From 9827ae0e5b171212d7c143550a2d09482a974c1b Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 4 Oct 2023 14:31:53 +0200
Subject: [PATCH] Get software from file
---
convert_to_modelcif.py | 21 ++++++++-------------
1 file changed, 8 insertions(+), 13 deletions(-)
diff --git a/convert_to_modelcif.py b/convert_to_modelcif.py
index 97a3f0e..3a01fc9 100755
--- a/convert_to_modelcif.py
+++ b/convert_to_modelcif.py
@@ -318,10 +318,9 @@ def _get_modelcif_ref_dbs(meta_json):
db_name = db_name.lower()
# if DB already exists, check URL and version
if db_name in sdb_dct:
- print("ALREADY THERE", sdb_dct[db_name])
# ToDo: switch URL to the actual URL read from JSON
if (
- sdb_dct[db_name].version == vdct["version"]
+ sdb_dct[db_name].version != vdct["version"]
or sdb_dct[db_name].url != db_info[db_name]["url"]
):
raise RuntimeError(
@@ -376,6 +375,7 @@ def _store_as_modelcif(
)
# create software list from feature metadata
+ # ToDo: store_as_modelcif should not use __meta__
sw_dct = _get_software_data(data_json["__meta__"])
# process scores
@@ -730,25 +730,20 @@ def _get_protocol_steps(modelcif_json):
"""Create the list of protocol steps with software and parameters used."""
protocol = []
# MSA/ monomer feature generation step
- # ToDo: get software from modelcif_json
step = {
"method_type": "coevolution MSA",
"step_name": "MSA generation",
"details": "Create sequence features for corresponding monomers.",
"input_data_group": "target_sequences",
"output_data_group": "monomer_pickle_files",
- "software_group": [
- "AlphaPulldown",
- "AlphaFold",
- "jackhmmer",
- "hhblits",
- "hhsearch",
- "hmmsearch",
- "hmmbuild",
- "kalign",
- ]
+ "software_group": []
# _ma_protocol_step.protocol_id
}
+ for sftwr in modelcif_json["__meta__"].values():
+ sftwr = sftwr["software"]
+ for tool in sftwr:
+ if tool not in step["software_group"]:
+ step["software_group"].append(tool)
protocol.append(step)
# modelling step
--
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