def mcs(sdf1, sdf2):
calc_cmd = "%s '%s' '%s'" % (mcs_cmd, sdf1, sdf2)
ret = popen(calc_cmd)
(status, mcs) = ret.split('\n', 1)
if status == 'error':
raise ExternalProgramError()
(status_code, m_size, size1, size2) = status.split()
m_size = int(m_size)
min_size = min(int(size1), int(size2))
max_size = max(int(size1), int(size2))
sim_min = m_size * 1. / min_size
sim_max = m_size * 1. / max_size
sim_tanimoto = m_size * 1. / (min_size + max_size - m_size)
mcs = sdf_to_smiles(mcs)
(s, title) = mcs.split(None, 1)
from hashlib import md5
return dict(
m_size=m_size,
sim_min='%.4f' % sim_min,
sim_max='%.4f' % sim_max,
sim_tanimoto='%.4f' % sim_tanimoto,
img='/similarity/renderer/' + s,
md5=md5(mcs).hexdigest(),
title=title,
smiles=mcs,
)
def mcs(sdf1, sdf2):
calc_cmd = "%s '%s' '%s'" % (mcs_cmd, sdf1, sdf2)
ret = popen(calc_cmd)
(status, mcs) = ret.split('\n', 1)
if status == 'error':
raise ExternalProgramError()
(status_code, m_size, size1, size2) = status.split()
m_size = int(m_size)
min_size = min(int(size1), int(size2))
max_size = max(int(size1), int(size2))
sim_min = m_size * 1. / min_size
sim_max = m_size * 1. / max_size
sim_tanimoto = m_size * 1. / (min_size + max_size - m_size)
mcs = sdf_to_smiles(mcs)
(s, title) = mcs.split(None, 1)
from hashlib import md5
return dict(
m_size=m_size,
sim_min='%.4f' % sim_min,
sim_max='%.4f' % sim_max,
sim_tanimoto='%.4f' % sim_tanimoto,
img='/similarity/renderer/' + s,
md5=md5(mcs).hexdigest(),
title=title,
smiles=mcs,
)
def main():
sdfs = sys.stdin.read()
similarity = args['similarity']
similarity = int(float(similarity) * 100)
compounds = int(args['compounds'])
with open(args['outfile'], 'w') as f:
for sdf in sdf_iter(StringIO(str(sdfs))):
query_id =""
parts = re.split('\s+',sdf_to_smiles(sdf).strip())
smile_query = parts[0]
if len(parts) > 1:
query_id = parts[1]
output = SimilaritySearch(smile_query, similarity, compounds)
for match in output.strip().split('\n'):
f.write(query_id +" "+match+"\n")
def main():
sdf = sys.stdin.read()
similarity = args['similarity']
similarity = int(float(similarity) * 100)
compounds = int(args['compounds'])
query = sdf_to_smiles(sdf)
try:
id_list = SimilaritySearch(query, similarity, compounds)
if id_list == 'error':
raise Exception
id_list = [str(cid) for cid in id_list]
output = '\n'.join(id_list)
except:
output = ''
f = open(args['outfile'], 'w')
f.write(output)
f.close()
def main():
sdf = sys.stdin.read()
similarity = args['similarity']
similarity = int(float(similarity) * 100)
compounds = int(args['compounds'])
query = sdf_to_smiles(sdf)
try:
id_list = SimilaritySearch(query, similarity, compounds)
if id_list == 'error':
raise Exception
id_list = [str(cid) for cid in id_list]
output = '\n'.join(id_list)
except:
output = ''
f = open(args['outfile'], 'w')
f.write(output)
f.close()
def main():
sdfs = sys.stdin.read()
similarity = args['similarity']
similarity = int(float(similarity) * 100)
numResults = int(args['compounds'])
with open(args['outfile'], 'w') as f:
for sdf in sdf_iter(StringIO(str(sdfs))):
query_id = ""
parts = re.split('\s+', sdf_to_smiles(sdf).strip())
smile_query = parts[0]
if len(parts) > 1:
query_id = parts[1]
matches = chembl_similarity(smile_query, similarity, numResults)
if matches != None:
for match in matches:
#print("match: "+str(match))
f.write(query_id + " " + match[0] + " " + match[1] + "\n")
def uploadCompound(request, resource = None, job_id = None):
if (request.method == 'GET') and (resource != u'job'):
return render_to_response('addCompounds.html',
dict(input_mode='smiles-input'),
context_instance=RequestContext(request))
else:
sdf = None
name = None
compid = None
smiles = None
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles'].split('\n')
for line in smiles:
if re.match(r"^\S+", line):
sdf = sdf + smiles_to_sdf(str(line))
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif resource == 'job':
input_mode = 'sdf-upload'
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
sdf = f.read()
f.close()
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = sdf.read()
except (InputError, InvalidInputError):
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
compid = str(request.POST['id'])
compid = re.match(r"^(\S{0,20})", compid).group(1)
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, 'Invalid drawing!')
