X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=28a060308bdccce5c6911a73b6f0a7998087a674;hb=2c4b03af8bd8f39f4a501fb0beeecf80d1946f63;hp=37f4dd1dd9f385273b7774dd9bf0ce412718e957;hpb=e2e36679ef19186908b21dfa586df5af0c3d6710;p=django_unres.git

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 37f4dd1..28a0603 100644
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -6,6 +6,9 @@ from .models import Task
 import datetime
 import os
 import subprocess
+import json
+from lazysignup.decorators import allow_lazy_user
+from lazysignup.utils import is_lazy_user
 
 res_codes = [
                 # 20 canonical amino acids
@@ -34,21 +37,47 @@ 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[24:26])
-              ires.append(i)
+              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':
@@ -59,16 +88,21 @@ def from_pdb(file):
     if sequence[-1] != 'G':
             sequence.append('X')
     seq=''.join(sequence)
-    if ires[0] != 1:
-            ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in 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,ssbond
+    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
@@ -86,16 +120,31 @@ def add(request):
             return redirect('add_min',task_id=task.id)
     return redirect('/')
 
-
 @login_required
 def add_min(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':'1BDD'}
+        form = TaskForm_min(initial=data)     
+     else:
         form = TaskForm_min(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
              task.type="min"
-             task.myfile1=form.cleaned_data["file1"]
+             pdbid=form.cleaned_data["pdbid"]
+
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
 
              seq,task.ssbond=from_pdb(task.myfile1)
              task.md_seq=""
@@ -103,12 +152,12 @@ def add_min(request,task_id):
                     task.md_seq=task.md_seq+seq[i:i+40]+" "
 
              task.ready=True
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')              
+             else:
+              return redirect('/')
     else:
         data= {'name':task.name}
         form = TaskForm_min(initial=data)
@@ -116,9 +165,14 @@ def add_min(request,task_id):
     basic_adv=True    
     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 
+@login_required
 def add_min_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':'1EI0','unres_ff':'opt-wtfsa-2'}
+        form = TaskForm_min_a(initial=data)     
+     else:
         form = TaskForm_min_a(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
@@ -129,23 +183,38 @@ def add_min_a(request,task_id):
              task.min_maxmin=form.cleaned_data["min_maxmin"]
              task.min_maxfun=form.cleaned_data["min_maxfun"]
              task.min_pdbout=form.cleaned_data["min_pdbout"]
-             task.myfile1=form.cleaned_data["file1"]
+
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             task.jobdirname = "_".join([basename, suffix])
+             
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
+
              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
              task.unres_ff=form.cleaned_data["unres_ff"]
+             task.boxx=form.cleaned_data["boxx"]
+             task.boxy=form.cleaned_data["boxy"]             
+             task.boxz=form.cleaned_data["boxz"]             
 
              seq,task.ssbond=from_pdb(task.myfile1)
              task.md_seq=""
              for i in range(0,len(seq),40):
                 task.md_seq=task.md_seq+seq[i:i+40]+" "
                                                            
-
              task.ready=True
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')             
+             else:
+              return redirect('/')
     else:
         data= {'name':task.name}
         form = TaskForm_min_a(initial=data)
@@ -157,6 +226,11 @@ def add_min_a(request,task_id):
 def add_md(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':'1IGD','md_start':'pdbstart',
+        'md_pdbref':True,'md_temp':200}
+        form = TaskForm_md(initial=data)     
+     else:
         form = TaskForm_md(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
@@ -165,8 +239,19 @@ def add_md(request,task_id):
              task.md_start=form.cleaned_data["md_start"]
              task.md_temp=form.cleaned_data["md_temp"]
              task.md_nstep=form.cleaned_data["md_nstep"]
-             
-             task.myfile1=form.cleaned_data["file1"]
+
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             task.jobdirname = "_".join([basename, suffix])
+
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
              task.md_pdbref=form.cleaned_data["md_pdbref"]             
 
              task.md_seq=""
@@ -182,12 +267,12 @@ def add_md(request,task_id):
                 task.ssbond=''
 
              task.ready=True
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')
+             else:
+              return redirect('/')
     else:
         data= {'name':task.name}
         form = TaskForm_md(initial=data)
@@ -195,15 +280,32 @@ def add_md(request,task_id):
     p_type='molecular dynamics'
     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 
+@login_required
 def add_md_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':'1L2Y','md_start':'extconf',
+         'md_pdbref':True,'md_mdpdb':True}
+        form = TaskForm_md_a(initial=data)     
+     else:
         form = TaskForm_md_a(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
              task.type="md"
 
-             task.myfile1=form.cleaned_data["file1"]
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             task.jobdirname = "_".join([basename, suffix])
+
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
              task.md_start=form.cleaned_data["md_start"]
              task.md_pdbref=form.cleaned_data["md_pdbref"]             
 
