Merge pull request #92 from MDverse/feat/add-sequence-for-atlas

Feat/add sequence for atlas

Author: pierrepo

docs/atlas.md

@@ -1,6 +1,8 @@
 # ATLAS
 
-ATLAS (Atlas of proTein moLecular dynAmicS) is an open-access data repository that gathers standardized molecular dynamics simulations of protein structures, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. All raw trajectories as well as the results of analysis are available for download.
+ATLAS (Atlas of proTein moLecular dynAmicS) is an open-access data repository that gathers standardized molecular dynamics simulations of protein structures,
+accompanied by their analysis in the form of interactive diagrams and trajectory visualisation.
+All raw trajectories as well as the results of analysis are available for download.
 
 - web site: <https://www.dsimb.inserm.fr/ATLAS/>
 - publication: [ATLAS: protein flexibility description from atomistic molecular dynamics simulations](https://academic.oup.com/nar/article/52/D1/D384/7438909), Nucleic Acids Research, 2024.
@@ -38,7 +40,8 @@ Example with dataset id `1k5n_A`:
 Remarks:
 
 - The title of the dataset is the protein name.
-- No comment or description is provided. We used the organism as description.
+- No comment or description is provided. We used the organism name as description.
+- Parameters of molecular dynamics simulations are provided through the API endpoint <https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters>.
 
 ### Metadata for files
 

src/mdverse_scrapers/scrapers/atlas.py

@@ -19,8 +19,9 @@
 )
 from ..core.toolbox import print_statistics
 from ..models.dataset import DatasetMetadata
-from ..models.enums import DatasetSourceName
+from ..models.enums import DatasetSourceName, ExternalDatabaseName, MoleculeType
 from ..models.scraper import ScraperContext
+from ..models.simulation import ExternalIdentifier, ForceFieldModel, Molecule, Software
 from ..models.utils import (
     export_list_of_models_to_parquet,
     normalize_datasets_metadata,
@@ -40,6 +41,14 @@
     ],
     "doi": "10.1093/nar/gkad1084",  # https://academic.oup.com/nar/article/52/D1/D384/7438909
     "external_link": ["https://www.dsimb.inserm.fr/ATLAS/"],
+    "software_name": "GROMACS",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "software_version": "v2019.6",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "forcefield_name": "CHARMM36m",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "forcefield_version": "July 2020",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "water_model": "TIP3P",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "simulation_temperature": 300,  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "simulation_time": "100 ns",  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
+    "simulation_timestep": 2,  # https://www.dsimb.inserm.fr/ATLAS/api/MD_parameters
 }
 
 
@@ -115,7 +124,7 @@ def extract_file_sizes_from_html(
     return files_metadata
 
 
-def scrape_metadata_for_a_dataset(
+def scrape_metadata_for_one_dataset(
     client: httpx.Client,
     chain_id: str,
     logger: "loguru.Logger" = loguru.logger,
@@ -165,6 +174,53 @@ def scrape_metadata_for_a_dataset(
         "doi": ATLAS_METADATA["doi"],
         "external_links": ATLAS_METADATA["external_link"],
     }
+    # Add molecules.
+    external_identifiers = []
+    if meta_json.get("PDB"):
+        external_identifiers.append(
+            ExternalIdentifier(
+                database_name=ExternalDatabaseName.PDB,
+                identifier=meta_json["PDB"].split("_", maxsplit=1)[0],
+            )
+        )
+    if meta_json.get("UniProt"):
+        external_identifiers.append(
+            ExternalIdentifier(
+                database_name=ExternalDatabaseName.UNIPROT,
+                identifier=meta_json["UniProt"],
+            )
+        )
+    metadata["molecules"] = [
+        Molecule(
+            name=meta_json.get("protein_name"),
+            sequence=meta_json.get("sequence"),
+            external_identifiers=external_identifiers,
+            type=MoleculeType.PROTEIN,
+        )
+    ]
+    # Add software.
+    metadata["software"] = [
+        Software(
+            name=ATLAS_METADATA["software_name"],
+            version=ATLAS_METADATA["software_version"],
+        )
+    ]
+    # Add forcefields and models.
+    metadata["forcefields_models"] = [
+        ForceFieldModel(
+            name=ATLAS_METADATA["forcefield_name"],
+            version=ATLAS_METADATA["forcefield_version"],
+        ),
+        ForceFieldModel(name=ATLAS_METADATA["water_model"]),
+    ]
+    # Add simulation temperature.
+    metadata["simulation_temperatures_in_kelvin"] = [
+        ATLAS_METADATA["simulation_temperature"]
+    ]
+    # Add simulation time.
+    metadata["simulation_times"] = [ATLAS_METADATA["simulation_time"]]
+    # Add simulation time step.
+    metadata["simulation_timesteps_in_fs"] = [ATLAS_METADATA["simulation_timestep"]]
     logger.info("Done.")
     return metadata
 
@@ -223,7 +279,7 @@ def scrape_all_datasets(
     datasets_meta = []
     logger.info("Starting scraping of all datasets...")
     for pdb_counter, pdb_chain in enumerate(pdb_chains, start=1):
-        metadata = scrape_metadata_for_a_dataset(client, pdb_chain, logger=logger)
+        metadata = scrape_metadata_for_one_dataset(client, pdb_chain, logger=logger)
         if metadata:
             datasets_meta.append(metadata)
         logger.info(