sdf = None
else:
input_mode = 'sdf-input'
sdf = request.POST['sdf']
if not sdf:
messages.error(request, 'No input found!')
elif 'pubchem' in request.POST:
cids = request.POST['pubchem']
cids = cids.split()
input_mode = 'pubchem'
filteredCIDs = []
for cid in cids[:]:
match = re.search("(\d{1,200})", cid)
if match:
filteredCIDs.append(int(match.group(1)))
if len(filteredCIDs) > 0:
try:
sdf = DownloadCIDs(filteredCIDs)
except:
messages.error(request,
'Invalid CIDs or no response from PubChem!'
)
sdf = None
else:
messages.error(request, 'Error: No valid CIDs entered!')
sdf = None
if not sdf:
return render_to_response('addCompounds.html',
dict(input_mode=input_mode,
post_data=request.POST),
context_instance=RequestContext(request))
newJob = createJob(request.user, 'Upload Compounds', '',
['--user='******'tools.views.view_job', job_id=newJob.id,
resource='')
def sdf2smiles(sdf):
sdf = sdf_to_smiles(sdf)
return HttpResponse(sdf, content_type='text/plain')
def search(request):
if request.is_ajax():
if 'application_id' in request.GET:
form = getAppForm(request.GET['application_id'], request.user)()
return HttpResponse(str(form))
else:
return HttpResponse("", status_code=404)
elif request.method != 'POST':
smi = ''
if 'smi' in request.GET:
smi = str(request.GET['smi'])
smi = urlunquote(smi)
allTags = Tag.allUserTagNames(request.user)
fields = {}
category = ApplicationCategories.objects.get(name="Search")
apps = Application.objects.filter(category=category).exclude(
name__exact="pubchemID2SDF")
fields['application'] = ModelChoiceField(queryset=apps, empty_label='')
form = type('%sForm' % 'choose application', (Form, ), fields)
return render(request, 'search.html',
dict(mode='form', smi=smi, appsForm=form, tags=allTags))
else:
sdf = None
smiles = None
compid = u'query'
form = None
application = None
application_id = None
if 'application' in request.POST:
application_id = request.POST['application']
application = Application.objects.get(id=application_id)
if 'tags' in request.POST:
givenTags = request.POST.getlist("tags")
compoundList = Compound.byTagNames(givenTags, request.user)
if len(compoundList) == 0:
messages.error(request,
"Error: No compounds found with selected tags")
else:
sdf = u''
for compound in compoundList:
sdf = sdf + compound.sdffile_set.all()[0].sdffile.rstrip(
) + '\n'
smiles = sdf_to_smiles(sdf)
elif 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles']
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = first_mol(sdf.read())
smiles = sdf_to_smiles(sdf)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid drawing!')
sdf = None
else:
try:
input_mode = 'sdf-input'
sdf = first_mol(request.POST['sdf'])
smiles = sdf_to_smiles(sdf)
except:
print(traceback.format_exc())
messages.error(request, 'Invalid input SDF!')
