-
Notifications
You must be signed in to change notification settings - Fork 22
/
QresFEP.py
executable file
·1190 lines (995 loc) · 49.7 KB
/
QresFEP.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
import argparse
import re
import os
import shutil
import sys
import glob
import functions as f
import settings as s
import IO
class Run(object):
"""
Setup residue FEPs using either a single or dual topology approach
"""
def __init__(self,
cofactor,
mutation,
include,
forcefield,
windows,
sampling,
system,
cluster,
rest_shell_width,
temperature,
replicates,
dual,
preplocation,
start,
*args,
**kwargs):
self.cofactor = [cofactor]
# Check whether all required files are there:
required = ['protein.pdb', 'water.pdb', 'protPREP.log']
if self.cofactor[0] != None:
extension = ['.pdb', '.lib', '.prm']
for filename in self.cofactor:
for line in extension:
required.append(filename + line)
for filename in required:
if os.path.exists(filename) == False:
required = ' '.join(required)
print("ERROR: {} are required files, exiting now.".format(required))
sys.exit()
if windows == None:
self.windows = s.WINDOWS
else:
self.windows = int(windows)
if sampling == None:
self.sampling = s.SAMPLING
else:
self.sampling = sampling
if temperature == None:
self.temperature = s.TEMPERATURE
else:
self.temperature = temperature
if replicates == None:
self.replicates = s.REPLICATES
else:
self.replicates = replicates
tmp = mutation.split(':')
if len(tmp) == 2:
self.chain = tmp[0]
self.mutation = re.split('(\d+)', tmp[1])
else:
self.chain = ' '
self.mutation = re.split('(\d+)', tmp[0])
self.include = include
self.forcefield = forcefield
self.preplocation = preplocation
self.lambdas = []
self.CYX = []
self.PDB = {}
self.PDB2Q = {}
self.systemsize = 0
self.system = system
self.cluster = cluster
self.rest_shell_width = rest_shell_width
self.FEPlist = []
self.dual = dual
self.start = start
self.dualMUT = {'0':[], '1':[]}
self.nonAA = False
self.replacements = {'ATOM_START_LIG1':'1',
'WATER_RESTRAINT':'',
'TEMP_VAR':self.temperature,
'RUN_VAR':self.replicates,
'RUNFILE':'run' + self.cluster + '.sh'
}
if self.start == '1':
self.replacements['EQ_LAMBDA'] = '1.000 0.000'
if self.start == '0.5':
self.replacements['EQ_LAMBDA'] = '0.500 0.500'
print(self.chain)
def checkFEP(self):
if len(self.mutation[0]) == 1:
AA_from = IO.AA(self.mutation[0])
else:
AA_from = self.mutation[0]
try:
if len(self.mutation[2]) == 1:
AA_to = IO.AA(self.mutation[2])
else:
AA_to = self.mutation[2]
except:
print("residue not found in library, assuming non-natural AA")
AA_to = 'X'
self.nonAA = True
mutation = '{}{}{}'.format(*self.mutation)
FEPdir = s.FF_DIR + '/.FEP/' + self.forcefield + '/' + AA_from + '_' + AA_to
if self.dual == True:
print('Generating dual topology inputfiles')
self.FEPlist = ['FEP1.fep']
self.FEPdir = None
elif not os.path.exists(FEPdir):
print('FATAL: no FEP files found for the {} mutation' \
'in {} exiting now.'.format(mutation,
FEPdir))
sys.exit()
else:
for line in sorted(glob.glob(FEPdir + '/FEP*.fep')):
line = line.split('/')
self.FEPlist.append(line[-1])
self.FEPdir = FEPdir
def create_environment(self):
self.directory = 'FEP_{}{}{}'.format(*self.mutation)
if not os.path.exists(self.directory):
os.makedirs(self.directory)
os.makedirs(self.directory + '/inputfiles')
files = {self.directory + '/inputfiles/' + self.forcefield + '.lib': \
s.FF_DIR + '/' + self.forcefield + '.lib',
