number of clusters <> 5

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index 50dab80..74779e2 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -620,6 +620,8 @@ class TaskForm_dock_a(forms.Form):
      remd_cluter_temp = forms.FloatField(label='TEMPER',
                   help_text='temperature for cluster analysis',initial=280)                  
 
+     remd_cluster_n = forms.IntegerField(label='NCLUST',initial=10,min_value=2,
+                    max_value=50,help_text='number of clusters')
 
      def clean(self):
              cleaned_data = super(TaskForm_dock_a, self).clean()

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 5248031..e2f0829 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -524,7 +524,8 @@ rm tmp_plik2.pdb act.rebuilt.pdb\n""")
           f.write(instance.name + ' UNRES server job'+ '\n')
           f.write('{:79}'.format('nres='+str(len(seq))
              +' one_letter rescale=2 PRINT_CART PDBOUT=1 iopt=1'
-             +' temper='+str(instance.remd_cluter_temp))+'&\n')
+             +' temper='+str(instance.remd_cluter_temp)
+             +' nclust='+str(instance.remd_cluster_n))+'&\n')
           if instance.md_2d != '':
                f.write('{:79}'.format(' WITH_DIHED_CONSTR')+'&\n')
           if instance.type == 'dock':

diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index 5629bf5..c235012 100644 (file)
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -86,6 +86,7 @@ class Task(models.Model):
     remd_model4 = models.TextField(default='')
     remd_model5 = models.TextField(default='')
     remd_models = models.TextField(default='')
+    remd_cluster_n = models.IntegerField(default=5)
 
 #saxs
     scal_rad = models.FloatField(default=1.0)

diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index 9fd9a03..c6bfd20 100644 (file)
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -349,6 +349,10 @@ Created {{ task.created_date  }}
                            <div class="col-md-6"> temperature for clustering</div>
                            <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
                        </li>           
+                       <li class="list-group-item task-item">
+                           <div class="col-md-6"> number of clusters</div>
+                           <div class="col-md-6">{{ task.remd_cluster_n}}</div>
+                       </li>           
                        {% if task.saxs_data != "" %}                   
                        <li class="list-group-item task-item">
                            <div class="col-md-6"> wsaxs </div>
@@ -638,7 +642,7 @@ Created {{ task.created_date  }}
        </div>
        </li>           
        
-               {% for iii in "12345" %}
+               {% for iii in range %}
 
                 {% with istr=forloop.counter|stringformat:"s" %}
                 {% with MODELi="MODEL"|add:istr|add:".pdb" %}
@@ -652,7 +656,7 @@ Created {{ task.created_date  }}
                          {% if not task.damino %}
                          after conversion to allatom 
                          {% endif %}
-                         {{ remd_models|index:forloop.counter|linebreaks }}
+                         {{ remd_models|index:iii|linebreaks }}
                          NGL viewer</div>
                          <div class="col-md-10" id={{viewporti}}
                          style="width:500px;height:500px;"> 

diff --git a/django_simple/todo/templates/details1.html b/django_simple/todo/templates/details1.html
index 27b5a1f..be13e07 100644 (file)
--- a/django_simple/todo/templates/details1.html
+++ b/django_simple/todo/templates/details1.html
@@ -1,5 +1,6 @@
 {% extends "base.html" %}
 
