t4 - t3)
if ML:
#Join information from clashes
with open(output_folder+'_clashes.log','w') as fwclash:
fwclash.write('Ch\tResN\tResT\tSClDist\tPhClSum\tPhClSc\n\n')
for ch,dires in dic_pos_aa.items():
for resn in dires:
stresn=str(resn)
outfold2 = output_folder + '/eval/' + ch + '/' + stresn
with open(outfold2+'/'+ ch+'_'+stresn + '_clash.log') as f: fr=f.readlines()
for l in fr[1:]: fwclash.write(ch+'\t'+stresn+'\t'+l)
fwclash.write('\n\n')
#Join information from interaction
with open(output_folder+'_interaction.log','w') as fwInt:
fwInt.write('Ch\tResN\tResT\tnSSb\tnHb\tnSalt\tnHydInt\tEnergy\n\n')
for ch,dires in dic_pos_aa.items():
for resn in dires:
stresn=str(resn)
outfold2 = output_folder + '/eval/' + ch + '/' + stresn
with open(outfold2+'/'+ ch+'_'+stresn + '_nInt.log') as f: fr=f.readlines()
for l in fr[1:]: fwInt.write(ch+'\t'+stresn+'\t'+l)
fwInt.write('\n\n')
# ROTAMER EVALUATION
DicRotResults={} # dic that contains rotamer results [ch][resn][restype]=Favored/Allowed/OUTLIER
for res in ['C', 'D', 'E', 'F', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y' ]:
fwrot=open(output_folder+'_rotamers.log','w')
#output labels in output_folder+'_rotamers.log'
fwrot.write('Ch\tResN')
for r in ['C', 'D', 'E', 'F', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']: fwrot.write('\t'+r)
DicRot=defaultdict(list) # dic that contains what residues were evaluated
for ch,dires in dic_pos_aa.items():
if ch not in DicRotResults: DicRotResults[ch]={}
for resn, lmut in dires.items():
if res in lmut: DicRot[ch].append(resn)
outfold2 = output_folder + '/eval/'
countatom=1
#for each amino acid type, output pdb file containing all of residues within this aa type
if not os.path.isfile(outfold2+res+'.pdb'):
with open(outfold2+res+'.pdb','w') as fwpdb:
for ch,lresn in DicRot.items():
for resn in lresn:
stresn=str(resn)
with open(output_folder+'/'+ch+'/'+stresn+'/'+stresn+res+'.pdb') as f: fr=f.readlines()
for l in fr:
if l.startswith('ATOM') and l[21]==ch and int(l[22:26])==resn:
#correct atom number
scountatom=str(countatom)
l='ATOM'+' '*(7-len(scountatom))+scountatom+l[11:]
if l[72]==' ': l=l[:72]+l[21]+l[73:]
fwpdb.write(l)
countatom+=1
#print (outfold2+res+'.pdb')
#print ('phenix.rotalyze '+outfold2+res+'.pdb > '+outfold2+res+'.log')
#exit()
for res in ['C', 'D', 'E', 'F', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']:
if not os.path.isfile(outfold2+res+'.log'): #os.system('phenix.rotalyze '+outfold2+res+'.pdb > '+outfold2+res+'.log')
if nproc > -1: # NOTE: PROCESSES es el numero de cores que quieres lanzar, default == numero de cores-1
# print "I found ", sym.REALPROCESSES, "CPUs." #NOTE: REALPROCESSES es el numero de cores de tu ordenador
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) < nproc:
print ('Running phenix.rotalyze',outfold2+res+'.pdb > ',outfold2+res+'.log')
process = multiprocessing.Process(target=phenixrotalize, args=('phenix.rotalyze', outfold2+res+'.pdb',outfold2+res+'.log'))
process.start()
time.sleep(0.1)
break
else:
print("FATAL ERROR: I cannot load correctly information of CPUs.")