}
if self.cofactor[0] != None:
for filename in self.cofactor:
files[self.directory + '/inputfiles/' + filename + '.lib'] = filename + '.lib'
for key in files:
shutil.copy(files[key], key)
def read_input(self):
block = 0
with open('protPREP.log') as infile:
for line in infile:
line = line.split()
if len(line) > 1:
if line[1] == 'center:':
self.sphere = line[2:]
if line[1] == 'radius:':
self.radius = line[2]
self.replacements['SPHERE'] = self.radius
if line[0] == 'Q_CYS1':
block = 1
if line[0] == 'pdbfile':
block = 2
if line[0][0] == '-':
block = 0
if block == 1:
if line[0].isdigit():
self.CYX.append([line[0], line[1]])
if block == 2 and len(line) > 2:
chain = line[2]
if chain not in self.PDB2Q:
self.PDB2Q[chain] = {}
self.PDB2Q[chain][line[1]] = line[0]
def readpdb(self):
atnr = 0
if len(self.mutation[2]) == 1:
if self.nonAA != True:
self.MUTresn = '{}2{}'.format(self.mutation[0],self.mutation[2])
else:
self.MUTresn = '{}2{}'.format(self.mutation[0],'X')
elif len(self.mutation[2]) == 3:
self.MUTresn = '{}2{}'.format(IO.AA(self.mutation[0]),IO.AA(self.mutation[2]))
#self.backbone = []
self.backbone = ['C', 'O', 'CA', 'N', 'H', 'HA']
# Read in the mutant residue
if self.dual == True:
MUT = []
with open(self.mutation[2] + '.pdb') as infile:
for line in infile:
line = IO.pdb_parse_in(line)
# The residue name should match the mutant residue number
# relative to Q numbering from protPREP.log
line[6] = int(self.PDB2Q[self.mutation[1]])
if line[2] in self.backbone:
continue
else:
MUT.append(line)
pdb_files = ['protein.pdb']
if self.cofactor[0] != None:
for line in self.cofactor:
pdb_files.append(line + '.pdb')
for pdb_file in pdb_files:
with open(pdb_file) as infile:
for line in infile:
if line.startswith(self.include):
atnr += 1
line = IO.pdb_parse_in(line)
if pdb_file != 'protein.pdb':
line[6] = resoffset + 1
line[1] = self.systemsize
line[1] = atnr
# Change to hybrid residue name
if self.dual == True:
if str(line[6]) == self.PDB2Q[self.mutation[1]]:
line[4] = self.MUTresn
# Generate the dual topology residue in the PDB dictionary
# Construct the PDB dictionary
try:
self.PDB[line[6]].append(line)
except:
self.PDB[line[6]] = [line]
if self.dual == True:
if str(line[6]) == self.PDB2Q[self.mutation[1]]:
if line[2] == 'O':
for MUTat in MUT:
atnr += 1
if MUTat[2] not in self.backbone:
# Atom name cannot be longer than 4 characters
#if len(MUTat[2]) <= 3:
# MUTat[2] = MUTat[2] + 'x'
#elif len(MUTat[2]) == 4:
# MUTat[2] = MUTat[2][0:1] + 'x'
MUTat[2] = MUTat[2].lower()
MUTat[1] = atnr
MUTat[4] = self.MUTresn
try:
self.PDB[MUTat[6]].append(MUTat)
except:
self.PDB[MUTat[6]] = [MUTat]
self.dualMUT['0'].append(MUTat)
self.dualMUT['1'].append(line)
self.systemsize += 1
resoffset = len(self.PDB)
def create_dual_lib(self):
FFlib = {}
self.merged_lib = {}
replacements = {}
if self.dual == False:
return None
headers =['[atoms]',
'[bonds]',
'[connections]',
'[impropers]',
'[info]'
]
if self.forcefield[0:4] == 'OPLS':
headers.append('[charge_groups]')
libfiles = [s.FF_DIR + '/' + self.forcefield + '.lib']
if self.nonAA == True:
libfiles.append(self.mutation[2] + '.lib')
for libfile in libfiles:
with open(libfile) as infile:
for line in infile:
if line[0] == '*':
continue
if line[0] == '{':
RESname = line.split('}')[0][1:]
continue
try:
FFlib[RESname].append(line)
except:
FFlib[RESname] = [line]
# Read the WT residue
if len(self.mutation[0]) == 1:
AA = AA(self.mutation[0])
else:
AA = self.mutation[0]
for line in FFlib[AA]:
if line.strip() in headers:
header = line.strip()
self.merged_lib[header] = []
else:
self.merged_lib[header].append(line)
# Add CA CBx bond
self.merged_lib['[bonds]'].append(' CA cb\n')
## Read the mutant residue
# Construct atom name replacements
if len(self.mutation[2]) == 1:
AA = IO.AA(self.mutation[2])
else:
AA = self.mutation[2]
for line in FFlib[AA]:
line = line.strip()
line = line.split()
if line != headers[0]:
if len(line) > 2:
atom = line[1]
if atom != 'H':
replacements[atom] = atom.lower()
if line == header[1]:
break
for line in FFlib[AA]:
if line.strip() in headers:
header = line.strip()
if line[0] == '!':
continue
if len(line.split()) < 2:
continue
else:
# connection flag only needs to be there once
if header == headers[2]:
continue
# Remove overlapping backbone definitions
if line.split()[0] == 'O' \
or line.split()[0] == 'C' \
or line.split()[0] == 'CA' \
or line.split()[0] == 'N' \
or line.split()[0] == 'H' \
or line.split()[0] == 'HA':
continue
if line.split()[1] == 'O' \
or line.split()[1] == 'C' \
or line.split()[1] == 'CA' \
or line.split()[1] == 'N' \
or line.split()[1] == 'H' \
or line.split()[1] == 'HA':
continue
# Merge the library on the reference
line = IO.replace(line, replacements)
self.merged_lib[header].append(line)
# Write out the merged library file
out = self.directory + '/inputfiles/' + self.MUTresn + '.lib'
with open(out, 'w') as outfile:
self.merged_lib['[charge_groups]'] = []
cnt = 0
outfile.write('{' + self.MUTresn + '}\n\n')
for header in headers:
outfile.write('\n ' + header + '\n')
if not header in self.merged_lib:
continue
for line in self.merged_lib[header]:
if header == '[atoms]':
cnt += 1
line = line.split()
outfile.write(' {:2d} {:<10}{:<10}{:<10}\n'.format(cnt,
line[1],
line[2],
line[3]))
else:
outfile.write(line)
def get_zeroforcebonded(self):
if self.dual == False:
return None
self.zerofk = {'[angles]':[],
'[bonds]':[],
'[impropers]':[],
'[torsions]':[]
}
prmfile = [s.FF_DIR + '/' + self.forcefield + '.prm']
libfile = self.directory + '/inputfiles/' + self.MUTresn + '.lib'
headers =['[options]',
'[atom_types]',
'[bonds]',
'[angles]',
'[torsions]',
'[impropers]'
]
# Write tmp qprep.inp and prm file
if self.nonAA == True:
prmfile.append(self.mutation[2] + '.prm')
prms = IO.read_prm(prmfile)
prm_tmp = self.directory + '/inputfiles/tmp.prm'
qprep_tmp = self.directory + '/inputfiles/tmp.inp'
pdb_tmp = self.directory + '/inputfiles/tmp.pdb'
# Write out PDB file
with open(pdb_tmp, 'w') as outfile:
mutPDB = self.PDB[int(self.PDB2Q[self.mutation[1]])]
for atom in mutPDB:
outfile.write(IO.pdb_parse_out(atom) + '\n')
with open(prm_tmp, 'w') as outfile:
for key in headers:
outfile.write(key + '\n')
for line in prms[key]:
outfile.write(line)
with open(qprep_tmp, 'w') as outfile:
outfile.write('rl {}\n'.format(libfile.split('/')[-1]))
outfile.write('rprm {}\n'.format(prm_tmp.split('/')[-1]))
outfile.write('rp {}\n'.format(pdb_tmp.split('/')[-1]))
outfile.write('boundary 1 {} {} {} {}\n'.format(self.sphere[0],
self.sphere[1],
self.sphere[2],
self.radius))
outfile.write('maketop tmp.top\n'.format(pdb_tmp))
outfile.write('q')
# run qprep to get bonded parameters to be set to zero
os.chdir(self.directory + '/inputfiles/')
qprep = s.Q_DIR[self.preplocation] + 'qprep'
options = ' < tmp.inp > tmp.out'
