Datasets:
File size: 11,705 Bytes
9619619 834a6f2 9619619 469c490 9619619 469c490 9619619 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 |
---
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<n<100K
---
# DynaRepo MDPosit
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) |