def get_mcs_indices_indigo(m_sdf, t_sdf, timeout=None, exact=False):
import indigo
indigo = indigo.Indigo()
m_mol = indigo.loadMolecule(m_sdf)
t_mol = indigo.loadMolecule(t_sdf)
# find common substructure
arr = indigo.createArray()
arr.arrayAdd(m_mol)
arr.arrayAdd(t_mol)
mcs = indigo.extractCommonScaffold(arr, 'exact' if exact else 'approx')
# match to scaffold
query = indigo.loadQueryMolecule(mcs.smiles())
m_match = indigo.substructureMatcher(m_mol).match(query)
t_match = indigo.substructureMatcher(t_mol).match(query)
# atom indices of match
m_atoms = [m_match.mapAtom(a) for a in query.iterateAtoms()]
t_atoms = [t_match.mapAtom(a) for a in query.iterateAtoms()]
m_indices = [a.index() for a in m_atoms if a is not None]
t_indices = [a.index() for a in t_atoms if a is not None]
return m_indices, t_indices
def do_GET(self):
if self.path.endswith("knocknock"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
self.wfile.write("You are welcome!")
return
if self.path.find('?') != -1:
self.path, self.query_string = \
self.path.split('?', 1)
else:
self.query_string = ''
self.globals = dict(cgi.parse_qsl(self.query_string))
if self.path.endswith("layout"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
mol = indigo.loadQueryMolecule(self.globals['smiles'])
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
SimpleHTTPServer.SimpleHTTPRequestHandler.do_GET(self)
def get_mcs_indices_indigo(m_sdf, t_sdf, timeout=None, exact=False):
import indigo
indigo = indigo.Indigo()
m_mol = indigo.loadMolecule(m_sdf)
t_mol = indigo.loadMolecule(t_sdf)
# find common substructure
arr = indigo.createArray()
arr.arrayAdd(m_mol)
arr.arrayAdd(t_mol)
mcs = indigo.extractCommonScaffold(arr, 'exact' if exact else 'approx')
# match to scaffold
query = indigo.loadQueryMolecule(mcs.smiles())
m_match = indigo.substructureMatcher(m_mol).match(query)
t_match = indigo.substructureMatcher(t_mol).match(query)
# atom indices of match
m_atoms = [m_match.mapAtom(a) for a in query.iterateAtoms()]
t_atoms = [t_match.mapAtom(a) for a in query.iterateAtoms()]
m_indices = [a.index() for a in m_atoms if a is not None]
t_indices = [a.index() for a in t_atoms if a is not None]
return m_indices, t_indices
def do_GET(self):
if self.path.endswith("knocknock"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
self.wfile.write("You are welcome!")
return
if self.path.find('?') != -1:
self.path, self.query_string = \
self.path.split('?', 1)
else:
self.query_string = ''
self.globals = dict(cgi.parse_qsl(self.query_string))
if self.path.endswith("layout"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
mol = indigo.loadQueryMolecule(self.globals['smiles'])
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
SimpleHTTPServer.SimpleHTTPRequestHandler.do_GET(self)
def handle_layout(request):
if request.method == "GET" and request.GET.has_key("smiles"):
moldata = request.GET["smiles"]
elif request.method == "POST" and request.POST.has_key("moldata"):
moldata = request.POST["moldata"]
else:
raise Http404
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return HttpResponse(content="Ok.\n" + mol.molfile(), mimetype="text/plain")
def handle_layout(request):
if request.method == 'GET' and request.GET.has_key("smiles"):
moldata = request.GET["smiles"]
elif request.method == 'POST' and request.POST.has_key("moldata"):
moldata = request.POST["moldata"]
else:
raise Http404
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return HttpResponse(content="Ok.\n" + mol.molfile(), mimetype='text/plain')
def do_POST(self):
ctype, pdict = cgi.parse_header(self.headers.getheader('content-type'))
if ctype == 'multipart/form-data':
if self.path.endswith("open"):
query = cgi.parse_multipart(self.rfile, pdict)
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
self.wfile.write("Ok.\n")
self.wfile.write(query['filedata'][0])
return
if self.path.endswith("save"):
query = cgi.parse_multipart(self.rfile, pdict)
filedata = query['filedata'][0]
first = filedata.split("\n")[0]
rest = "\n".join(filedata.split("\n")[1:])
self.send_response(200)
if first == "smi":
self.send_header('Content-type',
'chemical/x-daylight-smiles')
elif first == "mol":
self.send_header('Content-type', 'chemical/x-mdl-molfile')
else:
self.send_header('Content-type', 'text/plain')
self.send_header('Content-Disposition',
'attachment; filename=ketcher.' + first)
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
self.wfile.write(rest)
return
if self.path.endswith("layout"):
length = int(self.headers['content-length'])
self.globals = dict(cgi.parse_qsl(self.rfile.read(length)))
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
mol = indigo.loadQueryMolecule(self.globals['moldata'])
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
def do_GET(self):
if self.path.endswith("knocknock"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
self.wfile.write("You are welcome!")
