New argument --monomer_objects_dir

convert_to_modelcif.py

@@ -27,6 +27,8 @@ import modelcif.dumper
 import modelcif.model
 import modelcif.protocol
 
+from alphapulldown.utils import make_dir_monomer_dictionary
+
 # 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?
@@ -43,17 +45,25 @@ import modelcif.protocol
 # 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: check that PAE files are written to an associated file
+# ToDo: deal with `--max_template_date`, beta-barrel project has it as software
+#       parameter
 flags.DEFINE_string(
-    "ap_output", None, "AlphaPulldown pipeline output directory."
+    "ap_output", None, "AlphaPulldown pipeline output directory"
+)
+flags.DEFINE_list(
+    "monomer_objects_dir",
+    None,
+    "a list of directories where monomer objects are stored",
 )
 flags.DEFINE_integer(
     "model_selected",
     None,
-    "Model to be converted into ModelCIF, use '--select_all' to convert all "
+    "model to be converted into ModelCIF, use '--select_all' to convert all "
     + "models found in '--af2_output'",
 )
-flags.DEFINE_bool("compress", False, "Compress the ModelCIF file using Gzip")
-flags.mark_flags_as_required(["ap_output"])
+flags.DEFINE_bool("compress", False, "compress the ModelCIF file using Gzip")
+flags.mark_flags_as_required(["ap_output", "monomer_objects_dir"])
 
 FLAGS = flags.FLAGS
 
@@ -535,19 +545,19 @@ def _get_model_details(cmplx_name: str, data_json: dict) -> str:
 
 
 def _get_feature_metadata(
-    modelcif_json: dict, cmplx_name: str, prj_dir: str
+    modelcif_json: dict,
+    cmplx_name: str,
+    monomer_objects_dir: list,
 ) -> list:
     """Read metadata from a feature JSON file."""
     cmplx_name = cmplx_name.split("_and_")
-    prj_dir = os.path.join(prj_dir, "features_monomers")
-    if not os.path.isdir(prj_dir):
-        logging.info(f"No feature directory '{prj_dir}' found.")
-        sys.exit()
+    mnmr_obj_fls = make_dir_monomer_dictionary(monomer_objects_dir)
     if "__meta__" not in modelcif_json:
         modelcif_json["__meta__"] = {}
     for mnmr in cmplx_name:
         modelcif_json["__meta__"][mnmr] = {}
-        feature_json = os.path.join(prj_dir, f"{mnmr}_feature_metadata.json")
+        feature_json = f"{mnmr}_feature_metadata.json"
+        feature_json = os.path.join(mnmr_obj_fls[feature_json], feature_json)
         if not os.path.isfile(feature_json):
             logging.info(f"No feature metadata file '{feature_json}' found.")
             sys.exit()
@@ -826,6 +836,7 @@ def alphapulldown_model_to_modelcif(
     mdl: tuple,
     out_dir: str,
     prj_dir: str,
+    monomer_objects_dir: list,
     compress: bool = False,
 ) -> None:
     """Convert an AlphaPulldown model into a ModelCIF formatted mmCIF file.
@@ -836,7 +847,9 @@ def alphapulldown_model_to_modelcif(
     # ToDo: ENABLE logging.info(f"Processing '{mdl[0]}'...")
     modelcif_json = {}
     # fetch metadata
-    cmplx_name = _get_feature_metadata(modelcif_json, cmplx_name, prj_dir)
+    cmplx_name = _get_feature_metadata(
+        modelcif_json, cmplx_name, monomer_objects_dir
+    )
     # fetch/ assemble more data about the modelling experiment
     _get_model_info(
         modelcif_json,
@@ -963,6 +976,7 @@ def main(argv):
             mdl,
             model_dir,
             FLAGS.ap_output,
+            FLAGS.monomer_objects_dir,
             FLAGS.compress,
         )