From 8d0378b282005516ac220f29bb9d5df935efa77d Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 16 Nov 2023 13:13:47 +0100
Subject: [PATCH] Removed some ToDos
---
convert_to_modelcif.py | 7 -------
1 file changed, 7 deletions(-)
diff --git a/convert_to_modelcif.py b/convert_to_modelcif.py
index fbb6a84..0612cc8 100755
--- a/convert_to_modelcif.py
+++ b/convert_to_modelcif.py
@@ -46,7 +46,6 @@ from alphapulldown.utils import make_dir_monomer_dictionary
# ToDo: Example 1 from the GitHub repo mentions MMseqs2
# ToDo: Discuss input of protocol steps, feature creation has baits, sequences
# does modelling depend on mode?
-# ToDo: Option to add remaining models w PAE files to archive
# ToDo: deal with `--max_template_date`, beta-barrel project has it as software
# parameter
flags.DEFINE_string(
@@ -394,7 +393,6 @@ def _cmp_ref_dbs(db_dct, db_objs):
def _get_modelcif_ref_dbs(meta_json):
"""Get sequence databases used for monomer features."""
# vendor formatting for DB names/ URLs, extend on KeyError
- # ToDo: adapt to new JSON input
sdb_lst = {} # 'sequence database list' starts as dict since we need to
# compare DBs between the different monomers.
i = 0
@@ -1101,11 +1099,6 @@ def main(argv):
if __name__ == "__main__":
app.run(main)
-# ToDo: Question - option to include all the non-selected models in associated
-# data archive? This blows up storage size (especially if PAEs included),
-# but we did that already in the past. Idea is to have all models
-# available for... reproducibility and whatnot, but show the selected
-# (representative) of the modelling experiment/ study more prominently.
# ToDo: Things to look at: '_struct.title', '_struct.pdbx_model_details',
# 'data_', '_entry', maybe have a user-defined JSON document with things
# like that, including author names?
--
GitLab