Enhances CIF parsing in SampleModelFactory

Author: AndrewSazonov

src/easydiffraction/io/cif/serialize.py

@@ -130,9 +130,11 @@ def datablock_item_to_cif(datablock) -> str:
 
     header = f'data_{datablock._identity.datablock_entry_name}'
     parts: list[str] = [header]
+    # First categories
     for v in vars(datablock).values():
         if isinstance(v, CategoryItem):
             parts.append(v.as_cif)
+    # Then collections
     for v in vars(datablock).values():
         if isinstance(v, CategoryCollection):
             parts.append(v.as_cif)

src/easydiffraction/sample_models/sample_model/factory.py

@@ -11,6 +11,8 @@
 
 import gemmi
 
+from easydiffraction.core.category import CategoryCollection
+from easydiffraction.core.category import CategoryItem
 from easydiffraction.core.factory import FactoryBase
 from easydiffraction.sample_models.sample_model.base import SampleModelBase
 
@@ -126,56 +128,25 @@ def _pick_first_structural_block(
         except Exception:
             return doc[0]
 
-    # TODO: Move to a common CIF utility module? io.cif.parse?
-    @classmethod
-    def _create_model_from_block(
-        cls,
-        block: gemmi.cif.Block,
-    ) -> SampleModelBase:
-        """Build a model instance from a single CIF block."""
-        name = cls._extract_name_from_block(block)
-        model = SampleModelBase(name=name)
-        cls._set_space_group_from_cif_block(model, block)
-        cls._set_cell_from_cif_block(model, block)
-        cls._set_atom_sites_from_cif_block(model, block)
-        return model
-
     # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _extract_name_from_block(cls, block: gemmi.cif.Block) -> str:
         """Extract a model name from the CIF block name."""
-        return block.name or 'model'
-
-    # TODO: Move to a common CIF utility module? io.cif.parse?
-    @classmethod
-    def _set_space_group_from_cif_block(
-        cls,
-        model: SampleModelBase,
-        block: gemmi.cif.Block,
-    ) -> None:
-        """Populate the model's space group from a CIF block."""
-        model.space_group.from_cif(block)
-
-    # TODO: Move to a common CIF utility module? io.cif.parse?
-    @classmethod
-    def _set_cell_from_cif_block(
-        cls,
-        model: SampleModelBase,
-        block: gemmi.cif.Block,
-    ) -> None:
-        """Populate the model's unit cell from a CIF block."""
-        model.cell.from_cif(block)
+        # TODO: Need validator or normalization
+        return block.name
 
     # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
-    def _set_atom_sites_from_cif_block(
+    def _create_model_from_block(
         cls,
-        model: SampleModelBase,
         block: gemmi.cif.Block,
-    ) -> None:
-        """Populate the model's atom sites from a CIF block."""
-        model.atom_sites.from_cif(block)
-
-    # TODO: How to automatically parce and populate all categories?
-    #  for category in model.categories:
-    #      cls._set_category_from_cif_block(category, block)
+    ) -> SampleModelBase:
+        """Build a model instance from a single CIF block."""
+        name = cls._extract_name_from_block(block)
+        model = SampleModelFactory.create(name=name)
+        # TODO: Add property categories to the DatablockItem class
+        # Iterate over all categories and populate them from CIF
+        for category in vars(model).values():
+            if isinstance(category, (CategoryItem, CategoryCollection)):
+                category.from_cif(block)
+        return model