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 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 test_smiles(self):
inp = "O=C1NC%91=NC2NC=NC=21.[*:1]%91 |$;;;;;;;;;;_R1$|"
molfile = indigo.loadMolecule(inp).molfile()
r = make_request("smiles", (("moldata", molfile), ))
self.assertEquals(200, r.code)
status, smiles = r.read().split('\n', 1)
self.assertEquals(status, "Ok.")
self.assertEquals(inp, indigo.loadMolecule(smiles).canonicalSmiles())
def test_calculate_cip(self):
inp = "CCCN1C(=O)N=C(O)c2[nH]c[n]c12"
r = make_request("calculate_cip", (("moldata", inp), ))
self.assertEquals(200, r.code)
status, molfile = r.read().split('\n', 1)
self.assertEquals(status, "Ok.")
smiles = indigo.loadMolecule(molfile).canonicalSmiles()
self.assertEquals(smiles, "CCCN1C(=O)N=C(O)C2NC=NC1=2")
def test_aromatize(self):
inp = "N1=C(O)C2NC=NC=2N(CCC)C1=O"
r = make_request("aromatize", (("moldata", inp), ))
self.assertEquals(200, r.code)
status, molfile = r.read().split('\n', 1)
self.assertEquals(status, "Ok.")
smiles = indigo.loadMolecule(molfile).canonicalSmiles()
self.assertEquals(smiles, "CCCN1C(=O)N=C(O)c2[nH]c[n]c12")
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