exit()
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) == 0:
break
for res in ['C', 'D', 'E', 'F', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']:
with open(outfold2+res+'.log') as f: fr=f.readlines()
for l in fr[1:-1]:
ch=l[1]
resn=int(l[2:6])
l=l.split(':')
rottype=l[-1]
rotval=l[-2]
if resn not in DicRotResults[ch]: DicRotResults[ch][resn]={}
DicRotResults[ch][resn][res]=rotval
for ch,dicresnaarot in DicRotResults.items():
for resn,dicaarot in dicresnaarot.items():
fwrot.write('\n'+ch+'\t'+str(resn))
for aa,rotval in dicaarot.items():
fwrot.write('\t'+rotval)
for ch, dires in dic_pos_aa.items():
#print (ch)
RJB_lib.mkdir(output_folder + '/' + ch)
for resn, lmut in dires.items():
#print('resn', resn)
#print('lmut', lmut)
stresn=str(resn)
outfmc=output_folder + '/mainchain/' + ch + stresn + '.pdb'
if not os.path.isfile(outfmc):
dic = {}
for c1 in ch:
#print ('c1',c1)
for c in c1:
#print ('c',c)
#print ('dic_pdb[c][resn]',dic_pdb[c][resn])
dic[c] = {resn:dic_pdb[c][resn]}
RJB_lib.remove_Bfactor_occ_res_pdb(pdb_input=pdb,pdb_output=outfmc,dic_ch_resn=dic,AtomsExclude=[],AtomsInclude=['CA','N ','C ','O '])
# I was writing all atoms names to be excluded,but decided to do the opposite
# ['CB','CD','CE','CG','CZ','ND','NE','NZ','OD','SD','SG'] )
#['CB ' ,'SG ' ,'CG1','OD1','OD2','CG ','CD1','CD2','CE1','CE2', 'CZ','ND1','NE2','CG1','CG2', 'SD ','CE ','','','','','','',''] )
#A/ALA,C/CYS,D/ASP, F/PHE G/GLY0 H/HIS I/ILE L/LEU M/MET N/ASN
#wait coot jobs finish
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) == 0 :
break
####RUNNING PHENIX.POLDER
for ch, dires in dic_pos_aa.items():
# print ch
for resn, lmut in dires.items():
print ('\nEvaluating chain', ch, 'and residue', resn, ' with: ', ', '.join(lmut), ' (total: ', str(len(lmut)) + ')')
print ('Running phenix.polder to calculate CC of refine in chain(s)\n') # print lmut
# print resn
stresn = str(resn)
outfold = output_folder + '/' + ch + '/' + stresn + '/'
RJB_lib.mkdir(outfold)
if (not os.path.isfile(outfold + ch + '_' + stresn + '_polder.log')):
for a in lmut:
#print a
aa=amino_acid_list_3L[amino_acid_list.index(a)]
#polder section
outf=outfold+stresn+a+''
dic={ch:{resn:a}}
pdbinput=outfold+stresn+a+'.pdb'
#print dic
if not os.path.isfile( outf+'.log' ):
if NewNProcPolder > -1: #NOTE: PROCESSES es el numero de cores que quieres lanzar, default == numero de cores-1
# print "I found ", sym.REALPROCESSES, "CPUs." #NOTE: REALPROCESSES es el numero de cores de tu ordenador
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) < NewNProcPolder:
#process = multiprocessing.Process(target= RJB_lib.coot_run_rotamer_sphere_refinement_multi , args= ( pdb=pdb,mtz=mtz,output=outf,ch=ch,resn=resn,rest3L_mutate=aa , coot_path=False , polder_path=False ) )
if 'A' in lmut:
output_map=False
if a=='A':
output_map=True
else:
output_map=True
process = multiprocessing.Process(target= RJB_lib.run_phenix_polder_multiproc , args= ( pdbinput , mtz_init , dic , outf+'.log' , False , output_map , sidechainoption) )
#run_phenix_polder_multiproc ( pdb , mtz_init , dic , output , polder_path=polder_path, output_mtz=True) #dic should be dic[chain][resn]
#print 'Running phenix.polder to calculate CC of refine in chain(s)',ch,'and residue',stresn,'with side chain',aa,'from file:',pdbinput,'to save in:',outf+'.log\n'
process.start()
time.sleep(0.1)
break
else:
print ("FATAL ERROR: I cannot load correctly information of CPUs.")
