fredrikw
fredrikw
A short question/comment. Are you sure that gen3D will result in a minimization of a 3D structure? I think it will create a new one from scratch, without using the...
I cannot find it in the documentation right now, but due to the fact that `obabel -opng` commands can both add chemical data to an existing png file and create...
That was not the feature I was thinking about. That is just to create a png that normally show the title of the compound but you add MW to the...
@nbehrnd That looks lika bug...
These kind of problems are almost always due to a problem with the BABEL_DATADIR environment variable. Are you using a Conda install of OpenBabel? In that case, you could look...
Just a follow-up to my message above. That issue is taken care of by https://github.com/conda-forge/openbabel-feedstock/pull/22. If you run `conda update -c conda-forge openbabel` and make sure you get a version...
I cannot reproduce this (on OB 3.1.0 on wsl2, should be feature matched to 3.1.1) ``` >>> from openbabel import pybel >>> mol = pybel.readstring("smi", "O") >>> mol.addh() >>> mol.make3D()...
The first thing to try is with a recent version of Open Babel if you have the possibility. 2.4.1 is rather old.
Do every conversion end with the error or do you have an example of a successful SMILES to sdf conversion? Does it work without the --gen2D option?
Sorry for the spamming, I don't have access to an arm64 computer so I will ask you to do a couple of more things. Could you please check `obabel -ismi...