Simplified command line options for now.

convert_to_modelcif.py

@@ -3,68 +3,76 @@
 """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
+import os
+import sys
 
+from absl import app, flags, logging
 
-FLAGS = flags.FLAGS
-flags.DEFINE_list(
-    "metadata",
-    None,
-    "JSON files with information about experiment setup, one file per feature",
+
+# ToDo: Get options properly, best get the same names as used in existing
+#       scripts, e.g. could '--monomer_objects_dir' be used as feature
+#       directory/ directory with the feature JSON files?
+flags.DEFINE_string(
+    "ap_output", None, "AlphaPulldown pipeline output directory."
 )
-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'",
-)
 
+flags.mark_flags_as_required(["ap_output"])
 
-def _mark_model_selection_as_mutual_exclusive():
-    """Create & register a validator for model selection.
+FLAGS = flags.FLAGS
+
+# ToDo: implement a flags.register_validator() checking that files/ directories
+#       exist as expected.
 
-    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
+def alphapulldown_model_to_modelcif() -> None:
+    """Convert an AlphaPulldown model into a ModelCIF formatted mmCIF file.
 
-        if not_set_count == 1:
-            return True
-        return False
+    Metadata for the ModelCIF categories will be fetched from AlphaPulldown
+    output as far as possible. This expects modelling projects to exists in
+    AlphaPulldown's output directory structure."""
 
-    flags.register_multi_flags_validator(
-        ["model_selected", "select_all"],
-        _validate_mutual_exclusion_model_selection,
-        "Exactly one (and only one) argument needs to be set.",
-    )
 
+def _get_model_list(ap_dir, model_selected) -> list:
+    """Get the list of models to be converted.
 
-_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).
+    If `model_selected` is none, all models will be marked for conversion."""
+    # ToDo: Question - use 'ranked_*.pdb' or
+    #       'unrelaxed_model_*_multimer_v3_pred_0.pdb' models?
+
+    if model_selected is not None:
+        mdl_paths = os.path.join(ap_dir, "models")
+        cmplx = os.listdir(mdl_paths)
+        # For now, exactly 1 complex is expected in the 'models' subdirectory.
+        # If there are more, the 'model_selected' mechanism needs to be further
+        # tuned to get to the right model.
+        assert len(cmplx) == 1
+        cmplx = cmplx[0]
+        mdl_paths = os.path.join(
+            mdl_paths, cmplx, f"ranked_{model_selected}.pdb"
+        )
+        mdl_paths = [mdl_paths]
+
+    for mdl in mdl_paths:
+        if os.path.isfile(mdl):
+            logging.info(
+                f"Model file '{mdl}' does not exist or is not a regular file."
+            )
+            sys.exit()
+
+    # check that files actually exist
+
+    return []
 
 
 def main(argv):
     """Run as script."""
+    # pylint: disable=pointless-string-statement
     """
     Here, the metadata json files for each feature are in features_monomers/
     directory. The models are in models/ directory, and usually there are many
@@ -81,10 +89,22 @@ def main(argv):
     AlphaPulldown side and may be added now or later on. Let me know if it is
     critical for you now.
     """
+    # pylint: enable=pointless-string-statement
     del argv  # Unused.
 
+    # make list of selected models
+    model_conversions = _get_model_list(FLAGS.ap_output, FLAGS.model_selected)
+    # assemble selected models into ModelCIF files + associated data archives
+    alphapulldown_model_to_modelcif()
+
 
 if __name__ == "__main__":
     app.run(main)
 
-#  LocalWords:  ToDo
+# 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.
+
+#  LocalWords:  ToDo AlphaPulldown PAEs dir