sdf = None
if application_id != None:
AppFormSet = getAppForm(request.POST['application'], request.user)
form = AppFormSet(request.POST)
if form != None and form.is_valid():
commandOptions, optionsList = parseToolForm(form)
else:
sdf = None
messages.error(request, "Invalid form options!")
if not sdf:
print("no sdf found")
return redirect(structure_search.views.search)
smiles = re.search(r'(\S+)', smiles).group(1)
smiles = urlquote(smiles)
#print("command options: "+str(commandOptions))
if application.name == "PubChem Fingerprint Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
elif application.name == "ChEMBL Fingerprint Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
elif application.name == "ChEMBL EI Search":
newJob = createJob(request.user, application.name, optionsList,
commandOptions, sdf, smiles)
time.sleep(1)
return redirect(tools.views.view_job, job_id=newJob.id, resource='')
def uploadCompound(request, resource = None, job_id = None):
allTags = Tag.allUserTagNames(request.user)
if (request.method == 'GET') and (resource != u'job'):
return render(request,'addCompounds.html',
dict(input_mode='smiles-input',
tags=allTags))
else:
sdf = None
name = None
compid = None
smiles = None
compoundTags = []
input_mode='smiles-input'
if 'tags' in request.POST:
compoundTags = set(request.POST.getlist('tags'))
Tag.ensureAllExist(compoundTags,request.user)
#existingTags = set(allTags)
#print("compound tags: "+str(compoundTags))
#for newTag in compoundTags.difference(existingTags):
# print("creating new tag: "+newTag+" for user "+request.user.username)
# Tag.objects.create(name = newTag, user=request.user)
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles'].split('\n')
for line in smiles:
if re.match(r"^\S+", line):
sdf = sdf + smiles_to_sdf(str(line))
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif resource == 'job':
input_mode = 'sdf-upload'
job = updateJob(request.user, job_id)
f = open(job.output, 'r')
sdf = f.read()
f.close()
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = sdf.read().decode("utf-8")
except (InputError, InvalidInputError):
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
compid = str(request.POST['id'])
compid = re.match(r"^(\S{0,20})", compid).group(1)
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request, 'Invalid drawing!')
sdf = None
else:
input_mode = 'sdf-input'
sdf = request.POST['sdf']
if not sdf:
messages.error(request, 'No input found!')
elif 'pubchem' in request.POST:
cids = request.POST['pubchem']
cids = cids.split()
input_mode = 'pubchem'
filteredCIDs = []
for cid in cids[:]:
match = re.search("(\d{1,200})", cid)
if match:
filteredCIDs.append(int(match.group(1)))
if len(filteredCIDs) > 0:
try:
sdf = DownloadCIDs(cids)
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request,
'Invalid CIDs or no response from PubChem!'
)
sdf = None
else:
messages.error(request, 'Error: No valid CIDs entered!')
sdf = None
elif 'chembl' in request.POST:
cids = tuple(request.POST['chembl'].split())
if len(cids) > 0:
try:
sdfs = get_chembl_sdfs(cids)
sdf = "\n$$$$\n".join(sdfs)+"\n$$$$\n"
except:
print("Unexpected error:", sys.exc_info())
traceback.print_tb(sys.exc_info()[2])
messages.error(request,
'Invalid CIDs or no response from ChEMBL!'
