3 from django.db.models.signals import post_save, post_delete
4 from django.dispatch import receiver
5 from .models import Task
10 from string import Template
14 logger = logging.getLogger(__name__)
16 def seq_2d_xx(line,seq):
17 line=line.replace(" ","")
19 for ii in range(0,len(line)):
25 return("".join(lista))
27 def seq_2d_write(line):
28 line=line.replace(" ", "")
29 out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
31 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
32 for ii in range(1,len(line)-2):
34 if line[ii:ii+2]=='HH':
35 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
36 elif line[ii:ii+2]=='EE':
37 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
39 out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
42 def seq_2d_write_50(line):
43 line=line.replace(" ", "")
44 out='{:d}\n'.format(len(line))
46 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
47 for ii in range(1,len(line)-2):
49 if line[ii:ii+2]=='HH':
50 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
51 elif line[ii:ii+2]=='EE':
52 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
54 out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
57 def write_ssbond(ssbond):
60 ssbond=json.loads(ssbond)
64 list_sorted=sorted(list)
67 return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\
68 str(len(ssbond))+' '+' '.join(map(str,list))+'\n'
73 @receiver(post_save, sender=Task)
74 def write_on_task_save(sender, instance, **kwargs):
75 if instance.ready and not instance.done and instance.running==0:
76 if (not os.path.isdir(instance.jobdirname)):
77 os.mkdir(instance.jobdirname)
78 # os.chdir(instance.jobdirname)
82 #md=Template('nstep=$nstep ntwe=100 ntwx=100 dt=0.20 damax=10.0 lang=1'+
83 # 't_bath=300 reset_vel=0 respa ntime_split=1 maxtime_split=512 mdpdb')
84 #wrapper = textwrap.TextWrapper(width=70)
85 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
87 if instance.unres_ff =='FF2':
88 w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 &
89 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 &
90 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 &
91 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 &
92 CUTOFF=7.00000 WCORR4=0.00000"""
94 w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 &
95 WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 &
96 WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 &
97 WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 &
98 CUTOFF=7.00000 WCORR4=0.00000"""
101 with open(instance.jobdirname+'/file.inp','w') as f:
102 f.write(instance.name + ' UNRES server job'+ '\n')
104 if instance.type == 'min' :
106 control_line = 'SEED='+str(instance.md_seed)+' ' \
107 + instance.min_choice \
108 + ' pdbstart pdbref ' \
109 + ' BOXX='+str(instance.boxx) \
110 + ' BOXY='+str(instance.boxy) \
111 + ' BOXZ='+str(instance.boxz) +' '
112 if not instance.min_overlap:
113 control_line = control_line+'overlap '
114 if not instance.min_searchsc:
115 control_line = control_line+'nosearchsc '
116 if instance.min_pdbout:
117 control_line = control_line+'pdbout '
118 if instance.min_unres_pdb:
119 control_line = control_line+'unres_pdb '
121 type_line = 'print_min_ini print_min_res print_min_stat'\
122 +' MAXMIN='+str(instance.min_maxmin)\
123 +' MAXFUN='+str(instance.min_maxfun)
126 seq=instance.md_seq.replace(" ","")
134 nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
135 seq2 = ''.join([c for c in seq if c in nogly])
137 dimen3=(dimen3+len(seq2))*3
140 if instance.type == 'md' :
141 control_line = 'SEED='+str(instance.md_seed)+' '\
142 +instance.md_start +' md one_letter'\
143 + ' BOXX='+str(instance.boxx) \
144 + ' BOXY='+str(instance.boxy) \
145 + ' BOXZ='+str(instance.boxz) +' '
147 if instance.md_pdbref:
148 control_line = control_line+'pdbref '
150 type_line = ' reset_vel=0'\
151 +' t_bath='+str(instance.md_temp)\
152 +' nstep='+str(instance.md_nstep)\
153 +' ntwe='+str(instance.md_ntwe)\
154 +' ntwx='+str(instance.md_ntwx)\
155 +' dt='+str(instance.md_dt)
156 if instance.md_lang == 'langevin':
157 type_line = type_line + ' lang=1 '
158 type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
159 if instance.md_lang == 'berendsen':
160 type_line = type_line + ' lang=0 tbf '
161 type_line = type_line + 'tau_bath='+str(instance.md_tau)
162 if instance.md_respa:
