fix for missing mtz files

xchem · Jan 12, 2024 · f640aa1 · f640aa1
1 parent ba4ea76
commit f640aa1
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/src/xchemalign/aligner.py b/src/xchemalign/aligner.py
@@ -110,14 +110,17 @@ def get_datasets_from_crystals(crystals, output_path):
     reference_datasets = {}
     new_datasets = {}
     for dtag, crystal in crystals.items():
+        mtz_file = crystal[Constants.META_XTAL_FILES].get(Constants.META_XTAL_MTZ, {}).get(Constants.META_FILE)
+        if mtz_file is None:
+            mtz_path = "None"
+        else:
+            mtz_path = str(output_path / mtz_file)
+
         dataset = dt.Dataset(
             dtag=dtag,
             pdb=str(output_path / crystal[Constants.META_XTAL_FILES][Constants.META_XTAL_PDB][Constants.META_FILE]),
             xmap="",
-            mtz=str(
-                output_path
-                / crystal[Constants.META_XTAL_FILES].get(Constants.META_XTAL_MTZ, {}).get(Constants.META_FILE)
-            ),
+            mtz=mtz_path,
             # ligand_binding_events=LigandBindingEvents(
             #     ligand_ids=[
             #         LigandID(

diff --git a/src/xchemalign/collator.py b/src/xchemalign/collator.py
@@ -542,7 +542,6 @@ def run(self, meta):
         all_xtals, new_xtals = self._munge_history(meta)
         self.logger.info("writing metadata ...")
         self._write_metadata(new_meta)
-        self.logger.info("copying config ...")
         self._copy_config()
         self.logger.info("run complete")
         return new_meta
@@ -933,7 +932,9 @@ def _write_metadata(self, meta, suffix=""):
             yaml.dump(meta, stream, sort_keys=False)
 
     def _copy_config(self):
-        f = shutil.copy2(self.config_file, self.output_path / self.version_dir / 'config.yaml')
+        to_path = self.output_path / self.version_dir / 'config.yaml'
+        self.logger.info("copying config file", self.config_file, "to", to_path)
+        f = shutil.copy2(self.config_file, to_path)
         if not f:
             self.logger.warn("Failed to copy config file to {}".format((self.output_path / self.version_dir)))
             return False