X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=e7ee71653117be5f5c45c3b04e8f73c76ba09a13;hb=56595cc7938f5c7b53dd3ebe91b2a42f52cb89d1;hp=d9b8c7c0ba884a32ad7f6f9896148e30105ee32c;hpb=a3b7f27a81cf442cdeeaff5b9c9b52298c282f5a;p=django_unres.git diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index d9b8c7c..e7ee716 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -72,7 +72,7 @@ def write_ssbond(ssbond): @receiver(post_save, sender=Task) def write_on_task_save(sender, instance, **kwargs): - if instance.ready and not instance.done and instance.running==0: + if instance.ready and not instance.done and instance.running==0 and instance.pbsjob=='': if (not os.path.isdir(instance.jobdirname)): os.mkdir(instance.jobdirname) # os.chdir(instance.jobdirname) @@ -90,6 +90,12 @@ WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000 & WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000 & WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25 & CUTOFF=7.00000 WCORR4=0.00000""" + elif instance.unres_ff =='NEWCT-9P': + w="""WSC=0.81230 WSCP=1.20420 WELEC=0.87690 WBOND=1.00000 WANG=1.97730 & +WSCLOC=0.063657 WTOR=1.41540 WTORD=0.00000 WCORRH=0.00000 WCORR5=0.00000 & +WCORR6=0.00000 WEL_LOC=0.036638 WTURN3=1.45110 WTURN4=0.00000 WTURN6=0.00000 & +WSCCOR=0.00000 WVDWPP=0.33393 WHPB=1.00000 WSCP14=0.00000 & +CUTOFF=7.00000 WCORR4=0.00000""" else: w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542 & WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000 & @@ -117,6 +123,8 @@ CUTOFF=7.00000 WCORR4=0.00000""" control_line = control_line+'pdbout ' if instance.min_unres_pdb: control_line = control_line+'unres_pdb ' + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 ' type_line = 'print_min_ini print_min_res print_min_stat'\ +' MAXMIN='+str(instance.min_maxmin)\ @@ -146,8 +154,11 @@ CUTOFF=7.00000 WCORR4=0.00000""" if instance.md_pdbref: control_line = control_line+'pdbref ' + + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 cart' - type_line = 'reset_vel=0'\ + type_line = ' reset_vel=0'\ +' t_bath='+str(instance.md_temp)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ @@ -164,15 +175,21 @@ CUTOFF=7.00000 WCORR4=0.00000""" if instance.md_mdpdb: type_line = type_line + ' mdpdb ' - if instance.type == 'remd' : + if instance.type == 'remd' or instance.type == 'dock': control_line = 'SEED='+str(instance.md_seed)+' '\ +instance.md_start +' re one_letter'\ + ' BOXX='+str(instance.boxx) \ + ' BOXY='+str(instance.boxy) \ + ' BOXZ='+str(instance.boxz) +' ' + + if instance.type == 'dock': + control_line = control_line+'CONSTR_HOMOL=24 ' if instance.md_pdbref: control_line = control_line+'pdbref ' + + if instance.unres_ff =='NEWCT-9P': + control_line = control_line+'tormode=2 cart' cntrl_saxs='' if instance.saxs_data != '': @@ -184,7 +201,7 @@ CUTOFF=7.00000 WCORR4=0.00000""" cntrl_saxs=' nsaxs='+str(nsaxs)+' scal_rad='+str(instance.scal_rad) control_line += cntrl_saxs - type_line = 'reset_vel='+ str(instance.remd_nstex)\ + type_line = ' reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ +' ntwx='+str(instance.md_ntwx)\ @@ -197,8 +214,8 @@ CUTOFF=7.00000 WCORR4=0.00000""" type_line = type_line + 'tau_bath='+str(instance.md_tau) if instance.md_respa: type_line = type_line + ' respa ' - if instance.md_mdpdb: - type_line = type_line + ' mdpdb ' +# if instance.md_mdpdb: +# type_line = type_line + ' mdpdb ' type_line2 = 'nrep='+str(instance.remd_nrep) \ +' nstex='+str(instance.remd_nstex) \ @@ -220,15 +237,15 @@ CUTOFF=7.00000 WCORR4=0.00000""" f.write('{:79}'.format(element)+'&\n') f.write(word_list[-1]+'\n') - if instance.md_start == 'pdbstart': - if instance.type == 'remd' : + if instance.md_start == 'pdbstart' and instance.unres_ff !