Add delete_atoms method and use bonding info for add_hatoms SO107 #178
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dormrod
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Nov 26, 2024
GiulioIlBen
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Nov 29, 2024
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GiulioIlBen
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Dec 20, 2024
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I added a notebook for showing the add_hatoms and I decided to show also how to visualize molecules in the same notebook.
It would be nice to obtain the plt.Axes of the molecule as visualized in the notebook, but I couldn't figure out how to do it. Since this is off-topic, I think we can leave the notebook as it is.
GiulioIlBen
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Dec 20, 2024
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Description
Two small changes to
Molecule:delete_atoms: add a method to delete multiple atoms in a single call. This uses "partial success" so that all passed atoms will attempted to be deleted, even if one of them fails.add_hatoms: use a.infile to amsprep instead of a.xyzso bonding information is respected when adding h-atoms. Also perform a guess bonds on the output, if there were bonds on the original molecule.