Note: I turned logging off, otherwise a lot of time was spent spewing to
stderr:
from rdkit import Chem, rdBase
rdBase.DisableLog("rdApp.*")
On Sat, Dec 3, 2016 at 9:02 AM, Brian Kelley <fustiga...@gmail.com> wrote:
> 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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>
>
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