digichem-core 7.0.1__tar.gz → 7.0.3__tar.gz

{digichem_core-7.0.1 → digichem_core-7.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: digichem-core
-Version: 7.0.1
+Version: 7.0.3
 Summary: Open-source library for Digichem core components
 Project-URL: Homepage, https://github.com/Digichem-Project/digichem-core
 Project-URL: Documentation, https://doc.digi-chem.co.uk

{digichem_core-7.0.1 → digichem_core-7.0.3}/digichem/__init__.py

@@ -20,7 +20,7 @@ from digichem.datas import get_resource
 # development = prerelease is not None
 # # The full version number of this package.
 # __version__ = "{}.{}.{}{}".format(major_version, minor_version, revision, "-pre.{}".format(prerelease) if development else "")
-__version__ = "7.0.1"
+__version__ = "7.0.3"
 _v_parts = __version__.split("-")[0].split(".")
 major_version = int(_v_parts[0])
 minor_version = int(_v_parts[1])
@@ -39,7 +39,7 @@ __author__ = [
 ]
 
 # Program date (when we were last updated). This is changed automatically.
-_last_updated_string = "06/10/2025"
+_last_updated_string = "13/11/2025"
 last_updated = datetime.strptime(_last_updated_string, "%d/%m/%Y")
 
 # The sys attribute 'frozen' is our flag, '_MEIPASS' is the dir location.

{digichem_core-7.0.1 → digichem_core-7.0.3}/digichem/config/base.py

@@ -59,7 +59,7 @@ class Digichem_options(Configurable):
     render = Options(
         help = "Options for controlling the appearance of 3D molecule images.",
         enable_rendering = Option(help = "Set to False to disable image rendering.", type = bool, default = True),
-        engine = Option(help = "The rendering engine to use", choices = ["vmd", "batoms"], default = "vmd"),
+        engine = Option(help = "The rendering engine to use", choices = ["vmd", "batoms"], default = "batoms"),
         vmd = Options(help = "VMD specific options (only applies if engine == 'vmd'",
             executable = Option(help = "Path to the VMD (Visual Molecular Dynamics) executable", default = "vmd"),
             tachyon = Option(help = "The tachyon ray-tracing library, performs the actual rendering. Tachyon is typically packaged with VMD, but often isn't added to the path automatically", default = "tachyon"),

{digichem_core-7.0.1 → digichem_core-7.0.3}/digichem/result/excited_state.py

@@ -382,17 +382,16 @@ class Excited_state_transition(Result_object):
                 "label": self.ending_mo.label
             },
             "coefficient": float(self.coefficient),
-            "probability": float(self.probability **2)
+            "probability": float(self.probability)
         }
         
     @classmethod
-    def list_from_parser(self, parser):
+    def list_from_parser(self, parser, threshold = 1e-4):
         """
         Create a list of excited state transitions from an output file parser.
         
         :param parser: An output file parser.
-        :param alpha_mo_list: A Molecular_orbital_list object of the MOs of this system.
-        :param beta_mo_list: A Molecular_orbital_list object of the beta MOs of this system. This can be left as null for restricted calcs.
+        :param threshold: The threshold below which transitions will be discarded.
         :return: A list of Excited_state_transition objects.
         """
         try:
@@ -409,6 +408,10 @@ class Excited_state_transition(Result_object):
 
                 for (starting_mo_index, starting_mo_AB), (ending_mo_index, ending_mo_AB), coefficient in excited_state_transitions:
                     try:
+                        if coefficient **2 < threshold:
+                            # Skip tiny contributions.
+                            continue
+
                         data_list.append({
                             'starting_mo': MOs[starting_mo_AB][starting_mo_index],
                             'ending_mo': MOs[ending_mo_AB][ending_mo_index],