examples correction

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

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index a569298..d09ab98 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -66,7 +66,10 @@ 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:
@@ -97,7 +100,11 @@ 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 '
             
@@ -120,7 +127,11 @@ CUTOFF=7.00000 WCORR4=0.00000
 
        if instance.type == 'remd' :
           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.md_pdbref:
              control_line = control_line+'pdbref '
            
@@ -231,7 +242,7 @@ CUTOFF=7.00000 WCORR4=0.00000
         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()  
 
@@ -295,11 +306,15 @@ CUTOFF=7.00000 WCORR4=0.00000
               isampl=int(instance.md_nstep/instance.md_ntwx*nreplicas/8000)
 
           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)+' isampl='+str(isampl)+
+               ' einicheck=1 rescale=2 delta=0.02 cxfile classify')+'&\n')
+            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+                    ' BOXZ='+str(instance.boxz) +'\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)+' isampl='+str(isampl)+
+              ' einicheck=1 rescale=2 delta=0.02 cxfile')+'&\n')
+            f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+                    ' BOXZ='+str(instance.boxz) +'\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')
@@ -325,9 +340,11 @@ 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')
+             +' temper='+str(instance.remd_cluter_temp))+'&\n')
+          f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
+                  ' BOXZ='+str(instance.boxz) +'\n')
           f.write(w)
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')