From 1c260674ebd5c690868fadea76ecd86e8b7f0b74 Mon Sep 17 00:00:00 2001
From: Cezary Czaplewski <czarek@chem.univ.gda.pl>
Date: Wed, 5 Feb 2020 13:59:14 +0100
Subject: [PATCH] dock peptide

---
 django_simple/todo/forms.py                |    2 ++
 django_simple/todo/jobfiles.py             |    5 ++++-
 django_simple/todo/models.py               |    1 +
 django_simple/todo/templates/details.html  |    4 ++++
 django_simple/todo/templates/details1.html |    4 ++++
 django_simple/todo/views.py                |    1 +
 6 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index 04de3b2..f1f1ea7 100644
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -516,6 +516,8 @@ class TaskForm_dock(forms.Form):
                   help_text='total number of steps', max_value=10000000)
      md_seed = forms.IntegerField(label='SEED',initial=-39912345,
                   help_text='seed for random number generator')
+     dock_peptide = forms.BooleanField(required=False,initial=False,
+            label='dock peptide',help_text='no constrains on 2nd chain')                  
                   
      def clean(self):
              cleaned_data = super(TaskForm_dock, self).clean()
diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 9855b31..982f02d 100644
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -408,7 +408,10 @@ CUTOFF=7.00000 WCORR4=0.00000"""
            f2.write(line.replace('$ssbond',tmp_ss))
           elif 'cd $PBS_O_WORKDIR' in line and instance.type == 'dock':
             f2.write(line)
-            f2.write('../files/generator_v12a plik.pdb plik2.pdb 0 \n')
+            if instance.dock_peptide:
+             f2.write('../files/generator_v12a plik.pdb plik2.pdb 1 \n')
+            else:
+             f2.write('../files/generator_v12a plik.pdb plik2.pdb 0 \n')
             f2.write("sed '/END/q' plik.pdb |grep ATOM > plik1ter.pdb \n")
             f2.write("echo TER >>  plik1ter.pdb \n")
             f2.write("sed '/END/q' plik2.pdb |grep ATOM >> plik1ter.pdb \n")            
diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index ba4f3cb..d11b412 100644
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -94,6 +94,7 @@ class Task(models.Model):
 #dock
     myfile2 = models.FileField(default='',upload_to=user_directory_path2)        
     pdbcode2 = models.CharField(max_length=6,default='')
+    dock_peptide = models.BooleanField(default=False)
     
 # system    
     ready = models.BooleanField(default=False)
diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index 36e8e63..0c2a6cc 100644
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -253,6 +253,10 @@ Created {{ task.created_date  }}
 		            <div class="col-md-6"> pdb code2</div>
 		 	    <div class="col-md-6">{{ task.pdbcode2 }}</div>
 			</li>		
+		        <li class="list-group-item task-item">
+		            <div class="col-md-6"> dock_peptide</div>
+		 	    <div class="col-md-6">{{ task.dock_peptide }}</div>
+			</li>		
 			
 			{% endif %}
 		        <li class="list-group-item task-item">
diff --git a/django_simple/todo/templates/details1.html b/django_simple/todo/templates/details1.html
index 9573fe0..4860b27 100644
--- a/django_simple/todo/templates/details1.html
+++ b/django_simple/todo/templates/details1.html
@@ -253,6 +253,10 @@ Created {{ task.created_date  }}
 		            <div class="col-md-6"> pdb code2</div>
 		 	    <div class="col-md-6">{{ task.pdbcode2 }}</div>
 			</li>		
+		        <li class="list-group-item task-item">
+		            <div class="col-md-6"> dock_peptide</div>
+		 	    <div class="col-md-6">{{ task.dock_peptide }}</div>
+			</li>		
 			
 			{% endif %}
 		        <li class="list-group-item task-item">
diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 4cbd2e5..aea28ec 100644
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -750,6 +750,7 @@ def add_dock(request,task_id):
              task.md_pdbref=True
              task.md_respa=False
              task.ssbond=""
+             task.dock_peptide=form.cleaned_data["dock_peptide"]
 
              task.md_seq=""
 
-- 
1.7.9.5