+{% load index %}
 {% load i18n lazysignup_tags %}
 {% block content %}
 
@@ -339,6 +340,11 @@ Created {{ task.created_date  }}
                            <div class="col-md-6"> temperature for clustering</div>
                            <div class="col-md-6">{{ task.remd_cluter_temp}}</div>
                        </li>           
+                       <li class="list-group-item task-item">
+                           <div class="col-md-6"> number of clusters</div>
+                           <div class="col-md-6">{{ task.remd_cluster_n}}</div>
+                       </li>           
+
                        {% if task.saxs_data != "" %}                   
                        <li class="list-group-item task-item">
                            <div class="col-md-6"> wsaxs </div>
@@ -627,188 +633,45 @@ Created {{ task.created_date  }}
         <button onclick="plusDivs(1)">&#10095;</button>
        </div>
        </li>           
-                       
+       
+               {% for iii in range %}
+
+                {% with istr=forloop.counter|stringformat:"s" %}
+                {% with MODELi="MODEL"|add:istr|add:".pdb" %}
+                {% with viewporti="viewport_M"|add:istr %}
+                {% with toggleRefi="toggleRefM"|add:istr %}
+                {% with toggleSidechainsi="toggleSidechainsM"|add:istr %}
+
                         <div class="model">
-<!--                   <li class="list-group-item task-item">
-                         <div class="col-md-2"> model1 after conversion
-                         to allatom 
-                         {{ task.remd_model1|linebreaks }}
-                         </div>
-                         <div class="col-md-10"> 
-                         <a
-                         href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">
-                         <img
-                         src="/myfiles/download-file/{{task.jobdirname}}/model1.png" width="500">
-                         </a></div>
-                       </li> -->                       
-                       <li class="list-group-item task-item">
-                         <div class="col-md-2"> model1 
-                         {% if not task.damino %}
-                         after conversion to allatom 
-                         {% endif %}
-                         {{ task.remd_model1|linebreaks }}
-                         NGL viewer</div>
-                         <div class="col-md-10" id="viewport_M1"
-                         style="width:500px;height:500px;"> 
-                         </div>
-                       </li>
-                        <li class="list-group-item task-item">
-               <div class="col-md-12">
-               {% if task.md_pdbref %}
-               <button id="toggleRefM1">Reference structure on/off</button>
-               {% endif %}
-               <button id="toggleSidechainsM1">Side-chains on/off</button>
-               <a class="btn btn-default"
-               href="/myfiles/download-file/{{task.jobdirname}}/MODEL1.pdb">Download</a>               
-               </div>
-                        </li>
-                       
-                       </div>
-                       <div class="model">
-<!--                   <li class="list-group-item task-item">
-                         <div class="col-md-2"> model2 after conversion
-                         to allatom 
-                         {{ task.remd_model2|linebreaks }}
-                         </div>
-                         <div class="col-md-10"> 
-                         <a
-                         href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">
-                         <img
-                         src="/myfiles/download-file/{{task.jobdirname}}/model2.png" width="500">
-                         </a></div>
-                       </li> -->
-                       <li class="list-group-item task-item">
-                         <div class="col-md-2"> model2 
-                         {% if not task.damino %}
-                         after conversion to allatom
-                         {% endif %}
-                         {{ task.remd_model2|linebreaks }}
-                         NGL viewer</div>
-                         <div class="col-md-10" id="viewport_M2"
-                         style="width:500px;height:500px;"> 
-                         </div>
-                       </li>
-                        <li class="list-group-item task-item">
-               <div class="col-md-12">
-               {% if task.md_pdbref %}
-               <button id="toggleRefM2">Reference structure on/off</button>
-               {% endif %}
-               <button id="toggleSidechainsM2">Side-chains on/off</button>
-               <a class="btn btn-default"
-               href="/myfiles/download-file/{{task.jobdirname}}/MODEL2.pdb">Download</a>               
-               </div>
-                        </li>
-                       
-                       
-                       </div>
-                       <div class="model">
-<!--                   <li class="list-group-item task-item">
-                         <div class="col-md-2"> model3 after conversion
-                         to allatom 
-                         {{ task.remd_model3|linebreaks }}
-                         </div>
-                         <div class="col-md-10"> 
-                         <a
-                         href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">
-                         <img
-                         src="/myfiles/download-file/{{task.jobdirname}}/model3.png" width="500">
-                         </a></div>
-                       </li>-->
-                       <li class="list-group-item task-item">
-                         <div class="col-md-2"> model3 
-                         {% if not task.damino %}
-                         after conversion to allatom
-                         {% endif %}
-                         {{ task.remd_model3|linebreaks }}
-                         NGL viewer</div>
-                         <div class="col-md-10" id="viewport_M3"
-                         style="width:500px;height:500px;"> 
-                         </div>
-                       </li>
-                        <li class="list-group-item task-item">
-               <div class="col-md-12">
-               {% if task.md_pdbref %}
-               <button id="toggleRefM3">Reference structure on/off</button>
-               {% endif %}
-               <button id="toggleSidechainsM3">Side-chains on/off</button>
-               <a class="btn btn-default"
-               href="/myfiles/download-file/{{task.jobdirname}}/MODEL3.pdb">Download</a>               
-               </div>
-                        </li>
-                       
-                       </div>
-                       <div class="model">
-<!--                   <li class="list-group-item task-item">
-                         <div class="col-md-2"> model4 after conversion
-                         to allatom 
-                         {{ task.remd_model4|linebreaks }}
-                         </div>
-                         <div class="col-md-10"> 
-                         <a
-                         href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">
-                         <img
-                         src="/myfiles/download-file/{{task.jobdirname}}/model4.png" width="500">
-                         </a></div>
-                       </li>-->
-                       <li class="list-group-item task-item">
-                         <div class="col-md-2"> model4 
-                         {% if not task.damino %}
-                         after conversion to allatom
-                         {% endif %}
-                         {{ task.remd_model4|linebreaks }}
-                         NGL viewer</div>
-                         <div class="col-md-10" id="viewport_M4"
-                         style="width:500px;height:500px;"> 
-                         </div>
-                       </li>
-                        <li class="list-group-item task-item">
-               <div class="col-md-12">
-               {% if task.md_pdbref %}
-               <button id="toggleRefM4">Reference structure on/off</button>
-               {% endif %}
-               <button id="toggleSidechainsM4">Side-chains on/off</button>
-               <a class="btn btn-default"
-               href="/myfiles/download-file/{{task.jobdirname}}/MODEL4.pdb">Download</a>               
-               </div>
-                        </li>
-                       
-                       </div>
-                       <div class="model">
-<!--                   <li class="list-group-item task-item">
-                         <div class="col-md-2"> model5 after conversion
-                         to allatom 
-                         {{ task.remd_model5|linebreaks }}
-                         </div>
-                         <div class="col-md-10"> 
-                         <a
-                         href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">
-                         <img
-                         src="/myfiles/download-file/{{task.jobdirname}}/model5.png" width="500">
-                         </a></div>
-                       </li>-->
                        <li class="list-group-item task-item">
-                         <div class="col-md-2"> model5 
+                         <div class="col-md-2"> model {{ iii }}
                          {% if not task.damino %}
                          after conversion to allatom 
                          {% endif %}
-                         {{ task.remd_model5|linebreaks }}
+                         {{ remd_models|index:iii|linebreaks }}
                          NGL viewer</div>
-                         <div class="col-md-10" id="viewport_M5"
+                         <div class="col-md-10" id={{viewporti}}
                          style="width:500px;height:500px;"> 
                          </div>
                        </li>
                         <li class="list-group-item task-item">
                <div class="col-md-12">
                {% if task.md_pdbref %}
-               <button id="toggleRefM5">Reference structure on/off</button>
+               <button id={{toggleRefi}}>Reference structure on/off</button>
                {% endif %}
-               <button id="toggleSidechainsM5">Side-chains on/off</button>
+               <button id={{toggleSidechainsi}}>Side-chains on/off</button>
                <a class="btn btn-default"
-               href="/myfiles/download-file/{{task.jobdirname}}/MODEL5.pdb">Download</a>               
+               href="/myfiles/download-file/{{task.jobdirname}}/{{MODELi}}">Download</a>               
                </div>
                         </li>
-                       
                        </div>
+               {% endwith %}
+               {% endwith %}   
+                {% endwith %}
+                {% endwith %}
+                {% endwith %}
+                {% endfor %}   
+
                        {% endif %}
 
