digichem-core 6.0.2__tar.gz → 6.1.0__tar.gz

{digichem_core-6.0.2 → digichem_core-6.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: digichem-core
-Version: 6.0.2
+Version: 6.1.0
 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
@@ -25,7 +25,7 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
 Requires-Dist: adjusttext
 Requires-Dist: basis-set-exchange
-Requires-Dist: cclib
+Requires-Dist: cclib<2,>=1.7.1
 Requires-Dist: colour-science
 Requires-Dist: configurables
 Requires-Dist: deepmerge

{digichem_core-6.0.2 → digichem_core-6.1.0}/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__ = "6.0.2"
+__version__ = "6.1.0"
 _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 = "21/08/2024"
+_last_updated_string = "16/10/2024"
 last_updated = datetime.strptime(_last_updated_string, "%d/%m/%Y")
 
 # The sys attribute 'frozen' is our flag, '_MEIPASS' is the dir location.

{digichem_core-6.0.2 → digichem_core-6.1.0}/digichem/basis.py

@@ -62,7 +62,7 @@ class BSE_basis_set(dict):
         import basis_set_exchange.misc
         
         if elements_filter is not None and not isinstance(elements_filter, str):
-            elements_filter = ",".join(elements_filter)
+            elements_filter = ",".join((str(item) for item in elements_filter))
 
         if elements_filter is not None:
             elements_filter = basis_set_exchange.misc.expand_elements(elements_filter)

{digichem_core-6.0.2 → digichem_core-6.1.0}/digichem/parse/turbomole.py

@@ -25,9 +25,9 @@ class Turbomole_parser(Cclib_parser):
         """
         Sort a list of log files into a particular order, if required for this parser.
         """
-        from cclib.io.ccio import sort_turbomole_outputs
+        from cclib.parser.turbomoleparser import Turbomole
         
-        return sort_turbomole_outputs(log_files)
+        return Turbomole.sort_input(log_files)
     
     def duration_to_timedelta(self, duration_str):
         """

{digichem_core-6.0.2 → digichem_core-6.1.0}/digichem/result/atom.py

@@ -315,11 +315,18 @@ class Atom_list(Result_container, Unmergeable_container_mixin, Molecule_mixin):
             from rdkit.Chem import MolToSmiles
             from rdkit.Chem.rdmolops import RemoveHs
             
+            # TODO: Find some other way of generating SMILES.
+
             mol = self.to_rdkit_molecule()
-            mol = RemoveHs(mol)
+            try:
+                # TODO: rdkit is unreliable, this method can fail for lots of reasons...
+                mol = RemoveHs(mol)
+            except Exception:
+                pass
+                
             self._smiles = MolToSmiles(mol)
             return self._smiles
-            
+
             # # TODO: Handle cases where obabel isn't available
             # conv = Openprattle_converter.get_cls("xyz")(input_file = self.to_xyz(), input_file_type = "xyz")
             # # Cache the result in case we need it again.
@@ -450,10 +457,16 @@ class Atom_list(Result_container, Unmergeable_container_mixin, Molecule_mixin):
         """
         Get a representation of this result object in primitive format.
         """
+        try:
+            smiles = self.smiles
+        
+        except Exception:
+            smiles = None
+        
         dump_dict = {
             "formula": self.formula_string,
             "charge": self.charge,
-            "smiles": self.smiles,
+            "smiles": smiles,
             "exact_mass": {
                 "value": float(self.mass) if self.safe_get("mass") is not None else None,
                 "units": "g mol^-1" 

{digichem_core-6.0.2 → digichem_core-6.1.0}/pyproject.toml

@@ -12,7 +12,7 @@ description = "Open-source library for Digichem core components"
 dependencies = [
     "adjustText",
     "basis_set_exchange",
-    "cclib",
+    "cclib >= 1.7.1, < 2",
     "colour-science",
     "configurables",
     "deepmerge",

{digichem_core-6.0.2 → digichem_core-6.1.0}/digichem/file/base.py

@@ -29,6 +29,9 @@ class File_maker_ABC():
         """
         self.output = output
         self.file_path = {'file': self.output}
+        
+        # A flag of whether we have already created our output file.
+        self.done_file_creation = False
     
     def get_file(self, name = 'file'):
         """
@@ -160,9 +163,6 @@ class File_maker(File_maker_ABC):
         self.dont_modify = dont_modify
         self.use_existing = use_existing
         
-        # A flag of whether we have already created our output file.
-        self.done_file_creation = False
-        
         self.failed_file_creation = False
         
         self.full_path_names = full_path_names