From 22717880ad136636ec63123b02ada31400c9e64a Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 21 Aug 2023 10:40:43 +0200
Subject: [PATCH] Argument parsing (early version)
---
convert_to_modelcif.py | 90 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 90 insertions(+)
create mode 100755 convert_to_modelcif.py
diff --git a/convert_to_modelcif.py b/convert_to_modelcif.py
new file mode 100755
index 0000000..129f0d4
--- /dev/null
+++ b/convert_to_modelcif.py
@@ -0,0 +1,90 @@
+#!/usr/bin/env python3
+
+"""Take the output of the AlphaPulldown pipeline and turn it into a ModelCIF
+file with a lot of metadata in place."""
+
+from absl import app
+from absl import flags
+
+
+FLAGS = flags.FLAGS
+flags.DEFINE_list(
+ "metadata",
+ None,
+ "JSON files with information about experiment setup, one file per feature",
+)
+flags.DEFINE_string("af2_output", None, "Results of AlphaFold2 modelling")
+flags.DEFINE_integer(
+ "model_selected",
+ None,
+ "Model to be converted into ModelCIF, use '--select_all' to convert all "
+ + "models found in '--af2_output'",
+)
+flags.DEFINE_bool(
+ "select_all",
+ False,
+ "Convert all models found in '--af2_output' into ModelCIF, excludes "
+ + "'--model_selected'",
+)
+
+
+def _mark_model_selection_as_mutual_exclusive():
+ """Create & register a validator for model selection.
+
+ Enforce only one option is set, either '--select_all' or '--model_selected'.
+ Enforce that at least one of '--select_all' or '--model_selected' is set
+ (so this options will not pop up in `flags.mark_flags_as_required`).
+ """
+
+ def _validate_mutual_exclusion_model_selection(flags_dict):
+ not_set_count = 0
+ if flags_dict["model_selected"] is None:
+ not_set_count += 1
+ if flags_dict["select_all"] is False:
+ not_set_count += 1
+
+ if not_set_count == 1:
+ return True
+ return False
+
+ flags.register_multi_flags_validator(
+ ["model_selected", "select_all"],
+ _validate_mutual_exclusion_model_selection,
+ "Exactly one (and only one) argument needs to be set.",
+ )
+
+
+_mark_model_selection_as_mutual_exclusive()
+flags.mark_flags_as_required(["metadata", "af2_output"])
+# ToDo: implement a flags.register_validator() for 'metadata', checking that
+# the file exists and is readable.
+# ToDo: implement a flags.register_validator() for 'af2_output', checking that
+# the file directory exists and is readable (overkill: check directory
+# structure).
+
+
+def main(argv):
+ """Run as script."""
+ """
+ Here, the metadata json files for each feature are in features_monomers/
+ directory. The models are in models/ directory, and usually there are many
+ complexes modelled using different permutations of the monomeric features.
+ For the sake of size, I send you the models of only one dimer
+ cage_B_and_cage_C/ that was generated using features_monomers/cage_B.pkl
+ and features_monomers/cage_C.pkl accordingly.
+ Please note that typically all the cage_?_feature_metadata.json files are
+ identical in terms of used databases and software versions and generated
+ in one go.
+ However, theoretically they could be generated using different binaries/DBs
+ versions, so maybe it makes sense to compare them and store both/all
+ versions if they are different. This merging can be done on our
+ AlphaPulldown side and may be added now or later on. Let me know if it is
+ critical for you now.
+ """
+ del argv # Unused.
+
+
+if __name__ == "__main__":
+ app.run(main)
+
+# LocalWords: ToDo
--
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