Dear folks,
I have some old code which I would like to convert smoothly to rdkit.
I have set-up a MySQL database of molecules given MOL2 and SMILES. The
substructure search happens via frowns:
"
db_smiles = db.do('SELECT ligand_id, smiles FROM ligands;')
ligand_ids = []
for db_smile in db_smiles:
try:
db_can_smiles = Smiles.smilin(db_smile[1]).cansmiles()
match = pattern.match(Smiles.smilin(db_can_smiles))
if match != None:
ligand_ids.append(db_smile[0])
except:
pass #print "Warning: failed for to recognize \"%s\"
SMILES string<br>\n" %db_smile[1]
return ligand_ids
"
Do I necessarily need to convert MySQL to PostgreSQL? A quick google search
shows me that this should be feasible, but I have never done it so far.
Or can I just replace the frowns SMILES search by the RDkit SMILES search?
Cheers & Thanks,
Paul
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