Hi Brian, (Note that it's a good idea to edit the subject when replying to a digest.)
Let's get you set up with the Python bindings. Try it again from a clean build, and report what you find. Note that the 3.0 release requires that you have Swig and pass -DRUN_SWIG=TRUE (an oversight on our part). Regards, - Noel On Wed, 15 Apr 2020 at 19:14, Bennion, Brian via OpenBabel-discuss < openbabel-discuss@lists.sourceforge.net> wrote: > 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: openbabel-discuss-requ...@lists.sourceforge.net < > openbabel-discuss-requ...@lists.sourceforge.net> > Sent: Tuesday, April 14, 2020 6:55 AM > To: openbabel-discuss@lists.sourceforge.net > Subject: OpenBabel-discuss Digest, Vol 167, Issue 10 > > Send OpenBabel-discuss mailing list submissions to > openbabel-discuss@lists.sourceforge.net > > 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 > openbabel-discuss-requ...@lists.sourceforge.net > > You can reach the person managing the list at > openbabel-discuss-ow...@lists.sourceforge.net > > 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 <geoff.hutchi...@gmail.com> > To: "Bennion, Brian" <benni...@llnl.gov> > Cc: "openbabel-discuss@lists.sourceforge.net" > <openbabel-discuss@lists.sourceforge.net> > Subject: Re: [Open Babel] Operating on multi molecule sdf files > Message-ID: <ed95515b-3d5f-48a4-89eb-dad0a2adf...@gmail.com> > 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" <diallobaka...@gmail.com> > To: "openbabel-discuss@lists.sourceforge.net mailinglist" > <openbabel-discuss@lists.sourceforge.net> > 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: diallobaka...@gmail.com | 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 > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > ------------------------------ > > End of OpenBabel-discuss Digest, Vol 167, Issue 10 > ************************************************** > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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