X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=56711181829a32c922e3dcaa90bf24b1a08b1a1d;hb=322f15af60c70fccda4adeedd0dab84553880f3b;hp=45c3f249228a5b5b2d8e382128611b792a9e1264;hpb=a2e1f491fcf3227562136b78a511676b7b8f14d4;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 45c3f24..5671118 100644 --- a/django_simple/todo/views.py +++ b/django_simple/todo/views.py @@ -9,6 +9,7 @@ import subprocess import json from lazysignup.decorators import allow_lazy_user from lazysignup.utils import is_lazy_user +import random res_codes = [ # 20 canonical amino acids @@ -29,23 +30,49 @@ res_codes = [ three_to_one = dict(res_codes) -def load_pdbid(pdbid,dirname): - os.mkdir(dirname) +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) if len(pdbid)==4: file,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb', - dirname+'/plik.pdb') + dirname+'/'+filename) else: chain=pdbid[5] pdbid=pdbid[:4] pdb_tmp=urllib.urlopen('http://files.rcsb.org/download/'+pdbid+'.pdb') - with open(dirname+'/plik.pdb', 'w') as outfile: + with open(dirname+'/'+filename, 'w') as outfile: for line in pdb_tmp: if line[0:6] == 'SSBOND' and line[15] == chain and line[29] == chain: outfile.write(line) if line[0:6] == 'ATOM ' and line[21] == chain: outfile.write(line) + if line[0:6] == 'ENDMDL': + break pdb_tmp.close() - file=dirname+'/plik.pdb' + file=dirname+'/'+filename return(file) @@ -157,8 +184,9 @@ 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 @@ -277,7 +305,7 @@ def add_md(request,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} + 'md_pdbref':True,'md_temp':200,'md_seed':-39912345} form = TaskForm_md(initial=data) else: form = TaskForm_md(request.POST,request.FILES) @@ -288,6 +316,9 @@ 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.md_total_steps=task.md_nstep + if task.md_nstep<250000: + task.md_ntwx=100 basename = str(task.owner) suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S") @@ -313,6 +344,10 @@ def add_md(request,task_id): if task.md_start != "pdbstart": task.ssbond='' + if any(c.islower() for c in seq): + task.md_respa=False + task.damino=True + task.ready=True task.save() @@ -321,7 +356,7 @@ def add_md(request,task_id): else: return redirect('/') else: - data= {'name':task.name} + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} form = TaskForm_md(initial=data) basic_adv=True p_type='molecular dynamics' @@ -333,7 +368,7 @@ def add_md_a(request,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} + 'md_pdbref':True,'md_mdpdb':True,'md_seed':-39912345} form = TaskForm_md_a(initial=data) else: form = TaskForm_md_a(request.POST,request.FILES) @@ -372,6 +407,7 @@ def add_md_a(request,task_id): task.md_temp=form.cleaned_data["md_temp"] task.md_nstep=form.cleaned_data["md_nstep"] + task.md_total_steps=task.md_nstep task.md_ntwe=form.cleaned_data["md_ntwe"] task.md_ntwx=form.cleaned_data["md_ntwx"] task.md_dt=form.cleaned_data["md_dt"] @@ -381,6 +417,9 @@ def add_md_a(request,task_id): task.md_mdpdb=form.cleaned_data["md_mdpdb"] task.unres_ff=form.cleaned_data["unres_ff"] task.md_respa=form.cleaned_data["md_respa"] + if any(c.islower() for c in seq): + task.md_respa=False + task.damino=True task.boxx=form.cleaned_data["boxx"] task.boxy=form.cleaned_data["boxy"] task.boxz=form.cleaned_data["boxz"] @@ -394,7 +433,7 @@ def add_md_a(request,task_id): else: return redirect('/') else: - data= {'name':task.name} + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} form = TaskForm_md_a(initial=data) basic_adv=False p_type='molecular dynamics - advanced options' @@ -405,7 +444,7 @@ 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} + data= {'name':task.name,'pdbid':'1L2Y','md_pdbref':True,'md_seed':-39912345} form = TaskForm_remd(initial=data) else: form = TaskForm_remd(request.POST,request.FILES) @@ -441,6 +480,11 @@ def add_remd(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 task.ready=True @@ -452,7 +496,7 @@ def add_remd(request,task_id): else: return redirect('/') else: - data= {'name':task.name} + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} form = TaskForm_remd(initial=data) basic_adv=True p_type='replica exchange molecular dynamics' @@ -465,14 +509,14 @@ def add_remd_a(request,task_id): if request.method == 'POST': if '_example' in request.POST: data= {'name':task.name,'pdbid':'5G3Q:B','md_pdbref':True, - 'md_nstep':2000000,'md_lang':'berendsen','unres_ff':'FF2', + 'md_nstep':2000000,'md_lang':'berendsen','unres_ff':'FF2','md_seed':-39912345, 'remd_cluter_temp':290,'md_2d':'--EEEEEEE------EEEEEE------EEEEEE------HHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH---'} form = TaskForm_remd_a(initial=data) task.example='casp12' task.save() elif '_example_saxs' in request.POST: data= {'name':task.name,'pdbid':'5UJQ','md_pdbref':True, - 'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2', + 'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345, 'remd_cluter_temp':270, 'scal_rad':4.0,'wsaxs':100.0,'saxs_data': """ 0.5 1.33868e-02 @@ -513,6 +557,112 @@ def add_remd_a(request,task_id): 35.5 3.30592e-04 36.5 1.38359e-04"""} form = TaskForm_remd_a(initial=data) + elif '_example_saxs1' in request.POST: + data= {'name':task.name,'pdbid':'2KMS','md_pdbref':True,'md_start':'pdbstart', + 'md_2d':'----EEEEEE-EEEEE-------EEEEEEEEE--EEEEEE-EEEE---EEEEEEEEE-----EEEEEEE-EEE-HHHHH-EEEE-EEEEEEEEE----EEEEEE---EEE-----', + 'md_nstep':200000,'md_lang':'langevin','unres_ff':'FF2','md_seed':-39912345, + 'remd_cluter_temp':280, 'min_maxfun':50, + 'scal_rad':5.0,'wsaxs':1000.0,'saxs_data': +"""0.7100E-00 0.2036E-03 +0.1420E+01 0.4221E-03 +0.2130E+01 0.6548E-03 +0.2840E+01 0.9001E-03 +0.3550E+01 0.1156E-02 +0.4260E+01 0.1421E-02 +0.4970E+01 0.1692E-02 +0.5680E+01 0.1965E-02 +0.6390E+01 0.2239E-02 +0.7100E+01 0.2509E-02 +0.7810E+01 0.2772E-02 +0.8520E+01 0.3025E-02 +0.9230E+01 0.3265E-02 +0.9940E+01 0.3489E-02 +0.1065E+02 0.3694E-02 +0.1136E+02 0.3878E-02 +0.1207E+02 0.4039E-02 +0.1278E+02 0.4177E-02 +0.1349E+02 0.4289E-02 +0.1420E+02 0.4377E-02 +0.1491E+02 0.4439E-02 +0.1562E+02 0.4478E-02 +0.1633E+02 0.4493E-02 +0.1704E+02 0.4487E-02 +0.1775E+02 0.4461E-02 +0.1846E+02 0.4418E-02 +0.1917E+02 0.4361E-02 +0.1988E+02 0.4291E-02 +0.2059E+02 0.4211E-02 +0.2130E+02 0.4125E-02 +0.2201E+02 0.4034E-02 +0.2272E+02 0.3942E-02 +0.2343E+02 0.3850E-02 +0.2414E+02 0.3761E-02 +0.2485E+02 0.3677E-02 +0.2556E+02 0.3598E-02 +0.2627E+02 0.3526E-02 +0.2698E+02 0.3462E-02 +0.2769E+02 0.3405E-02 +0.2840E+02 0.3356E-02 +0.2911E+02 0.3315E-02 +0.2982E+02 0.3280E-02 +0.3053E+02 0.3251E-02 +0.3124E+02 0.3226E-02 +0.3195E+02 0.3205E-02 +0.3266E+02 0.3186E-02 +0.3337E+02 0.3167E-02 +0.3408E+02 0.3147E-02 +0.3479E+02 0.3125E-02 +0.3550E+02 0.3099E-02 +0.3621E+02 0.3068E-02 +0.3692E+02 0.3031E-02 +0.3763E+02 0.2987E-02 +0.3834E+02 0.2937E-02 +0.3905E+02 0.2878E-02 +0.3976E+02 0.2812E-02 +0.4047E+02 0.2739E-02 +0.4118E+02 0.2658E-02 +0.4189E+02 0.2571E-02 +0.4260E+02 0.2478E-02 +0.4331E+02 0.2381E-02 +0.4402E+02 0.2279E-02 +0.4473E+02 0.2174E-02 +0.4544E+02 0.2068E-02 +0.4615E+02 0.1960E-02 +0.4686E+02 0.1853E-02 +0.4757E+02 0.1748E-02 +0.4828E+02 0.1644E-02 +0.4899E+02 0.1544E-02 +0.4970E+02 0.1447E-02 +0.5041E+02 0.1355E-02 +0.5112E+02 0.1267E-02 +0.5183E+02 0.1184E-02 +0.5254E+02 0.1106E-02 +0.5325E+02 0.1033E-02 +0.5396E+02 0.9646E-03 +0.5467E+02 0.9008E-03 +0.5538E+02 0.8411E-03 +0.5609E+02 0.7852E-03 +0.5680E+02 0.7327E-03 +0.5751E+02 0.6831E-03 +0.5822E+02 0.6360E-03 +0.5893E+02 0.5909E-03 +0.5964E+02 0.5475E-03 +0.6035E+02 0.5055E-03 +0.6106E+02 0.4646E-03 +0.6177E+02 0.4245E-03 +0.6248E+02 0.3853E-03 +0.6319E+02 0.3467E-03 +0.6390E+02 0.3089E-03 +0.6461E+02 0.2719E-03 +0.6532E+02 0.2357E-03 +0.6603E+02 0.2007E-03 +0.6674E+02 0.1669E-03 +0.6745E+02 