New NAGL docs take 2 #21
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Co-authored-by: Matt Thompson <[email protected]>
lilyminium
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Mar 9, 2023
docs/theory.md
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| In a molecular graph, atoms are nodes and bonds are edges. A molecular graph can store extra information in its nodes and edges; in a Lewis structure, this is things like an atom's element and lone pairs, or a bond's bond order or stereochemistry, but for a molecular graph they can be anything. Element and bond order are usually somewhere near the top of the list. Envisioning a molecule as a graph lets us apply computer science techniques designed for graphs to molecules. | ||
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| Note that a particular molecular species may have more than one molecular graph topology that represents it. This most commonly happens with tautomers and resonance forms. NAGL operates on molecular graphs, and on the OpenFF [`Molecule`] class, and it doesn't try to be clever about whether two molecules are the same or not. If you want tautomers to produce the same charges, you may need to prepare your dataset accordingly. |
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(Non-blocking, since the ResonanceEnumerator is not very well documented and hidden in utils) -- this might be a good place to eventually mention the ResonanceEnumerator which will enumerate all resonance forms of a molecule so that properties such as formal charges or hybridisation can be averaged.
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OK I think this is ready for review! |
This reverts commit 70d5013.
More docstrings!
lilyminium
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Mar 22, 2023
Co-authored-by: Lily Wang <[email protected]>
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This PR adds documentation. Replaces #12 with a branch that has a clean history of not touching the main codebase.
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