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Published 20 hours ago • verified publisher icon a-r-j

H coords are not included when constructing molecule graph from SDF file

Open chris-clem opened this issue 5 months ago • 1 comments

Describe the bug H atoms are not included in coords when constructing molecule graph with add_hs=True and path.

To Reproduce Colab reproducing the bug: https://colab.research.google.com/drive/122CTepC6O_-R-jbLArcbdqSQOiQseB-H?usp=sharing

Expected behavior If config.add_hs is True, rdmol = Chem.AddHs(rdmol, addCoords=True) needs to be executed before creating the coords list. Otherwise an IndexError occurs when nodes are added in https://github.com/a-r-j/graphein/blob/master/graphein/molecule/graphs.py#L79.

Happy to open a PR fixing the bug.

chris-clem avatar Jun 02 '25 10:06 chris-clem