Here are some number from my laptop for parsing:
Normal Smiles parser:
=================
Proper Smiles 11K/s
Non Smiles words: 94K/s
Don't make molecules (n.b. accepts some 'bad' smiles like C1CCC3)
=================
Proper Smiles: 110K/s
Non Smiles words: 130K/s
If I had to pick, I would just use the normal MolFromSmiles, if you don't
expect many actual smiles strings in your corpus, it's plenty fast.
Cheers,
Brian
On Fri, Dec 2, 2016 at 5:08 PM, Andrew Dalke <da...@dalkescientific.com>
wrote:
> On Dec 2, 2016, at 10:05 PM, Brian Kelley wrote:
> > Here is a very old version of Andrew's parser in code form: ... It was
> fairy well tested on the sigma catalog back in the day. It might be fun to
> resurrect use it in some form.
>
> There's also my OpenSMILES parser written for Ragel:
>
> https://bitbucket.org/dalke/opensmiles-ragel
>
> Taking that path goes more along the lines of what NextMove has done.
>
> BTW, upon consideration,
>
> >> [^]]* # ignore anything up to the ']'
>
> should be more restrictive and exclude '[', ' ', newline ... or really,
> only allow those characters which are valid after the element (+, -, 0-9,
> @, :, T, H, and a few others).
>
> The exercise is left for the students. ;)
>
>
> Andrew
> da...@dalkescientific.com
>
>
>
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