pdbid:chain added

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index e87cdcc..6d47368 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -7,6 +7,52 @@ from .models import FF_CHOICE
 import json
 import urllib
 
+def pdb_code_chain(pdbid):
+
+    msg=''
+    chain=''
+    if len(pdbid)>4:
+       if pdbid[4]!=':':
+         return('use : between pdb code and chain id, like 5G3Q:B to select single chain')
+       chain=pdbid[5]
+       pdbid=pdbid[:4]    
+    
+    test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
+    if test.code != 200:
+          msg = 'wrong pdb code'
+    else:
+          msg=pdb_missing_res_chain(test,chain)
+    test.close()
+    return(msg)
+
+def pdb_missing_res_chain(file,chain):
+   msg=''
+   newchain = True
+   ires=[]
+   for line in file:
+      if line[0:6] == 'ATOM  ' and line[13:15] == 'CA' and (line[21] == chain or chain==''):
+               i = int(line[22:26])
+               ch = line[21]
+               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)+' of chain '+ch+\
+                   ', server cannot add missing residues to PDB file - please repair the structure using e.g. Modeller'
+                 break
+      if line[0:3] == 'TER':
+               newchain = True
+      if line[0:3] == 'END':
+               break
+   
+   if len(ires) == 0:
+               msg='wrong chain id'
+   return(msg)
+
+
 def code_2d(line):
    msg=''
    set ='HEC-'
@@ -78,9 +124,9 @@ class TaskForm_min(forms.Form):
      name = forms.CharField(max_length=20)
      file1 = forms.FileField(label='Upload a PDB file',required=False,
       help_text='continuous (without breaks) protein chains,use TER to divide chains')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
 
      def clean(self):
              cleaned_data = super(TaskForm_min, self).clean()
@@ -93,15 +139,9 @@ class TaskForm_min(forms.Form):
                 self.add_error('file1', msg)
               
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
-                 if msg != '':
+               msg=pdb_code_chain(pdbid)
+               if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)
@@ -123,9 +163,9 @@ class TaskForm_min_a(forms.Form):
                   help_text='maximum number of function evaluations')
      file1 = forms.FileField(label='Upload a PDB file',required=False,
         help_text='continuous (without breaks) protein chains,use TER to divide chains')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
 
      min_unres_pdb = forms.BooleanField(required=False,label='uploaded input unres PDB',
                   help_text='(CA and CB atoms only, CB represents SC in UNRES)')
@@ -148,15 +188,9 @@ class TaskForm_min_a(forms.Form):
                 self.add_error('file1', msg)
               
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
+                 msg=pdb_code_chain(pdbid)
                  if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)
@@ -176,9 +210,9 @@ class TaskForm_md(forms.Form):
                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')
      md_temp = forms.FloatField(label='temperature',initial=300,
                   help_text='bath temperature')
@@ -210,15 +244,9 @@ class TaskForm_md(forms.Form):
                 self.add_error('md_seq', msg)
 
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
+                 msg=pdb_code_chain(pdbid)
                  if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)
@@ -245,9 +273,9 @@ class TaskForm_md_a(forms.Form):
 
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')                  
      md_temp = forms.FloatField(label='temperature',initial=300,
                   help_text='bath temperature')
@@ -301,15 +329,9 @@ class TaskForm_md_a(forms.Form):
                 self.add_error('md_seq', msg)
 
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
+                 msg=pdb_code_chain(pdbid)
                  if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)
@@ -333,9 +355,9 @@ class TaskForm_remd(forms.Form):
                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')                  
      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
                   help_text='total number of steps')
@@ -364,15 +386,9 @@ class TaskForm_remd(forms.Form):
                 self.add_error('md_seq', msg)
 