return
if self.path.find('?') != -1:
self.path, self.query_string = \
self.path.split('?', 1)
else:
self.query_string = ''
self.globals = dict(cgi.parse_qsl(self.query_string))
if self.path.endswith("layout"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
smiles = self.globals['smiles']
if '>>' in smiles or smiles.startswith('$RXN'):
rxn = indigo.loadQueryReaction(smiles)
rxn.layout()
self.wfile.write("Ok.\n")
self.wfile.write(rxn.rxnfile())
else:
mol = indigo.loadQueryMolecule(smiles)
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
if self.path.endswith("automap"):
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
smiles = self.globals['smiles']
if 'mode' in self.globals:
mode = self.globals['mode']
else:
mode = 'discard'
rxn = indigo.loadQueryReaction(smiles)
if not smiles.startswith('$RXN'):
rxn.layout()
rxn.automap(mode)
self.wfile.write("Ok.\n")
self.wfile.write(rxn.rxnfile())
return
SimpleHTTPServer.SimpleHTTPRequestHandler.do_GET(self)
def do_POST(self):
ctype, pdict = cgi.parse_header(self.headers.getheader('content-type'))
if ctype == 'multipart/form-data':
if self.path.endswith("open"):
query = cgi.parse_multipart(self.rfile, pdict)
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
self.wfile.write("Ok.\n");
self.wfile.write(query['filedata'][0]);
return
if self.path.endswith("save"):
query = cgi.parse_multipart(self.rfile, pdict)
filedata = query['filedata'][0]
first = filedata.split("\n")[0]
rest = "\n".join(filedata.split("\n")[1:])
self.send_response(200)
if first == "smi":
self.send_header('Content-type', 'chemical/x-daylight-smiles')
elif first == "mol":
self.send_header('Content-type', 'chemical/x-mdl-molfile')
else:
self.send_header('Content-type', 'text/plain')
self.send_header('Content-Disposition', 'attachment; filename=ketcher.' + first)
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
self.wfile.write(rest)
return
if self.path.endswith("layout"):
length = int(self.headers['content-length'])
self.globals = dict(cgi.parse_qsl(self.rfile.read(length)))
self.send_response(200)
self.send_header('Content-type', 'text/plain')
# Allow CORS and x-json
self.send_header('Access-Control-Allow-Origin', '*')
self.send_header('Access-Control-Expose-Headers', 'x-json')
self.end_headers()
mol = indigo.loadQueryMolecule(self.globals['moldata'])
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
def handle_layout(request):
if request.method == 'GET' and request.GET.has_key("smiles"):
moldata = request.GET["smiles"]
elif request.method == 'POST' and request.POST.has_key("moldata"):
moldata = request.POST["moldata"]
else:
raise Http404
if '>>' in moldata or moldata.startswith('$RXN'):
rxn = indigo.loadQueryReaction(moldata)
rxn.layout()
return HttpResponse(content="Ok.\n" + rxn.rxnfile(), mimetype='text/plain')
else:
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return HttpResponse(content="Ok.\n" + mol.molfile(), mimetype='text/plain')
def load_moldata(self, is_query=False):
moldata = self.fields.getfirst('moldata')
if moldata.startswith('$RXN'):
if is_query:
md = indigo.loadQueryReaction(moldata)
else:
md = indigo.loadReaction(moldata)
is_rxn = True
else:
if is_query:
md = indigo.loadQueryMolecule(moldata)
else:
md = indigo.loadMolecule(moldata)
is_rxn = False
return md, is_rxn
def load_moldata(self, is_query=False):
moldata = self.fields.getfirst('moldata')
if moldata.startswith('$RXN'):
if is_query:
md = indigo.loadQueryReaction(moldata)
else:
md = indigo.loadReaction(moldata)
is_rxn = True
else:
if is_query:
md = indigo.loadQueryMolecule(moldata)
else:
md = indigo.loadMolecule(moldata)
is_rxn = False
return md, is_rxn
def on_layout(self):
moldata = None
if self.method == 'GET' and 'smiles' in self.fields:
moldata = self.fields.getfirst('smiles')
elif self.is_form_request() and 'moldata' in self.fields:
moldata = self.fields.getfirst('moldata')
if moldata:
if '>>' in moldata or moldata.startswith('$RXN'):
rxn = indigo.loadQueryReaction(moldata)
rxn.layout()
return ["Ok.\n", rxn.rxnfile()]
else:
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return ["Ok.\n", mol.molfile()]
self.notsupported()
def handle_layout(request):
if request.method == 'GET' and request.GET.has_key("smiles"):
moldata = request.GET["smiles"]
elif request.method == 'POST' and request.POST.has_key("moldata"):
moldata = request.POST["moldata"]
else:
raise Http404
if '>>' in moldata or moldata.startswith('$RXN'):
rxn = indigo.loadQueryReaction(moldata)
rxn.layout()
return HttpResponse(content="Ok.\n" + rxn.rxnfile(),
mimetype='text/plain')
else:
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return HttpResponse(content="Ok.\n" + mol.molfile(),
mimetype='text/plain')
def on_layout(self):
moldata = None
if self.method == 'GET' and 'smiles' in self.fields:
moldata = self.fields.getfirst('smiles')
elif self.is_form_request() and 'moldata' in self.fields:
moldata = self.fields.getfirst('moldata')
if moldata:
if '>>' in moldata or moldata.startswith('$RXN'):
rxn = indigo.loadQueryReaction(moldata)
rxn.layout()
return ["Ok.\n",
rxn.rxnfile()]
else:
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
return ["Ok.\n",
mol.molfile()]
self.notsupported()
def do_POST(self):
ctype, pdict = cgi.parse_header(self.headers.getheader('content-type'))
if ctype == 'multipart/form-data':
if self.path.endswith("open"):
query = cgi.parse_multipart(self.rfile, pdict)
self.send_response(200)
self.send_header('Content-type', 'text/html')
self.end_headers()
self.wfile.write("<html><body onload=\"parent.ui.loadMoleculeFromFile()\" title=\"");
self.wfile.write(base64.b64encode("Ok.\n"));
self.wfile.write(base64.b64encode(query['filedata'][0]));
self.wfile.write("\"></body></html>");
return
if self.path.endswith("save"):
query = cgi.parse_multipart(self.rfile, pdict)
filedata = query['filedata'][0]
lines = filedata.splitlines()
first = lines[0].strip()
rest = "\n".join(lines[1:])
self.send_response(200)
if first == "smi":
self.send_header('Content-type', 'chemical/x-daylight-smiles')
elif first == "mol":
if rest.startswith('$RXN'):
first = "rxn"
self.send_header('Content-type', 'chemical/x-mdl-rxnfile')
else:
self.send_header('Content-type', 'chemical/x-mdl-molfile')
else:
self.send_header('Content-type', 'text/plain')
self.send_header('Content-Length', len(rest))
self.send_header('Content-Disposition', 'attachment; filename=ketcher.' + first)
self.end_headers()
self.wfile.write(rest)
return
if self.path.endswith("layout"):
length = int(self.headers['content-length'])
self.globals = dict(cgi.parse_qsl(self.rfile.read(length)))
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
moldata = self.globals['moldata']
if '>>' in moldata or moldata.startswith('$RXN'):
rxn = indigo.loadQueryReaction(moldata)
rxn.layout()
self.wfile.write("Ok.\n")
self.wfile.write(rxn.rxnfile())
else:
mol = indigo.loadQueryMolecule(moldata)
mol.layout()
self.wfile.write("Ok.\n")
self.wfile.write(mol.molfile())
return
if self.path.endswith("automap"):
length = int(self.headers['content-length'])
self.globals = dict(cgi.parse_qsl(self.rfile.read(length)))
self.send_response(200)
self.send_header('Content-type', 'text/plain')
self.end_headers()
moldata = self.globals['moldata']
if 'mode' in self.globals:
mode = self.globals['mode']
else:
mode = 'discard'
rxn = indigo.loadQueryReaction(moldata)
if not moldata.startswith('$RXN'):
rxn.layout()
rxn.automap(mode)
self.wfile.write("Ok.\n")
self.wfile.write(rxn.rxnfile())
return
