Greg,
Thanks for this.
I, for one, think it is useful - not in a "parse this particular smiles
string" fashion.
But consider this use case. I have 8,000,000 molecules in a few hundred
smiles files on which I am calculating descriptors on the cloud. I only
have access to log files.
I get some ten thousand "SMILES Parse Error" without any additional info.
Also, I think this error should be just one line (no need to bloat log
files with redundant static data).
These should have a bit of static info which is the same for both (so you
can grep on that) and must have (on the same line) the offending smiles
string, which you could extract easily with regex, so I suggest something
structured like:
In [2]: Chem.MolFromSmiles('Ccc1XXXcCCC')
[06:06:25] SMILES Parse Error: Ccc1XXXcCCC (reason: unknown atoms X)
In [3]: Chem.MolFromSmiles('C1C')
[06:06:28] SMILES Parse Error: C1C (reason: unclosed ring for input)
In the words of the master, as it stands:
Useless, it is. More info, I need.
>From smiles errors, young Padawan must learn.
Jean-Paul Ebejer
Early Stage Researcher
InhibOx Ltd
Pembroke House
36-37 Pembroke Street
Oxford
OX1 1BP
UK
(+44 / 0) 1865 262 034
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On 10 May 2011 05:14, Greg Landrum <[email protected]> wrote:
> Best,
> -greg
>
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