digichem-core 6.0.0rc1__tar.gz → 6.0.1__tar.gz

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/.github/workflows/python-main-pull.yml

@@ -8,7 +8,7 @@ on:
     branches: [ "main" ]
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
   build:

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: digichem-core
-Version: 6.0.0rc1
+Version: 6.0.1
 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
@@ -53,6 +53,10 @@ This is Digichem-core, the open-source library for Digichem. If you are looking
  - Alternatively, if you are looking for the full Digichem program, try [Build-boy](https://github.com/Digichem-Project/build-boy)
  - If you'd like more information on the Digichem project, check out the [website](https://www.digi-chem.co.uk)
 
+## Documentation
+
+Please refer to the main Digichem [documentation](https://doc.digi-chem.co.uk) for further reading.
+
 ## Dependencies
 
  - adjustText
@@ -93,4 +97,4 @@ Documentation coming soon.
 
 Digichem-core is licensed under the BSD-3-Clause license, but some files are licensed separately. See [COPYING.md](COPYING.md) for full details.
 
-The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).
+The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/README.md

@@ -9,6 +9,10 @@ This is Digichem-core, the open-source library for Digichem. If you are looking
  - Alternatively, if you are looking for the full Digichem program, try [Build-boy](https://github.com/Digichem-Project/build-boy)
  - If you'd like more information on the Digichem project, check out the [website](https://www.digi-chem.co.uk)
 
+## Documentation
+
+Please refer to the main Digichem [documentation](https://doc.digi-chem.co.uk) for further reading.
+
 ## Dependencies
 
  - adjustText
@@ -49,4 +53,4 @@ Documentation coming soon.
 
 Digichem-core is licensed under the BSD-3-Clause license, but some files are licensed separately. See [COPYING.md](COPYING.md) for full details.
 
-The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).
+The Digichem logo and branding is Copyright Digichem 2024, you may not use them in any way (although you are welcome to look at them).

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/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__ = "6.0.0-pre.1"
+__version__ = "6.0.1"
 _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 = "31/05/2024"
+_last_updated_string = "01/08/2024"
 last_updated = datetime.strptime(_last_updated_string, "%d/%m/%Y")
 
 # The sys attribute 'frozen' is our flag, '_MEIPASS' is the dir location.

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/config/base.py

@@ -72,7 +72,7 @@ Possible options are:
         batoms = Options(help = "Beautiful Atoms/Blender specific options (only applies if engine == 'batoms'",
             blender = Option(help = "Path to the blender executable, in which beautiful atoms should be installed", default = None),
             cpus = Option(help = "The number of CPUs/threads to use. This option is overridden if running in a calculation environemnt (where it uses the same number of CPUs as the calculation did)", type = int, default = 1),
-            render_samples = Option(help = "The number of render samples (or passes) to use. Higher values result in higher image quality and greater render times", type = int, default = 256),
+            render_samples = Option(help = "The number of render samples (or passes) to use. Higher values result in higher image quality and greater render times", type = int, default = 64),
             perspective = Option(help = "The perspective mode", choices = ["orthographic", "perspective"], default = "orthographic")
             # TODO: Colour options.
         ),
@@ -318,4 +318,4 @@ To disable the maximum width, set to null.""", type = int, default = 1500),
         except FileNotFoundError as e:
             # We lost the race, give up.
             raise Exception("Failed to write settings to file '{}'; one of the parent directories does not exist".format(path)) from e
-    
+    

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/data/batoms/batoms-renderer.py

@@ -210,8 +210,8 @@ def main():
     parser.add_argument("--isovalues", help = "List of isovalues to render", nargs = "*", type = float, default = [])
     parser.add_argument("--isotype", help = "Whether to render positive, negative or both isosurfaces for each isovalue", choices = ["positive", "negative", "both"], default = "both")
     parser.add_argument("--isocolor", help = "The colouring method to use for isosurfaces", choices = ["sign", "cube"], default = "sign")
-    parser.add_argument("--primary-color", help = "RGBA for one of the colors to use for isosurfaces", type = float, nargs = 4, default = [0.1, 0.1, 0.9, 0.7])
-    parser.add_argument("--secondary-color", help = "RGBA for the other color to use for isosurfaces", type = float, nargs = 4, default = [1, 0.058, 0.0, 0.7])
+    parser.add_argument("--primary-color", help = "RGBA for one of the colors to use for isosurfaces", type = float, nargs = 4, default = [0.1, 0.1, 0.9, 0.65])
+    parser.add_argument("--secondary-color", help = "RGBA for the other color to use for isosurfaces", type = float, nargs = 4, default = [1, 0.058, 0.0, 0.65])
     parser.add_argument("--style", help = "Material style for isosurfaces", choices = ('default', 'metallic', 'plastic', 'ceramic', 'mirror'), default = "default")
     parser.add_argument("--cpus", help = "Number of parallel CPUs to use for rendering", type = int, default = 1)
     parser.add_argument("--use-gpu", help = "Whether to enable GPU rendering", action = "store_true")
@@ -243,6 +243,10 @@ def main():
     if args.rotations is not None:
         rotations = [yaml.safe_load(rotation) for rotation in args.rotations]
     
