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 '
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')
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':
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)))
' 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(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)))
+' 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 != '':