3DCS evaluates a molecular representation along three axes. Each evaluator supports two metric versions:
--metric-version paper(default): the definitions used for the published tables, so that those tables can be regenerated.--metric-version v2: an alternative set of definitions (full-precision inputs, separate kernel bandwidths, neighbour and population choices), described metric by metric on each page.
| Axis | Dataset (EscheWang/3dcs config) |
Paper tables | Definitions |
|---|---|---|---|
| Geometry | rotation |
Table 1 | metrics/geometry.md |
| Chirality | chirality |
Tables 2, 4 | metrics/chirality.md |
| Energy | traj_energies (+ traj_frames for embedding generation) |
Tables 3, 6, 7 | metrics/energy.md |
Common conventions:
- Representation distances
Δare computed within one molecule (all conformers of a rotation molecule, all stereoisomer conformers of a chirality parent, or one trajectory window). RDKit bit vectors always use the Tanimoto distance. - The chirality evaluator uses the Euclidean distance by default (
--distance euclidean), which is what the published Table 2 used;--distance cosineis available. The geometry evaluator reports both cosine and Euclidean spaces (--metrics); Table 1 uses cosine. The energy evaluator uses the cosine distance. - Scores are averaged per molecule (or per trajectory window) and then over molecules; non-finite
per-molecule values are excluded from the mean.
summary.csvreports the number of finite values.
The reproduction scripts and the reference values for each table are in ../reproduce/.