# Somehow Q is very annoying with this < > input style so had to implement
# another function that just calls os.system instead of using the preferred
# subprocess module....
IO.run_command(qprep, options, string = True)
with open('tmp.out') as infile:
for line in infile:
line = line.split()
if len(line) < 3:
continue
if line[1] != 'Missing':
continue
# Create zero fk angles
if line[2] == 'angle':
angle_prm = '{:11}{:11}{:11}{: 8.2f}{:>12.7}\n'.format(line[-3],
line[-2],
line[-1],
0.0,
110.0)
self.zerofk['[angles]'].append(angle_prm)
# Create zero fk torsions
if line[2] == 'torsion':
torsion_prm='{:11}{:11}{:11}{:11}{:<10.3f}{: d}.000{:>10s}{:>10s}\n'.format(line[-4],
line[-3],
line[-2],
line[-1],
0.0,
1,
'0.000',
'1')
self.zerofk['[torsions]'].append(torsion_prm)
# ADD REMOVE FUNCTIONS FOR TMP FILES HERE
# for tmp in glob.glob('tmp*'):
# os.remove(tmp)
os.chdir('../../')
def merge_prm(self):
headers =['[options]',
'[atom_types]',
'[bonds]',
'[angles]',
'[torsions]',
'[impropers]'
]
prmfiles = [s.FF_DIR + '/' + self.forcefield + '.prm']
if self.cofactor[0] != None:
for filename in self.cofactor:
prmfiles.append(filename + '.prm')
if self.nonAA == True:
prmfiles.append(self.mutation[2] + '.prm')
prms = IO.read_prm(prmfiles)
prm_merged = self.directory + '/inputfiles/' + self.forcefield + '_merged.prm'
self.prm_merged = self.forcefield + '_merged.prm'
with open (prm_merged, 'w') as outfile:
for key in headers:
outfile.write(key + '\n')
for line in prms[key]:
outfile.write(line)
if self.dual == True:
if key in self.zerofk:
outfile.write('! Zero order bonds dual topology\n')
for line in self.zerofk[key]:
outfile.write(line)
outfile.write('\n')
def write_pdb(self):
PDBout = self.directory + '/inputfiles/complex.pdb'
self.PDBout = 'complex.pdb'
with open(PDBout, 'w') as outfile:
for key in self.PDB:
for line in self.PDB[key]:
outline = IO.pdb_parse_out(line) + '\n'
outfile.write(outline)
def select_waters(self):
src = 'water.pdb'
tgt = self.directory + '/inputfiles/water.pdb'
cofactor_coordinates = []
waters_remove = []
waters = {}
if self.cofactor[0] != None:
for line in self.cofactor:
with open(line + '.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
cofactor_coordinates.append([line[8], line[9], line[10]])
with open (src) as infile, open (tgt, 'w') as outfile:
outfile.write('{} SPHERE\n'.format(self.radius))
for line in infile:
line = IO.pdb_parse_in(line)
coord_wat = [line[8], line[9], line[10]]
try:
waters[line[6]].append(line)
except:
waters[line[6]] = [line]
for coord_co in cofactor_coordinates:
if f.euclidian_overlap(coord_wat, coord_co, 1.6) == True:
waters_remove.append(line[6])
for key in waters:
if key not in waters_remove:
for water in waters[key]:
outfile.write(IO.pdb_parse_out(water) + '\n')
def write_qprep(self):
replacements = {'PRM':self.prm_merged,
'PDB':self.PDBout,
'CENTER':'{} {} {}'.format(*self.sphere),
'SPHERE':self.radius,
}
if self.system == 'protein':
replacements['SOLVENT'] = '4 water.pdb'
elif self.system == 'water':
replacements['SOLVENT'] = '1 HOH'
elif self.system == 'vacuum':
replacements['solvate']='!solvate'
