X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=61d2c45b4347c8bbb984e4ac87fa5c532eb60c24;hb=5a52e318fbba09f787c91fadc8d364d16c2d452d;hp=856c22eca6b181c5503d8d81b43fbd67059fbb33;hpb=00fcf7b84f8d27f314f1e5a6296e402ec6252bc1;p=django_unres.git diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index 856c22e..61d2c45 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -13,18 +13,60 @@ import textwrap logging.basicConfig() logger = logging.getLogger(__name__) +def seq_2d_xx(line,seq): + line=line.replace(" ","") + lista=list(line) + for ii in range(0,len(line)): + if seq[ii]=='X': + if ii>0: + lista[ii-1]='-' + if ii+10: + if len(list)>0: return str(len(list))+' '+' '.join(map(str,list_sorted))+'\n'+\ str(len(ssbond))+' '+' '.join(map(str,list))+'\n' - else: + else: return '0\n' @@ -42,20 +84,18 @@ def write_on_task_save(sender, instance, **kwargs): #wrapper = textwrap.TextWrapper(width=70) #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep))) - if instance.unres_ff =='E0LL2Y': + if instance.unres_ff =='FF2': w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954 & 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 -""" +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 & WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000 & WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000 & -CUTOFF=7.00000 WCORR4=0.00000 -""" +CUTOFF=7.00000 WCORR4=0.00000""" with open(instance.jobdirname+'/file.inp','w') as f: @@ -65,7 +105,10 @@ CUTOFF=7.00000 WCORR4=0.00000 control_line = 'SEED='+str(instance.md_seed)+' ' \ + instance.min_choice \ - + ' pdbstart pdbref BOXX=1000. BOXY=1000. BOXZ=1000. ' + + ' pdbstart pdbref ' \ + + ' BOXX='+str(instance.boxx) \ + + ' BOXY='+str(instance.boxy) \ + + ' BOXZ='+str(instance.boxz) +' ' if not instance.min_overlap: control_line = control_line+'overlap ' if not instance.min_searchsc: @@ -88,7 +131,7 @@ CUTOFF=7.00000 WCORR4=0.00000 if seq[-1]=='X': dimen3-=1 - nogly ='CDSQKIPTFNHLRWAVEYM' + nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym' seq2 = ''.join([c for c in seq if c in nogly]) dimen3=(dimen3+len(seq2))*3 @@ -96,11 +139,15 @@ CUTOFF=7.00000 WCORR4=0.00000 if instance.type == 'md' : control_line = 'SEED='+str(instance.md_seed)+' '\ - +instance.md_start +' md one_letter BOXX=1000. BOXY=1000. BOXZ=1000. ' + +instance.md_start +' md one_letter'\ + + ' BOXX='+str(instance.boxx) \ + + ' BOXY='+str(instance.boxy) \ + + ' BOXZ='+str(instance.boxz) +' ' + if instance.md_pdbref: control_line = control_line+'pdbref ' - type_line = 'reset_vel=0'\ + type_line = 'restart reset_vel=0'\ +' t_bath='+str(instance.md_temp)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ @@ -117,14 +164,30 @@ 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=1000. BOXY=1000. BOXZ=1000. ' + +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=20 ' + if instance.md_pdbref: control_line = control_line+'pdbref ' - + + cntrl_saxs='' + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + nsaxs=0 + for line in lines: + if len(line.split())==2: + nsaxs+=1 + 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 = 'restart reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ +' ntwx='+str(instance.md_ntwx)\ @@ -161,10 +224,14 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(word_list[-1]+'\n') if instance.md_start == 'pdbstart': + 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') @@ -183,15 +250,30 @@ CUTOFF=7.00000 WCORR4=0.00000 for element in word_list[:-1]: f.write('{:79}'.format(element)+'&\n') f.write(word_list[-1]+'\n') - - f.write(w) + + if instance.saxs_data != '': + w+=' wsaxs='+str(instance.wsaxs) + f.write(w+'\n') if instance.type == 'min' or instance.md_start == 'pdbstart': - f.write('plik.pdb\n') + if instance.type == 'dock': + f.write('model01.pdb\n') + else: + f.write('plik.pdb\n') f.write(write_ssbond(instance.ssbond)) - f.write('0\n') - + if instance.md_2d == '': + f.write('0\n') + 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(10,21): + f.write('model'+str(i)+'.pdb\n') if instance.type == 'md' and instance.md_start != 'pdbstart': @@ -200,7 +282,12 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(str(len(seq))+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') - f.write('0\n0\n') + f.write('0\n') + if instance.md_2d == '': + f.write('0\n') + else: + f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + if instance.type == 'remd' and instance.md_start != 'pdbstart': @@ -209,14 +296,24 @@ CUTOFF=7.00000 WCORR4=0.00000 f.write(str(len(seq))+'\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') - f.write('0\n0\n') + f.write('0\n') + if instance.md_2d == '': + f.write('0\n') + else: + f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq))) + if instance.saxs_data != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') if instance.type == 'min': os.chdir(instance.jobdirname) - if instance.unres_ff =='E0LL2Y': + if instance.unres_ff =='FF2': shutil.copy('../files/pbs.csh','.') else: shutil.copy('../files/pbs_new.csh','pbs.csh') @@ -224,19 +321,20 @@ CUTOFF=7.00000 WCORR4=0.00000 os.chdir('..') elif instance.type == 'md': os.chdir(instance.jobdirname) - if instance.unres_ff =='E0LL2Y': + if instance.unres_ff =='FF2': f1 = open('../files/pbs_md.csh', 'r') else: f1 = open('../files/pbs_md_new.csh', 'r') f2 = open('pbs.csh', 'w') for line in f1: - f2.write(line.replace('$dimen3',str(dimen3) )) + f2.write(line.replace('$dimen3',str(dimen3)+' '+str(instance.md_temp) )) 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() ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) @@ -252,9 +350,24 @@ CUTOFF=7.00000 WCORR4=0.00000 pbs = '#PBS -l nodes='+str(nodes)+':ppn=4' else: pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta) + + tmp_ss='' + if instance.ssbond!='': + ix=[] + ii=0 + for i in range(0,len(seq)): + if seq[i]=='X': + ii=ii+1 + ix.append(ii) + l=[] + ss=json.loads(instance.ssbond) + for e in ss: + l.append(e[0]-ix[e[0]]) + l.append(e[1]-ix[e[1]]) + tmp_ss=' '.join(map(str,l)) os.chdir(instance.jobdirname) - if instance.unres_ff =='E0LL2Y': + if instance.unres_ff =='FF2': f1 = open('../files/pbs8.csh', 'r') else: f1 = open('../files/pbs8_new.csh', 'r') @@ -262,11 +375,23 @@ CUTOFF=7.00000 WCORR4=0.00000 for line in f1: if '#PBS -l nodes=4:ppn=4' in line: f2.write(line.replace('#PBS -l nodes=4:ppn=4', pbs)) + elif '$ssbond' in line: + f2.write(line.replace('$ssbond',tmp_ss)) + elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock': + f2.write(line) + f2.write('../files/generator_v7 plik.pdb plik2.pdb\n') else: tmp1=json.loads(instance.remd_multi_t) f2.write(line.replace('$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 @@ -275,21 +400,60 @@ 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('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ - ' einicheck=1 rescale=2 delta=0.02 cxfile classify\n') + f.write('{:79}'.format('SEED='+str(instance.md_seed)+ + ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n') else: - f.write('SEED='+str(instance.md_seed)+' isampl='+str(isampl)+ - ' einicheck=1 rescale=2 delta=0.02 cxfile\n') + 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=20')+'&\n') + f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ + ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') + f.write('nres='+str(len(seq))+' one_letter\n') for i in range(0,len(seq),80): f.write(seq[i:i+80]+'\n') f.write(write_ssbond(instance.ssbond)) - - f.write(w) + 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(10,21): + 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 != '': + 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: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') + saxs_r.append(tmp[0]) + saxs_P.append(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() + + f.write(w+'\n') f.write('\n') f.write('nt='+str(instance.remd_nrep)+' replica read_iset\n') tmp1=json.loads(instance.remd_multi_t) @@ -307,13 +471,34 @@ CUTOFF=7.00000 WCORR4=0.00000 with open(instance.jobdirname+'/file_cluster.inp','w') as f: f.write(instance.name + ' UNRES server job'+ '\n') - f.write('nres='+str(len(seq)) + f.write('{:79}'.format('nres='+str(len(seq)) +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1' - +' temper='+str(instance.remd_cluter_temp)+'\n') - f.write(w) + +' 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=20')+'&\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(10,21): + 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 != '': + lines=instance.saxs_data.split('\n') + for line in lines: + tmp=line.split() + if len(tmp)==2: + f.write(tmp[0]+' '+tmp[1]+'\n') os.chdir(instance.jobdirname) ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)