+
+#---v
+ if instance.use_nmr:
+ f.write('ndist='+repr(instance.linijek_nmr)+' restr_type=12 scal_peak=')
+ f.write(repr(instance.nmr_scal)+' fordepth_peak='+repr(instance.nmr_fordepth))
+ f.write(' slope_peak='+repr(instance.nmr_slope)+'\n')
+ if (instance.myfile3=='files/N1008_AmbiR-trunc.txt'):
+ fnmr = open(instance.jobdirname+'/../files/N1008_AmbiR-trunc.txt', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+ else:
+ fnmr = open(instance.jobdirname+'/plik3.nmr', 'r')
+ for linmr in fnmr:
+ f.write(linmr)
+ fnmr.close()
+#---^
+
+ 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 != '':
+ 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 == 'dock' and instance.md_seq2 != '':
+ with open(instance.jobdirname+'/file2.inp','w') as f:
+ f.write(instance.name + ' chain2 random start'+ '\n')
+ control_line = 'SEED='+str(instance.md_seed)+' '\
+ +'rand_conf md one_letter'\
+ + ' BOXX=1000 BOXY=1000 BOXZ=1000 '
+
+ if instance.unres_ff =='NEWCT-9P':
+ control_line = control_line+'tormode=2 cart'
+
+ type_line = ' reset_vel=0'\
+ +' t_bath=300'\
+ +' nstep=100000'\
+ +' ntwe=10000'\
+ +' ntwx=100000'\
+ +' dt=0.2 lang=1 scal_fric=0.02 respa mdpdb '
+
+ wrapper = textwrap.TextWrapper(width=70)
+ word_list = wrapper.wrap(text=control_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ word_list = wrapper.wrap(text=type_line)
+ for element in word_list[:-1]:
+ f.write('{:79}'.format(element)+'&\n')
+ f.write(word_list[-1]+'\n')
+
+ f.write(w+'\n')
+
+ seq=instance.md_seq2.replace(" ","")
+ f.write(str(len(seq))+'\n')
+ for i in range(0,len(seq),80):
+ f.write(seq[i:i+80]+'\n')
+ f.write('0\n')
+ f.write('0\n')
+