# bit ugly to join the coordinates again but in Qligfep these were never split.
# so the f.get_density expects a string not a list.
center = ' '.join(self.sphere)
radius = float(self.radius)
target_density = f.get_density('protein.pdb', center, radius)
replacements['SOLUTEDENS'] = f'{target_density:.5f}'
src = s.INPUT_DIR + '/qprep_resFEP.inp'
self.qprep = self.directory + '/inputfiles/qprep.inp'
libraries = [self.forcefield + '.lib']
if self.cofactor[0] != None:
for filename in self.cofactor:
libraries.append(filename + '.lib')
with open(src) as infile, open(self.qprep, 'w') as outfile:
if self.dual == True:
outfile.write('rl ' + self.MUTresn + '.lib\n')
for line in infile:
line = IO.replace(line, replacements)
if line.startswith('!Added'):
for libraryfile in libraries:
outfile.write('rl ' + libraryfile + '\n')
continue
if line.startswith('!addbond'):
for CYX in self.CYX:
outline = 'addbond {}:SG {}:SG y\n'.format(*CYX)
outfile.write(outline)
continue
outfile.write(line)
def run_qprep(self):
os.chdir(self.directory + '/inputfiles/')
qprep = s.Q_DIR[self.preplocation] + 'qprep'
options = ' < qprep.inp > qprep.out'
# Somehow Q is very annoying with this < > input style so had to implement
# another function that just calls os.system instead of using the preferred
# subprocess module....
IO.run_command(qprep, options, string = True)
os.chdir('../../')
def get_lambdas(self):
self.lambdas = IO.get_lambdas(self.windows, self.sampling)
def write_EQ(self):
self.replacements['SPHERE'] = '{:<7}'.format(float(self.radius) - self.rest_shell_width)
for line in self.PDB[int(self.PDB2Q[self.chain][self.mutation[1]])]:
if line[2] == 'CA' and self.system == 'water' \
or line[2] == 'CA' and self.system == 'vacuum': \
self.replacements['WATER_RESTRAINT'] = '{} {} 1.0 0 0'.format(line[1],
line[1])
self.replacements['ATOM_END'] = '{}'.format(self.systemsize)
for EQ_file in glob.glob(s.INPUT_DIR + '/eq*.inp'):
src = EQ_file
EQ_file = EQ_file.split('/')
tgt = self.directory + '/inputfiles/' + EQ_file[-1]
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
self.replacements['SPHERE'] = self.radius
def write_MD(self):
# Get restraint for water and vacuum systems
#for line in self.PDB[int(self.PDB2Q[self.mutation[1]])]:
# if line[2] == 'CA' and self.system == 'water' \
# or line[2] == 'CA' and self.system == 'vacuum': \ self.replacements['WATER_RESTRAINT'] = '{} {} 1.0 0 0'.format(line[1],
# line[1])
self.replacements['SPHERE'] = '{:<7}'.format(float(self.radius) - self.rest_shell_width)
if self.start == '1':
for i in range(0, int(self.windows) + 1):
j = int(self.windows) - i
lambda1 = self.lambdas[i].replace(".", "")
lambda2 = self.lambdas[j].replace(".", "")
if self.lambdas[i] == '1.000':
src = s.INPUT_DIR + '/md_1000_0000.inp'
else:
src = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
self.replacements['FLOAT_LAMBDA1'] = self.lambdas[i]
self.replacements['FLOAT_LAMBDA2'] = self.lambdas[j]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(lambda1,
lambda2)
self.replacements['FILE'] = 'md_{}_{}'.format(lambda1,
lambda2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(lambda1,
lambda2)
# This needs to be a function at one point
if self.start == '0.5':
self.mdfiles = ['md_0500_0500']
half = int((len(self.lambdas)-1)/2)
lambda1 = self.lambdas[0:half]