)
sdf = None
else:
print("no chembl cids given")
messages.error(request, 'Error: No valid ChEMBL CIDs entered!')
sdf = None
if not sdf:
return render('addCompounds.html',
dict(input_mode=input_mode,
post_data=request.POST,
tags=compoundTags))
jobArgs = ['--user='******'dedup' in request.POST:
jobArgs += ["--deduplicate"]
newJob = createJob(request.user, 'Upload Compounds', '',jobArgs , sdf)
time.sleep(2)
return redirect(tools.views.view_job, job_id=newJob.id,
resource='')
def search(request):
application = Application.objects.get(name='EI Search')
AppFormSet = getAppForm(application.id, request.user)
if request.method != 'POST':
smi = ''
if 'smi' in request.GET:
smi = str(request.GET['smi'])
smi = urlunquote(smi)
form = AppFormSet()
form = str(form)
return render_to_response('search.html', dict(mode='form',
smi=smi, form=form),
context_instance=RequestContext(request))
else:
sdf = None
smiles = None
compid = u'query'
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles']
sdf = smiles_to_sdf(str(smiles))
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = first_mol(sdf.read())
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, 'Invalid drawing!')
sdf = None
else:
try:
input_mode = 'sdf-input'
sdf = first_mol(request.POST['sdf'])
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, 'Invalid input SDF!')
sdf = None
form = AppFormSet(request.POST)
if form.is_valid():
commandOptions, optionsList = parseToolForm(form)
else:
sdf = None
messages.error(request, "Invalid form options!")
if not sdf:
return redirect('eisearch.views.search')
smiles = re.search(r'(\S+)', smiles).group(1)
smiles = urlquote(smiles)
newJob = createJob(request.user, 'EI Search', optionsList,
commandOptions, sdf, smiles)
time.sleep(1)
return redirect('tools.views.view_job', job_id=newJob.id,resource='')
def sdf2smiles(sdf):
sdf = sdf_to_smiles(sdf)
return HttpResponse(sdf, mimetype='text/plain')
def search(request):
application = Application.objects.get(name='EI Search')
AppFormSet = getAppForm(application.id, request.user)
if request.method != 'POST':
smi = ''
if 'smi' in request.GET:
smi = str(request.GET['smi'])
smi = urlunquote(smi)
form = AppFormSet()
form = str(form)
return render_to_response('search.html',
dict(mode='form', smi=smi, form=form),
context_instance=RequestContext(request))
else:
sdf = None
smiles = None
compid = u'query'
if 'smiles' in request.POST:
input_mode = 'smiles-input'
sdf = u''
try:
smiles = request.POST['smiles']
sdf = smiles_to_sdf(str(smiles))
except:
messages.error(request, 'Error: Invalid SMILES string!')
sdf = None
elif 'sdf' in request.FILES:
input_mode = 'sdf-upload'
try:
sdf = request.FILES['sdf']
sdf = first_mol(sdf.read())
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, 'Invalid SDF!')
sdf = None
elif 'sdf' in request.POST:
if 'draw' in request.POST:
input_mode = 'draw'
sdf = request.POST['sdf'] + '$$$$'
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + ' ' + compid
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, 'Invalid drawing!')
sdf = None
else:
try:
input_mode = 'sdf-input'
sdf = first_mol(request.POST['sdf'])
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, 'Invalid input SDF!')
sdf = None
form = AppFormSet(request.POST)
if form.is_valid():
commandOptions, optionsList = parseToolForm(form)
else:
sdf = None
messages.error(request, "Invalid form options!")
if not sdf:
return redirect('eisearch.views.search')
smiles = re.search(r'(\S+)', smiles).group(1)
smiles = urlquote(smiles)
if request.POST['algorithm'] == u'fp':
newJob = createJob(request.user, 'Fingerprint Search', optionsList,
commandOptions, sdf, smiles)
else:
newJob = createJob(request.user, 'EI Search', optionsList,
commandOptions, sdf, smiles)
time.sleep(1)
return redirect('tools.views.view_job', job_id=newJob.id, resource='')
def search(request):
application = Application.objects.get(name="EI Search")
AppFormSet = getAppForm(application.id, request.user)
if request.method != "POST":
smi = ""
if "smi" in request.GET:
smi = str(request.GET["smi"])
smi = urlunquote(smi)
form = AppFormSet()
form = str(form)
return render_to_response(
"search.html", dict(mode="form", smi=smi, form=form), context_instance=RequestContext(request)
)
else:
sdf = None
smiles = None
compid = u"query"
if "smiles" in request.POST:
input_mode = "smiles-input"
sdf = u""
try:
smiles = request.POST["smiles"]
sdf = smiles_to_sdf(str(smiles))
except:
messages.error(request, "Error: Invalid SMILES string!")
