--- 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 task_categories: - token-classification tags: - chemistry - biology - medical - synthetic size_categories: - 10K\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\` (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\\` in this repository; corresponds to Dynarepo’s remote path `/projects//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\\` is enumerated in that accession’s `records.jsonl` `files[]` entries with `name`, `downloadUrl` (relative to `/projects//files/`), `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\` 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\`) - **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\\`. 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//files/`), `length` (bytes), `contentType`, and a small `metadata` dict (e.g., `{project: , md: }` 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)