From 743319e57337fb86ea5bccf9b68455efef84a5e4 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 8 Nov 2023 16:18:48 +0100
Subject: [PATCH] Get reference databases from JSON
---
convert_to_modelcif.py | 48 ++++++++++++++++++++++++------------------
1 file changed, 28 insertions(+), 20 deletions(-)
diff --git a/convert_to_modelcif.py b/convert_to_modelcif.py
index d1c18ea..a2c3747 100755
--- a/convert_to_modelcif.py
+++ b/convert_to_modelcif.py
@@ -4,6 +4,7 @@
file with a lot of metadata in place."""
from typing import Tuple
+import datetime
import gzip
import hashlib
import json
@@ -346,45 +347,52 @@ def _get_modelcif_protocol(
return protocol
+def _cast_release_date(release_date):
+ """Type cast a date into datetime.date"""
+ # "AF2" has a special meaning, those DBs did not change since the first
+ # release of AF2. This information is needed in the model-producing
+ # pipeline.
+ if release_date is None or release_date == "AF2":
+ return None
+
+ try:
+ return datetime.datetime.strptime(release_date, "%Y-%m-%d %H:%M:%S")
+ except ValueError:
+ logging.warning(
+ f"Unsupported release date format found: {release_date}"
+ )
+ raise
+
+
def _get_modelcif_ref_dbs(meta_json):
"""Get sequence databases used for monomer features."""
# vendor formatting for DB names/ URLs, extend on KeyError
- db_info = {
- "uniref90": {
- "name": "UniRef90",
- "url": "https://ftp.uniprot.org/pub/databases/uniprot/uniref/"
- + "uniref90/",
- },
- "mgnify": {"name": "MGnify", "url": None},
- "bfd": {"name": "BFD", "url": None},
- "small_bfd": {"name": "Reduced BFD", "url": None},
- "uniref30": {"name": "UniRef30", "url": None},
- "uniprot": {"name": "UniProt", "url": None},
- "pdb70": {"name": "PDB70", "url": None},
- "pdb_seqres": {"name": "PDB seqres", "url": None},
- "colabfold": {"name": "ColabFold", "url": None},
- }
+ # ToDo: adapt to new JSON input
sdb_dct = {} # 'sequence database list', starts as dict
for data in meta_json.values():
for db_name, vdct in data["databases"].items():
- db_name = db_name.lower()
+ if vdct["version"] == "NA":
+ vdct["version"] = None
+ vdct["release_date"] = _cast_release_date(vdct["release_date"])
# if DB already exists, check URL and version
if db_name in sdb_dct:
# ToDo: switch URL to the actual URL read from JSON
if (
sdb_dct[db_name].version != vdct["version"]
- or sdb_dct[db_name].url != db_info[db_name]["url"]
+ or sdb_dct[db_name].url != vdct["location_url"][0]
):
raise RuntimeError(
"Database versions or URLs differ for "
+ f"'{db_name}': '{sdb_dct[db_name].version}/ "
+ f"{sdb_dct[db_name].url}' vs. '{vdct['version']}/ "
- + f"{db_info[db_name]['url']}'"
+ + f"{vdct['location_url'][0]}'"
)
+ # ToDo: deal with DBs with multiple URLs
sdb_dct[db_name] = modelcif.ReferenceDatabase(
- db_info[db_name]["name"],
- db_info[db_name]["url"],
+ db_name,
+ vdct["location_url"][0],
version=vdct["version"],
+ release_date=vdct["release_date"],
)
return sdb_dct.values()
--
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