0.1345E-03 +0.6816E+02 0.1038E-03 +0.6887E+02 0.7482E-04 +0.6958E+02 0.4782E-04 +0.7029E+02 0.2286E-04"""} + form = TaskForm_remd_a(initial=data) else: form = TaskForm_remd_a(request.POST,request.FILES) if form.is_valid(): @@ -548,6 +698,7 @@ def add_remd_a(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 task.md_dt=form.cleaned_data["md_dt"] task.md_lang=form.cleaned_data["md_lang"] task.md_tau=form.cleaned_data["md_tau"] @@ -558,6 +709,10 @@ def add_remd_a(request,task_id): task.md_ntwx=form.cleaned_data["md_ntwx"] task.md_ntwe=form.cleaned_data["md_ntwe"] task.md_respa=form.cleaned_data["md_respa"] + if any(c.islower() for c in seq): + task.md_respa=False + task.damino=True + # task.remd_traj1file=form.cleaned_data["remd_traj1file"] # task.remd_rest1file=form.cleaned_data["remd_rest1file"] @@ -575,13 +730,210 @@ def add_remd_a(request,task_id): task.save() return redirect('addmlist',task_id=task.id) else: - data= {'name':task.name} + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} form = TaskForm_remd_a(initial=data) basic_adv=False 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 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':'1BON:A','pdbid2':'1BON:B','md_seed':-12396738,'md_nstep':500000} + form = TaskForm_dock(initial=data) + else: + form = TaskForm_dock(request.POST,request.FILES) + if form.is_valid(): + task.name=form.cleaned_data["name"] + task.type="dock" + + 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: + task.myfile1=load_pdbid(pdbid,task.jobdirname) + task.pdbcode=pdbid + else: + task.myfile1=form.cleaned_data["file1"] + + 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" + 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) + + + 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=seq1+'X'+seq2 + + for i in range(0,len(seq),40): + task.md_seq=task.md_seq+seq[i:i+40]+" " + + 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() + if is_lazy_user(request.user): + return redirect('/details1/'+str(task.owner)+'/'+str(task.id)+'/') + else: + return redirect('/') + else: + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} + form = TaskForm_dock(initial=data) + basic_adv=True + p_type='docking' + return render(request, 'edit.html', {'form': form, 'task':task, 'basic_adv':basic_adv, 'p_type':p_type}) + +@login_required +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_dock_a(initial=data) + else: + form = TaskForm_dock_a(request.POST,request.FILES) + if form.is_valid(): + task.name=form.cleaned_data["name"] + task.type="dock" + + 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: + task.myfile1=load_pdbid(pdbid,task.jobdirname) + task.pdbcode=pdbid + else: + task.myfile1=form.cleaned_data["file1"] + + pdbid2=form.cleaned_data["pdbid2"] + if pdbid2: + task.myfile2=load_pdbid(pdbid2,task.jobdirname,'plik2.pdb') + task.pdbcode2=pdbid2 + 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="" + + 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=seq1+'X'+seq2 + + for i in range(0,len(seq),40): + task.md_seq=task.md_seq+seq[i:i+40]+" " + + 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.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.save() + return redirect('addmlist',task_id=task.id) + + else: + data= {'name':task.name,'md_seed':-random.randint(10000000,99999999)} + 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}) + + + +@login_required def addmlist(request,task_id): task = get_object_or_404(Task, id=task_id) if request.method == 'POST': @@ -635,6 +987,67 @@ def details1(request,user_id,task_id): def delete(request, task_id): Task.objects.get(id=task_id).delete() return redirect('/') + +@login_required +def restart(request, task_id): + task = get_object_or_404(Task, id=task_id) + restart0(task) + return redirect('/') + +def add_restart_inp(): + with open('file.inp','r') as f1, open ('file.inp.tmp','w') as f2: + for line in f1: + if 'reset_vel=' in line: + f2.write('{:79}'.format('restart'+line[7:])) + else: + f2.write(line) + os.remove('file.inp') + os.rename('file.inp.tmp','file.inp') + return + +def restart0(task): + if os.path.isfile(task.jobdirname+'/finished'): + os.remove(task.jobdirname+'/finished') + task.running =1 + task.done=False + task.md_total_steps = task.md_total_steps+task.md_nstep + task.save() + if task.type == 'md': + os.chdir(task.jobdirname) + 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': + os.chdir(task.jobdirname) + add_restart_inp() + tmp1=json.loads(task.remd_multi_m) + nreplicas=sum(map(int, tmp1)) + with open('file_wham.inp','r') as f1, open ('file_wham.tmp','w') as f2: + for line in f1: + if 'rec_end=' in line: + rec=task.md_total_steps/task.md_ntwx + f2.write('nfile_cx=1 rec_start='+str(rec/10) + +' rec_end='+str(rec)+' totraj='+str(nreplicas)+'\n') + elif 'isampl=' in line: + if task.md_total_steps/task.md_ntwx*nreplicas<=8000: + isampl=1 + else: + isampl=int(task.md_total_steps/task.md_ntwx*nreplicas/8000) + f2.write('{:79}'.format(' isampl='+str(isampl))+'&\n') + else: + f2.write(line) + os.remove('file_wham.inp') + os.rename('file_wham.tmp','file_wham.inp') + ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs8.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + os.chdir('..') + return + +def restart1(request, user_id, task_id): + task = get_object_or_404(Task, id=task_id) + user = task.owner + restart0(task) + return redirect('/details1/'+str(user)+'/'+str(task.id)+'/') + def refresh_done1(request, task_id): task = get_object_or_404(Task, id=task_id) @@ -659,6 +1072,7 @@ 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) @@ -682,7 +1096,8 @@ def refresh_done(request): return render(request, "index.html", { 'tasks': tasks , 'variable' : variable, - 'alldone': alldone + 'alldone': alldone, + 'tasks_count':tasks_count }) @@ -709,7 +1124,7 @@ def refresh_done0(task): if 'Total wall' in line: text=text+line - elif task.type=='remd': + elif task.type=='remd' or task.type=='dock': j=0 text="Acceptance for replica exchanges and number of exchange attempts\n" for line in f: @@ -727,7 +1142,7 @@ def refresh_done0(task): task.results_text=text - if task.md_pdbref and task.type=='remd': + if task.md_pdbref and task.type=='remd' or task.type=='dock' and task.md_seq2 == '': for i in range(1,6): try: @@ -766,10 +1181,38 @@ def refresh_done0(task): task.remd_model4=task.remd_model4+text elif i==5: task.remd_model5=task.remd_model5+text + + if task.type=='dock': + for i in range(1,6): + 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] + 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': + if task.type=='remd' or task.type=='dock': with open(task.jobdirname+'/file_cluster_clust.out_000', 'r') as f: for line in f: @@ -780,15 +1223,15 @@ def refresh_done0(task): if i>6: break if i==1: - task.remd_model1=task.remd_model1+' Cluster1 probability= '+line1.split()[2] + 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] + 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] + 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] + 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.remd_model5=task.remd_model5+' Cluster5 probability= '+line1.split()[-2] @@ -796,6 +1239,20 @@ def refresh_done0(task): elif os.path.isfile(task.jobdirname+'/file_GB000.stat') and not task.done: if (task.type=='min'): task.running =1 + with open(task.jobdirname+'/file.out_GB000', 'r') as f: + line='' + for line in f: + pass + if line != '': + last = line.split()[0] + else: + last = 0 + try: + task.running=int(1+int(last)*100.0/task.min_maxmin) + except: + pass + if task.running>100: + task.running=100 else: with open(task.jobdirname+'/file_GB000.stat', 'r') as f: line='' @@ -812,3 +1269,24 @@ 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