Hi all, I just got this message, and I am pretty sure the CDK does this wrong too... the original problem was that InChI generation failed, because a SDF was read wrongly...
So, I was wondering how many CDK users are relying on MDL molfile bond order 4 = aromatic? Some time ago, the CDK introduced the STRICT and RELAXED mode for reading files, tuning to what extend the true specification should be used, and the MDL molfile reader already complains about certain errors, which it will allows in RELAXED mode. (And Cactvs seems to take the same approach, as written below.) I'll verify the below claim, but I'm sure this is true, so I will file a bug report and make the appropriate patch... ---------- Forwarded message ---------- From: Wolf-D.Ihlenfeldt <w...@....> Date: Wed, Sep 30, 2009 at 7:52 PM Subject: Re: [InChI-discuss] Aromatic molecules To: inchi-disc...@lists.sourceforge.net <snip> Vincent, This is *NOT* a bug, but rather a rare and laudable example of a proper implementation of an MDL Molfile reader. Bonds type 4 are NOT aromatic bonds. They are query bonds for database searches. This is clearly defined in the MDL format specification. These MUST NOT be used to encode normal structure data files. File a bug report with the suppliers of whatever tool you used to write you file. Your options: a) Fix your input files. b) Use a tool which provides advanced interpretation of Molfile to deal with peculiarities and common misencodings, such as the Cactvs toolkit. It is free for academic use, is available from www.xemistry.com, has full InChI support and the capability to restore a proper KekulĂ© scheme from misapplied query bond encodings. <snip> ---------- End Forwarded message ---------- Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