sdf = None
elif "sdf" in request.FILES:
input_mode = "sdf-upload"
try:
sdf = request.FILES["sdf"]
sdf = first_mol(sdf.read())
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, "Invalid SDF!")
sdf = None
elif "sdf" in request.POST:
if "draw" in request.POST:
input_mode = "draw"
sdf = request.POST["sdf"] + "$$$$"
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + " " + compid
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, "Invalid drawing!")
sdf = None
else:
try:
input_mode = "sdf-input"
sdf = first_mol(request.POST["sdf"])
smiles = sdf_to_smiles(sdf)
except:
messages.error(request, "Invalid input SDF!")
sdf = None
form = AppFormSet(request.POST)
if form.is_valid():
commandOptions, optionsList = parseToolForm(form)
else:
sdf = None
messages.error(request, "Invalid form options!")
if not sdf:
return redirect("eisearch.views.search")
smiles = re.search(r"(\S+)", smiles).group(1)
smiles = urlquote(smiles)
if request.POST["algorithm"] == u"fp":
newJob = createJob(request.user, "Fingerprint Search", optionsList, commandOptions, sdf, smiles)
else:
newJob = createJob(request.user, "EI Search", optionsList, commandOptions, sdf, smiles)
time.sleep(1)
return redirect("tools.views.view_job", job_id=newJob.id, resource="")
def uploadCompound(request, *args, **kargs):
if request.method == "GET":
return render_to_response(
"addCompounds.html", dict(input_mode="smiles-input"), context_instance=RequestContext(request)
)
else:
sdf = None
name = None
compid = None
smiles = None
if "smiles" in request.POST:
input_mode = "smiles-input"
sdf = u""
try:
smiles = request.POST["smiles"].split("\n")
for line in smiles:
if re.match(r"^\S+", line):
sdf = sdf + smiles_to_sdf(str(line))
except:
messages.error(request, "Error: Invalid SMILES string!")
sdf = None
elif "sdf" in request.FILES:
input_mode = "sdf-upload"
try:
sdf = request.FILES["sdf"]
sdf = sdf.read()
except (InputError, InvalidInputError):
messages.error(request, "Invalid SDF!")
sdf = None
elif "sdf" in request.POST:
if "draw" in request.POST:
input_mode = "draw"
sdf = request.POST["sdf"] + "$$$$"
compid = str(request.POST["id"])
compid = re.match(r"^(\S{0,20})", compid).group(1)
try:
smiles = sdf_to_smiles(sdf)
smiles = re.match(r"^(\S+)", smiles).group(1)
smiles = smiles + " " + compid
sdf = smiles_to_sdf(smiles)
except:
messages.error(request, "Invalid drawing!")
sdf = None
else:
input_mode = "sdf-input"
sdf = request.POST["sdf"]
if not sdf:
messages.error(request, "No input found!")
elif "pubchem" in request.POST:
cids = request.POST["pubchem"]
cids = cids.split()
input_mode = "pubchem"
filteredCIDs = []
for cid in cids[:]:
match = re.search("(\d{1,200})", cid)
if match:
filteredCIDs.append(int(match.group(1)))
if len(filteredCIDs) > 0:
try:
sdf = DownloadCIDs(filteredCIDs)
except:
messages.error(request, "Invalid CIDs or no response from PubChem!")
sdf = None
else:
messages.error(request, "Error: No valid CIDs entered!")
sdf = None
if not sdf:
return render_to_response(
"addCompounds.html",
dict(input_mode=input_mode, post_data=request.POST),
context_instance=RequestContext(request),
)
newJob = createJob(request.user, "Upload Compounds", "", "--user="******"tools.views.view_job", job_id=newJob.id, resource="")
