New crystalform and assemblies documentation

scripts/collate.py

@@ -0,0 +1,32 @@
+import argparse
+
+from xchemalign import utils
+from xchemalign.collator import Collator
+
+
+def main():
+    parser = argparse.ArgumentParser(description="collator")
+
+    parser.add_argument("-c", "--config-file", default="config.yaml", help="Configuration file")
+    parser.add_argument("-l", "--log-file", help="File to write logs to")
+    parser.add_argument("--log-level", type=int, default=0, help="Logging level")
+    parser.add_argument("-v", "--validate", action="store_true", help="Only perform validation")
+
+    args = parser.parse_args()
+    logger = utils.Logger(logfile=args.log_file, level=args.log_level)
+    logger.info("collator: ", args)
+
+    c = Collator(args.config_file, logger=logger)
+
+    meta, num_errors, num_warnings = c.validate()
+
+    if not args.validate:
+        if meta is None or num_errors:
+            print("There are errors, cannot continue")
+            exit(1)
+        else:
+            c.run(meta)
+
+
+if __name__ == "__main__":
+    main()

xchemalign/aligner.py

@@ -190,10 +190,6 @@ def __init__(self, version_dir, metadata, xtalforms, assemblies, logger=None):
             self.xtalforms_file = Path(xtalforms)
         else:
             self.xtalforms_file = self.base_dir / Constants.XTALFORMS_FILENAME  # e.g. path/to/xtalforms.yaml
-        if assemblies:
-            self.assemblies_file = Path(assemblies)
-        else:
-            self.assemblies_file = self.base_dir / Constants.ASSEMBLIES_FILENAME  # e.g. path/to/assemblies.yaml
         if logger:
             self.logger = logger
         else:
@@ -234,7 +230,7 @@ def run(self):
     def _write_output(self, collator_dict, aligner_dict):
         # keep a copy of the xtaforms and assemblies configs
         self._copy_file_to_version_dir(self.xtalforms_file)
-        self._copy_file_to_version_dir(self.assemblies_file)
+        # self._copy_file_to_version_dir(self.assemblies_file)
 
         collator_dict[Constants.META_XTALFORMS] = aligner_dict[Constants.META_XTALFORMS]
         collator_dict[Constants.META_CONFORMER_SITES] = aligner_dict[Constants.META_CONFORMER_SITES]
@@ -313,7 +309,7 @@ def _perform_alignments(self, meta):
         # Load the fs model for the new output dir
         fs_model = dt.FSModel.from_dir(output_path)
         fs_model.xtalforms = self.xtalforms_file
-        fs_model.assemblies = self.assemblies_file
+        # fs_model.assemblies = self.assemblies_file
         if source_fs_model:
             fs_model.alignments = source_fs_model.alignments
             fs_model.reference_alignments = source_fs_model.reference_alignments
@@ -331,16 +327,21 @@ def _perform_alignments(self, meta):
         datasets, reference_datasets, new_datasets = get_datasets_from_crystals(crystals, self.base_dir)
 
         # Get assemblies
-        if source_fs_model:
-            assemblies: dict[str, dt.Assembly] = _load_assemblies(source_fs_model.assemblies, self.assemblies_file)
-        else:
-            assemblies = _load_assemblies(fs_model.assemblies, self.assemblies_file)
-
-        # Get xtalforms
-        if source_fs_model:
-            xtalforms: dict[str, dt.XtalForm] = _load_xtalforms(source_fs_model.xtalforms, self.xtalforms_file)
-        else:
-            xtalforms = _load_xtalforms(fs_model.xtalforms, self.xtalforms_file)
+        # if source_fs_model:
+        #     assemblies: dict[str, dt.Assembly] = _load_assemblies(source_fs_model.assemblies, self.assemblies_file)
+        # else:
+        #     assemblies = _load_assemblies(fs_model.assemblies, self.assemblies_file)
+        #
+        # # Get xtalforms
+        # if source_fs_model:
+        #     xtalforms: dict[str, dt.XtalForm] = _load_xtalforms(source_fs_model.xtalforms, self.xtalforms_file)
+        # else:
+        #     xtalforms = _load_xtalforms(fs_model.xtalforms, self.xtalforms_file)
+        xtalforms, assemblies = _load_xtalforms_and_assemblies(
+            source_fs_model.xtalforms,
+            source_fs_model.assemblies,
+            self.xtalforms_file
+        )
 
         # Get the dataset assignments
         if source_fs_model:
@@ -745,7 +746,6 @@ def main():
     parser.add_argument("-d", "--version-dir", required=True, help="Path to version dir")
     parser.add_argument("-m", "--metadata_file", default=Constants.METADATA_XTAL_FILENAME, help="Metadata YAML file")
     parser.add_argument("-x", "--xtalforms", help="Crystal forms YAML file")
-    parser.add_argument("-a", "--assemblies", help="Assemblies YAML file")
     parser.add_argument("-l", "--log-file", help="File to write logs to")
     parser.add_argument("--log-level", type=int, default=0, help="Logging level")
     parser.add_argument("--validate", action="store_true", help="Only perform validation")
@@ -755,7 +755,7 @@ def main():
 
     logger = utils.Logger(logfile=args.log_file, level=args.log_level)
 
-    a = Aligner(args.version_dir, args.metadata_file, args.xtalforms, args.assemblies, logger=logger)
+    a = Aligner(args.version_dir, args.metadata_file, args.xtalforms, logger=logger)
     num_errors, num_warnings = a.validate()
 
     if not args.validate:

xchemalign/collator.py

@@ -26,8 +26,8 @@
 
 from rdkit import Chem
 
-from . import utils, dbreader
-from .utils import Constants
+from xchemalign import utils, dbreader
+from xchemalign.utils import Constants
 
 
 def generate_xtal_dir(input_path: Path, xtal_name: str):