        {% endif %}             
@@ -836,8 +699,9 @@ $('.majorpointslegend').click(function(){
 
 {% if task.type == "remd" or task.type == "dock" %}
 <script>
-function display_model(numstr){
+function display_model(num){
 
+ numstr=num.toString();
 {% if task.md_pdbref %}
   var stage = new NGL.Stage("viewport_M"+numstr);
   stage.setParameters( { backgroundColor: "white",fogFar: 60, fogNear: 45 } );
@@ -947,7 +811,7 @@ function (event) {
 },false);
 
 
-display_model("1")
+display_model(1)
 
 
 var slideIndex = 1;
@@ -974,20 +838,8 @@ function showDivs(n) {
   }
   x[slideIndex-1].style.display = "block";
   
-  if (lista[slideIndex-1] == 0 && slideIndex == 2) {
-    display_model("2")  
-  }
-  
-  if (lista[slideIndex-1] == 0 && slideIndex == 3) {
-     display_model("3")  
-  }
-
-  if (lista[slideIndex-1] == 0 && slideIndex == 4) {
-     display_model("4")  
-  }
-
-  if (lista[slideIndex-1] == 0 && slideIndex == 5) {
-     display_model("5")  
+  if (lista[slideIndex-1] == 0) {
+    display_model(slideIndex)  
   }
     
   

diff --git a/django_simple/todo/templatetags/index.py b/django_simple/todo/templatetags/index.py
index 07353ad..c5af2d0 100644 (file)
--- a/django_simple/todo/templatetags/index.py
+++ b/django_simple/todo/templatetags/index.py
@@ -3,5 +3,10 @@ register = template.Library()
 
 @register.filter
 def index(indexable, i):
-    return indexable[i-1]
+    try:
+     ele=indexable[i-1]
+    except:
+     ele=''
+    return ele
+     
     
\ No newline at end of file

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index bd70a61..4db3747 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -10,6 +10,10 @@ import json
 from lazysignup.decorators import allow_lazy_user
 from lazysignup.utils import is_lazy_user
 import random
+import logging
+
+logging.basicConfig()
+logger = logging.getLogger(__name__)
 
 res_codes = [
                 # 20 canonical amino acids
@@ -836,8 +840,10 @@ def add_dock_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_pdbref':True,'md_seed':-39912345}
+        data= {'name':task.name,'pdbid':'2HPL:A','md_seq':'DDLYG','dock_peptide':True,'md_seed':-39912345,'md_nstep':600000}
         form = TaskForm_dock_a(initial=data)     
+        task.example='dock_peptide'
+        task.save()
      else:
         form = TaskForm_dock_a(request.POST,request.FILES)
         if form.is_valid():
@@ -859,6 +865,7 @@ def add_dock_a(request,task_id):
              if pdbid2:
               task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb')
               task.pdbcode2=pdbid2
+              seq2,ssbond2=from_pdb(task.myfile2)
              else:
               task.myfile2=form.cleaned_data["file2"]
               if not task.myfile2:
@@ -906,6 +913,7 @@ def add_dock_a(request,task_id):
              task.md_ntwe=form.cleaned_data["md_ntwe"]
 
              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
+             task.remd_cluster_n=form.cleaned_data["remd_cluster_n"]
              task.unres_ff=form.cleaned_data["unres_ff"]
 
              if any(c.islower() for c in seq):
@@ -955,6 +963,12 @@ def addmlist(request,task_id):
         'temperatures':
         '["270", "280", "290", "300", "310", "320", "330", "340"]'
         }
+      elif  task.example == 'dock_peptide':
+        data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
+        '["4", "8", "4", "4", "4", "4", "4", "4"]',
+        'temperatures':
+        '["270", "280", "290", "300", "310", "320", "330", "345"]'
+        }
       elif task.unres_ff == 'FF2':
         data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing':
         '["1", "1", "1", "1", "1", "1", "1", "1"]',
@@ -984,12 +998,21 @@ def details(request,task_id):
      remd_models.append(task.remd_model3)
      remd_models.append(task.remd_model4)
      remd_models.append(task.remd_model5)
-    return render(request, "details.html",{'task':task,'remd_models':remd_models})
+    return render(request, "details.html",{'task':task,'remd_models':remd_models,'range':range(1,task.remd_cluster_n+1)})
 
 
 def details1(request,user_id,task_id):
     task = get_object_or_404(Task, id=task_id)
-    return render(request, "details1.html",{'task':task})
+    try:
+     remd_models=json.loads(task.remd_models)
+    except:
+     remd_models=[]
+     remd_models.append(task.remd_model1)
+     remd_models.append(task.remd_model2)
+     remd_models.append(task.remd_model3)
+     remd_models.append(task.remd_model4)
+     remd_models.append(task.remd_model5)
+    return render(request, "details1.html",{'task':task,'remd_models':remd_models,'range':range(1,task.remd_cluster_n+1)})
 
 
 @login_required
@@ -1160,17 +1183,17 @@ def refresh_done0(task):
          task.results_text=text
 
 
+         remd_models=[]
          if task.md_pdbref and task.type=='remd' or task.type=='dock' and task.md_seq2 == '':
          
-          remd_models=[]
-          for i in range(1,6):
+          for i in range(1,task.remd_cluster_n+1):
            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()
-                 remd_models.append('Cluster'+str(i)+' '.join(line.split()[-3:]))
+                 remd_models.append('Cluster'+str(i)+' '+' '.join(line.split()[-3:]))
            except EnvironmentError:
             print 'file_wham_T*pdb open error'
-          for i in range(1,6):
+          for i in range(1,task.remd_cluster_n+1):
             with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f:
                text=''
                for line in f:
@@ -1184,7 +1207,7 @@ def refresh_done0(task):
                remd_models[i-1]=remd_models[i-1]+text
           
           if task.type=='dock':
-           for i in range(1,6):
+           for i in range(1,task.remd_cluster_n+1):
             with open(task.jobdirname+'/dockq_'+str(i)+'.out', 'r') as f:
                text=''
                for line in f:
@@ -1202,7 +1225,7 @@ def refresh_done0(task):
                    text=text+' DockQ='+line.split()[1]
 
                remd_models[i-1]=remd_models[i-1]+text
-
+#               logger.warning("models %d %s" % (i,remd_models))
 
          if task.type=='remd' or task.type=='dock':  
           with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f:
@@ -1212,15 +1235,16 @@ def refresh_done0(task):
                 i=0
                 for line1 in f:
                   i+=1
-                  if i>6:
+                  if i>task.remd_cluster_n:
                        break
                   try:
-                    remd_models[i-1]=remd_models[i-1]+' Cluster'+str(i)+'probability= '+line1.split()[-2]
+                    remd_models[i-1]=remd_models[i-1]+' Cluster'+str(i)+' probability= '+line1.split()[-2]
                   except:
-                    print i
+                    if len(line1.split())==4:
+                     remd_models.append(' Cluster'+str(i)+' probability= '+line1.split()[-2])
                      
          task.remd_models=json.dumps(remd_models)
-
+#         logger.warning("models%s" % task.remd_models)
          task.save()
       elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done:
          if (task.type=='min'):