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Merged
evasnow1992 merged 1 commit into from
Apr 2, 2026
Merged

Add conformer RMSD docs and fix MMFF benchmark build after API change #126

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4 changes: 3 additions & 1 deletion benchmarks/mmff_multimol_bench.cpp
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Expand Up @@ -110,7 +110,9 @@ std::vector<std::vector<double>> runNvMolKit(std::vector<RDKit::ROMol*>& molsPtr
", batch_size=" + std::to_string(batchSize) +
", num_concurrent_batches=" + std::to_string(batchesPerGpu) + ", backend=" + backendStr;
ankerl::nanobench::Bench().epochIterations(1).epochs(1).run(benchName, [&]() {
energies = nvMolKit::MMFF::MMFFOptimizeMoleculesConfsBfgs(molsPtrs, maxIters, 100.0, perfOptions, backend);
nvMolKit::MMFFProperties properties;
properties.nonBondedThreshold = 100.0;
energies = nvMolKit::MMFF::MMFFOptimizeMoleculesConfsBfgs(molsPtrs, maxIters, properties, perfOptions, backend);
});
return energies;
}
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10 changes: 10 additions & 0 deletions docs/api/nvmolkit.rst
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Expand Up @@ -76,6 +76,16 @@ Substructure Search
substructure.SubstructSearchConfig
substructure.SubstructMatchResults

Conformer RMSD
--------------

.. autosummary::
:toctree: generated/
:template: function_template.rst

conformerRmsd.GetConformerRMSMatrix
conformerRmsd.GetConformerRMSMatrixBatch

Types
-----

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2 changes: 2 additions & 0 deletions docs/index.rst
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Expand Up @@ -123,6 +123,8 @@ nvMolKit currently supports the following features:
* Supports SMILES and recursive SMARTS-based query molecules via RDKit
* Does not yet support chirality-aware matching, enhanced stereochemistry, or other advanced RDKit ``SubstructMatchParameters`` options

* **Conformer RMSD**: GPU-accelerated pairwise RMSD matrix computation for conformer ensembles

.. _async-results:

Asynchronous GPU Results
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