secondary structure restraints correction

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

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index fd7fd7c..25532da 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -13,6 +13,47 @@ 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 ii in range(1,len(line)-2):
+     i+=1
+     if line[ii:ii+2]=='HH':
+       out=out+'{:5d}{:8.3f}{:8.3f}\n'.format(i,50.0,20.0)
+     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):
+   line=line.replace(" ", "")
+   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 ii in range(1,len(line)-2):
+     i+=1
+     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 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):
    list=[]
    if ssbond!='':
@@ -90,7 +131,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if seq[-1]=='X':
             dimen3-=1
   
-       nogly ='CDSQKIPTFNHLRWAVEYM'
+       nogly ='CDSQKIPTFNHLRWAVEYMcdsqkiptfnhlrwaveym'
        seq2 = ''.join([c for c in seq if c in nogly])
   
        dimen3=(dimen3+len(seq2))*3
@@ -211,8 +252,10 @@ 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))
-          f.write('0\n')
-
+          if instance.md_seq_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_seq_2d,seq)))
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -221,7 +264,12 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
 
        if instance.type == 'remd' and instance.md_start != 'pdbstart':
 
@@ -230,7 +278,12 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           f.write(str(len(seq))+'\n')
           for i in range(0,len(seq),80):
              f.write(seq[i:i+80]+'\n')
-          f.write('0\n0\n')
+          f.write('0\n')
+          if instance.md_2d == '':
+            f.write('0\n')
+          else:
+            f.write(seq_2d_write(seq_2d_xx(instance.md_2d,seq)))
+
 
        if instance.saxs_data != '':
              lines=instance.saxs_data.split('\n')
@@ -322,19 +375,23 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_pdbref:
             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)+cntrl_saxs +'\n')
           else:    
             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)+
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
+          f.write('BOXX='+str(instance.boxx)+' BOXY='+str(instance.boxy)+
                     ' BOXZ='+str(instance.boxz)+cntrl_saxs +'\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')
 
           f.write(write_ssbond(instance.ssbond))
 
+          if 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')
              lines=instance.saxs_data.split('\n')
@@ -366,12 +423,16 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           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')
+          if instance.md_2d != '':
+               f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\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.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: