Hi Robert,Thanks for sending the supporting files to Geoff, I am working that
issue too. If you need further clarifications, please let me know, i shall send
the required information. Thank you Geoff for your mail
--- On Thu, 2/4/10, Robert DeLisle <[email protected]> wrote:
From: Robert DeLisle <[email protected]>
Subject: Re: [Open Babel] Unexpected result - by obprop
To: "Geoffrey Hutchison" <[email protected]>
Cc: "Vinay M" <[email protected]>, "babel"
<[email protected]>
Received: Thursday, February 4, 2010, 8:35 PM
Geoff,
Attached is the original example.sdf from Vinay in which bonding is properly
defined. As per my notes, when this is converted to canonical SMILES and then
back to SDF, the bonding is incorrect. Also, some properties are different for
the original SDF and the Babel-generated canonical SMILES.
If you need any other files post-conversion, please let me know and I'll send
them. I assume that you'll be able to reproduce the problem but just in case a
version difference leads to different results, I'm happy to supply additional
files should you need them.
-Kirk
On Thu, Feb 4, 2010 at 1:00 PM, Geoffrey Hutchison <[email protected]>
wrote:
On Jan 26, 2010, at 12:20 PM, Robert DeLisle wrote:
> you get a different bonding pattern. See attached. It appears that babel is
> having issues with the bonding pattern (due to aromaticity detection?) of the
> tricycle.
This is clear. I'm sorry, since I'm a bit late coming into this. Can someone
send me the actual SDF file, so I can see why the aromaticity/kekule assignment
is failing. Craig did a lot of work for v2.2.3 to make sure this is right. Both
Craig and I have been hunting down problems like this, and this looks very
familiar to a number of test cases.
Thanks,
-Geoff
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