More context. I have 500K ligands in a single sdf file. The names for each ligand was found after the sdf file was created. I would like to either replace the label at the top with the appropriate title or add to a property value. Unfortunately, I and others at LLNL have never been able to compile python bindings to obabel. I am not familiar with pybabel but can look at it. Due to the source of the sdf files RDKit chokes on about 50% of them so manipulation is not easy there.
Brian -----Original Message----- From: [email protected] <[email protected]> Sent: Tuesday, April 14, 2020 6:55 AM To: [email protected] Subject: OpenBabel-discuss Digest, Vol 167, Issue 10 Send OpenBabel-discuss mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/openbabel-discuss or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of OpenBabel-discuss digest..." Today's Topics: 1. Re: Operating on multi molecule sdf files (Geoffrey Hutchison) 2. Structure size scaling in 2D depiction (Bakary N'tji Diallo) ---------------------------------------------------------------------- Message: 1 Date: Tue, 14 Apr 2020 09:53:59 -0400 From: Geoffrey Hutchison <[email protected]> To: "Bennion, Brian" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [Open Babel] Operating on multi molecule sdf files Message-ID: <[email protected]> Content-Type: text/plain; charset="utf-8" > After reading the docs I think that adding individual properties to > individual molecules in a multi molecule sdf files is probably not possible? > I have an sdf file with 500k molecules and I would like to add a little > unique identifier that isn?t a supported descriptor to each molecule and then > write out the altered sdf file. Personally, I'd do this with a quick Python script, since a Pybel molecule has a data property: https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule.data <https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule.data> -Geoff -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Mon, 13 Apr 2020 21:07:56 +0200 From: "Bakary N'tji Diallo" <[email protected]> To: "[email protected] mailinglist" <[email protected]> Subject: [Open Babel] Structure size scaling in 2D depiction Message-ID: <CABWhgwRcq0kT1451K=JUeiH8=bu1xjo+qwsjkoj6hpjfwyg...@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear all, I have the following depiction for a structure file. As you can see the first compound is scaled up. [image: image.png] Is there way to maintain a uniform structure size. I am using the following command: "obabel structure.smi -O out.svg -xC -xe -d" Thanks Best regards -- Bakary N?tji DIALLO PhD Student (Bioinformatics) <http://linkedin.com/in/bakarydiallo>, Research Unit in Bioinformatics (RUBi) <https://rubi.ru.ac.za/> Mail: [email protected] | Skype: diallobakary4 Tel: +27798233845 | +223 74 56 57 22 | +223 97 39 77 14 -------------- next part -------------- An HTML attachment was scrubbed... -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 33868 bytes Desc: not available ------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------ End of OpenBabel-discuss Digest, Vol 167, Issue 10 ************************************************** _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
