Merge pull request #89 from molssi-seamm/dev

Significant internal enhancement to property handling.

HISTORY.rst

@@ -1,6 +1,12 @@
 =======
 History
 =======
+2024.12.7 -- Significant internal enhancement to property handling.
+    * An internal change, allowing listing and getting properties with wildcards,
+      working with multiple values at once. This is a significant change, but should
+      not affect the user interface. Also consolidated the property handling code for
+      configurations vs systems.
+
 2024.11.27.1 -- Added support for charge in chemical formulae
     * Added support for charge in chemical formulae, e.g. [H2 O]+.
 

molsystem/configuration_properties.py

@@ -58,25 +58,37 @@ def exists(self, name):
         """A thin wrapper of the _Properties method."""
         return self.properties.exists(name)
 
-    def get(self, _property="all", include_system_properties=False):
-        """Get the given property value for this configuration.
+    def get(
+        self,
+        pattern="*",
+        match="glob",
+        include_system_properties=False,
+        types=["float", "int", "str", "json"],
+    ):
+        """Get the property value(s)
 
         Parameters
         ----------
-        _property : int or str
-            The id or name of the property.
+        pattern : str = "*"
+            The pattern of the property.
+        match : str="glob"
+            Whether to use exact, glob, or 'like' matching.
         include_system_properties : bool=False
-            Whether to include properties that are on the system, not any configuration
+            For a configuration, whether to include properties that are on the system.
+        types : [str] = ["float", "int", "str", "json"]
+            The type of results to return.
 
         Returns
         -------
-        int, float, or str
-            The value of the property.
+        {str: {str: value}}
+            The matching property values.
         """
         return self.properties.get(
             self._cid,
-            _property,
+            pattern=pattern,
+            match=match,
             include_system_properties=include_system_properties,
+            types=types,
         )
 
     def id(self, name):
@@ -98,35 +110,43 @@ def known_properties(self):
         """List the known properties."""
         return self.properties.known_properties()
 
-    def list(self):
-        """Return all of the property names for the current configuration.
-        Returns
-        -------
-        [str]
-            The names of the properties for the configuration.
-        """
-        sql = "SELECT name FROM property WHERE id IN ("
-        sql += "SELECT property FROM float_data WHERE configuration = ?"
-        sql += "UNION SELECT property FROM int_data WHERE configuration = ?"
-        sql += "UNION SELECT property FROM str_data WHERE configuration = ?"
-        sql += ")"
+    def list(
+        self,
+        pattern="*",
+        match="glob",
+        include_system_properties=False,
+        as_ids=False,
+        types=["float", "int", "str", "json"],
+    ):
+        """Get the list of matching properties for the configuration.
 
-        self.properties.cursor.execute(sql, (self._cid, self._cid, self._cid))
-        return [row[0] for row in self.properties.cursor]
+        Parameters
+        ----------
+        pattern : str = "*"
+            The pattern of the property.
+        match : str="glob"
+            Whether to use exact, glob, or 'like' matching.
+        include_system_properties : bool=False
+            Whether to include properties that are on the system, not any configuration
+        as_ids : bool=False
+            Whether to return the ids rather than names
+        types : [str] = ["float", "int", "str", "json"]
+            The type of results to return.
 
-    def list_ids(self):
-        """Return all of the property ids for the current configuration.
         Returns
         -------
-        [int]
-            The names of the properties for the configuration.
+        [str] or [int]
+            The matching properties.
         """
-        sql = "SELECT property FROM float_data WHERE configuration = ?"
-        sql += "UNION SELECT property FROM int_data WHERE configuration = ?"
-        sql += "UNION SELECT property FROM str_data WHERE configuration = ?"
-
-        self.properties.cursor.execute(sql, (self._cid, self._cid, self._cid))
-        return [row[0] for row in self.properties.cursor]
+        return self.properties.list(
+            self._cid,
+            is_system=False,
+            pattern=pattern,
+            match=match,
+            include_system_properties=include_system_properties,
+            as_ids=as_ids,
+            types=types,
+        )
 
     def metadata(self, _property):
         """The metadata for a property

molsystem/openbabel.py

@@ -78,8 +78,8 @@ def to_OBMol(self, properties=None):
             pair.SetValue(str(self.spin_multiplicity))
             ob_mol.CloneData(pair)
 
-        if properties == "all":
-            data = self.properties.get("all", include_system_properties=True)
+        if properties is not None:
+            data = self.properties.get(properties, include_system_properties=True)
             for key, value in data.items():
                 pair.SetAttribute(key)
                 pair.SetValue(str(value))
@@ -318,7 +318,7 @@ def to_sdf_text(self):
         """
         obConversion = ob.OBConversion()
         obConversion.SetOutFormat("sdf")
-        obMol = self.to_OBMol(properties="all")
+        obMol = self.to_OBMol(properties="*")
         title = f"SEAMM={self.system.name}/{self.name}"
         obMol.SetTitle(title)
         text = obConversion.WriteString(obMol)