| # processed_data |
| |
| The small tables the notebooks read, committed so the figures redraw from a fresh clone. |
| Every one is the output of a script in this repo run against inputs far too large to |
| commit — the deposited mmCIFs (~2 GB), the prediction store (tens of GB), a count-ECFP4 |
| fingerprint matrix over half a million PDB molecules. Committing the *results* is what |
| makes the notebook runnable without fetching any of that. |
| |
| `run_pipeline.sh` writes the curation half of this directory. The analysis half needs |
| inputs that are not obtainable by a script — see `docs/reproducing.md`. |
|
|
| ## What run_pipeline.sh writes, and what is here now |
| |
| | file | written by | grain | |
| |---|---|---| |
| | `peptide_manifest.json` | `characterize_peptides.py` | one record per peptide chain considered | |
| | `edge_cases.csv` | `characterize_peptides.py`, via `edge_cases.py` | one row per flagged case per chain | |
| | `cyclization_classes.csv` | `cyclization_classes.py` | one row per buildable chain: the collapsed class, and whether the entry list's annotation agrees | |
|
|
| The two checks' outputs are **not** here. They describe one config tree, so they live beside |
| it: `<CONFIG_DIR>/config_fidelity_<MODEL>.tsv`, `check_summary.csv` and `check_summary.md`, |
| together with the `edge_case_decisions.yaml` that produced them. A check result separated |
| from the configs it judged is not interpretable. |
|
|
|
|
| At the time of writing that is **291 buildable peptide chains** out of 945 peptide chain |
| records across 347 passing entries. It was 315 until 2026-09-14, when |
| `characterize_peptides.py` stopped inheriting an entry's `is_cyclic` flag onto every peptide |
| chain of that entry and started asking each chain whether any of its own bonds closes a |
| ring: 26 chains left and 2 joined. `n` is not a constant anywhere: it changes with the |
| entry list, the notebook prints it, and a change shows up in `edge_cases.csv`. |
|
|
| ## The analysis tables |
|
|
| All four are present and all were regenerated at **n = 291** on 2026-09-14. |
| `notebooks/pretzel_ground_truth.ipynb` runs end to end from this directory and writes ten |
| figures. |
|
|
| | directory | written by | regenerating it needs | how long | |
| |---|---|---|---| |
| | `novelty/` | `analysis/novelty/novelty_search.py` | the 477 MB fingerprint matrices, see `fingerprints/README.md` | ~10 s | |
| | `peptide_profile/` | `analysis/dataset_profile.py` | the manifest only | ~5 s | |
| | `pocket/` | `analysis/pockets/*` | the mmCIF mirror and a `foldseek` binary | ~15 min | |
| | `bond_geometry/<MODEL>/` | `analysis/bond_geometry.py` | the mmCIFs, the CCD, and that model's configs and predictions | ~20 s per model | |
|
|
| `pocket/` does **not** need `pxmeter` installed, whatever earlier drafts of this file and |
| `docs/reproducing.md` said. `analysis/pockets/pocketlib.py` transcribes PXMeter's pocket |
| definition — alpha carbons within 10 A, a fixed radius PXMeter does not make configurable — |
| and cites it in a comment. Nothing imports the package. The dependencies are gemmi, numpy, |
| rdkit and a `foldseek` binary on the path. |
|
|
| The 15 minutes for `pocket/` is almost all two steps: the all-against-all foldseek search in |
| `similarity.py` (~9 min, of which the SuCOS pass over 10,332 scoring pairs is most) and the |
| solvent-accessible-surface pass in `pocket_chemistry.py` (~5 min). |
|
|
| `bond_geometry/` holds **Protenix only**. It is the one model re-run against the audited |
| config set; AF3, Boltz2 and HighFold3 were last run on v8, whose inputs differ for 84 of the |
| chains they cover, and they are left out until they are re-run rather than put on the same |
| forest plot. AF2 is out of scope — 13 chains is too few to read as a distribution. The |
| notebook derives its model list from the directories here, so re-adding one is exactly |
| "drop its table in"; `bond_geometry/README.md` has the command and the provenance. |
|
|
| ## fingerprints/ |
|
|
| Ignored except for its README, because the RCSB-wide matrix is 477 MB and over GitHub's |
| 100 MB per-file limit. `novelty/` holds the *results* of the search those matrices feed, |
| which is what the notebook reads — so the figures redraw without them and only re-running |
| the search itself needs them. |
|
|
| ## Why outputs/ is not committed beside this |
|
|
| `outputs/ssot/` would hold the same numbers as this directory, regenerated from it in under |
| a minute. Two copies of one set of counts is two places able to disagree about n. This |
| directory is the committed input; `outputs/` is the product, and it is ignored. |
|
|
