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dock peptide
author
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Wed, 5 Feb 2020 12:59:14 +0000
(13:59 +0100)
committer
Cezary Czaplewski
<czarek@chem.univ.gda.pl>
Wed, 5 Feb 2020 12:59:14 +0000
(13:59 +0100)
django_simple/todo/forms.py
patch
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django_simple/todo/jobfiles.py
patch
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blob
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django_simple/todo/models.py
patch
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django_simple/todo/templates/details.html
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django_simple/todo/templates/details1.html
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django_simple/todo/views.py
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diff --git
a/django_simple/todo/forms.py
b/django_simple/todo/forms.py
index
04de3b2
..
f1f1ea7
100644
(file)
--- 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')
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()
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
(file)
--- 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 $PBS_O_WORKDIR' in line and instance.type == 'dock':
f2.write(line)
f2.write(line.replace('$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")
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
(file)
--- 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
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)
# 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
(file)
--- 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>
<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">
{% 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
(file)
--- 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>
<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">
{% 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
(file)
--- 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.md_pdbref=True
task.md_respa=False
task.ssbond=""
+ task.dock_peptide=form.cleaned_data["dock_peptide"]
task.md_seq=""
task.md_seq=""