I want to know what is the officially used file extension for files containing SMILES and SMARTS strings. Somewhere I see .SMI/.SMA and somewhere its the full .SMILES/.SMARTS.
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$\begingroup$ It is just like .htm or .html, both are same $\endgroup$– FreddyOct 9, 2014 at 2:26
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1$\begingroup$ DOS\Win systems traditionally accept only three character file extensions, while Unix/Linux systems can handle longer ones. It is just a technicality, depends on software what they accept/recognize. $\endgroup$– GregOct 9, 2014 at 7:40
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2 Answers
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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.
answered Oct 9, 2014 at 2:23
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$\begingroup$ Thanks for the info. (Can't up-vote because it requires at least 15 reps :) ) $\endgroup$– user6834Oct 9, 2014 at 2:50
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Slightly beside the point, but here is what Daylight says:
The "chemical" MIME type, championed by H. Rzepa of Imperial College, London, is (hopefully) nearing ratification. Should this happen, SMILES will almost certainly appear as MIME subtype, i.e., the MIME type: chemical/smiles. Until that blessed day, the IETF recommendation is to use something like application/x-smiles or x-chemical/x-smiles.
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$\begingroup$ Yes, that's something we use internally for SMILES format, clipboard operations and while requesting SMILES data from our components. $\endgroup$– user6834Oct 9, 2014 at 2:07
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$\begingroup$ Sadly, if you look at the date, that was 1998. MIME types are also somewhat passé. $\endgroup$ Oct 9, 2014 at 2:09
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$\begingroup$ @GeoffHutchison, why do you say MIME types are passé?? They are still heavily used in the modern web, in the Linked Data web even more! $\endgroup$ Aug 13, 2016 at 11:32
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$\begingroup$ @EgonWillighagen I see far, far too much data on the web as text, generic XML or other generic types. Software is then left to infer that this text file is really SMILES or PDB, because of source or formatting. $\endgroup$ Aug 14, 2016 at 4:02