lambda2 = self.lambdas[half+1:]
# Write out the middle file
self.replacements['FILE_N'] = 'md_0500_0500'
src = s.INPUT_DIR + '/md_0500_0500.inp'
tgt = self.directory + '/inputfiles/md_0500_0500.inp'
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
# Write out part 1 of the out files
src = s.INPUT_DIR + '/md_XXXX_XXXX.inp'
for i in range(0, len(lambda1)):
l1 = lambda1[(half - i) - 1].replace(".", "")
l2 = lambda2[i].replace(".", "")
self.replacements['FLOAT_LAMBDA1'] = lambda1[(half - i) - 1]
self.replacements['FLOAT_LAMBDA2'] = lambda2[i]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(l1,
l2)
self.replacements['FILE'] = 'md_{}_{}'.format(l1,
l2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(l1,
l2)
self.mdfiles.append('md_{}_{}'.format(l1,l2))
# And part 2
self.replacements['FILE_N'] = 'md_0500_0500'
for i in range(0, len(lambda1)):
l1 = lambda2[i].replace(".", "")
l2 = lambda1[(half - i) - 1].replace(".", "")
self.replacements['FLOAT_LAMBDA1'] = lambda2[i]
self.replacements['FLOAT_LAMBDA2'] = lambda1[(half - i) - 1]
tgt = self.directory + '/inputfiles/md_{}_{}.inp'.format(l1,
l2)
self.replacements['FILE'] = 'md_{}_{}'.format(l1,
l2)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
outline = IO.replace(line, self.replacements)
outfile.write(outline)
## Store previous file
self.replacements['FILE_N'] = 'md_{}_{}'.format(l1,
l2)
self.mdfiles.append('md_{}_{}'.format(l1,l2))
self.replacements['SPHERE'] = self.radius
def write_runfile(self):
ntasks = getattr(s, self.cluster)['NTASKS']
src = s.INPUT_DIR + '/run.sh'
tgt = self.directory + '/inputfiles/run' + self.cluster + '.sh'
EQ_files = sorted(glob.glob(self.directory + '/inputfiles/eq*.inp'))
if self.start == '1':
MD_files = reversed(sorted(glob.glob(self.directory + '/inputfiles/md*.inp')))
elif self.start == '0.5':
MD_files = self.mdfiles[1:]
half = int((len(MD_files)/2))
md_1 = MD_files[0:half]
md_2 = MD_files[half:]
replacements = IO.merge_two_dicts(self.replacements, getattr(s, self.cluster))
replacements['FEPS'] = ' '.join(self.FEPlist)
with open(src) as infile, open(tgt, 'w') as outfile:
for line in infile:
if line.strip() == '#SBATCH -A ACCOUNT':
try:
replacements['ACCOUNT']
except:
line = ''
outline = IO.replace(line, replacements)
outfile.write(outline)
if line.strip() == '#EQ_FILES':
for line in EQ_files:
file_base = line.split('/')[-1][:-4]
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n'.format(ntasks,
file_base,
file_base)
outfile.write(outline)
if line.strip() == '#RUN_FILES':
if self.start == '1':
for line in MD_files:
file_base = line.split('/')[-1][:-4]
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n'.format(ntasks,
file_base,
file_base)
outfile.write(outline)
elif self.start == '0.5':
outline = 'time mpirun -np {} $qdyn {}.inp' \
' > {}.log\n\n'.format(ntasks,
'md_0500_0500',
'md_0500_0500')
outfile.write(outline)
for i, md in enumerate(md_1):
outline1 = 'time mpirun -np {:d} $qdyn {}.inp' \
' > {}.log &\n'.format(int(int(ntasks)/2),
md_1[i],
md_1[i])
outline2 = 'time mpirun -np {:d} $qdyn {}.inp' \
' > {}.log\n'.format(int(int(ntasks)/2),
md_2[i],
md_2[i])
outfile.write(outline1)
outfile.write(outline2)
outfile.write('\n')
def write_submitfile(self):
IO.write_submitfile(self.directory, self.replacements)
def write_FEPfile(self):
