MREMD different default temperatures for new ff

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

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 2ec8735..9822a30 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -6,6 +6,7 @@ from .models import Task
 import datetime
 import os
 import subprocess
+import json
 
 res_codes = [
                 # 20 canonical amino acids
@@ -34,18 +35,47 @@ def seq_add_x(sequence):
 def from_pdb(file):
     sequence = []
     ssbond = []
+    ssbond_ch = []
+    ires = []
+    chain_start = {}
+    chain_end = {}
+    unres_shift = {}
+    chain=[]
+    ichain=0
+    newchain = True
+    
     for line in file:
+            if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:':
+              tmp=line[18:]
+              chain_=tmp.split(', ')
+              chain_[-1]=chain_[-1][0]
+              chain.extend(chain_)
+    
             if line[0:6] == 'ATOM  ' and line[13:15] == 'CA':
               aa = three_to_one.get(line[17:20])
-              sequence.append(aa)
+              i = int(line[22:26])
+              if newchain or i!=ires[-1]:
+                sequence.append(aa)
+                ires.append(i)
+                if newchain:
+                 if len(chain)>0:
+                  chain_start[chain[ichain]]=i
+                 newchain = False
             if line[0:3] == 'TER':
               sequence.append('XX')
+              if len(chain)>0:
+               chain_end[chain[ichain]]=i
+              ichain=ichain+1
+              newchain = True
             if line[0:6] == 'SSBOND':
               b=[]
               b.append(int(line[17:21]))
               b.append(int(line[31:35]))
               ssbond.append(b)
-                                                                                    
+              c = []
+              c.append((line[15:16]))
+              c.append((line[29:30]))
+              ssbond_ch.append(c)                                                                      
             if line[0:3] == 'END':
               break
     while sequence[-1] == 'XX':
@@ -56,13 +86,21 @@ def from_pdb(file):
     if sequence[-1] != 'G':
             sequence.append('X')
     seq=''.join(sequence)
-    return seq,ssbond
+#    if ires[0] != 1:
+#            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond]
+    i=0
+    for c in chain:
+      unres_shift[c]=i+chain_start[c]
+      i=i-(chain_end[c]-chain_start[c])-3
+    ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)]     
+
+    return seq,json.dumps(ssbond)
 
 
 @login_required
 def index(request):
     user = request.user
-    tasks = Task.objects.filter(owner=user)
+    tasks = Task.objects.filter(owner=user).order_by('-created_date')
     variable = ''
     return render(request, "index.html", {
             'tasks': tasks
@@ -315,6 +353,7 @@ def add_remd_a(request,task_id):
              task.remd_nrep=form.cleaned_data["remd_nrep"]
              task.remd_nstex=form.cleaned_data["remd_nstex"]
              task.md_ntwx=form.cleaned_data["md_ntwx"]             
+             task.md_ntwe=form.cleaned_data["md_ntwe"]
 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 
@@ -347,12 +386,20 @@ def addmlist(request,task_id):
              task.save()
              return redirect('/')
     else:
+      if task.unres_ff == 'E0LL2Y':
         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
         '["1", "1", "1", "1", "1", "1", "1", "1"]',
         'temperatures':
         '["270", "280", "290", "300", "310", "320", "330", "345"]'
         }
-        form = TaskForm_list(task.remd_nrep,initial=data)
+      else: 
+        data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
+        '["1", "1", "1", "1", "1", "1", "1", "1"]',
+        'temperatures':
+        '["250", "260", "270", "280", "290", "300", "315", "330"]'
+        }
+      
+      form = TaskForm_list(task.remd_nrep,initial=data)
     p_type='replica exchange molecular dynamics - advanced options'
     return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type})
 
@@ -369,7 +416,7 @@ def delete(request, task_id):
 @login_required
 def refresh_done(request):
     user = request.user
-    tasks = Task.objects.filter(owner=user)
+    tasks = Task.objects.filter(owner=user).order_by('-created_date')
     for task in tasks:
       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
          task.done=True
@@ -414,6 +461,7 @@ def refresh_done(request):
          if task.md_pdbref and task.type=='remd':
          
           for i in range(1,6):
+           try:
             with open(task.jobdirname+'/file_wham_T'+str(int(task.remd_cluter_temp))+'K_000'+str(i)+'.pdb', 'r') as f:
                  line=f.readline()
                  if i==1:
@@ -426,7 +474,8 @@ def refresh_done(request):
                      task.remd_model4=' '.join(line.split()[-6:])
                  elif i==5:
                      task.remd_model5=' '.join(line.split()[-6:])
-
+           except EnvironmentError:
+            print 'file_wham_T*pdb open error'
           for i in range(1,6):
             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
                text=''