UNRES-Dock peptide sequence no pdb

[django_unres.git] / django_simple / todo / jobfiles.py

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index e7ee716..5248031 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -408,6 +408,17 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            f2.write(line.replace('$ssbond',tmp_ss))
           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
             f2.write(line)
+            if instance.md_seq2 !='':
+             f2.write("""setenv FGPROCS 2
+setenv POT GB
+setenv PREFIX file2
+setenv OUT1FILE YES
+/users2/local/mpich2-1.4.1p1_intel/bin/mpirun -machinefile $PBS_NODEFILE -np 2 $UNRES_BIN
+/users2/local/pulchra306/pulchra -q -g file2_MD000.pdb
+cat file2_MD000.rebuilt.pdb |grep -v TER |grep -v END > tmp_plik2.pdb
+/users2/local/mmtsb/perl/convpdb.pl -renumber 1 -out generic tmp_plik2.pdb > act.rebuilt.pdb
+/users2/local/scwrl4/Scwrl4 -h -i act.rebuilt.pdb -o plik2.pdb
+rm tmp_plik2.pdb act.rebuilt.pdb\n""")
             if instance.dock_peptide:
              f2.write('../files/generator_v13 plik.pdb plik2.pdb 1 \n')
             else:
@@ -542,6 +553,44 @@ CUTOFF=7.00000 WCORR4=0.00000"""
               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')
+          
+      
       os.chdir(instance.jobdirname)  
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
       os.chdir('..')