exit()
####RUNNING PHENIX.POLDER MAIN CHAIN
for ch, dires in dic_pos_aa.items():
# print ch
for resn, lmut in dires.items():
print ('Running phenix.polder to calculate RSCC of main chain atoms of residue',resn,'in chain(s)', ch)
#print '\n' # print lmut
# print resn
stresn = str(resn)
outfmc = output_folder + '/mainchain/' + ch + stresn + '_polder.log'
if (not os.path.isfile(outfmc)):
#polder section
dic={ch:{resn:a}}
pdbinput=outfmc[:-11]+'.pdb'
#print dic
if not os.path.isfile( outfmc ):
if NewNProcPolder > -1: #NOTE: PROCESSES es el numero de cores que quieres lanzar, default == numero de cores-1
# print "I found ", sym.REALPROCESSES, "CPUs." #NOTE: REALPROCESSES es el numero de cores de tu ordenador
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) < NewNProcPolder:
#process = multiprocessing.Process(target= RJB_lib.coot_run_rotamer_sphere_refinement_multi , args= ( pdb=pdb,mtz=mtz,output=outf,ch=ch,resn=resn,rest3L_mutate=aa , coot_path=False , polder_path=False ) )
output_map=True
process = multiprocessing.Process(target= RJB_lib.run_phenix_polder_multiproc , args= ( pdbinput , mtz_init , dic , outfmc , False , output_map , 'OnlyMainChain') )
#run_phenix_polder_multiproc ( pdb , mtz_init , dic , output , polder_path=polder_path, output_mtz=True) #dic should be dic[chain][resn]
#print 'Running phenix.polder to calculate CC of refine in chain(s)',ch,'and residue',stresn,'with side chain',aa,'from file:',pdbinput,'to save in:',outf+'.log\n'
process.start()
time.sleep(0.1)
break
else:
print ("FATAL ERROR: I cannot load correctly information of CPUs.")
exit()
while 1:
time.sleep(0.1)
if len(multiprocessing.active_children()) == 0:
break
#Dictionary of CC1/3
dicallSC={}
print ('Building Summary of polder RSCC (cc13) of side chain atoms')
###SUMMARY RESULTS PHENIX.POLDER BY CHAIN AND BY RESIDUE NUMBER
quitt = False
for ch, dires in dic_pos_aa.items():
dicallSC[ch]={}
# print ch
for resn, lmut in dires.items():
dicallSC[ch][resn]=[]
stresn=str(resn)
outfold=output_folder+'/'+ch+'/'+stresn+'/'
#if not os.path.isfile(outfold+ch+'_'+stresn+'_polder.log'):
ou2=open(outfold+ch+'_'+stresn+'_polder.log','w')
ou2.write('Residue\tCC1,3\tR\tRfree\tRimp\tRfImp\tRimp')
lisel=[]
for a in lmut:
aa=amino_acid_list_3L[amino_acid_list.index(a)]
outlog=outfold+stresn+a+'.log'
try: di=RJB_lib.extract_CC_R_Rfree_from_polder_log (outlog)
except:
print ('Failure extracting CC, R, Rfree of file:',outlog)
di = False
quitt = True
#exit()
if di!=False:
lisel.append( (a,di['cc13'],di) )
if dic_pdb[ch[0]][resn]==a: dicallSC[ch][resn].append( [a+'!',di['cc13']] )
else: dicallSC[ch][resn].append( [a,di['cc13']] )
#d={'cc13':cc13,'rmodel':rmodel,'rfreemodel':rfreemodel,'rexcl':rexcl,'rfreeexcl':rfreeexcl,'rimpr':rimpr,'rfreeimpr':rfreeimpr}
#'\t'+di['cc13']+'\t'+di[]+'\t'++'\t'+)
lisel=sorted(lisel,key=(lambda item: item[1]), reverse=True)
#for i in lisel[0]:
for i in lisel:
di=i[2]
for key,value in di.items():
di[key]='%.3f'%(value)
tab=['cc13','rmodel','rfreemodel','rimpr','rfreeimpr','rsimpr']
ou2.write('\n'+i[0])
if dic_pdb[ch[0]][resn]==i[0]:
ou2.write('!')
for t in tab: