Add conformer RMSD alignment modes

[scal444]

Distinguishes between two different common RDKit RMSD paths - the conformer RMSD matrix we were allegedly replacing in the first place aligns on a single conformer, whereas a true pairwise RMSD aligns individually.

Since the previous RMSD implementation worked by computing RMSD without actually aligning mols, we needed significant code to match. We could have done this via the original kabsch mechanism, but would give up an O(n) for O(n^2) path for the align on 0 mechanism.

[greptile-apps]

Greptile Summary

Adds pairwise and first-conformer RMSD alignment modes while preserving pairwise alignment as the public default.

• Extends the Python and Boost.Python APIs with alignment-mode selection.
• Adds CUDA kernels that align each conformer to conformer zero before calculating RMSDs.
• Supports single-molecule and batched execution, including explicit CUDA streams and square output.
• Adds tests covering RDKit agreement, input immutability, mixed conformer counts, validation, and stream behavior.

Confidence Score: 5/5

The PR appears safe to merge, with no concrete blocking or independently actionable non-blocking issues identified.

The public wrappers consistently route the new mode, the CUDA buffers remain valid through stream-ordered work, and the added tests cover the principal single, batch, and explicit-stream paths.

Important Files Changed

Filename	Overview
nvmolkit/conformerRmsd.py	Adds validated alignment-mode selection and forwards it consistently through single and batch public APIs.
nvmolkit/conformerRmsd.cpp	Extends both native bindings with the first-conformer alignment flag and forwards argument order consistently from the public wrapper.
src/conformer_rmsd.cu	Implements shared rigid-alignment moments, quaternion rotation, and single/batch first-conformer alignment kernels without an established correctness defect.
src/conformer_rmsd_mol.cpp	Allocates temporary aligned-coordinate buffers and safely orders alignment, RMSD calculation, and asynchronous deallocation on the supplied stream.
nvmolkit/tests/test_conformer_rmsd.py	Adds broad regression coverage for alignment semantics, batching, validation, immutability, and explicit streams.

_{Reviews (1): Last reviewed commit: "Add conformer RMSD alignment modes" | Re-trigger Greptile}

[scal444]

Fixes #277

@evasnow1992 I think starting at the python layer for review makes the most sense, our docstrings now spell out the modes explicitly and what they do.

[evasnow1992]

Changes look good for me. Thank you for clearly distinguish the two modes.