From f3bfe6e521044d61dee2d8e267d3bd5ed6ba44f7 Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Tue, 12 Dec 2017 01:56:30 +0100
Subject: [PATCH] missing residues error for pdb file or id

---
 django_simple/todo/forms.py |   78 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index bfbd094..8fda381 100644
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -7,6 +7,29 @@ from .models import FF_CHOICE
 import json
 import urllib
 
+def pdb_missing_res(file):
+   msg=''
+   newchain = True
+   ires=[]
+   for line in file:
+      if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
+               i = int(line[22:26])
+               if ires and i==ires[-1]:
+                 continue
+               if newchain or i==ires[-1]+1:
+                 ires.append(i)
+                 newchain = False
+               else:
+                 msg = 'chain breaks between residues '+\
+                   str(ires[-1])+' and '+str(i)+\
+                   ', server cannot add missing residues to PDB file'
+                 break
+      if line[0:3] == 'TER':
+               newchain = True
+      if line[0:3] == 'END':
+               break
+   
+   return(msg)
 
 class MultiWidgetBasic(forms.MultiWidget):
     def __init__(self, count, attrs=None):
@@ -66,7 +89,17 @@ class TaskForm_min(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
+
             
 class TaskForm_min_a(forms.Form):
      name = forms.CharField(max_length=20)
@@ -111,7 +144,16 @@ class TaskForm_min_a(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
 
 
 class TaskForm_md(forms.Form):
@@ -164,7 +206,16 @@ class TaskForm_md(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
 
                         
 class TaskForm_md_a(forms.Form):
@@ -239,7 +290,16 @@ class TaskForm_md_a(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
 
 
 class TaskForm_remd(forms.Form):
@@ -289,7 +349,16 @@ class TaskForm_remd(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
 
                              
 class TaskForm_remd_a(forms.Form):
@@ -369,7 +438,16 @@ class TaskForm_remd_a(forms.Form):
                if test.code != 200:
                  msg = 'wrong pdb code'
                  self.add_error('pdbid', msg)
+               else:
+                 msg=pdb_missing_res(test)
+                 if msg != '':
+                   self.add_error('pdbid',msg)
                test.close()
+               
+             if file1:
+                 msg=pdb_missing_res(file1)
+                 if msg != '':
+                   self.add_error('file1',msg)
 
 
 
-- 
1.7.9.5