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
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)
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)
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
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()
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")
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})
'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"]',
@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
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)
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
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:
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:
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'):
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
projects / django_unres.git / blobdiff