X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=61d5b618223d8be3864a5eb2beb3d9af34a8bb54;hb=041ac85ddbd6a090a7b0973acb8caaa6a1db2089;hp=521517a72ad81d8af2fa99914762a8ad1009b929;hpb=591ac48194b207c02ffd7cda59c1c9709a114498;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 521517a..61d5b61 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -5,6 +5,10 @@ from .forms import * from .models import Task import datetime import os +import subprocess +import json +from lazysignup.decorators import allow_lazy_user +from lazysignup.utils import is_lazy_user res_codes = [ # 20 canonical amino acids @@ -14,6 +18,8 @@ res_codes = [ ('LEU', 'L'), ('ARG', 'R'), ('TRP', 'W'), ('ALA', 'A'), ('VAL', 'V'), ('GLU', 'E'), ('TYR', 'Y'), ('MET', 'M'), ('HSD', 'H'),('HSE', 'H'),('HSP', 'H'), + ('HIE', 'H'), ('HID', 'H'),('HIP', 'H'), + ('CYX', 'C'), ] three_to_one = dict(res_codes) @@ -31,21 +37,50 @@ def seq_add_x(sequence): def from_pdb(file): sequence = [] ssbond = [] + ssbond_ch = [] + ires = [] + chain_start = {} + chain_end = {} + unres_shift = {} + chain=[] + ichain=0 + newchain = True + for line in file: + if line[0:6] == 'COMPND' and line[11:17] == 'CHAIN:': + tmp=line[18:] + chain_=tmp.split(', ') + chain_[-1]=chain_[-1][0] + chain.extend(chain_) + if line[0:6] == 'ATOM ' and line[13:15] == 'CA': aa = three_to_one.get(line[17:20]) - sequence.append(aa) + i = int(line[22:26]) + if newchain or i!=ires[-1]: + sequence.append(aa) + ires.append(i) + if newchain: + if len(chain)>0: + chain_start[chain[ichain]]=i + newchain = False if line[0:3] == 'TER': sequence.append('XX') + if len(chain)>0: + chain_end[chain[ichain]]=i + ichain=ichain+1 + newchain = True if line[0:6] == 'SSBOND': b=[] b.append(int(line[17:21])) b.append(int(line[31:35])) ssbond.append(b) - + c = [] + c.append((line[15:16])) + c.append((line[29:30])) + ssbond_ch.append(c) if line[0:3] == 'END': break - if sequence[-1] == 'XX': + while sequence[-1] == 'XX': del sequence[-1] if sequence[0] != 'G': sequence.insert(0,'X') @@ -53,13 +88,22 @@ def from_pdb(file): if sequence[-1] != 'G': sequence.append('X') seq=''.join(sequence) - return seq,ssbond +# if ires[0] != 1: +# ssbond=[ [e[0]-ires[0]+1,e[1]-ires[0]+1] for e in ssbond] + i=0 + for c in chain: + unres_shift[c]=i+chain_start[c] + i=i-(chain_end[c]-chain_start[c])-3 + ssbond=[ [e[0]-unres_shift[c[0]]+1,e[1]-unres_shift[c[1]]+1] for e,c in zip(ssbond,ssbond_ch)] + + return seq,json.dumps(ssbond) @login_required def index(request): user = request.user - tasks = Task.objects.filter(owner=user) + tasks = Task.objects.filter(owner=user).order_by('-created_date') + variable = '' return render(request, "index.html", { 'tasks': tasks }) @@ -76,16 +120,31 @@ def add(request): return redirect('add_min',task_id=task.id) return redirect('/') - @login_required 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="" @@ -93,12 +152,12 @@ 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() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: data= {'name':task.name} form = TaskForm_min(initial=data) @@ -106,9 +165,14 @@ def add_min(request,task_id): basic_adv=True return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) +@login_required 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"] @@ -119,22 +183,38 @@ 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"] + task.boxy=form.cleaned_data["boxy"] + task.boxz=form.cleaned_data["boxz"] seq,task.ssbond=from_pdb(task.myfile1) task.md_seq="" 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() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: data= {'name':task.name} form = TaskForm_min_a(initial=data) @@ -146,6 +226,11 @@ 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"] @@ -154,8 +239,19 @@ 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="" @@ -171,12 +267,12 @@ 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() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: data= {'name':task.name} form = TaskForm_md(initial=data) @@ -184,15 +280,32 @@ def add_md(request,task_id): p_type='molecular dynamics' return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) +@login_required 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"] @@ -218,15 +331,19 @@ def add_md_a(request,task_id): task.md_tau=form.cleaned_data["md_tau"] 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.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() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: data= {'name':task.name} form = TaskForm_md_a(initial=data) @@ -238,13 +355,30 @@ 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 task.md_seq="" if task.md_start == "pdbstart" or task.md_pdbref: @@ -264,12 +398,12 @@ 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() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: data= {'name':task.name} form = TaskForm_remd(initial=data) @@ -277,15 +411,33 @@ def add_remd(request,task_id): p_type='replica exchange molecular dynamics' return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) +@login_required 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"] @@ -308,14 +460,17 @@ def add_remd_a(request,task_id): task.md_scal_fric=form.cleaned_data["md_scal_fric"] task.remd_nrep=form.cleaned_data["remd_nrep"] 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.remd_traj1file=form.cleaned_data["remd_traj1file"] # task.remd_rest1file=form.cleaned_data["remd_rest1file"] + task.boxx=form.cleaned_data["boxx"] + task.boxy=form.cleaned_data["boxy"] + task.boxz=form.cleaned_data["boxz"] + task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"] - - basename = str(task.owner) - suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S") - task.jobdirname = "_".join([basename, suffix]) + task.unres_ff=form.cleaned_data["unres_ff"] task.save() return redirect('addmlist',task_id=task.id) @@ -326,7 +481,7 @@ def add_remd_a(request,task_id): p_type='replica exchange molecular dynamics - advanced options' return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) - +@login_required def addmlist(request,task_id): task = get_object_or_404(Task, id=task_id) if request.method == 'POST': @@ -337,14 +492,25 @@ def addmlist(request,task_id): task.ready=True task.save() - return redirect('/') + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') else: + if task.unres_ff == 'E0LL2Y': data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': '["1", "1", "1", "1", "1", "1", "1", "1"]', 'temperatures': '["270", "280", "290", "300", "310", "320", "330", "345"]' } - form = TaskForm_list(task.remd_nrep,initial=data) + else: + data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': + '["1", "1", "1", "1", "1", "1", "1", "1"]', + 'temperatures': + '["250", "260", "270", "280", "290", "300", "315", "330"]' + } + + form = TaskForm_list(task.remd_nrep,initial=data) p_type='replica exchange molecular dynamics - advanced options' return render(request, 'edit_lista.html', {'form': form, 'task':task, 'p_type':p_type}) @@ -353,16 +519,64 @@ def details(request,task_id): task = get_object_or_404(Task, id=task_id) return render(request, "details.html",{'task':task}) + +def details1(request,user_id,task_id): + task = get_object_or_404(Task, id=task_id) + return render(request, "details1.html",{'task':task}) + + @login_required def delete(request, task_id): Task.objects.get(id=task_id).delete() return redirect('/') +def refresh_done1(request, task_id): + task = get_object_or_404(Task, id=task_id) + user = task.owner + refresh_done0(task) + + proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE) + njob=0 + nq=0 + for line in proc.stdout: + if 'piasek4' in line: + if line.split()[1]=='test_server': + njob+=1 + if line.split()[-2]=='Q': + nq+=1 + variable='Idle jobs='+str(nq)+' Total jobs='+str(njob) + + return redirect('/details1/'+str(user)+'/'+str(task.id)+'/') + + @login_required def refresh_done(request): user = request.user - tasks = Task.objects.filter(owner=user) + tasks = Task.objects.filter(owner=user).order_by('-created_date') for task in tasks: + refresh_done0(task) + + proc = subprocess.Popen('/opt/torque/bin/qstat', stdout=subprocess.PIPE) + njob=0 + nq=0 + for line in proc.stdout: + if 'piasek4' in line: + if line.split()[1]=='test_server': + njob+=1 + if line.split()[-2]=='Q': + nq+=1 + variable='Idle jobs='+str(nq)+' Total jobs='+str(njob) + + if is_lazy_user(request.user): + return redirect('/details1/'+str(user)+'/'+str(task.id)+'/') + else: + return render(request, "index.html", { + 'tasks': tasks , + 'variable' : variable + }) + + +def refresh_done0(task): if os.path.isfile(task.jobdirname+'/finished') and not task.done: task.done=True @@ -387,37 +601,104 @@ def refresh_done(request): 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 - task.results_text=text + if task.md_pdbref and task.type=='remd': + + for i in range(1,6): + 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() + if i==1: + task.remd_model1='Cluster1 '+' '.join(line.split()[-3:]) + elif i==2: + task.remd_model2='Cluster2 '+' '.join(line.split()[-3:]) + elif i==3: + task.remd_model3='Cluster3 '+' '.join(line.split()[-3:]) + elif i==4: + task.remd_model4='Cluster4 '+' '.join(line.split()[-3:]) + elif i==5: + task.remd_model5='Cluster5 '+' '.join(line.split()[-3:]) + except EnvironmentError: + print 'file_wham_T*pdb open error' + for i in range(1,6): + with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f: + text='' + for line in f: + if 'RMSD of the common residues=' in line: + text=' RMSD='+line.split()[5] + if 'TM-score =' in line: + text=text+' TMscore='+line.split()[2] + if 'GDT-TS-score=' in line: + text=text+' GDT_TS='+line.split()[1] + + if i==1: + task.remd_model1=task.remd_model1+text + elif i==2: + task.remd_model2=task.remd_model2+text + elif i==3: + task.remd_model3=task.remd_model3+text + elif i==4: + task.remd_model4=task.remd_model4+text + elif i==5: + task.remd_model5=task.remd_model5+text + + + + if task.type=='remd': + with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f: + + for line in f: + if 'sumprob' in line: + i=0 + for line1 in f: + i+=1 + if i>6: + break + if i==1: + task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2] + elif i==2: + task.remd_model2=task.remd_model2+' Cluster2 probability= '+line1.split()[2] + elif i==3: + task.remd_model3=task.remd_model3+' Cluster3 probability= '+line1.split()[2] + elif i==4: + task.remd_model4=task.remd_model4+' Cluster4 probability= '+line1.split()[2] + elif i==5: + task.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[2] + + + task.save() elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done: if (task.type=='min'): task.running =1 else: with open(task.jobdirname+'/file_GB000.stat', 'r') as f: + line='' for line in f: pass - if line: + if line != '': last = line.split()[0] else: last = 0 - task.running=1+int(last)*100.0/task.md_nstep + task.running=int(1+int(last)*100.0/task.md_nstep) if task.running>100: task.running=100 task.save() - return redirect('/') + + + return