163 type_line = type_line + ' respa '
164 if instance.md_mdpdb:
165 type_line = type_line + ' mdpdb '
167 if instance.type == 'remd' or instance.type == 'dock':
168 control_line = 'SEED='+str(instance.md_seed)+' '\
169 +instance.md_start +' re one_letter'\
170 + ' BOXX='+str(instance.boxx) \
171 + ' BOXY='+str(instance.boxy) \
172 + ' BOXZ='+str(instance.boxz) +' '
174 if instance.type == 'dock':
175 control_line = control_line+'CONSTR_HOMOL=20 '
177 if instance.md_pdbref:
178 control_line = control_line+'pdbref '
181 if instance.saxs_data != '':
182 lines=instance.saxs_data.split('\n')
185 if len(line.split())==2:
187 cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad)
188 control_line += cntrl_saxs
190 type_line = ' reset_vel='+ str(instance.remd_nstex)\
191 +' nstep='+str(instance.md_nstep)\
192 +' ntwe='+str(instance.md_ntwe)\
193 +' ntwx='+str(instance.md_ntwx)\
194 +' dt='+str(instance.md_dt)
195 if instance.md_lang == 'langevin':
196 type_line = type_line + ' lang=1 '
197 type_line = type_line + 'scal_fric='+str(instance.md_scal_fric)
198 if instance.md_lang == 'berendsen':
199 type_line = type_line + ' lang=0 tbf '
200 type_line = type_line + 'tau_bath='+str(instance.md_tau)
201 if instance.md_respa:
202 type_line = type_line + ' respa '
203 # if instance.md_mdpdb:
204 # type_line = type_line + ' mdpdb '
206 type_line2 = 'nrep='+str(instance.remd_nrep) \
207 +' nstex='+str(instance.remd_nstex) \
208 +' tlist mlist sync nsyn='+str(instance.remd_nstex)\
209 +' traj1file rest1file TRAJCACHE=200'
211 if instance.md_start == 'pdbstart':
212 type_line = type_line + ' preminim cart'
214 wrapper = textwrap.TextWrapper(width=70)
216 word_list = wrapper.wrap(text=control_line)
217 for element in word_list[:-1]:
218 f.write('{:79}'.format(element)+'&\n')
219 f.write(word_list[-1]+'\n')
221 word_list = wrapper.wrap(text=type_line)
222 for element in word_list[:-1]:
223 f.write('{:79}'.format(element)+'&\n')
224 f.write(word_list[-1]+'\n')
226 if instance.md_start == 'pdbstart':
227 if instance.type == 'remd' or instance.type == 'dock':
228 f.write('print_min_ini print_min_res print_min_stat maxfun='+
229 str(instance.min_maxfun)+'\n')
231 f.write('print_min_ini print_min_res print_min_stat\n')
234 if instance.type == 'remd' or instance.type == 'dock':
235 word_list = wrapper.wrap(text=type_line2)
236 for element in word_list[:-1]:
237 f.write('{:79}'.format(element)+'&\n')
238 f.write(word_list[-1]+'\n')
240 tmp1=json.loads(instance.remd_multi_t)
242 word_list = wrapper.wrap(text=string1.join(tmp1))
243 for element in word_list[:-1]:
244 f.write('{:79}'.format(element)+'&\n')
245 f.write(word_list[-1]+'\n')
247 tmp1=json.loads(instance.remd_multi_m)
249 word_list = wrapper.wrap(text=string1.join(tmp1))
250 for element in word_list[:-1]:
251 f.write('{:79}'.format(element)+'&\n')
252 f.write(word_list[-1]+'\n')
254 if instance.saxs_data != '':
255 w+=' wsaxs='+str(instance.wsaxs)
259 if instance.type == 'min' or instance.md_start == 'pdbstart':
260 if instance.type == 'dock':
261 f.write('model01.pdb\n')
263 f.write('plik.pdb\n')
264 f.write(write_ssbond(instance.ssbond))
265 if instance.md_2d == '':
268 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
270 if instance.type == 'dock':
271 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
272 f.write('READ2SIGMA START_FROM_MODELS\n')
273 for i in range(1,10):
274 f.write('model0'+str(i)+'.pdb\n')
275 for i in range(10,21):
276 f.write('model'+str(i)+'.pdb\n')
278 if instance.type == 'md' and instance.md_start != 'pdbstart':
280 if instance.md_pdbref:
281 f.write('plik.pdb\n')
282 f.write(str(len(seq))+'\n')
283 for i in range(0,len(seq),80):
284 f.write(seq[i:i+80]+'\n')
286 if instance.md_2d == '':
289 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
292 if instance.type == 'remd' and instance.md_start != 'pdbstart':
294 if instance.md_pdbref:
295 f.write('plik.pdb\n')
296 f.write(str(len(seq))+'\n')
297 for i in range(0,len(seq),80):
298 f.write(seq[i:i+80]+'\n')
300 if instance.md_2d == '':
303 f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
306 if instance.saxs_data != '':
307 lines=instance.saxs_data.split('\n')
311 f.write(tmp[0]+' '+tmp[1]+'\n')
314 if instance.type == 'min':
315 os.chdir(instance.jobdirname)
316 if instance.unres_ff =='FF2':
317 shutil.copy('../files/pbs.csh','.')