='NEWCT-9P': + if instance.type == 'remd' or instance.type == 'dock': f.write('print_min_ini print_min_res print_min_stat maxfun='+ str(instance.min_maxfun)+'\n') else: f.write('print_min_ini print_min_res print_min_stat\n') - if instance.type == 'remd' : + if instance.type == 'remd' or instance.type == 'dock': word_list = wrapper.wrap(text=type_line2) for element in word_list[:-1]: f.write('{:79}'.format(element)+'&\n') @@ -254,12 +271,26 @@ CUTOFF=7.00000 WCORR4=0.00000""" if instance.type == 'min' or instance.md_start == 'pdbstart': - f.write('plik.pdb\n') + if instance.type == 'dock': + f.write('plik1ter.pdb\n') + else: + f.write('plik.pdb\n') f.write(write_ssbond(instance.ssbond)) if instance.md_2d == '': f.write('0\n') else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA START_FROM_MODELS\n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') if instance.type == 'md' and instance.md_start != 'pdbstart': @@ -272,6 +303,9 @@ CUTOFF=7.00000 WCORR4=0.00000""" if instance.md_2d == '': f.write('0\n') else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) @@ -286,6 +320,9 @@ CUTOFF=7.00000 WCORR4=0.00000""" if instance.md_2d == '': f.write('0\n') else: + if instance.unres_ff =='NEWCT-9P': + f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) + else: f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) @@ -301,6 +338,8 @@ CUTOFF=7.00000 WCORR4=0.00000""" os.chdir(instance.jobdirname) if instance.unres_ff =='FF2': shutil.copy('../files/pbs.csh','.') + elif instance.unres_ff =='NEWCT-9P': + shutil.copy('../files/pbs_newct-9p.csh','pbs.csh') else: shutil.copy('../files/pbs_new.csh','pbs.csh') ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) @@ -309,6 +348,8 @@ CUTOFF=7.00000 WCORR4=0.00000""" os.chdir(instance.jobdirname) if instance.unres_ff =='FF2': f1 = open('../files/pbs_md.csh', 'r') + elif instance.unres_ff =='NEWCT-9P': + f1 = open('../files/pbs_md_newct-9p.csh', 'r') else: f1 = open('../files/pbs_md_new.csh', 'r') f2 = open('pbs.csh', 'w') @@ -355,6 +396,8 @@ CUTOFF=7.00000 WCORR4=0.00000""" os.chdir(instance.jobdirname) if instance.unres_ff =='FF2': f1 = open('../files/pbs8.csh', 'r') + elif instance.unres_ff =='NEWCT-9P': + f1 = open('../files/pbs8_newct-9p.csh', 'r') else: f1 = open('../files/pbs8_new.csh', 'r') f2 = open('pbs8.csh', 'w') @@ -363,11 +406,27 @@ CUTOFF=7.00000 WCORR4=0.00000""" f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs)) elif '$ssbond' in line: f2.write(line.replace('$ssbond',tmp_ss)) + elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock': + f2.write(line) + if instance.dock_peptide: + f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n') + else: + f2.write('../files/generator_v13 plik.pdb plik2.pdb 0 \n') + f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n") + f2.write("echo TER >> plik1ter.pdb \n") + f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n") else: tmp1=json.loads(instance.remd_multi_t) f2.write(line.replace('$temperatures','"'+" ".join(tmp1)+'" '+str(nreplicas))) f1.close() f2.close() + + f1 = open('file.seq', 'w') + for i in range(0,len(seq),80): + f1.write(seq[i:i+80]+'\n') + f1.write('\n') + f1.close() + os.chdir('..') # write wham & cluster input @@ -376,15 +435,19 @@ CUTOFF=7.00000 WCORR4=0.00000""" isampl=1 else: isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000) - + f.write('{:79}'.format(' isampl='+str(isampl))+'&\n') if instance.md_pdbref: - f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ + f.write('{:79}'.format('SEED='+str(instance.md_seed)+ ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n') else: - f.write('{:79}'.format('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ + f.write('{:79}'.format('SEED='+str(instance.md_seed)+ ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n') if instance.md_2d != '': f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n') + if instance.type == 'dock': + f.write('{:79}'.format(' n_ene=19 CONSTR_HOMOL=24')+'&\n') + if instance.unres_ff =='NEWCT-9P': + f.write('{:79}'.format('tormode=2 ')+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') @@ -394,6 +457,14 @@ CUTOFF=7.00000 WCORR4=0.00000""" f.write(write_ssbond(instance.ssbond)) + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA \n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') + if instance.md_2d != '': f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) @@ -401,6 +472,7 @@ CUTOFF=7.00000 WCORR4=0.00000""" saxs_r=[] saxs_P=[] saxs_norm=0 + r_last=None fsaxs = open(instance.jobdirname+'/saxs.data', 'w') lines=instance.saxs_data.split('\n') for line in lines: @@ -409,7 +481,11 @@ CUTOFF=7.00000 WCORR4=0.00000""" f.write(tmp[0]+' '+tmp[1]+'\n') saxs_r.append(tmp[0]) saxs_P.append(float(tmp[1])) - saxs_norm += float(tmp[1]) + if r_last==None: + r_last=float(tmp[0]) + else: + saxs_norm += float(tmp[1])*(float(tmp[0])-r_last) + r_last=float(tmp[0]) for r,p in zip(saxs_r,saxs_P): fsaxs.write('{} {}\n'.format(r,p/saxs_norm)) fsaxs.close() @@ -427,7 +503,10 @@ CUTOFF=7.00000 WCORR4=0.00000""" f.write('file_MD000\n') if instance.md_pdbref: f.write('pdbref\n') - f.write('plik.pdb\n') + if instance.type == 'dock': + f.write('plik1ter.pdb\n') + else: + f.write('plik.pdb\n') with open(instance.jobdirname+'/file_cluster.inp','w') as f: @@ -437,12 +516,23 @@ CUTOFF=7.00000 WCORR4=0.00000""" +' temper='+str(instance.remd_cluter_temp))+'&\n') if instance.md_2d != '': f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n') + if instance.type == 'dock': + f.write('{:79}'.format(' CONSTR_HOMOL=24')+'&\n') + if instance.unres_ff =='NEWCT-9P': + f.write('{:79}'.format('tormode=2 ')+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') f.write(w+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) + if instance.type == 'dock': + f.write('HOMOL_DIST=0.1 HOMOL_ANGLE=1.0 HOMOL_THETA=1.0 HOMOL_SCD=1.0 DIST_CUT=15.0 &\n') + f.write('READ2SIGMA \n') + for i in range(1,10): + f.write('model0'+str(i)+'.pdb\n') + for i in range(10,25): + f.write('model'+str(i)+'.pdb\n') if instance.md_2d != '': f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) if instance.saxs_data != '': @@ -455,14 +545,28 @@ CUTOFF=7.00000 WCORR4=0.00000""" os.chdir(instance.jobdirname) ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) os.chdir('..') + + output = str(ret_code.communicate()[0]) + output=output.strip() + if output=='': + output='error' + logger.warning("PBS \"%s\" " % output) + instance.pbsjob = output + instance.save() - print ret_code.stdout.readlines() +# print ret_code.stdout.readlines() logger.warning("Dir \"%s\" has been saved." % instance.jobdirname) @receiver(post_delete, sender=Task) def delete_on_task_del(sender, instance, **kwargs): if instance.jobdirname: if os.path.isdir(instance.jobdirname): + if not instance.done: + ret_code_qdel = subprocess.Popen(' /opt/torque/bin/qdel '+str(instance.pbsjob), shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + output = str(ret_code_qdel.communicate()[0]) + output=output.strip() + logger.warning("PBS qdel \"%s\" " % instance.pbsjob) + logger.warning("QDEL \"%s\" " % output) shutil.rmtree(instance.jobdirname) logger.warning("Dir \"%s\" has been rm." % instance.jobdirname) \ No newline at end of file