Re: [Rdkit-discuss] a SMILES that rdkit cannot read

[Greg Landrum]

Hi,

On Mon, Sep 19, 2016 at 5:33 AM, 杨弘宾  wrote:

>When I used rdkit to parse a smi file, I found that there was a SMILES
> that rdkit cannot parse, and no any error or warning.
>
>
> version: Release_2016_03_1
> >>> mol = Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')
> >>> print mol
> None
>
> This compound can be read by OpenBabel. But I have no idea why it didnot
> work.
>

I don't know why OpenBabel accepts it, but there's definitely an error in
that SMILES. This part: "=N/#N" has a single bond (the "/") directly
followed by a triple bond (the "#"), and that's not legal SMILES.

I do see an error message when I try the SMILES:

In [2]: mol = Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')
[06:04:54] SMILES Parse Error: syntax error for input:
'N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O'

and find it a bit odd that you don't. What operating system are you using
and how are you running the code?

Best,
-greg
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[Rdkit-discuss] a SMILES that rdkit cannot read

[杨弘宾]

hi,? ? When I used rdkit to parse a smi file, I found that there was a SMILES 
that rdkit cannot parse, and no any error or?warning.

version: Release_2016_03_1>>>?mol = 
Chem.MolFromSmiles('N(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')>>> print molNone

This compound can be read by OpenBabel. But I have no idea why it didnot work.



Hongbin Yang 杨弘宾

Research: Toxicophore and Chemoinformatics
Pharmaceutical Science, School of Pharmacy

East China University of Science and Technology?


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