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
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Today's Topics:
1. Re: Operating on multi molecule sdf files (Geoffrey Hutchison)
2. Structure size scaling in 2D depiction (Bakary N'tji Diallo)
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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>
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> 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
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Date: Mon, 13 Apr 2020 21:07:56 +0200
From: "Bakary N'tji Diallo" <diallobaka...@gmail.com>
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Subject: [Open Babel] Structure size scaling in 2D depiction
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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
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