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Add a persistent GPU SubstructLibrary - #357
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One comment, not a blocker but may be beneficial to address. Other changes look good to me.
SubstructLibrary is the GPU counterpart of RDKit's SubstructLibrary: molecules are copied in once and packed and uploaded at finalize(), then any number of queries run against them. Molecules get IDs in the order they are added and become searchable at the next finalize(); queries keep searching the previously finalized molecules until then. Each GPU holds its molecules as one packed batch, new molecules go to the GPU with the fewest, and results are merged in ID order. Molecules the packed format cannot represent are matched with RDKit on the CPU. Each GPU keeps one search workspace, and calls are serialized by the library lock. Also rename the resident-search API from NVIDIA-BioNeMo#351 to the codebase's host and device vocabulary: ResidentTargetBatch / makeResidentTargetBatch become PersistentDeviceTargets / makePersistentDeviceTargets, hasSubstructMatchResident becomes a hasSubstructMatch overload, and ResidentSubstructSearchWorkspace becomes SubstructSearchWorkspace. Declare mergeBatch() in molecules.h so the library can append packed batches.
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SubstructLibrary is the GPU counterpart of RDKit's SubstructLibrary: molecules are copied in once and packed and uploaded at finalize(), then any number of queries run against them. Molecules get IDs in the order they are added and become searchable at the next finalize(); queries keep searching the previously finalized molecules until then. Each GPU holds its molecules as one packed batch, new molecules go to the GPU with the fewest, and results are merged in ID order. Molecules the packed format cannot represent are matched with RDKit on the CPU.
Also changed up naming schemes from the previous PR to be a bit clearer.
PR 3 for #350