X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=django_simple%2Ftodo%2Fviews.py;h=33276acee3b1973d718ae0707fcea2a3d0f1b5bd;hb=03c96699333f5c45ba11d3e1da84b4f471e52ace;hp=c513fbf903de4c2a60d06a38e57aa16a9bed336a;hpb=18720bfd2db199afb2ebf034b3206fc07f16c1ad;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index c513fbf..33276ac 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 @@ -20,16 +21,75 @@ 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 load_pdbid(pdbid,dirname): + os.mkdir(dirname) + if len(pdbid)==4: + file,header=urllib.urlretrieve('http://files.rcsb.org/download/'+pdbid+'.pdb', + dirname+'/plik.pdb') + 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: + 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) + pdb_tmp.close() + file=dirname+'/plik.pdb' + + return(file) + + +def seq_2d_from_pdb(seq_2d,seq): + if seq_2d =='': + return(seq_2d) + seq_2d=seq_2d.replace('C', '-') + seq_2d_tmp='' + ii=0 + for i in range(0,len(seq)): + if seq[i]=='X': + seq_2d_tmp=seq_2d_tmp+'-' + else: + if len(seq_2d)>ii: + seq_2d_tmp=seq_2d_tmp+seq_2d[ii] + ii+=1 + tmp='' + for i in range(0,len(seq_2d_tmp),40): + tmp=tmp+seq_2d_tmp[i:i+40]+" " + return(tmp) + +def seq_2d_add_x(seq_2d,seq,seq_form): + if seq_2d =='': + return(seq_2d) + seq_2d=seq_2d[:len(seq_form)] + seq_2d=seq_2d.replace('C', '-') + if seq_form[0] !='X' and seq[0] == 'X': + seq_2d='-'+seq_2d + if seq_form[-1] !='X' and seq[-1] == 'X': + seq_2d=seq_2d+'-' + seq_2d=seq_2d[:len(seq)] + tmp='' + for i in range(0,len(seq_2d),40): + tmp=tmp+seq_2d[i:i+40]+" " + return(tmp) + def seq_add_x(sequence): - if sequence[0] != 'G': + if sequence[0] != 'G' and sequence[0] != 'g' and sequence[0] != 'X': sequence='X'+sequence - if sequence[-1] != 'G': + if sequence[-1] != 'G' and sequence[-1] != 'g' and sequence[-1] != 'X': sequence=sequence+'X' - set ='CDSQKIPTFNGHLRWAVEYMX' + set ='CDSQKIPTFNGHLRWAVEYMXcdsqkiptfnhlrwaveym' sequence = ''.join([c for c in sequence if c in set]) return(sequence) @@ -42,32 +102,24 @@ def from_pdb(file): chain_start = {} chain_end = {} unres_shift = {} - chain=[] - ichain=0 + chain_sorted=[] newchain = True - + i='' 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]) i = int(line[22:26]) + ch = line[21:22] if newchain or i!=ires[-1]: sequence.append(aa) ires.append(i) if newchain: - if len(chain)>0: - chain_start[chain[ichain]]=i + chain_start[ch]=i + chain_sorted.extend(ch) newchain = False - if line[0:3] == 'TER': + if line[0:3] == 'TER' and i != '': sequence.append('XX') - if len(chain)>0: - chain_end[chain[ichain]]=i - ichain=ichain+1 + chain_end[ch]=i newchain = True if line[0:6] == 'SSBOND': b=[] @@ -80,6 +132,8 @@ def from_pdb(file): ssbond_ch.append(c) if line[0:3] == 'END': break + if not sequence[-1] == 'XX': + chain_end[ch]=i while sequence[-1] == 'XX': del sequence[-1] if sequence[0] != 'G': @@ -91,7 +145,7 @@ def from_pdb(file): # 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: + for c in chain_sorted: 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)] @@ -105,7 +159,7 @@ 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 @@ -139,9 +193,7 @@ def add_min(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -177,7 +229,7 @@ def add_min_a(request,task_id): if form.is_valid(): task.name=form.cleaned_data["name"] task.type="min" - task.min_choice=form.cleaned_data["min_choice"] +# task.min_choice=form.cleaned_data["min_choice"] task.min_overlap=form.cleaned_data["min_overlap"] task.min_searchsc=form.cleaned_data["min_searchsc"] task.min_maxmin=form.cleaned_data["min_maxmin"] @@ -190,9 +242,7 @@ def add_min_a(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -228,7 +278,7 @@ 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) @@ -246,9 +296,7 @@ def add_md(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -274,7 +322,7 @@ 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' @@ -286,7 +334,7 @@ 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) @@ -300,9 +348,7 @@ def add_md_a(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -312,8 +358,11 @@ def add_md_a(request,task_id): task.md_seq="" if task.md_start == "pdbstart" or task.md_pdbref: seq,task.ssbond=from_pdb(task.myfile1) + task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq) else: seq=seq_add_x(form.cleaned_data["md_seq"]) + task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"]) + for i in range(0,len(seq),40): task.md_seq=task.md_seq+seq[i:i+40]+" " @@ -332,6 +381,7 @@ 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"] @@ -345,7 +395,7 @@ 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' @@ -356,7 +406,7 @@ 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) @@ -371,9 +421,7 @@ def add_remd(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -405,7 +453,7 @@ 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' @@ -417,13 +465,15 @@ 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) + data= {'name':task.name,'pdbid':'5G3Q:B','md_pdbref':True, + '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':'E0LL2Y', + '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 @@ -464,6 +514,112 @@ 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(): @@ -476,9 +632,7 @@ def add_remd_a(request,task_id): 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.myfile1=load_pdbid(pdbid,task.jobdirname) task.pdbcode=pdbid else: task.myfile1=form.cleaned_data["file1"] @@ -488,8 +642,11 @@ def add_remd_a(request,task_id): task.md_seq="" if task.md_start == "pdbstart" or task.md_pdbref: seq,task.ssbond=from_pdb(task.myfile1) + task.md_2d=seq_2d_from_pdb(form.cleaned_data["md_2d"],seq) else: seq=seq_add_x(form.cleaned_data["md_seq"]) + task.md_2d=seq_2d_add_x(form.cleaned_data["md_2d"],seq,form.cleaned_data["md_seq"]) + for i in range(0,len(seq),40): task.md_seq=task.md_seq+seq[i:i+40]+" " @@ -502,10 +659,12 @@ def add_remd_a(request,task_id): 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.md_respa=form.cleaned_data["md_respa"] # task.remd_traj1file=form.cleaned_data["remd_traj1file"] # task.remd_rest1file=form.cleaned_data["remd_rest1file"] @@ -523,7 +682,7 @@ 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' @@ -545,7 +704,13 @@ def addmlist(request,task_id): else: return redirect('/') else: - if task.unres_ff == 'E0LL2Y': + if task.example == 'casp12': + data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': + '["2", "2", "2", "2", "2", "2", "2", "2"]', + 'temperatures': + '["270", "280", "290", "300", "310", "320", "330", "340"]' + } + elif task.unres_ff == 'FF2': data= {'name':task.name,'nrep':task.remd_nrep,'multiplexing': '["1", "1", "1", "1", "1", "1", "1", "1"]', 'temperatures': @@ -601,8 +766,11 @@ 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 @@ -620,7 +788,8 @@ def refresh_done(request): else: return render(request, "index.html", { 'tasks': tasks , - 'variable' : variable + 'variable' : variable, + 'alldone': alldone })