X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;ds=sidebyside;f=django_simple%2Ftodo%2Fviews.py;h=0edb463c6e72335ba1957f93a41504e5fb90e652;hb=44795ccd472cf97e058eff3e635f4a8c6b3ba58f;hp=3d959f19a7cbd8184a8b3572eb0402f8a820c0b1;hpb=b016dd2317a9654a9997f747a24686b0e95d83ab;p=django_unres.git diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py index 3d959f1..0edb463 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 @@ -29,6 +30,27 @@ res_codes = [ 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) @@ -82,7 +104,7 @@ def from_pdb(file): unres_shift = {} chain_sorted=[] newchain = True - + i='' for line in file: if line[0:6] == 'ATOM ' and line[13:15] == 'CA': aa = three_to_one.get(line[17:20]) @@ -95,7 +117,7 @@ def from_pdb(file): 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') chain_end[ch]=i newchain = True @@ -171,9 +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"] @@ -222,9 +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"] @@ -260,7 +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) @@ -278,9 +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"] @@ -306,7 +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' @@ -318,7 +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) @@ -332,9 +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"] @@ -381,7 +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' @@ -392,7 +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) @@ -407,9 +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"] @@ -441,7 +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' @@ -453,13 +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':'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 @@ -512,9 +526,7 @@ 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"] @@ -541,6 +553,7 @@ 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"] @@ -563,7 +576,7 @@ 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' @@ -585,7 +598,13 @@ def addmlist(request,task_id): else: return redirect('/') else: - if task.unres_ff == 'FF2': + 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':