Thanks. It's really a obvious error.I ran it in jupyter via browser. Both
docker/ubuntu and windows were tested and found that jupyter won't give error.
Ipython or python in terminal(cmd) would show this error.
Why not raise a python error or warning?
Hongbin Yang
From: Greg LandrumDate: 2016-09-19 12:08To: 杨弘宾CC: rdkit-discussSubject: Re:
[Rdkit-discuss] a SMILES that rdkit cannot readHi,
On Mon, Sep 19, 2016 at 5:33 AM, 杨弘宾 <yanyangh...@163.com> 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('CCCCN(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.
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('CCCCN(CC(O)C1=C\C(=N/#N)\C(=O)C=C1)N=O')[06:04:54] SMILES
Parse Error: syntax error for input:
'CCCCN(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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