@@ -230,14 +332,18 @@ def add_md_a(request,task_id):
              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
              task.unres_ff=form.cleaned_data["unres_ff"]
+             task.boxx=form.cleaned_data["boxx"]
+             task.boxy=form.cleaned_data["boxy"]             
+             task.boxz=form.cleaned_data["boxz"]             
+
              
              task.ready=True
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')             
+             else:
+              return redirect('/')
     else:
         data= {'name':task.name}
         form = TaskForm_md_a(initial=data)
@@ -249,12 +355,28 @@ def add_md_a(request,task_id):
 def add_remd(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':'1L2Y','md_pdbref':True}
+        form = TaskForm_remd(initial=data)     
+     else:
         form = TaskForm_remd(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
              task.type="remd"
              task.md_start=form.cleaned_data["md_start"]
-             task.myfile1=form.cleaned_data["file1"]
+
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             task.jobdirname = "_".join([basename, suffix])
+
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
              task.md_pdbref=form.cleaned_data["md_pdbref"]
              task.md_ntwx=task.remd_nstex 
 
@@ -276,12 +398,12 @@ def add_remd(request,task_id):
 
              task.ready=True
              
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')             
+             else:
+              return redirect('/')
     else:
         data= {'name':task.name}
         form = TaskForm_remd(initial=data)
@@ -289,15 +411,33 @@ def add_remd(request,task_id):
     p_type='replica exchange molecular dynamics'
     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 
+@login_required
 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':1000000,'md_lang':'berendsen','unres_ff':'opt-wtfsa-2',
+         'remd_cluter_temp':270}
+        form = TaskForm_remd_a(initial=data)     
+     else:
         form = TaskForm_remd_a(request.POST,request.FILES)
         if form.is_valid():
              task.name=form.cleaned_data["name"]
              task.type="remd"
 
-             task.myfile1=form.cleaned_data["file1"]
+             basename = str(task.owner)
+             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
+             task.jobdirname = "_".join([basename, suffix])
+
+             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.pdbcode=pdbid
+             else:
+              task.myfile1=form.cleaned_data["file1"]
              task.md_start=form.cleaned_data["md_start"]  
              task.md_pdbref=form.cleaned_data["md_pdbref"]                        
 
@@ -325,13 +465,13 @@ def add_remd_a(request,task_id):
 #             task.remd_traj1file=form.cleaned_data["remd_traj1file"]
 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 
+             task.boxx=form.cleaned_data["boxx"]
+             task.boxy=form.cleaned_data["boxy"]             
+             task.boxz=form.cleaned_data["boxz"]             
+
              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
              task.unres_ff=form.cleaned_data["unres_ff"]
              
-             basename = str(task.owner)
-             suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")
-             task.jobdirname = "_".join([basename, suffix])
-             
              task.save()
              return redirect('addmlist',task_id=task.id)
     else:
@@ -341,7 +481,7 @@ def add_remd_a(request,task_id):
     p_type='replica exchange molecular dynamics - advanced options'
     return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type})
 
-
+@login_required
 def addmlist(request,task_id):
     task = get_object_or_404(Task, id=task_id)
     if request.method == 'POST':
@@ -352,14 +492,25 @@ def addmlist(request,task_id):
              task.ready=True
              
              task.save()
-             return redirect('/')
+             if is_lazy_user(request.user):
+              return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/')              
+             else:
+              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})
 
@@ -368,16 +519,64 @@ def details(request,task_id):
     task = get_object_or_404(Task, id=task_id)
     return render(request, "details.html",{'task':task})
 
+
+def details1(request,user_id,task_id):
+    task = get_object_or_404(Task, id=task_id)
+    return render(request, "details1.html",{'task':task})
+
+
 @login_required
 def delete(request, task_id):
     Task.objects.get(id=task_id).delete()
     return redirect('/')
 
+def refresh_done1(request, task_id):
+    task = get_object_or_404(Task, id=task_id)
+    user = task.owner
+    refresh_done0(task)
+
+    proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
+    njob=0
+    nq=0
+    for line in proc.stdout:
+      if 'piasek4' in line:
+        if line.split()[1]=='test_server':
+          njob+=1
+          if line.split()[-2]=='Q':
+            nq+=1
+    variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
+
+    return redirect('/details1/'+str(user)+'/'+str(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:
+      refresh_done0(task)
+
+    proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
+    njob=0
+    nq=0
+    for line in proc.stdout:
+      if 'piasek4' in line:
+        if line.split()[1]=='test_server':
+          njob+=1
+          if line.split()[-2]=='Q':
+            nq+=1
+    variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
+
+    if is_lazy_user(request.user):
+     return redirect('/details1/'+str(user)+'/'+str(task.id)+'/')
+    else:
+     return render(request, "index.html", {
+                'tasks': tasks ,
+                'variable' : variable
+                        })
+
+      
+def refresh_done0(task):
       if os.path.isfile(task.jobdirname+'/finished') and not task.done:
          task.done=True
 
@@ -421,6 +620,7 @@ 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:
@@ -433,7 +633,8 @@ 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=''
@@ -499,20 +700,5 @@ def refresh_done(request):
              task.running=100
          task.save()
 
-    proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE)
-    njob=0
-    nq=0
-    for line in proc.stdout:
-      if 'piasek4' in line:
-        if line.split()[1]=='test_server':
-          njob+=1
-          if line.split()[-2]=='Q':
-            nq+=1
-    variable='Idle jobs='+str(nq)+' Total jobs='+str(njob)
-
-    return render(request, "index.html", {
-                'tasks': tasks ,
-                'variable' : variable
-                        })
     
-#   return redirect('/')        
+      return