remd preminim maxfun input

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

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 4d9270c..df2ce65 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -13,19 +13,30 @@ import textwrap
 logging.basicConfig()
 logger = logging.getLogger(__name__)
 
+def seq_2d_xx(line,seq):
+   line=line.replace(" ","")
+   lista=list(line)
+   for ii in range(0,len(line)):
+    if seq[ii]=='X':
+      if ii>0:
+            lista[ii-1]='-'
+      if ii+1<len(line):
+            lista[ii+1]='-'
+   return("".join(lista)) 
+
 def seq_2d_write(line):
    line=line.replace(" ", "")
    out='{:d}\n{:6.1f}\n'.format(len(line),50.0)
    for i in range(1,4):
      out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
-   for e in line[:-3]:
+   for ii in range(1,len(line)-2):
      i+=1
-     if e=='-':
-       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
-     elif e=='H':
+     if line[ii:ii+2]=='HH':
        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
-     elif e=='E':
+     elif line[ii:ii+2]=='EE':
        out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0)
+     else:
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0)
    return(out)
 
 def seq_2d_write_50(line):
@@ -33,14 +44,14 @@ def seq_2d_write_50(line):
    out='{:d}\n'.format(len(line))
    for i in range(1,4):
      out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
-   for e in line[:-3]:
+   for ii in range(1,len(line)-2):
      i+=1
-     if e=='-':
-       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)
-     elif e=='H':
+     if line[ii:ii+2]=='HH':
        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0,50.0)
-     elif e=='E':
+     elif line[ii:ii+2]=='EE':
        out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,180.0,40.0,50.0)
+     else:
+       out=out+'{:5d}{:8.3f}{:8.3f}{:8.3f}\n'.format(i,0.0,180.0,50.0)     
    return(out)
 
 def write_ssbond(ssbond):
@@ -73,7 +84,7 @@ def write_on_task_save(sender, instance, **kwargs):
 #wrapper = textwrap.TextWrapper(width=70)
 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
 
-     if  instance.unres_ff =='E0LL2Y':
+     if  instance.unres_ff =='FF2':
       w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
@@ -210,6 +221,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        f.write(word_list[-1]+'\n')
           
        if instance.md_start == 'pdbstart':
+        if instance.type == 'remd' :
+         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')
 
        
@@ -241,10 +256,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
        if instance.type == 'min' or instance.md_start == 'pdbstart':
           f.write('plik.pdb\n')
           f.write(write_ssbond(instance.ssbond))
-          if instance.md_seq_2d == '':
+          if instance.md_2d == '':
             f.write('0\n')
           else:
-            f.write(seq_2d_write(instance.md_seq_2d))
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -257,7 +272,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_2d == '':
             f.write('0\n')
           else:
-            f.write(seq_2d_write(instance.md_2d))
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
@@ -271,7 +286,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_2d == '':
             f.write('0\n')
           else:
-            f.write(seq_2d_write(instance.md_2d))
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
 
 
        if instance.saxs_data != '':
@@ -284,7 +299,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
         
      if instance.type == 'min':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         shutil.copy('../files/pbs.csh','.')
       else:
         shutil.copy('../files/pbs_new.csh','pbs.csh')
@@ -292,7 +307,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       os.chdir('..')
      elif instance.type == 'md':
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs_md.csh', 'r')
       else:
         f1 = open('../files/pbs_md_new.csh', 'r') 
@@ -305,6 +320,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
       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()
 
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)      
@@ -337,7 +353,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
         tmp_ss=' '.join(map(str,l))
 
       os.chdir(instance.jobdirname)
-      if  instance.unres_ff =='E0LL2Y':
+      if  instance.unres_ff =='FF2':
         f1 = open('../files/pbs8.csh', 'r')
       else:
         f1 = open('../files/pbs8_new.csh', 'r')
@@ -379,7 +395,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write(write_ssbond(instance.ssbond))
 
           if instance.md_2d != '':
-             f.write(seq_2d_write_50(instance.md_2d))
+             f.write(seq_2d_write_50(seq_2d_xx(instance.md_2d,seq)))
 
           if instance.saxs_data != '':
              fsaxs = open(instance.jobdirname+'/saxs.data', 'w')
@@ -421,7 +437,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
              f.write(seq[i:i+80]+'\n')
           f.write(write_ssbond(instance.ssbond))
           if instance.md_2d != '':
-             f.write(seq_2d_write_50(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: