Update README.md

README.md

@@ -1,5 +1,171 @@
-# INRIA Dynarepo Flattened Dataset
+---
+configs:
+- config_name: default
+  data_files:
+  - split: train
+    path:
+    - data/files/*/*screenshot*.jpg
+    - data/files/*/screenshot.jpg
+    - data/files/*/clusters_*_screenshot_*.jpg
+    - data/files/*/*.jpg
+    - data/files/*/*.jpeg
+    - data/files/*/*.png
+- config_name: manifests
+  data_files:
+  - split: train
+    path:
+    - data/files/*/records.jsonl
+    - data/files/*/project.json
+    - data/files/all_records.jsonl
+- config_name: structures
+  data_files:
+  - split: train
+    path:
+    - data/files/*/*.pdb
+    - data/files/*/*.tpr
+- config_name: trajectories
+  data_files:
+  - split: train
+    path:
+    - data/files/*/*.xtc
+    - data/files/*/*.trr
+    - data/files/*/*.dcd
+    - data/files/*/*.bin
+    - data/files/*/pca_trajectory_*.bin
+license: gpl
+---
 
-This repository contains flattened per-MD records exported from the INRIA Dynarepo.
+# DynaRepo MDPosit
 
-Data is located under `data/records.jsonl`.
+This repository mirrors Molecular Dynamics (MD) project metadata and files laid out per accession as exposed by Dynarepo. It includes global and per-accession manifests, project-level JSON, and the actual files (structures, trajectories, derived PCA binaries, and analysis screenshots). Field names and shapes follow Dynarepo’s documented model.
+
+
+## Overview
+
+### How to consume
+
+- **Stream-parse**: Read the file line-by-line and `json.loads` each object to enumerate replicas and their artifacts.
+- **Relate to `project_example.json`**: Each line mirrors an item in `flattened_md_records` and can be joined back to project-level fields if needed.
+- **Concatenate across accessions**: You can build a global manifest by concatenating multiple `data\files\<ACCESSION>\records.jsonl` files.
+- **Field semantics**: Follow the Dynarepo docs: [Meta](https://dynarepo.inria.fr/#/meta), [Statistics](https://dynarepo.inria.fr/#/statistics), [Help](https://dynarepo.inria.fr/#/help).
+
+
+## Understanding `all_records.jsonl` (global flattened per-accession manifest)
+
+- **Source**: Global, line-delimited aggregation of per-replica records across all accessions. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help).
+- **Where it lives**: `data\files\all_records.jsonl`.
+- **What it is**: A JSON Lines file where each line mirrors a single replica entry from per-accession `records.jsonl` (fields include `project_identifier`, `accession`, `md_index`, `md_name`, `analyses`, `metadata`, and `files`).
+- **How to use**: Stream-parse line by line, filter by `accession` or `analyses`, and group by `accession`/`md_index` to enumerate all replicas and their artifacts across the dataset. Field semantics are identical to per-accession records and follow Dynarepo docs.
+
+## Remote folder contents in `data\files\<ACCESSION>` (A0098 example)
+
+- **Source**: Mirrors the per-accession file repository exposed by Dynarepo. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help).
+- **Where it appears**: Under `data\files\<ACCESSION>\` in this repository; corresponds to Dynarepo’s remote path `/projects/<ACCESSION>/files`.
+- **What you will typically find** (A0098 shown):
+  - Core descriptors: `project.json` (~5.18 kB), `records.jsonl` (~43.3 kB)
+  - Core MD simulation assets: `topology.tpr` (~1.71 MB), `structure.pdb` (~397 kB), `trajectory.xtc` (~93.5 MB), `trajectory.bin` (~294 MB)
+  - PCA-derived binaries: `pca_trajectory_01.bin` … `pca_trajectory_05.bin` (5 files, ~237 kB each)
+  - Cluster analysis screenshots:
+    - `clusters_00_screenshot_00.jpg` … `clusters_00_screenshot_20.jpg` (21 images, ~16–21 kB each)
+    - `clusters_01_screenshot_00.jpg` … `clusters_01_screenshot_19.jpg` (20 images, ~16–21 kB each)
+  - Cover/preview: `screenshot.jpg` (~20.7 kB)
+- **Relationship to manifests**:
+  - Every file present under `data\files\<ACCESSION>\` is enumerated in that accession’s `records.jsonl` `files[]` entries with `name`, `downloadUrl` (relative to `/projects/<ACCESSION>/files/<name>`), `length` (bytes), and `contentType`.
+  - The same inventory is summarized in `project.json` under its `files` section (e.g., `list`, `filenotes`, `merged`) and joined into `flattened_md_records` for per-replica views.
+- **Notes**: Exact counts and sizes vary by accession and by which analyses were run; additional analysis types will add further artifacts alongside those listed above.
+
+## Understanding `project.json` (Dynarepo dataset A0098)
+
+- **Source**: Dataset metadata follows the Dynarepo model. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help).
+- **Where it appears**: Each dataset under `data\files\<ACCESSION>` includes a project-level JSON with this schema. This repository provides a canonical example in `project_example.json`.
+- **What it is**: A single, self-contained description of an MD project combining high-level project metadata, per-replica MD records, file inventory, topology, references, analysis results, and summaries. It is designed to be directly consumable by Dynarepo services and UIs.
+
+### High-level structure
+
+- **`project`**: Core project info and global metadata
+  - Keys: `accession`, `published`, `metadata` (e.g., `NAME`, `DESCRIPTION`, `AUTHORS`, `PROGRAM`, `VERSION`, `TYPE`, `METHOD`, `LICENSE`, `PDBIDS`, `REFERENCES`, simulation params like `FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, box sizes, system counts), `mds` (replica names), `analyses` (available analysis types), `files` (canonical file names), `mdIndex`/`mdNumber`/`refframe`.
+- **`flattened_md_records`**: One entry per MD replica with the replica’s `metadata` and a resolved `files` list including `downloadUrl`, `length`, and `contentType`.
+- **`files`**:
+  - `list`: canonical file names present in the project
+  - `filenotes`: storage-level details (size, content type, upload date)
+  - `merged`: convenient join of name, URL, size, and metadata
+- **`topology`**: Atoms, residues, chains, bonding, and external references used to build the system.
+- **`references`**: Protein and PDB references (e.g., UniProt IDs, sequences, domains) and cross-links to PDB entries.
+- **`analyses`**: Machine-readable outputs per analysis (e.g., `clusters`, `dist-perres`, `energies`, `fluctuation`, `hbonds`, `interactions`, `pca`, `pockets`, `rgyr`, `rmsd*`, `sasa`, `tmscores`).
+- **`summaries`**: Compact keys/metrics for quick inspection and validation.
+
+### How this maps to datapoint A0098
+
+- **Accession**: `A0098` (see `data\files\A0098\records.jsonl` for the per-replica lines used to populate `flattened_md_records`).
+- **Project metadata examples** (from A0098):
+  - `metadata.NAME`: "Dynarepo 5FZT"
+  - `metadata.PDBIDS`: `["5FZT"]`
+  - `metadata.REFERENCES`: `["P26039", "Q96QB1"]`
+  - Simulation constants: `FRAMESTEP: 0.1`, `TIMESTEP: 2`, `TEMP: 310`, `ENSEMBLE: "NPT"`, `FF: ["CHARMM36m"]`, `WAT: "TIP3P"`, `BOXTYPE: "Dodecahedron"`
+  - System scale: `mdFrames: 5001`, `mdAtoms: 4900`, `PROTRES: 329`, `SYSTATS: 4900`
+- **Files commonly present**: `topology.tpr`, `structure.pdb`, `trajectory.xtc`, `trajectory.bin`, `pca_trajectory_*.bin`, and analysis screenshots (e.g., `clusters_*_screenshot_*.jpg`).
+- **Analyses present**: `clusters`, `clusters-00`, `clusters-01`, `dist-perres`, `energies`, `fluctuation`, `hbonds`, `interactions`, `pca`, `rgyr`, `rmsd-pairwise`, `rmsd-perres`, `rmsds`, `sasa`, `tmscores`.
+
+## Understanding `records.jsonl` (per-replica manifest in `data\files\<ACCESSION>`)
+
+- **Source**: Per-MD replica records consistent with Dynarepo’s flattened MD model. See: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), and [Dynarepo Help](https://dynarepo.inria.fr/#/help).
+- **Where it appears**: For each accession, a `records.jsonl` lives under `data\files\<ACCESSION>\`. This repository includes `data\files\A0098\records.jsonl`. A compact illustration is also provided at the repository root as `records._examplejsonl`.
