Update GPCRmd scraper

README.md

@@ -132,7 +132,7 @@ The scraping takes about 2 h.
 Scrape GPCRmd to collect molecular dynamics (MD) datasets and files related to G-protein-coupled receptors (GPCRs), a major family of membrane proteins and common drug targets.
 
 ```bash
-uv run -m scripts.scrape_gpcrmd
+uv run scrape-gpcrmd --output-dir data
 ```
 
 This command will:

docs/gpcrmd.md

@@ -0,0 +1,113 @@
+# GPCRmd
+
+> GPCRmd is an online platform for visualizing, analyzing, and sharing molecular dynamics simulations of G-protein-coupled receptors (GPCRs), a key family of membrane proteins and common drug targets.
+
+- web site: https://www.gpcrmd.org/
+- documentation: https://gpcrmd-docs.readthedocs.io/en/latest/index.html
+- API: https://www.gpcrmd.org/api/
+  - `version v1.3`
+
+No account / token is needed to access GPCRmd API.
+
+
+## Finding molecular dynamics datasets and files
+
+Although GPCRmd provides a public API to discover molecular dynamics datasets, **some important metadata fields and all file-level information are not exposed via the API**. For this reason, web scraping of the dataset page is required to retrieve complete dataset descriptions and file metadata.
+
+### Datasets
+
+In GPCRmd, datasets (a simulation and its related files) are called "dynamic".
+
+API entrypoint to search for all datasets at once:
+
+- Path: /search_all/info/
+- [documentatation](https://gpcrmd-docs.readthedocs.io/en/latest/api.html#main-gpcrmd-api)
+
+
+#### Dataset metadata retrieved via API:
+
+| Field              | Description                         |
+| ------------------ | ----------------------------------- |
+| `dyn_id`           | *Unique dynamic (dataset) identifier* |
+| `modelname`        | *Name of the simulated model*         |
+| `timestep`         | *MD integration timestep*             |
+| `atom_num`         | *Number of atoms*                     |
+| `mysoftware`       | *MD engine used*                      |
+| `software_version` | *Version of the MD engine*            |
+| `forcefield`       | *Force field and model name*          |
+| `forcefield_version` | *Force field and model version*     |
+| `creation_timestamp` | *Dataset creation date*             |
+| `dataset_url`        | *URL of the dataset web page*       |
+
+#### Dataset metadata retrieved via web scraping (URL provided by the API):
+
+| Field                | Description                                |
+| -------------------- | ------------------------------------------ |
+| `description`        | *Full textual description of the simulation* |
+| `authors`            | *Dataset authors*                           |
+| `simulation_time`    | *Total simulation length*                   |
+
+
+### Files
+
+The GPCRmd API does not provide any endpoint to access file-level metadata. All file information must therefore be extracted from the dataset web page. Two file categories are available: **simulation output files** and **simulation protocol and starting files**.
+
+For example, the files corresponding to the dataset` 7` (https://www.gpcrmd.org/dynadb/dynamics/id/7/) include these files:
+- https://www.gpcrmd.org/dynadb/files/Dynamics/10166_trj_7.dcd
+- https://www.gpcrmd.org/dynadb/files/Dynamics/10167_dyn_7.psf
+- https://www.gpcrmd.org/dynadb/files/Dynamics/10168_dyn_7.pdb
+
+
+#### File metadata retrieved via web scraping (URL provided by the API):
+
+| Field      | Description            |
+| ---------- | ---------------------- |
+| `file_name`  | *Name of the file*     |
+| `file_type` | *File extension*      |
+| `file_path`| *Public download URL*    |
+| `file_size`| *File size in bytes*    |
+
+> 💡 File size is obtained using an HTTP `HEAD` request on the file path, **avoiding file download**.
+
+
+## Examples
+### Dataset ID 2316
+
+- [Dataset on GPCRmd GUI](https://www.gpcrmd.org/dynadb/dynamics/id/2316/)
+- [Dataset on GPCRmd API](https://www.gpcrmd.org/api/search_dyn/info/2316)
+
+
+#### Dataset metadata (API + scraping)
+
+| Field              | Description                         |
+| ------------------ | ----------------------------------- |
+| `dyn_id`           | *2316* |
+| `modelname`        | *FFA2_TUG1375_Gi1-TUG1375*        |
+| `timestep`         | *2*             |
+| `atom_num`         | *4829*                     |
+| `mysoftware`       | *AMBER PMEMD.CUDA*                     |
+| `software_version` | *2020*            |
+| `forcefield`       | *ff19SB/lipid21/GAFF2*         |
+| `forcefield_version` | *ff19SB/lipid21*     |
+| `creation_timestamp` | *2025-05-13*            |
+| `dataset_url`        | *https://www.gpcrmd.org/dynadb/dynamics/id/2316/*     |
+| `description`        | *Simulation aims to observe structural features of FFA2 without an orthosteric agonist and G-protein, which will be compared to docking-based simulations of allosteric activators...* |
+| `authors`            | *Abdul-Akim Guseinov, University of Glasgow*                           |
+| `simulation_time`    | *3.0 µs*                   |
+
+
+- [files on GPCRmd GUI](https://www.gpcrmd.org/api/search_dyn/info/2316) (accessible via the *Technical Information* section)
+
+#### Example file from the dataset
+
+| Field      | Description            |
+| ---------- | ---------------------- |
+| `file_name`  | *tmp_dyn_0_2667.pdb*    |
+| `file_type` | *pdb*     |
+| `file_path`| *https://www.gpcrmd.org/dynadb/files/Dynamics/dyn2667/tmp_dyn_0_2667.pdb* |
+| `file_size`| *1 024 bytes*    |
+
+
+## References 
+
+Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S. et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods. 2020;17(8):777-787. doi:[10.1038/s41592-020-0884-y](https://www.nature.com/articles/s41592-020-0884-y)

pyproject.toml

@@ -47,3 +47,4 @@ build-backend = "uv_build"
 scrape-zenodo = "mdverse_scrapers.scrapers.zenodo:main"
 scrape-figshare = "mdverse_scrapers.scrapers.figshare:main"
 scrape-nomad = "mdverse_scrapers.scrapers.nomad:main"
+scrape-gpcrmd = "mdverse_scrapers.scrapers.gpcrmd:main"