Add properties to Structure and Molecule (#3264)

* Add 'properties' to Structure and Molecule

* add properties in copy methods

* fix structure copy

* setting structure properties in more places

* test struct with props to/from JSON str

* assert '"test_property": 42' in json_str

* fix Structure properties when reading from string

* make Molecule.from_str case insensitive

* Molecule.to() support both .yaml and .yml extension

* Molecule.from_file() support both .yaml and .yml extension

* add .yml test case in TestIMolecule.test_to_from_file_string()

* fix NameError: name 'pybel' is not defined in BabelMolAdaptor.from_str()

* update properties doc str: mention props be serialized when writing the structure to JSON or YAML but is
                lost when converting to other formats.

* fix mypy

* fix test_valid_magmom_struct regex

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: gpetretto

pymatgen/analysis/gb/grain.py

@@ -67,6 +67,7 @@ def __init__(
         oriented_unit_cell: Structure,
         validate_proximity: bool = False,
         coords_are_cartesian: bool = False,
+        properties: dict | None = None,
     ) -> None:
         """
         Makes a GB structure, a structure object with additional information
@@ -109,6 +110,8 @@ def __init__(
                 that are less than 0.01 Ang apart. Defaults to False.
             coords_are_cartesian (bool): Set to True if you are providing
                 coordinates in Cartesian coordinates. Defaults to False.
+            properties (dict): dictionary containing properties associated
+                with the whole GrainBoundary.
         """
         self.oriented_unit_cell = oriented_unit_cell
         self.rotation_axis = rotation_axis
@@ -125,6 +128,7 @@ def __init__(
             validate_proximity=validate_proximity,
             coords_are_cartesian=coords_are_cartesian,
             site_properties=site_properties,
+            properties=properties,
         )
 
     def copy(self):

pymatgen/analysis/magnetism/analyzer.py

@@ -553,16 +553,16 @@ def matches_ordering(self, other: Structure) -> bool:
         b_positive = CollinearMagneticStructureAnalyzer(other, overwrite_magmom_mode="normalize", make_primitive=False)
 
         b_negative = b_positive.structure.copy()
-        b_negative.add_site_property("magmom", np.multiply(-1, b_negative.site_properties["magmom"]))
+        b_negative.add_site_property("magmom", -np.array(b_negative.site_properties["magmom"]))
 
-        b_negative = CollinearMagneticStructureAnalyzer(
+        analyzer = CollinearMagneticStructureAnalyzer(
             b_negative, overwrite_magmom_mode="normalize", make_primitive=False
         )
 
         b_positive = b_positive.get_structure_with_spin()
-        b_negative = b_negative.get_structure_with_spin()
+        analyzer = analyzer.get_structure_with_spin()
 
-        return a.matches(b_positive) or a.matches(b_negative)
+        return a.matches(b_positive) or a.matches(analyzer)
 
     def __str__(self):
         """