What is the official file extension for SMILES and SMARTS files
I don't think I've ever seen anything proposed as "official," though I admit I don't use Daylight's official toolkit.

Open Babel accepts:


.smi
.smiles
.can (ideally canonical SMILES, but that matters more for writing, not reading)


I haven't seen many SMARTS files, but I would suspect both .sma and .smarts are out there "in the wild."

Incidentally, this is probably something to bring up with the OpenSMILES effort. I know there's an OpenSMARTS specification started as well.