if self.dual == True:
run.write_dualFEPfile()
if self.dual == False:
run.write_singleFEPfile()
def write_singleFEPfile(self):
RES_list = self.PDB[int(self.PDB2Q[self.chain][self.mutation[1]])]
RES_dic = {}
block = 0
empty = ['[change_charges]',
'[FEP]',
'[atom_types]',
'[change_atoms]',
'[softcore]',
'[bond_types]'
]
atom_map = {}
print(RES_list)
for line in RES_list:
RES_dic[line[2].strip()] = line
for src in sorted(glob.glob(self.FEPdir + '/FEP*.fep')):
tgt = self.directory + '/inputfiles/' + src.split('/')[-1]
with open (src) as infile, open (tgt, 'w') as outfile:
for line in infile:
if line.strip() == '[atoms]':
outfile.write(line)
block = 1
if line.strip() == '[change_bonds]':
outfile.write(line)
block = 2
if line.strip() in empty:
block = 0
if block == 0:
outfile.write(line)
if block == 1:
if line.strip() != '[atoms]':
line = line.split()
if len(line) > 1 and line[0] != '!charge':
atnr = RES_dic[line[3]][1]
atom_map[line[0]] = atnr
try:
comment = line[4]
except:
comment = ' '
outline = ('{:7s}{:<7d}{:5s}{:5s}{:5s}\n'.format(line[1],
atnr,
'!',
line[3],
comment))
outfile.write(outline)
else:
outfile.write('\n')
if block == 2:
if line.strip != '[change_bonds]':
line = line.split()
if len(line) > 1 and line[0] != '!charge':
at_1 = atom_map[line[0]]
at_2 = atom_map[line[1]]
outline = '{:<7d}{:<7d}{:5s}{:5s}\n'.format(at_1,
at_2,
line[2],
line[3])
outfile.write(outline)
else:
outfile.write('\n')
def write_dualFEPfile(self):
# The vdW paramers need to be extracted from the reference .prm file
prmfiles = [s.FF_DIR + '/' + self.forcefield + '.prm']
if self.nonAA == True:
prmfiles.append(self.mutation[2] + '.prm')
vdw_prms = IO.read_prm(prmfiles)['[atom_types]']
## Next, we start to construct the FEP file
with open(self.directory + '/inputfiles/FEP1.fep', 'w') as outfile:
# First create the file header
outfile.write('! Dual topology QresFEP: ' + self.MUTresn + '\n\n')
outfile.write('[FEP]\n')
outfile.write('states 2\n')
outfile.write('softcore_use_max_potential on \n\n')
# Write out [atoms] section
outfile.write('[atoms]\n')
cnt = 0
res_ID = int(self.PDB2Q[self.mutation[1]])
for line in self.PDB[res_ID]:
cnt += 1
outfile.write('{:4d} {:4d} ! {:<4s}\n'.format(cnt, line[1], line[2]))
outfile.write('\n')
# Write out [change_charges] section
cnt = 0
outfile.write('[change_charges]\n')
for line in self.merged_lib['[atoms]']:
cnt += 1
line = line.split()
if line[1][0].islower() == False:
if line[1] in self.backbone:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[3],
line[3]))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
line[3],
'0.0000'))
else:
outfile.write('{:4d}{:>10s}{:>10s}\n'.format(cnt,
'0.0000',
line[3]))
outfile.write('\n')
# Write out [atom_types] section
outfile.write('[atom_types]\n')
for line in vdw_prms:
line = line.split()
if len(line) >= 7:
outfile.write('{:<8s}{:>10s}{:>10s}{:>10s}'\
'{:>10s}{:>10s}{:>10s}{:>10s}\n'.format(line[0],
line[1],
line[3],
'0.0000',
'0.0000',
line[4],
line[5],
line[6],
))
# Write out DUM entry
outfile.write('{:<8s}{:>10s}{:>10s}{:>10s}'\
'{:>10s}{:>10s}{:>10s}{:>10s}\n'.format('DUM',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'0.0000',
'1.0080',
))
outfile.write('\n')
# Write out [change_atoms] section
outfile.write('[change_atoms]\n')
cnt = 0
for line in self.merged_lib['[atoms]']: