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API and guide docs for new forcefield classes#139

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scal444 merged 3 commits intoNVIDIA-Digital-Bio:mainfrom
scal444:docs-forcefield
Apr 27, 2026
Merged

API and guide docs for new forcefield classes#139
scal444 merged 3 commits intoNVIDIA-Digital-Bio:mainfrom
scal444:docs-forcefield

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@scal444 scal444 commented Apr 24, 2026

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scal444 added 3 commits April 24, 2026 15:35
Introduce a new docs/forcefield.rst guide covering the batched MMFF/UFF
APIs, and link it into the Guides toctree. Add the batchedForcefield
classes to the API reference alongside the optimize-confs entry points.
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scal444 commented Apr 24, 2026

docs.zip
@evasnow1992 rendered is probably easier to review, attached the html tree

@scal444 scal444 requested a review from evasnow1992 April 24, 2026 19:46
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greptile-apps Bot commented Apr 24, 2026

Greptile Summary

This PR adds API documentation entries for the new MMFFBatchedForcefield, UFFBatchedForcefield, MMFFBatchElement, and UFFBatchElement classes, and a new forcefield.rst user guide covering GPU-accelerated force field optimization. The guide is well-written with accurate cross-references and useful code examples.

  • P1 – shared template change: Adding :inherited-members: to class_template.rst affects all classes documented with that template (MorganFingerprintGenerator, SubstructSearchConfig, AsyncGpuResult, etc.), not just the new forcefield classes. If any of those classes inherit non-trivial public methods, those will now appear in existing API pages unexpectedly. A dedicated template or per-block option is the safer approach.

Confidence Score: 3/5

Safe to merge after verifying the intended scope of the :inherited-members: change in the shared class template.

One P1 finding: :inherited-members: added to the shared class_template.rst unintentionally changes API doc rendering for all existing classes, not just the new forcefield ones. The impact depends on the inheritance hierarchy of existing classes and should be confirmed before merging.

docs/_templates/class_template.rst — the :inherited-members: addition has broader scope than the PR title implies.

Important Files Changed

Filename Overview
docs/_templates/class_template.rst Adds :inherited-members: globally to the shared class autodoc template, which will affect all existing classes documented with it, not only the new forcefield classes.
docs/api/nvmolkit.rst Adds autosummary entries for MMFFBatchedForcefield, MMFFBatchElement, UFFBatchedForcefield, and UFFBatchElement under the correct MMFF/UFF Optimization sections using class_template.rst.
docs/forcefield.rst New guide covering GPU-accelerated MMFF/UFF force fields; code examples are clear and :ref: targets are valid, but several code blocks depend on mols defined in an earlier block without explicit note.
docs/index.rst Adds forcefield to the Guides toctree — straightforward and correct.

Reviews (1): Last reviewed commit: "Allow inherited members in API docs" | Re-trigger Greptile

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Changes look good to me.

@scal444 scal444 merged commit 158aa69 into NVIDIA-Digital-Bio:main Apr 27, 2026
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