X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fjobfiles.py;h=61d2c45b4347c8bbb984e4ac87fa5c532eb60c24;hb=5a52e318fbba09f787c91fadc8d364d16c2d452d;hp=d9b8c7c0ba884a32ad7f6f9896148e30105ee32c;hpb=a3b7f27a81cf442cdeeaff5b9c9b52298c282f5a;p=django_unres.git diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py index d9b8c7c..61d2c45 100644 --- a/django_simple/todo/jobfiles.py +++ b/django_simple/todo/jobfiles.py @@ -147,7 +147,7 @@ CUTOFF=7.00000 WCORR4=0.00000""" 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)\ @@ -164,12 +164,15 @@ 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=20 ' if instance.md_pdbref: control_line = control_line+'pdbref ' @@ -184,7 +187,7 @@ 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 = 'restart reset_vel='+ str(instance.remd_nstex)\ +' nstep='+str(instance.md_nstep)\ +' ntwe='+str(instance.md_ntwe)\ +' ntwx='+str(instance.md_ntwx)\ @@ -221,14 +224,14 @@ CUTOFF=7.00000 WCORR4=0.00000""" f.write(word_list[-1]+'\n') if instance.md_start == 'pdbstart': - if instance.type == 'remd' : + 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 +257,23 @@ 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('model01.pdb\n') + else: + f.write('plik.pdb\n') f.write(write_ssbond(instance.ssbond)) 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': @@ -363,11 +377,21 @@ 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 $PBS_O_WORKDIR' in line and instance.type == 'dock': + f2.write(line) + f2.write('../files/generator_v7 plik.pdb plik2.pdb\n') else: tmp1=json.loads(instance.remd_multi_t) f2.write(line.replace('$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 @@ -376,15 +400,17 @@ 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=20')+'&\n') f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+ ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\n') @@ -394,6 +420,14 @@ 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(10,21): + f.write('model'+str(i)+'.pdb\n') + if instance.md_2d != '': f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq))) @@ -401,6 +435,7 @@ 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 +444,11 @@ 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() @@ -437,12 +476,21 @@ 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=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 != '':