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
+                 msg=pdb_code_chain(pdbid)
                  if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)
@@ -398,9 +414,9 @@ class TaskForm_remd_a(forms.Form):
                      widget=forms.Textarea(attrs={'cols': 70, 'rows': 2}))
      file1 = forms.FileField(label='Upload a PDB file',required=False,
                   help_text='starting structure for pdbstart/reference structure')
-     pdbid = forms.CharField(min_length=4,max_length=4,required=False,
-      widget=forms.TextInput(attrs={'size':4, 'maxlength':4, 'title':'PDB code'}),
-      label='or PDB code')                   
+     pdbid = forms.CharField(min_length=4,max_length=6,required=False,
+      widget=forms.TextInput(attrs={'size':6, 'maxlength':6, 'title':'PDB code or PDB code:chain id'}),
+      label='or PDB code (:chain)')                   
      md_pdbref = forms.BooleanField(required=False,label='PDB reference structure')                  
      md_nstep = forms.IntegerField(label='NSTEP',initial=200000,
                   help_text='total number of steps')
@@ -470,15 +486,9 @@ class TaskForm_remd_a(forms.Form):
                 self.add_error('md_seq', msg)
 
              if pdbid:
-               test=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')     
-               if test.code != 200:
-                 msg = 'wrong pdb code'
-                 self.add_error('pdbid', msg)
-               else:
-                 msg=pdb_missing_res(test)
+                 msg=pdb_code_chain(pdbid)
                  if msg != '':
                    self.add_error('pdbid',msg)
-               test.close()
                
              if file1:
                  msg=pdb_missing_res(file1)

diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index 2103d7f..bc2fac6 100644 (file)
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -30,7 +30,7 @@ class Task(models.Model):
 #       return json.loads(self.ssbond)
 
     unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='FF2')
-    pdbcode = models.CharField(max_length=4,default='')
+    pdbcode = models.CharField(max_length=6,default='')
 # minimization
     min_choice = models.CharField(max_length=20,choices=MIN_CHOICE,default='minimize cart')
     min_overlap = models.BooleanField(default=False)

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 3d959f1..7045a7c 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -29,6 +29,27 @@ res_codes = [
 
 three_to_one = dict(res_codes)
 
+def load_pdbid(pdbid,dirname):
+    os.mkdir(dirname)
+    if len(pdbid)==4:
+       file,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
+                     dirname+'/plik.pdb')     
+    else:
+       chain=pdbid[5]
+       pdbid=pdbid[:4]
+       pdb_tmp=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb')
+       with open(dirname+'/plik.pdb', 'w') as outfile:
+        for line in pdb_tmp:
+          if line[0:6] == 'SSBOND' and line[15] == chain and line[29] == chain:
+            outfile.write(line)
+          if line[0:6] == 'ATOM  ' and line[21] == chain:
+            outfile.write(line)
+       pdb_tmp.close()
+       file=dirname+'/plik.pdb'
+       
+    return(file)
+
+
 def seq_2d_from_pdb(seq_2d,seq):
     if seq_2d =='':
       return(seq_2d)
@@ -171,9 +192,7 @@ def add_min(request,task_id):
              task.jobdirname = "_".join([basename, suffix])
 
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]
@@ -222,9 +241,7 @@ def add_min_a(request,task_id):
              
              pdbid=form.cleaned_data["pdbid"]
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]
@@ -278,9 +295,7 @@ def add_md(request,task_id):
 
              pdbid=form.cleaned_data["pdbid"]
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]
@@ -332,9 +347,7 @@ def add_md_a(request,task_id):
 
              pdbid=form.cleaned_data["pdbid"]
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]
@@ -407,9 +420,7 @@ def add_remd(request,task_id):
 
              pdbid=form.cleaned_data["pdbid"]
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]
@@ -512,9 +523,7 @@ def add_remd_a(request,task_id):
 
              pdbid=form.cleaned_data["pdbid"]
              if pdbid:
-              os.mkdir(task.jobdirname)
-              task.myfile1,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb',
-                     task.jobdirname+'/plik.pdb')     
+              task.myfile1=load_pdbid(pdbid,task.jobdirname)
               task.pdbcode=pdbid
              else:
               task.myfile1=form.cleaned_data["file1"]