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"]
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"]
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()
if is_lazy_user(request.user):
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"]
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=""
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()
if is_lazy_user(request.user):
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"]
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()
if is_lazy_user(request.user):
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
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()
if is_lazy_user(request.user):
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':500000,'md_lang':'berendsen','unres_ff':'opt-wtfsa-2',
+ 'remd_cluter_temp':280}
+ 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"]
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:
elif task.type=='remd':
j=0
- text="Acceptance for replica exchanges\n"
+ text="Acceptance for replica exchanges and number of exchange attempts\n"
for line in f:
if 'ACC' in line:
j+=1
- text=text+line
+ text=text+' '.join(line.split()[2:])+"\n"
if j==task.remd_nrep:
j=1
- text="Acceptance for replica exchanges\n"+line
+ text="Acceptance for replica exchanges and number of exchange attempts\n"+' '.join(line.split()[2:])+"\n"
if 'Total wall' in line:
text=text+line
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:
- task.remd_model1=' '.join(line.split()[-6:])
+ task.remd_model1='Cluster1 '+' '.join(line.split()[-3:])
elif i==2:
- task.remd_model2=' '.join(line.split()[-6:])
+ task.remd_model2='Cluster2 '+' '.join(line.split()[-3:])
elif i==3:
- task.remd_model3=' '.join(line.split()[-6:])
+ task.remd_model3='Cluster3 '+' '.join(line.split()[-3:])
elif i==4:
- task.remd_model4=' '.join(line.split()[-6:])
+ task.remd_model4='Cluster4 '+' '.join(line.split()[-3:])
elif i==5:
- task.remd_model5=' '.join(line.split()[-6:])
+ task.remd_model5='Cluster5 '+' '.join(line.split()[-3:])
except EnvironmentError:
print 'file_wham_T*pdb open error'
for i in range(1,6):