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Add DCLV 3D descriptors - #373
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scal444 merged 6 commits intoOct 23, 2026
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Port RDKit's DoubleCubicLatticeVolume (Double Cubic Lattice Method surface area and volume) as seven scalar properties in a new Dclv family, one per getter: DCLVSurfaceArea, DCLVPolarSurfaceArea, DCLVVolume, DCLVVDWVolume, DCLVPolarVolume, DCLVCompactness and DCLVPackingDensity. Any selection shares one kernel launch. One warp per conformer centers the coordinates on RDKit's centre of gravity in float64, then per atom gathers neighbors in shared memory (falling back to a full scan past 128) and tests RDKit's 320 dots. The probe-expanded dots serve every property but DCLVVDWVolume and the bare van der Waals dots serve DCLVVDWVolume and DCLVPackingDensity; each set is tested only when a requested property needs it. DclvOptions exposes probeRadius, includeSandP and includeHs. Custom radii, isProtein and includeLigand are not supported. Conformers with a dummy atom (radius 0), on which RDKit crashes, and rows with non-finite coordinates produce NaN. On 484 ChEMBL conformers FULL matches RDKit to 3e-15 relative and SINGLE to 1.2e-6 relative with no surface-dot flips, so the kernel computes in the requested precision apart from the existing float64 centering.
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 [Medium impact] The reviewed changes appear safe to merge; no actionable issues remain.
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evasnow1992
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Oct 22, 2026
| rows = [] | ||
| for mol in mols: | ||
| for conf in mol.GetConformers(): | ||
| dclv = rdMolDescriptors.DoubleCubicLatticeVolume(mol, probeRadius=options.probeRadius, confId=conf.GetId()) |
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The reference here uses the default-radii constructor, which RDKit 2025.09.1 doesn't have. Since 2025.09.1 is the documented minimum, may consider passing the radii explicitly. Same at descriptors3d_bench.py:146 and test_descriptors3d_dclv_bench.py
evasnow1992
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Oct 22, 2026
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One rdkit version specific issue on the test and benchmark files. Other changes look good to me.
RDKit 2025.09.1's Python DoubleCubicLatticeVolume has no default-radii constructor. The Python test reference, descriptors3d_bench.py and its tests now pass per-atom van der Waals radii from the periodic table, which match the defaults of later RDKit releases exactly. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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