319 shutil.copy('../files/pbs_new.csh','pbs.csh')
320 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
322 elif instance.type == 'md':
323 os.chdir(instance.jobdirname)
324 if instance.unres_ff =='FF2':
325 f1 = open('../files/pbs_md.csh', 'r')
327 f1 = open('../files/pbs_md_new.csh', 'r')
328 f2 = open('pbs.csh', 'w')
330 f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) ))
334 f1 = open('file.seq', 'w')
335 for i in range(0,len(seq),80):
336 f1.write(seq[i:i+80]+'\n')
340 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
343 # instance.type == 'remd'
344 tmp1=json.loads(instance.remd_multi_m)
345 nreplicas=sum(map(int, tmp1))
346 # hardcoded for 4 core nodes with FGPROC=2
347 nodes=int(nreplicas*2/4)
348 reszta = nreplicas*2-nodes*4
350 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4'
352 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
355 if instance.ssbond!='':
358 for i in range(0,len(seq)):
363 ss=json.loads(instance.ssbond)
365 l.append(e[0]-ix[e[0]])
366 l.append(e[1]-ix[e[1]])
367 tmp_ss=' '.join(map(str,l))
369 os.chdir(instance.jobdirname)
370 if instance.unres_ff =='FF2':
371 f1 = open('../files/pbs8.csh', 'r')
373 f1 = open('../files/pbs8_new.csh', 'r')
374 f2 = open('pbs8.csh', 'w')
376 if '#PBS -l nodes=4:ppn=4' in line:
377 f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs))
378 elif '$ssbond' in line:
379 f2.write(line.replace('$ssbond',tmp_ss))
380 elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
382 f2.write('../files/generator_v7 plik.pdb plik2.pdb\n')
384 tmp1=json.loads(instance.remd_multi_t)
385 f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas)))
389 f1 = open('file.seq', 'w')
390 for i in range(0,len(seq),80):
391 f1.write(seq[i:i+80]+'\n')
397 # write wham & cluster input
398 with open(instance.jobdirname+'/file_wham.inp','w') as f:
399 if instance.md_nstep/instance.md_ntwx*nreplicas<=8000:
402 isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
403 f.write('{:79}'.format(' isampl='+str(isampl))+'&\n')
404 if instance.md_pdbref:
405 f.write('{:79}'.format('SEED='+str(instance.md_seed)+
406 ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
408 f.write('{:79}'.format('SEED='+str(instance.md_seed)+
409 ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
410 if instance.md_2d != '':
411 f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
412 if instance.type == 'dock':
413 f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=20')+'&\n')
414 f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
415 ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
417 f.write('nres='+str(len(seq))+' one_letter\n')
418 for i in range(0,len(seq),80):
419 f.write(seq[i:i+80]+'\n')
421 f.write(write_ssbond(instance.ssbond))
423 if instance.type == 'dock':
424 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
425 f.write('READ2SIGMA \n')
426 for i in range(1,10):
427 f.write('model0'+str(i)+'.pdb\n')
428 for i in range(10,21):
429 f.write('model'+str(i)+'.pdb\n')
431 if instance.md_2d != '':
432 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
434 if instance.saxs_data != '':
439 fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
440 lines=instance.saxs_data.split('\n')
444 f.write(tmp[0]+' '+tmp[1]+'\n')
445 saxs_r.append(tmp[0])
446 saxs_P.append(float(tmp[1]))
450 saxs_norm += float(tmp[1])*(float(tmp[0])-r_last)
452 for r,p in zip(saxs_r,saxs_P):
453 fsaxs.write('{} {}\n'.format(r,p/saxs_norm))
458 f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n')
459 tmp1=json.loads(instance.remd_multi_t)
461 f.write('nr=1 temp='+element+' fi=0.0 0.0 0.0 0.0 0.0\n')
462 f.write('kh= 0.0 Q0=0.0\n')
463 rec=instance.md_nstep/instance.md_ntwx
464 f.write('nfile_cx=1 rec_start='+str(rec/10)
465 +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n')
466 f.write('file_MD000\n')
467 if instance.md_pdbref:
469 f.write('plik.pdb\n')
472 with open(instance.jobdirname+'/file_cluster.inp','w') as f:
473 f.write(instance.name + ' UNRES server job'+ '\n')
474 f.write('{:79}'.format('nres='+str(len(seq))
475 +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
476 +' temper='+str(instance.remd_cluter_temp))+'&\n')
477 if instance.md_2d != '':
478 f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
479 if instance.type == 'dock':
480 f.write('{:79}'.format(' CONSTR_HOMOL=20')+'&\n')
481 f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
482 ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n')
484 for i in range(0,len(seq),80):
485 f.write(seq[i:i+80]+'\n')
486 f.write(write_ssbond(instance.ssbond))
487 if instance.type == 'dock':
488 f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n')
489 f.write('READ2SIGMA \n')
490 for i in range(1,10):
491 f.write('model0'+str(i)+'.pdb\n')
492 for i in range(10,21):
493 f.write('model'+str(i)+'.pdb\n')
494 if instance.md_2d != '':
495 f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
496 if instance.saxs_data != '':
497 lines=instance.saxs_data.split('\n')
501 f.write(tmp[0]+' '+tmp[1]+'\n')
503 os.chdir(instance.jobdirname)
504 ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
507 print ret_code.stdout.readlines()
508 logger.warning("Dir \"%s\" has been saved." % instance.jobdirname)
510 @receiver(post_delete, sender=Task)
511 def delete_on_task_del(sender, instance, **kwargs):
512 if instance.jobdirname:
513 if os.path.isdir(instance.jobdirname):
514 shutil.rmtree(instance.jobdirname)
515 logger.warning("Dir \"%s\" has been rm." % instance.jobdirname)