README.md

# OMol-Descriptors-4M

Post-DFT interpretive descriptors (partial charges, bond orders, QTAIM topology,
fuzzy and surface integrations, ORCA globals) for the 4M-structure wavefunction
subset of OMol25. Built with the open `generator` pipeline by wrapping Multiwfn
and ORCA post-analysis on geometries and wavefunctions inherited from the
OMol25 release (wB97M-V / def2-TZVPD).

- Corpus size: 3,986,738 structures across 80+ elements and 34 verticals.
- License: CC-BY-4.0, inheriting OMol25 terms.
- Pipeline: https://github.com/santi921/qtaim_generator

## Repository Layout

```
OMol-Descriptors-4M/
  train/        # 3,189,390 structures
  val/          #   399,690 structures
  test/         #   415,913 structures
  holdouts/
    h1_metal_ligand/      # 15,030 structures
    h3_reactivity/        # 12,507 structures
    h6_lanthanide_ligand/ #  2,589 structures
    h7_large_systems/     # 18,200 structures
    h8_large_net_charge/  # 12,393 structures
```

Each split folder (and each holdout folder) contains the same eight LMDB files
described below. Held-out structures are removed from `train/val/test` so the
same structure is never both in-distribution and stress-test. Overlaps between
held-out sets are allowed.

## LMDB Files

Every LMDB inside a split is keyed on the same string identifier

```
k = relpath(job_folder, root).replace("/", "__")
```

so any combination of descriptors joins by key on the full corpus. Cross-LMDB
key alignment holds to within 4 records on the 4M-key index.

| File | What it stores | What you get from it |
|------|----------------|----------------------|
| `structure.lmdb` | pymatgen `Molecule` (positions, elements), total spin and charge, RDKit-derived bond list, external identifiers | Geometry, connectivity, spin/charge state, source IDs |
| `charge.lmdb` | per-atom charges nested by scheme | Hirshfeld, CM5, ADCH, Becke, Mulliken (ORCA), Loewdin (ORCA); plus total dipole on Hirshfeld/CM5 and total + per-atom dipoles on ADCH/Becke |
| `qtaim.lmdb` | per-structure dict of critical points keyed by atom ID (nuclear CP) or atom-pair (bond CP) | 26 scalar fields per CP including rho, laplacian, ellipticity, kinetic and potential energy densities; ring/cage CPs and non-nuclear attractors where present; QTAIM bond presence is recoverable from BCP keys |
| `bond.lmdb` | bond-order schemes keyed by directed atom-pair string `"{i}_{El_i}_to_{j}_{El_j}"` | `fuzzy_bond`, `mayer_orca`, `loewdin_orca` |
| `fuzzy.lmdb` | per-atom Multiwfn fuzzy integrations | `becke_fuzzy_density`, `hirsh_fuzzy_density`; spin counterparts on open-shell records |
| `other.lmdb` | molecular descriptors from ESP and ALIE surface analysis | surface volume and area, signed mean and variance, polarity index, internal charge separation; plus `mpp_full`, `sdp_full`, `mpp_heavy`, `sdp_heavy` |
| `orca.lmdb` | ORCA-derived globals | total SCF energy, HOMO/LUMO orbital energies, dipole vector and magnitude, gradient RMS, energy components, rotational constants, quadrupole, S^2; filtered via `DEFAULT_ORCA_FILTER` when consumed by the converter |
| `timings.lmdb` | per-job step durations | Provenance only, not used by the converter |

### Coverage

Five of the seven analytic LMDBs show no corrupt or incomplete records. The
two with failures are `qtaim` (25 missing, 0.0006%) and `orca` (1,607 missing,
0.0403%). ORCA failures concentrate on physically hard cases (solvated
biomolecules, scaled-separation electrolytes, open-shell TM redox); geometry
and Multiwfn-side descriptors stay valid on those records. Every charge scheme,
bond-order scheme, full QTAIM topology, and ORCA globals reaches >= 99% on each
of the 34 verticals.

## Held-Out Evaluation Sets

Each holdout folder is a standalone copy of the eight LMDBs above, restricted
to the structures selected for that stress test. Headline metric per set is
`Delta = metric_holdout - metric_main_test`.

- **H1 - Metal-ligand pairs (15,030):** eleven (TM, partner) bond pairs sampled
  stratified across log-spaced frequency bands. Selection uses true bonds
  (Mayer or fuzzy bond order >= 0.3) from `bond.lmdb`, not element
  co-occurrence. Probes rare metal-ligand chemistry transfer while keeping
  every element represented in training.

- **H3 - Reactivity (12,507):** composition-stratified subsample of `tm_react`
  (5k), `electrolytes_reactivity` (5k), and `pmechdb` (2.5k). Tests
  non-equilibrium and transition-state-adjacent geometries.

- **H6 - Lanthanide-ligand pairs (2,589):** same construction as H1 applied
  to (Ln, partner) bonds across five Ln-bearing verticals. Probes rare f-block
  bonding while keeping every lanthanide represented in training.

- **H7 - Large systems (18,200):** structures with more than 250 atoms. Size
  extrapolation regime where fuzzy integration and grid-based QTAIM are most
  expensive and per-atom DFT signal-to-noise is hardest to maintain.

- **H8 - Large net charges (12,393):** structures with `|net_charge| > 4`.
  The high-charge tail where partial-charge schemes disagree most and SCF is
  most sensitive to functional and basis.




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license: cc-by-4.0
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