Update partial charge assignment docs#313
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mikemhenry merged 2 commits intomainfrom Dec 20, 2023
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mattwthompson
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Nov 29, 2023
| If they do _not_ contain partial charges, the `openff-toolkit` charging method [`Molecule.compute_partial_charges_am1bcc`](https://open-forcefield-toolkit.readthedocs.io/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.compute_partial_charges_am1bcc) is used to assign partial charges. | ||
| The [canonical AM1-BCC charging method](https://docs.eyesopen.com/toolkits/cookbook/python/modeling/am1-bcc.html) is used to assign ELF10 charges if the OpenEye Toolkit is available. | ||
| If not, [Antechamber](http://ambermd.org/antechamber/) from the [AmberTools](http://ambermd.org/AmberTools.php) distribution (which uses the `sqm` semiempirical quantum chemical package) is used to assign AM1-BCC charges (`antechamber -c bcc`). | ||
| If the provided molecule(s) contain nonzero (user-specified) partial charges (stored in the `Molecule.partial_charges` attribute), those partial charges will be used. |
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To be frank, I would like to insert a comment to be explicit about how this behavior differs from SMIRNOFF (and the toolkit)
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I think it could be helpful to add the note, better to be explicit about this behavior, I guess. On that note, do we want to support overriding this default behavior and forcing the toolkit to generate them if the user specifies it? (For future changes/PRs).
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I'm seeing this error: Which I've seen many times before but keep forgetting the source of |
ijpulidos
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Nov 29, 2023
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This looks great, thanks!
| If they do _not_ contain partial charges, the `openff-toolkit` charging method [`Molecule.compute_partial_charges_am1bcc`](https://open-forcefield-toolkit.readthedocs.io/en/latest/api/generated/openff.toolkit.topology.Molecule.html#openff.toolkit.topology.Molecule.compute_partial_charges_am1bcc) is used to assign partial charges. | ||
| The [canonical AM1-BCC charging method](https://docs.eyesopen.com/toolkits/cookbook/python/modeling/am1-bcc.html) is used to assign ELF10 charges if the OpenEye Toolkit is available. | ||
| If not, [Antechamber](http://ambermd.org/antechamber/) from the [AmberTools](http://ambermd.org/AmberTools.php) distribution (which uses the `sqm` semiempirical quantum chemical package) is used to assign AM1-BCC charges (`antechamber -c bcc`). | ||
| If the provided molecule(s) contain nonzero (user-specified) partial charges (stored in the `Molecule.partial_charges` attribute), those partial charges will be used. |
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I think it could be helpful to add the note, better to be explicit about this behavior, I guess. On that note, do we want to support overriding this default behavior and forcing the toolkit to generate them if the user specifies it? (For future changes/PRs).
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This materializes my understanding of the internals into the README