Hi Stan,
Based on your conversation with Pascal, it sounds like a confirmed bug -
are you happy to file it in our issue tracker (
https://github.com/openbabel/openbabel/issues)? I can do it with the info
you've provided, but it works better if you do it, as you will get updates
when someone fixes it or has queries.
- Noel
On 13 November 2017 at 13:40, Stanley P Kolis <kolis_stan...@lilly.com>
wrote:
> Hey Pascal—
>
>
>
> Thanks for putting the time into this and for expanding the ‘To:’ list to
> see if anyone else can help.
>
>
>
> The error does happen with multiple different ChemDraw files. I am using
> ChemDraw Professional v. 16.0.0.82 (68) (probably should have sent you that
> information before…I apologize). It could be a ChemDraw versioning
> problem? Unfortunately, I don’t have access to an older version of
> ChemDraw to see if that makes a difference.
>
>
>
> I have attached a new ChemDraw file with some generic structures in it.
> This raises the same error I have seen with the other files. I have also
> included a screenshot of the OpenBabel GUI conversion of the same .cdx file.
>
>
>
> Thanks again for all your help.
>
>
>
> Stan
>
>
>
> *Stanley (Stan) P. Kolis*
> Research Advisor, Small Molecule Design & Development
> Eli Lilly and Company
> Lilly Corporate Center, Indianapolis IN 46285 U.S.A.
> +1 317.433.3982 (office) | +1 317.494.2583 (mobile)
> sko...@lilly.com | www.lilly.com
> [image: LillyLogo_EmailSig2.jpg]
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>
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>
>
>
>
>
>
>
>
> *From:* Pascal Muller [mailto:pascal.jm.mul...@gmail.com]
> *Sent:* Monday, November 13, 2017 5:29 AM
>
> *To:* Stanley P Kolis <kolis_stan...@lilly.com>; babel <
> openbabel-discuss@lists.sourceforge.net>
> *Subject:* [EXTERNAL] Re: [Open Babel] Problem Converting .cdx files
> using Pybel
>
>
>
> Hi,
>
>
>
>
>
> Replying to the list, I think other may have better answer than mine.
>
>
>
>
>
> Hello Pascal—
>
>
>
> Thanks for the response and working through this.
>
>
>
> I have responded to your questions below.
>
>
>
> Stan
>
>
>
>
>
>
>
>
>
> *From:* Pascal Muller [mailto:pascal.jm.mul...@gmail.com]
> *Sent:* Friday, November 10, 2017 5:00 AM
> *To:* Stanley P Kolis <kolis_stan...@lilly.com>; babel <
> openbabel-discuss@lists.sourceforge.net>
> *Subject:* [EXTERNAL] Re: [Open Babel] Problem Converting .cdx files
> using Pybel
>
>
>
> Dear Stan,
>
>
>
> OpenBabel Version: 2.4.1
>
> Operating System: Windows/Jupyter Notebook
>
>
>
> I have been trying to use the instructions at this link
> <https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html> and also
> in the original Chemistry Central Journal
> <https://ccj.springeropen.com/articles/10.1186/1752-153X-2-5>
> publication. I am able to convert .sdf files over to .smi files without
> any problem. However, when I try to convert .cdx files to .sdf or .smi
> files, the system crashes and I get an error in the command window that
> tells me that there is no ‘ChemDraw Header’ that pybel/openbabel is
> expecting to see.
>
>
>
> I have included a .cdx file that I’ve been using. Any chance that you
> guys can help me figure out what’s going on?
>
>
>
>
>
> With the command line (Open Babel 2.4.1, Linux)
>
> obabel -icdx multiNitroCompounds.cdx -OmultiNitroCompounds.sdf
>
>
>
> the conversion is done without problem, but with one warning: "Alias O2N
> was not chemically interpreted"
>
> · *I see the same error message as above when working from the
> command line and the jupyter notebook.*
>
> Indeed, nitro groups are not all represented in the same way in the sdf
> file (see picture).
>
> I think that it should not be linked to the "no ChemDraw header" message,
> however.
>
> What's the message exactly? May you share the corresponding part of your
> Pybel script?
>
> · *The attached pdf shows the error messages received in the
> Jupyter notebook and at the command prompt in the background.*
>
> · *Script is pretty simple:*
>
> o *import pybel as pb*
>
> o *allmols = [mol for mol in pb.readfile(“cdx”, “untitled.cdx”)]*
>
>
>
> Indeed, I have the same error than you using pybel:
>
>
>
> ==============================
>
> *** Open Babel Warning in Expand
>
> Alias O2N was not chemically interpreted
>
>
>
> ==============================
>
> *** Open Babel Error in CDXReader
>
> Invalid file, no ChemDraw Header
>
> terminate called without an active exception
>
> Aborted
>
>
>
>
>
> It seems than the .cdx file may somehow badly formated, raising an error
> originating in chemdrawcdx.cpp.
>
>
>
> I have not ChemDraw installed, so I can't test other cdx file.
>
> Does another .cdx file raise the same error?
>
>
>
> Best regards,
>
> Pascal
>
>
>
>
>
>
>
> Without using Pybel, does the Open Babel GUI convert the .cdx file?
>
> · *The Open Babel GUI does work to do the conversion (to both the
> .sdf and .smi formats).*
>
> · *This is a good short-term fix, but would still like to be able
> to call the conversion script from other files I’ve written.*
>
>
>
> Regards,
>
> Pascal
>
>
>
>
>
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