From 56e79678d88f1b25b4c15ce3ac8047b6fa6faa35 Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Fri, 19 Jan 2018 09:36:37 +0100
Subject: [PATCH] secondary structure restraints correction

---
 django_simple/todo/jobfiles.py |   41 +++++++++++++++++++++++++---------------
 django_simple/todo/views.py    |    2 +-
 2 files changed, 27 insertions(+), 16 deletions(-)

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 4d9270c..25532da 100644
--- 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):
@@ -244,7 +255,7 @@ CUTOFF=7.00000 WCORR4=0.00000"""
           if instance.md_seq_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_seq_2d,seq)))
 
        if instance.type == 'md' and instance.md_start != 'pdbstart':
 
@@ -257,7 +268,7 @@ 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 +282,7 @@ 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 != '':
@@ -379,7 +390,7 @@ 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 +432,7 @@ 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:
diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 0387f29..5909fae 100644
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -39,7 +39,7 @@ def seq_2d_from_pdb(seq_2d,seq):
       if seq[i]=='X':
          seq_2d_tmp=seq_2d_tmp+'-'
       else:
-         if len(seq_2d)>=ii:
+         if len(seq_2d)>ii:
             seq_2d_tmp=seq_2d_tmp+seq_2d[ii]
             ii+=1
     tmp=''
-- 
1.7.9.5