X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=a29ae69c4a6c101241abb130a9fb36329242bee5;hb=f37d464d427e561556e76a1c37a3a74f23b56c97;hp=521a3000111eabb4667cf3820456aa95b4b34b9f;hpb=73008923acaf643aab7d5af2b559831ff0529489;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 521a300..a29ae69 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -20,16 +20,21 @@ res_codes = [ ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'), ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'), ('CYX', 'C'), + ('DCY', 'c'), ('DAS', 'd'), ('DSN', 's'), ('DGN', 'q'), + ('DLY', 'k'), ('DIL', 'i'), ('DPR', 'p'), ('DTH', 't'), + ('DPN', 'f'), ('DSG', 'n'), ('DHI', 'h'), + ('DLE', 'l'), ('DAR', 'r'), ('DTR', 'w'), ('DAL', 'a'), + ('DVA', 'v'), ('DGL', 'e'), ('DTY', 'y'), ('MED', 'm'), ] three_to_one = dict(res_codes) def seq_add_x(sequence): - if sequence[0] != 'G': + if sequence[0] != 'G' and sequence[0] != 'g': sequence='X'+sequence - if sequence[-1] != 'G': + if sequence[-1] != 'G' and sequence[-1] != 'g': sequence=sequence+'X' - set ='CDSQKIPTFNGHLRWAVEYMX' + set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnghlrwaveym' sequence = ''.join([c for c in sequence if c in set]) return(sequence) @@ -105,7 +110,7 @@ def index(request): tasks = Task.objects.filter(owner=user).order_by('-created_date') variable = '' return render(request, "index.html", { - 'tasks': tasks + 'tasks': tasks, 'alldone': 0 }) @login_required @@ -124,11 +129,27 @@ def add(request): 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="" @@ -136,9 +157,6 @@ 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() if is_lazy_user(request.user): @@ -156,6 +174,10 @@ def add_min(request,task_id): 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"] @@ -166,7 +188,20 @@ 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"] @@ -178,11 +213,7 @@ def add_min_a(request,task_id): 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): @@ -200,6 +231,11 @@ 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"] @@ -208,8 +244,19 @@ 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="" @@ -225,9 +272,6 @@ 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() if is_lazy_user(request.user): @@ -245,12 +289,28 @@ def add_md(request,task_id): 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"] @@ -277,15 +337,13 @@ 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.md_respa=form.cleaned_data["md_respa"] 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() if is_lazy_user(request.user): @@ -303,12 +361,28 @@ 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 @@ -330,9 +404,6 @@ 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() if is_lazy_user(request.user): @@ -348,14 +419,75 @@ def add_remd(request,task_id): @login_required def add_remd_a(request,task_id): + from django.core.files.uploadedfile import UploadedFile 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) + elif '_example_saxs' in request.POST: + data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True, + 'md_nstep':200000,'md_lang':'langevin','unres_ff':'E0LL2Y', + 'remd_cluter_temp':270, + 'scal_rad':4.0,'wsaxs':100.0,'saxs_data': +""" 0.5 1.33868e-02 + 1.5 1.95880e-02 + 2.5 2.68896e-02 + 3.5 3.43737e-02 + 4.5 4.07099e-02 + 5.5 4.47875e-02 + 6.5 4.63486e-02 + 7.5 4.60514e-02 + 8.5 4.49130e-02 + 9.5 4.36744e-02 +10.5 4.26085e-02 +11.5 4.17464e-02 +12.5 4.11217e-02 +13.5 4.07835e-02 +14.5 4.06776e-02 +15.5 4.06060e-02 +16.5 4.03241e-02 +17.5 3.96655e-02 +18.5 3.85756e-02 +19.5 3.70537e-02 +20.5 3.50982e-02 +21.5 3.27236e-02 +22.5 3.00046e-02 +23.5 2.70643e-02 +24.5 2.40044e-02 +25.5 2.08595e-02 +26.5 1.76342e-02 +27.5 1.43802e-02 +28.5 1.12281e-02 +29.5 8.34574e-03 +30.5 5.87354e-03 +31.5 3.88732e-03 +32.5 2.39755e-03 +33.5 1.36323e-03 +34.5 7.06686e-04 +35.5 3.30592e-04 +36.5 1.38359e-04"""} + 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"] @@ -380,6 +512,7 @@ def add_remd_a(request,task_id): task.remd_nstex=form.cleaned_data["remd_nstex"] task.md_ntwx=form.cleaned_data["md_ntwx"] task.md_ntwe=form.cleaned_data["md_ntwe"] + task.md_respa=form.cleaned_data["md_respa"] # task.remd_traj1file=form.cleaned_data["remd_traj1file"] # task.remd_rest1file=form.cleaned_data["remd_rest1file"] @@ -387,13 +520,12 @@ def add_remd_a(request,task_id): 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.scal_rad = form.cleaned_data["scal_rad"] + task.saxs_data = form.cleaned_data["saxs_data"] + task.wsaxs = form.cleaned_data["wsaxs"] task.save() return redirect('addmlist',task_id=task.id) @@ -476,8 +608,11 @@ def refresh_done1(request, task_id): def refresh_done(request): user = request.user tasks = Task.objects.filter(owner=user).order_by('-created_date') + alldone = 1 for task in tasks: refresh_done0(task) + if not task.done: + alldone=0 proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE) njob=0 @@ -495,7 +630,8 @@ def refresh_done(request): else: return render(request, "index.html", { 'tasks': tasks , - 'variable' : variable + 'variable' : variable, + 'alldone': alldone }) @@ -524,15 +660,15 @@ def refresh_done0(task): 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 @@ -547,15 +683,15 @@ def refresh_done0(task): 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):