Chemical formulas option for system names, cleaner tables.

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.11.29 -- Chemical formulas option for system names, cleaner tables.
+    * Added chemical formula to possible names for systems and configurations.
+    * Truncated results put in tables, based on units, to make more readable.
+
 2024.11.3 -- Bugfix: removed debug printing in the flowchart
     * Removed debug printing that was accidentally left in the flowchart code.
 

seamm/node.py

@@ -48,6 +48,20 @@ def scale(data, factor):
     return result
 
 
+def_fmt = {
+    "kJ/mol": 3,
+    "kcal/mol": 3,
+    "kJ/mol/Å": 3,
+    "kcal/mol/Å": 3,
+    "eV": 3,
+    "E_h": 6,
+    "E_h/a0": 6,
+    "E_h/Å": 6,
+    "debye": 3,
+    "Å": 3,
+}
+
+
 class Node(collections.abc.Hashable):
     """The base class for nodes (steps) in flowcharts.
 
@@ -590,34 +604,7 @@ def get_system_configuration(
                 )
 
             # Attend to naming
-            if "system name" in P:
-                if P["system name"] == "keep current name":
-                    pass
-                elif P["system name"] == "use SMILES string":
-                    system.name = configuration.smiles
-                elif P["system name"] == "use Canonical SMILES string":
-                    system.name = configuration.canonical_smiles
-                else:
-                    # Presume it is a string, perhaps with variables.
-                    if len(kwargs) == 0:
-                        system.name = str(P["system name"])
-                    else:
-                        system.name = str(P["system name"]).format(**kwargs)
-            if "configuration name" in P:
-                if P["configuration name"] == "keep current name":
-                    pass
-                elif P["configuration name"] == "use SMILES string":
-                    configuration.name = configuration.smiles
-                elif P["configuration name"] == "use Canonical SMILES string":
-                    configuration.name = configuration.canonical_smiles
-                else:
-                    # Presume it is a string, perhaps with variables.
-                    if len(kwargs) == 0:
-                        configuration.name = str(P["configuration name"])
-                    else:
-                        configuration.name = str(P["configuration name"]).format(
-                            **kwargs
-                        )
+            seamm.standard_parameters.set_names(system, configuration, P, **kwargs)
 
         return (system, configuration)
 
@@ -1074,12 +1061,17 @@ def store_results(
         results = self.parameters["results"].value
 
         json_data = {}
+        metadata = self.metadata["results"]
         for key, value in results.items():
-            if key not in data or data[key] is None:
+            if key not in metadata:
                 continue
 
-            # The metadata describing this result
-            result_metadata = self.metadata["results"][key]
+            result_metadata = metadata[key]
+            if "standard name" in result_metadata:
+                key = result_metadata["standard name"]
+
+            if key not in data or data[key] is None:
+                continue
 
             # Store the value in the database as a property.
             if "property" in value and value["property"]:
@@ -1164,7 +1156,7 @@ def store_results(
 
             # Store in a table
             if "table" in value:
-                tablename = value["table"]
+                tablename = self.get_value(value["table"])
                 column = self.get_value(value["column"])
                 # Does the table exist?
                 if not self.variable_exists(tablename):
@@ -1293,7 +1285,12 @@ def store_results(
                             if units != current_units:
                                 if result_metadata["dimensionality"] == "scalar":
                                     tmp = Q_(data[key], current_units)
-                                    table.at[row_index, column] = tmp.m_as(units)
+                                    if units in def_fmt:
+                                        table.at[row_index, column] = round(
+                                            tmp.m_as(units), def_fmt[units]
+                                        )
+                                    else:
+                                        table.at[row_index, column] = tmp.m_as(units)
                                 else:
                                     factor = Q_(1, current_units).m_as(units)
                                     tmp = scale(data[key], factor)
@@ -1302,7 +1299,9 @@ def store_results(
                                     )
                             else:
                                 if result_metadata["dimensionality"] == "scalar":
-                                    table.at[row_index, column] = data[key]
+                                    table.at[row_index, column] = round(
+                                        data[key], def_fmt[units]
+                                    )
                                 else:
                                     table.at[row_index, column] = json.dumps(
                                         data[key], separators=(",", ":")

seamm/standard_parameters.py

@@ -55,12 +55,12 @@
         "default_units": "",
         "enumeration": (
             "keep current name",
-            "title",
             "use SMILES string",
             "use Canonical SMILES string",
             "use IUPAC name",
             "use InChI",
             "use InChIKey",
+            "use chemical formula",
         ),
         "format_string": "s",
         "description": "System name:",
@@ -72,13 +72,13 @@
         "default_units": "",
         "enumeration": (
             "keep current name",
-            "title",
             "use SMILES string",
             "use Canonical SMILES string",
             "use IUPAC name",
             "use InChI",
             "use InChIKey",
             "sequential",
+            "use chemical formula",
         ),
         "format_string": "s",
         "description": "Configuration name:",
@@ -129,6 +129,8 @@ def structure_handling_description(P, **kwargs):
         text += " The name of the system will be its InChI."
     elif sysname == "use InChIKey":
         text += " The name of the system will be its InChIKey."
+    elif sysname == "use chemical formula":
+        text += " The name of the system will be its chemical formula."
     else:
         tmp = safe_format(sysname, **kwargs)
         text += f" The name of the system will be '{tmp}'."
@@ -146,6 +148,8 @@ def structure_handling_description(P, **kwargs):
         text += " The name of the configuration will be its InChI."
     elif confname == "use InChIKey":
         text += " The name of the configuration will be its InChIKey."
+    elif confname == "use chemical formula":
+        text += " The name of the configuration will be its chemical formula."
     else:
         tmp = safe_format(confname, **kwargs)
         text += f" The name of the configuration will be '{tmp}'."
@@ -269,6 +273,8 @@ def set_names(system, configuration, P, _first=True, **kwargs):
         system.name = configuration.inchi
     elif sysname == "use InChIKey":
         system.name = configuration.inchikey
+    elif sysname == "use chemical formula":
+        system.name = configuration.formula[0]
     else:
         system.name = safe_format(sysname, **kwargs)
 
@@ -287,6 +293,8 @@ def set_names(system, configuration, P, _first=True, **kwargs):
         configuration.name = configuration.inchi
     elif confname == "use InChIKey":
         configuration.name = configuration.inchikey
+    elif confname == "use chemical formula":
+        configuration.name = configuration.formula[0]
     else:
         configuration.name = safe_format(confname, **kwargs)
 

seamm/tk_node.py

@@ -1133,7 +1133,10 @@ def setup_results(self):
             table.cell(row, 6, w)
             widgets.append(w)
             e = ttk.Entry(frame, width=15)
-            e.insert(0, key.replace(" ", "_"))
+            if "standard name" in entry:
+                e.insert(0, entry["standard name"].replace(" ", "_"))
+            else:
+                e.insert(0, key.replace(" ", "_"))
             table.cell(row, 7, e)
             widgets.append(e)
 
@@ -1151,7 +1154,10 @@ def setup_results(self):
             w.bind("<Return>", self._table_cb)
             w.bind("<FocusOut>", self._table_cb)
             e = ttk.Entry(frame, width=15)
-            e.insert(0, key.replace("_", " "))
+            if "standard name" in entry:
+                e.insert(0, entry["standard name"].replace("_", " "))
+            else:
+                e.insert(0, key.replace("_", " "))
             table.cell(row, 10, e)
             widgets.append(e)