+- **What it is**: A JSON Lines file; each line describes one MD replica and its files.
+
+### Record shape (keys you will see per line)
+
+- **Top-level identifiers**: `project_identifier`, `accession`, `published`
+- **Replica info**: `md_index` (0-based), `md_name` (e.g., "replica 1"), `chains` (if applicable)
+- **Analyses available**: `analyses` (e.g., `clusters`, `rmsds`, `pca`, `sasa`, ...)
+- **`metadata` object**: Biology and simulation parameters used by Dynarepo UIs and services. Common fields include `NAME`, `DESCRIPTION`, `AUTHORS`, `GROUPS`, `CONTACT`, `PROGRAM`, `VERSION`, `TYPE`, `METHOD`, `LICENSE` (and `LINKCENSE`), `PDBIDS`, `REFERENCES`, sequences/domains (`PROTSEQ`, `NUCLSEQ`, `DOMAINS`), simulation setup (`FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, `BOXTYPE`), system sizes (`SYSTATS`, `SYSTRES`, `PROTATS`, `PROTRES`, ...), optional `INTERACTIONS`, box sizes (`BOXSIZEX/Y/Z`), and per-replica summaries like `mdAtoms` and `mdFrames`.
+- **`files` array**: One entry per stored artifact with `name`, `downloadUrl` (relative to `/projects/<ACCESSION>/files/<name>`), `length` (bytes), `contentType`, and a small `metadata` dict (e.g., `{project: <id>, md: <index>}` or per-file stats for derived binaries).
+
+Typical files for A0098 include `topology.tpr`, `structure.pdb`, `trajectory.xtc`, `trajectory.bin`, `pca_trajectory_*.bin`, and analysis screenshots like `clusters_*_screenshot_*.jpg`.
+
+### Example (A0098, truncated line 1)
+
+```json
+{
+  "project_identifier": "A0098",
+  "accession": "A0098",
+  "published": true,
+  "md_index": 0,
+  "md_name": "replica 1",
+  "analyses": ["clusters", "pca", "rmsds", "sasa", "..."],
+  "metadata": {
+    "NAME": "Dynarepo 5FZT",
+    "PDBIDS": ["5FZT"],
+    "FRAMESTEP": 0.1,
+    "TIMESTEP": 2,
+    "TEMP": 310,
+    "ENSEMBLE": "NPT",
+    "FF": ["CHARMM36m"],
+    "WAT": "TIP3P",
+    "mdAtoms": 4900,
+    "mdFrames": 5001
+  },
+  "files": [
+    {"name": "topology.tpr", "downloadUrl": "/projects/A0098/files/topology.tpr", "length": 1712912, "contentType": "application/octet-stream"},
+    {"name": "structure.pdb", "downloadUrl": "/projects/A0098/files/structure.pdb", "length": 396935, "contentType": "chemical/x-pdb"},
+    {"name": "trajectory.xtc", "downloadUrl": "/projects/A0098/files/trajectory.xtc", "length": 93513296, "contentType": "application/octet-stream"}
+    // ... more files omitted ...
+  ]
+}
+```
+
+
+### Contributing
+
+When creating a new project JSON for another accession, minimally review/update:
+
+- **Identifiers**: `project.accession`, `project.identifier`, and `metadata.NAME`
+- **Biology**: `metadata.PDBIDS`, `metadata.REFERENCES` (UniProt), sequences/domains in `references`
+- **Simulation**: `FRAMESTEP`, `TIMESTEP`, `TEMP`, `ENSEMBLE`, `FF`, `WAT`, box sizes, atom/residue counts
+- **Replicas**: `mds` list and `flattened_md_records[*].md_index/md_name`
+- **Files**: Ensure `files.list`, `files.merged`, and each replica’s `files[]` match your storage paths and sizes
+- **Analyses**: Keep only the analyses you actually produced and include their data payloads
+
+For reference on field meanings and expected shapes, consult the Dynarepo documentation: [Meta](https://dynarepo.inria.fr/#/meta), [Statistics](https://dynarepo.inria.fr/#/statistics), [Help](https://dynarepo.inria.fr/#/help).
+
+
+**References**: [Dynarepo Meta](https://dynarepo.inria.fr/#/meta), [Dynarepo Statistics](https://dynarepo.inria.fr/#/statistics), [Dynarepo Help](https://dynarepo.inria.fr/#/help)