# Stage 2 Format Compatibility Matrix

## Current parser

Stage 2 currently uses MDAnalysis for topology/trajectory parsing.

## Confirmed working

| Gate | Topology | Trajectory | Status |
|---|---|---|---|
| Public AdK single-job gate | PSF | DCD | PASS |
| Public AdK 5-job gate | PSF | DCD | PASS |
| Public AdK 10-job gate | PSF | DCD | PASS |
| Researcher-style browser upload gate | PSF | DCD | PASS |
| PDB + DCD format compatibility gate | PDB | DCD | PASS |
| GRO + XTC format compatibility gate | GRO | XTC | PASS |

## Confirmed public-alpha statement

Confirmed today:

- PSF + DCD path works on public AdK-derived examples.
- PDB + DCD path works on public AdK-derived example.
- GRO + XTC path works on public AdK-derived example.
- Browser upload path works.
- Worker download/hash path works.
- Descriptive RMSD/RMSF/Rg path works.

## Candidate formats requiring validation

These formats are candidates because they are commonly supported by MDAnalysis, but they must be validated before being presented as confirmed production support.

| Role | Candidate formats |
|---|---|
| Topology | PRMTOP, TPR |
| Trajectory | TRR, NetCDF, PDB trajectory |
| Metadata | JSON, CSV |

## Not yet confirmed

- arbitrary GRO + XTC outside the public AdK-derived gate
- arbitrary PDB + XTC
- arbitrary PRMTOP + NetCDF
- arbitrary TPR + XTC/TRR
- ligand systems
- membrane systems
- water/solvent-heavy systems
- very large trajectories
- multipart upload above single-upload limit
- concurrent user uploads

## Claim boundary

Format compatibility validates parsing and descriptive metrics only.

A parsed trajectory does not imply:

- stability prediction
- mechanism proof
- binding prediction
- biological truth
- clinical or pharma-grade decision support