Jan H. Jensen comments

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                                            Jan H. Jensen

atomic valence of O atom inconsistent with RDkit

I need a specific example

Parsing nciatlas geometries

Yeah, xyz2mol wants charge=0 on that line and nothing else. If you can come up with some fancy regex expression that correctly extracts the charge, I'd be happy to look...

Need for tutorial on how to save .svgs

For relatively large grids, f.write(img.data) stops writing after about 1099 lines. Any ideas?

Need for tutorial on how to save .svgs

@samoturk turns out I forgot to close the file :)

pdbbind_nn.py no longer working.

For some reason I am now getting a different error: https://colab.research.google.com/drive/1yZUVSwqSyytjryB6-aj0iEuUOE3IcRPw?usp=sharing

Building a multiclass classification model | Practical Cheminformatics

The precision for the activator really took a hit when oversampling. It's true that in the standard approach you hardly get any activator predictions, but when you do, there's a...

sdf file is empty while converting from xyz file

xyz2mol is now implemented in RDKit (see the readme file), so I don't really maintain xyz2mol actively. But do let me know if the RDKit implementation is not working for...

sdf file is empty while converting from xyz file

Your molecule works fine for me. Are you using a +1 charge?

Convert xyz file with several structures in it (different molecules or same molecule, conformers)

No, that's not currently possible

unexpected ligand pka values

For some reason the code is assigning the wrong atom type to these Ns. For example for 6W8I N50 is assigned to be a tertiary N (N33), but should be...