aminoacid list update and chain without CA correction

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

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 5909fae..2db5186 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)
@@ -82,7 +103,7 @@ def from_pdb(file):
     unres_shift = {}
     chain_sorted=[]
     newchain = True
-    
+    i=''
     for line in file:
             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
               aa = three_to_one.get(line[17:20])
@@ -95,7 +116,7 @@ def from_pdb(file):
                  chain_start[ch]=i
                  chain_sorted.extend(ch)
                  newchain = False
-            if line[0:3] == 'TER':
+            if line[0:3] == 'TER' and i != '':
               sequence.append('XX')
               chain_end[ch]=i
               newchain = True
@@ -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"]
@@ -209,7 +228,7 @@ def add_min_a(request,task_id):
         if form.is_valid():
              task.name=form.cleaned_data["name"]
              task.type="min"
-             task.min_choice=form.cleaned_data["min_choice"]
+#             task.min_choice=form.cleaned_data["min_choice"]
              task.min_overlap=form.cleaned_data["min_overlap"]
              task.min_searchsc=form.cleaned_data["min_searchsc"]
              task.min_maxmin=form.cleaned_data["min_maxmin"]
@@ -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"]
@@ -453,13 +464,15 @@ def add_remd_a(request,task_id):
     task = get_object_or_404(Task, id=task_id)
     if request.method == 'POST':
      if '_example' in request.POST:
-        data= {'name':task.name,'pdbid':'1E0G','md_pdbref':True,
-         'md_nstep':500000,'md_lang':'berendsen','unres_ff':'opt-wtfsa-2',
-         'remd_cluter_temp':280}
-        form = TaskForm_remd_a(initial=data)     
+        data= {'name':task.name,'pdbid':'5G3Q:B','md_pdbref':True,
+         'md_nstep':2000000,'md_lang':'berendsen','unres_ff':'FF2',
+         'remd_cluter_temp':290,'md_2d':'--EEEEEEE------EEEEEE------EEEEEE------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH---'}
+        form = TaskForm_remd_a(initial=data)    
+        task.example='casp12'
+        task.save() 
      elif '_example_saxs' in request.POST:
         data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True,
-         'md_nstep':200000,'md_lang':'langevin','unres_ff':'E0LL2Y',
+         'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2',
          'remd_cluter_temp':270, 
          'scal_rad':4.0,'wsaxs':100.0,'saxs_data':
 """ 0.5     1.33868e-02
@@ -512,9 +525,7 @@ 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"]
@@ -585,7 +596,13 @@ def addmlist(request,task_id):
              else:
               return redirect('/')
     else:
-      if task.unres_ff == 'E0LL2Y':
+      if task.example == 'casp12':
+        data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
+        '["2", "2", "2", "2", "2", "2", "2", "2"]',
+        'temperatures':
+        '["270", "280", "290", "300", "310", "320", "330", "340"]'
+        }
+      elif task.unres_ff == 'FF2':
         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
         '["1", "1", "1", "1", "1", "1", "1", "1"]',
         'temperatures':