X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=4db374750591bc07de6cca8f49d0e90c695c7651;hb=d368b6f6d2c47c7f30ca7a0d8dfb02c73de314da;hp=cd552cc1b33624ca4f5dccdb2abb39370c732f8e;hpb=1d54e2e65e14bc385a2479676d3722f2f2b998ec;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index cd552cc..4db3747 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -10,6 +10,10 @@ import json from lazysignup.decorators import allow_lazy_user from lazysignup.utils import is_lazy_user import random +import logging + +logging.basicConfig() +logger = logging.getLogger(__name__) res_codes = [ # 20 canonical amino acids @@ -30,6 +34,29 @@ res_codes = [ three_to_one = dict(res_codes) +def dock_box(file): + import math + coord = list() + for line in file: + if line[0:6] == 'ATOM ' and line[13:15] == 'CA': + x=float(line[30:38]) + y=float(line[38:46]) + z=float(line[46:54]) + coord.append([x, y, z]) + if line[0:3] == 'END': + break + maxd=0 + l=len(coord) + for i in xrange(l): + for j in xrange(i+1,l): + p1=coord[i] + p2=coord[j] + d=(p1[0]-p2[0])**2 + (p1[1]-p2[1])**2 + (p1[2]-p2[2])**2 + if d > maxd: + maxd=d + return math.sqrt(maxd) + + def load_pdbid(pdbid,dirname,filename='plik.pdb'): if (not os.path.isdir(dirname)): os.mkdir(dirname) @@ -161,8 +188,9 @@ def index(request): user = request.user tasks = Task.objects.filter(owner=user).order_by('-created_date') variable = '' + tasks_count = Task.objects.filter(owner=user).count() return render(request, "index.html", { - 'tasks': tasks, 'alldone': 0 + 'tasks': tasks, 'alldone': 0, 'tasks_count':tasks_count }) @login_required @@ -717,7 +745,7 @@ def add_dock(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_seed':-39912345} + data= {'name':task.name,'pdbid':'1BON:A','pdbid2':'1BON:B','md_seed':-12396738,'md_nstep':500000} form = TaskForm_dock(initial=data) else: form = TaskForm_dock(request.POST,request.FILES) @@ -740,19 +768,28 @@ def add_dock(request,task_id): if pdbid2: task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb') task.pdbcode2=pdbid2 + seq2,ssbond2=from_pdb(task.myfile2) else: task.myfile2=form.cleaned_data["file2"] + if not task.myfile2: + seq2=seq_add_x(form.cleaned_data["md_seq"]) + task.md_seq2=seq2 + else: + seq2,ssbond2=from_pdb(task.myfile2) task.md_ntwx=task.remd_nstex task.md_start="pdbstart" - task.md_pdbref=True + task.remd_multi_m='["3", "3", "3", "3", "3", "3", "3", "3"]' + if task.md_seq2 =='': + task.md_pdbref=True task.md_respa=False task.ssbond="" + task.dock_peptide=form.cleaned_data["dock_peptide"] task.md_seq="" seq1,ssbond1=from_pdb(task.myfile1) - seq2,ssbond2=from_pdb(task.myfile2) + if seq1[-1]=='X' and seq2[0]=='X': seq=seq1+seq2 @@ -767,13 +804,23 @@ def add_dock(request,task_id): task.md_seed=form.cleaned_data["md_seed"] task.md_nstep=form.cleaned_data["md_nstep"] + task.md_total_steps=task.md_nstep if any(c.islower() for c in seq): task.md_respa=False task.damino=True - + box1=dock_box(task.myfile1) + if task.myfile2: + box2=dock_box(task.myfile2) + else: + box2=len(task.md_seq2)*2.0 + task.boxx=(box1+box2)*1.2+20 + task.boxy=(box1+box2)*1.2+20 + task.boxz=(box1+box2)*1.2+20 + task.ready=True + task.save() @@ -793,14 +840,15 @@ def add_dock_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_pdbref':True,'md_seed':-39912345} - form = TaskForm_remd(initial=data) + data= {'name':task.name,'pdbid':'2HPL:A','md_seq':'DDLYG','dock_peptide':True,'md_seed':-39912345,'md_nstep':600000} + form = TaskForm_dock_a(initial=data) + task.example='dock_peptide' + task.save() else: - form = TaskForm_remd(request.POST,request.FILES) + form = TaskForm_dock_a(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.type="dock" basename = str(task.owner) suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S") @@ -812,40 +860,81 @@ def add_dock_a(request,task_id): task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] - task.md_pdbref=form.cleaned_data["md_pdbref"] - task.md_ntwx=task.remd_nstex + + pdbid2=form.cleaned_data["pdbid2"] + if pdbid2: + task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb') + task.pdbcode2=pdbid2 + seq2,ssbond2=from_pdb(task.myfile2) + else: + task.myfile2=form.cleaned_data["file2"] + if not task.myfile2: + seq2=seq_add_x(form.cleaned_data["md_seq"]) + task.md_seq2=seq2 + else: + seq2,ssbond2=from_pdb(task.myfile2) + + task.md_ntwx=task.remd_nstex + task.md_start="pdbstart" + if task.md_seq2 =='': + task.md_pdbref=True + task.md_respa=False + task.ssbond="" + task.dock_peptide=form.cleaned_data["dock_peptide"] + task.md_seq="" - if task.md_start == "pdbstart" or task.md_pdbref: - seq,task.ssbond=from_pdb(task.myfile1) + + seq1,ssbond1=from_pdb(task.myfile1) + + if seq1[-1]=='X' and seq2[0]=='X': + seq=seq1+seq2 + elif seq1[-1]!='X' and seq2[0]!='X': + seq=seq1+'XX'+seq2 else: - seq=seq_add_x(form.cleaned_data["md_seq"]) + seq=seq1+'X'+seq2 + for i in range(0,len(seq),40): task.md_seq=task.md_seq+seq[i:i+40]+" " - if task.md_start != "pdbstart": - task.ssbond='' - task.md_seed=form.cleaned_data["md_seed"] task.md_nstep=form.cleaned_data["md_nstep"] + task.md_total_steps=task.md_nstep + + task.md_dt=form.cleaned_data["md_dt"] + task.md_lang=form.cleaned_data["md_lang"] + task.md_tau=form.cleaned_data["md_tau"] + task.md_scal_fric=form.cleaned_data["md_scal_fric"] + task.min_maxfun=form.cleaned_data["min_maxfun"] + 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_cluter_temp=form.cleaned_data["remd_cluter_temp"] + task.remd_cluster_n=form.cleaned_data["remd_cluster_n"] + task.unres_ff=form.cleaned_data["unres_ff"] if any(c.islower() for c in seq): task.md_respa=False task.damino=True + box1=dock_box(task.myfile1) + if task.myfile2: + box2=dock_box(task.myfile2) + else: + box2=len(task.md_seq2)*2.0 + task.boxx=(box1+box2)*1.2+20 + task.boxy=(box1+box2)*1.2+20 + task.boxz=(box1+box2)*1.2+20 - task.ready=True - - task.save() - if is_lazy_user(request.user): - return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') - else: - return redirect('/') + return redirect('addmlist',task_id=task.id) + else: data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} - form = TaskForm_remd(initial=data) + form = TaskForm_dock_a(initial=data) basic_adv=False p_type='docking - advanced options' return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) @@ -874,6 +963,12 @@ def addmlist(request,task_id): 'temperatures': '["270", "280", "290", "300", "310", "320", "330", "340"]' } + elif task.example == 'dock_peptide': + data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': + '["4", "8", "4", "4", "4", "4", "4", "4"]', + 'temperatures': + '["270", "280", "290", "300", "310", "320", "330", "345"]' + } elif task.unres_ff == 'FF2': data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': '["1", "1", "1", "1", "1", "1", "1", "1"]', @@ -894,12 +989,30 @@ def addmlist(request,task_id): @login_required def details(request,task_id): task = get_object_or_404(Task, id=task_id) - return render(request, "details.html",{'task':task}) + try: + remd_models=json.loads(task.remd_models) + except: + remd_models=[] + remd_models.append(task.remd_model1) + remd_models.append(task.remd_model2) + remd_models.append(task.remd_model3) + remd_models.append(task.remd_model4) + remd_models.append(task.remd_model5) + return render(request, "details.html",{'task':task,'remd_models':remd_models,'range':range(1,task.remd_cluster_n+1)}) def details1(request,user_id,task_id): task = get_object_or_404(Task, id=task_id) - return render(request, "details1.html",{'task':task}) + try: + remd_models=json.loads(task.remd_models) + except: + remd_models=[] + remd_models.append(task.remd_model1) + remd_models.append(task.remd_model2) + remd_models.append(task.remd_model3) + remd_models.append(task.remd_model4) + remd_models.append(task.remd_model5) + return render(request, "details1.html",{'task':task,'remd_models':remd_models,'range':range(1,task.remd_cluster_n+1)}) @login_required @@ -936,7 +1049,7 @@ def restart0(task): add_restart_inp() ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) os.chdir('..') - elif task.type == 'remd': + elif task.type == 'remd' or task.type == 'dock': os.chdir(task.jobdirname) add_restart_inp() tmp1=json.loads(task.remd_multi_m) @@ -957,6 +1070,15 @@ def restart0(task): f2.write(line) os.remove('file_wham.inp') os.rename('file_wham.tmp','file_wham.inp') + if task.type == 'dock': + with open('pbs8.csh','r') as f1, open ('pbs8.tmp','w') as f2: + for line in f1: + if 'generator_v13' in line: + f2.write('#'+line) + else: + f2.write(line) + os.remove('pbs8.csh') + os.rename('pbs8.tmp','pbs8.csh') ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) os.chdir('..') return @@ -991,6 +1113,7 @@ def refresh_done1(request, task_id): def refresh_done(request): user = request.user tasks = Task.objects.filter(owner=user).order_by('-created_date') + tasks_count = Task.objects.filter(owner=user).count() alldone = 1 for task in tasks: refresh_done0(task) @@ -1014,7 +1137,8 @@ def refresh_done(request): return render(request, "index.html", { 'tasks': tasks , 'variable' : variable, - 'alldone': alldone + 'alldone': alldone, + 'tasks_count':tasks_count }) @@ -1059,25 +1183,17 @@ def refresh_done0(task): task.results_text=text - if task.md_pdbref and task.type=='remd': + remd_models=[] + if task.md_pdbref and task.type=='remd' or task.type=='dock' and task.md_seq2 == '': - for i in range(1,6): + for i in range(1,task.remd_cluster_n+1): 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:]) + remd_models.append('Cluster'+str(i)+' '+' '.join(line.split()[-3:])) except EnvironmentError: print 'file_wham_T*pdb open error' - for i in range(1,6): + for i in range(1,task.remd_cluster_n+1): with open(task.jobdirname+'/tmscore'+str(i)+'.out', 'r') as f: text='' for line in f: @@ -1088,20 +1204,30 @@ def refresh_done0(task): 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': + remd_models[i-1]=remd_models[i-1]+text + + if task.type=='dock': + for i in range(1,task.remd_cluster_n+1): + with open(task.jobdirname+'/dockq_'+str(i)+'.out', 'r') as f: + text='' + for line in f: + if 'Fnat' in line: + text=' Fnat='+line.split()[1] + if 'iRMS' in line: + text=text+' iRMS='+line.split()[1] + if 'LRMS' in line: + text=text+' LRMS='+line.split()[1] + if 'CAPRI' in line and not 'DockQ_CAPRI' in line: + text=text+' CAPRI='+line.split()[1] + if 'DockQ_CAPRI' in line: + text=text+' DockQ_CAPRI= '+line.split()[1] + if 'DockQ ' in line: + text=text+' DockQ='+line.split()[1] + + remd_models[i-1]=remd_models[i-1]+text +# logger.warning("models %d %s" % (i,remd_models)) + + if task.type=='remd' or task.type=='dock': with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f: for line in f: @@ -1109,21 +1235,16 @@ def refresh_done0(task): i=0 for line1 in f: i+=1 - if i>6: + if i>task.remd_cluster_n: 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] + try: + remd_models[i-1]=remd_models[i-1]+' Cluster'+str(i)+' probability= '+line1.split()[-2] + except: + if len(line1.split())==4: + remd_models.append(' Cluster'+str(i)+' probability= '+line1.split()[-2]) - - + task.remd_models=json.dumps(remd_models) +# logger.warning("models%s" % task.remd_models) task.save() elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done: if (task.type=='min'): @@ -1158,3 +1279,24 @@ def refresh_done0(task): return + +@login_required +def zip_all_files(request, task_id): + import os, zipfile + from django.http import HttpResponse + from wsgiref.util import FileWrapper + from django.core.files.temp import NamedTemporaryFile + + task = get_object_or_404(Task, id=task_id) + + temp=NamedTemporaryFile() + archive = zipfile.ZipFile(temp, 'w', zipfile.ZIP_DEFLATED) + for (dirpath, dirnames, filenames) in os.walk(task.jobdirname): + for file1 in filenames: + archive.write(dirpath+"/"+file1,file1) + archive.close() + temp.seek(0) + wrapper = FileWrapper(temp) + response = HttpResponse(wrapper, content_type='application/zip') + response['Content-Disposition'] = 'attachment; filename=all.zip' + return response