Add device-side ETKDG conformer pruning

[Matthew-Neba]

Summary

• Adds conformer pruning for ETKDG device output. Fixes Device output Pruning for ETKDG #160.
• Keeps conformer coordinates on the target GPU instead of copying them to the CPU for pruning.
• Matches RDKit's ordered greedy pruning behavior, including heavy-atom and symmetry-aware RMSD comparisons.

[greptile-apps]

Greptile Summary

Adds GPU-resident, RDKit-compatible ordered conformer pruning to ETKDG device output.

• Builds heavy-atom and symmetry mappings through RDKit.
• Performs greedy RMSD selection and coordinate compaction on the target GPU.
• Preserves molecule ownership and renumbers retained conformers within each molecule.
• Adds coverage for device pruning, symmetry, heavy-atom comparisons, interleaved results, and metadata.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains.

Important Files Changed

Filename	Overview
src/conformer/device_conformer_pruning.cpp	Prepares RDKit atom mappings, launches pruning, and compacts retained coordinates while preserving device-result metadata; no follow-up-eligible issue was identified.
src/conformer_rmsd.cu	Adds symmetry-aware aligned RMSD and ordered greedy pruning kernels; no follow-up-eligible issue was identified.
src/etkdg.cpp	Enables pruning after device-output collection while leaving the host conformer path unchanged.
tests/test_etkdg_device_output.cu	Expands coverage for device pruning behavior, ordering, symmetry, heavy atoms, compaction, and conformer-index renumbering.

_{Reviews (3): Last reviewed commit: "Merge official/main into pr-265" | Re-trigger Greptile}

[scal444]

Thanks for closing another feature gap! I'll be able to review this later today or tomorrow. Don't worry about the python build failures, I need to fix our CI from our v0.6 version bump. C++ build is the important one to look at.

[scal444]

Looks great! A few small things, and one performance suggestion that can definitely be left to a followup, or handled here.

[Matthew-Neba]

Awesome! Thanks for taking a look, will fix those issues and take another deep look before the weekend

[scal444]

Also our CI should be fixed now so if you rebase onto or merge in main, those unrelated failures should go away

[Matthew-Neba]

Applied the fixes. Also applied your suggestion to use a list of the retained conformers so that we don't waste time on those no ops; although it was done in place with the list containing conformers ( groupedConfIds) + a pointer (retainedCount) instead of allocating another buffer for the list.

[scal444]

Approved pending CI, thanks!

[Matthew-Neba]

I am faling during the build phase of the CI/CD pipeline, but it seems it is due to a Github issue, A Github action is timing out. Can you please trigger a rerun?