+    # Remove the starting cube object.
+    bpy.ops.object.select_all(action='SELECT')
+    bpy.ops.object.delete()
+
     # Load the input data.
     mol = add_molecule(
         args.cube_file,
@@ -326,6 +330,11 @@ def main():
     # Enable to add an outline.
     #bpy.context.scene.render.use_freestyle = True
     
+    # We have plenty of memory to play with, use one tile.
+    bpy.context.scene.cycles.tile_x = args.resolution
+    bpy.context.scene.cycles.tile_y = args.resolution
+    bpy.context.scene.cycles.tile_size = args.resolution
+
     # Performance options.
     bpy.context.scene.render.threads_mode = 'FIXED'
     bpy.context.scene.render.threads = args.cpus

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/file/prattle.py

@@ -155,22 +155,20 @@ class Openprattle_converter():
         inputs = self.input_file        
         
         # GO.
-        try:
-            done_process = subprocess.run(
-                sig,
-                input = inputs,
-                stdout = subprocess.PIPE,
-                stderr = subprocess.PIPE,
-                # TODO: Using universal newlines is probably not safe here; some formats are binary (.cdx etc...)
-                universal_newlines = True,
-                check = True,
-            )
-
-        except CalledProcessError as e:
-            self.handle_logging(e.stderr)
-            raise
+        done_process = subprocess.run(
+            sig,
+            input = inputs,
+            stdout = subprocess.PIPE,
+            stderr = subprocess.PIPE,
+            # TODO: Using universal newlines is probably not safe here; some formats are binary (.cdx etc...)
+            universal_newlines = True,
+        )
 
+        # This can throw exceptions.
         self.handle_logging(done_process.stderr)
+
+        if done_process.returncode != 0:
+            raise Digichem_exception("prattle subprocess returned code {}".format(done_process.returncode))
         
         # Return our output.
         return done_process.stdout if output_file is None else None
@@ -178,17 +176,20 @@ class Openprattle_converter():
     def handle_logging(self, raw_output):
         """
         """
+        exceptions = []
         for raw_message in raw_output.split("\n"):
             if raw_message == "":
                 # Nothing returned, nothing to do.
-                return
+                continue
             
             # Each message should be in JSON, but check.
             try:
                 message = json.loads(raw_message)
                 message_text = message['message']
                 if message['exception']:
-                    message_text += "\n" + message['exception']
+                    exceptions.append(Exception(message['exception']))
+                    continue
+                    #message_text += "\n" + message['exception']
                 digichem.log.get_logger().log(
                     message['levelno'],
                     message_text
@@ -196,6 +197,9 @@ class Openprattle_converter():
 
             except Exception:
                 digichem.log.get_logger().error("Unexpected output from oprattle: '{}'".format(raw_message), exc_info=False)
+
+        if len(exceptions) > 0:
+            raise exceptions[0]
     
 
 

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/input/digichem_input.py

@@ -496,5 +496,5 @@ def si_from_file(file_name, file_type = None, *, gen3D = None, **kwargs):
                 return Digichem_coords.from_com(com_file, file_name = file_name, **kwargs)
             
         except:
-            raise ValueError("Could not parse input coordinates from '{}'".format(file_name))
+            raise ValueError("Could not parse coordinates from '{}'".format(file_name))
     

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/result/atom.py

@@ -501,7 +501,7 @@ class Atom_list(Result_container, Unmergeable_container_mixin, Molecule_mixin):
         # Then coordinates.
         # No effort is made here to truncate coordinates to a certain precision.
         for atom in self:
-            xyz += "{}    {:f}    {:f}    {:f}\n".format(atom.element.symbol, atom.coords[0], atom.coords[1], atom.coords[2])
+            xyz += "{}    {:f}    {:f}    {:f}\n".format(atom.element.symbol, float(atom.coords[0]), float(atom.coords[1]), float(atom.coords[2]))
         
         return xyz
     
@@ -698,7 +698,7 @@ class Atom(Atom_ABC):
         :param data: The data to parse.
         :param result_set: The partially constructed result set which is being populated.
         """
-        return [self(atom_dict.get('index', index +1), atom_dict['element'], (atom_dict['coords']['x']['value'], atom_dict['coords']['y']['value'], atom_dict['coords']['z']['value']), atom_dict['mass']['value']) for index, atom_dict in enumerate(data)]
+        return [self(atom_dict.get('index', index +1), atom_dict['element'], (float(atom_dict['coords']['x']['value']), float(atom_dict['coords']['y']['value']), float(atom_dict['coords']['z']['value'])), atom_dict['mass']['value']) for index, atom_dict in enumerate(data)]
     
     @classmethod
     def list_from_parser(self, parser):
@@ -729,7 +729,7 @@ class Atom(Atom_ABC):
         zip_data = zip_longest(atomnos, atomcoords, atommasses, fillvalue = None)
         
         # Loop through and rebuild our objects.
-        return [self(index+1, atomic_number, tuple(coords), mass) for index, (atomic_number, coords, mass) in enumerate(zip_data)]
+        return [self(index+1, atomic_number, (float(coords[0]), float(coords[1]), float(coords[2])), mass) for index, (atomic_number, coords, mass) in enumerate(zip_data)]
     
     @classmethod
     def list_from_coords(self, coords):

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/result/metadata.py

@@ -162,6 +162,7 @@ class Metadata(Result_object):
             pressure = None,
             orbital_spin_type = None,
             digichem_version = None,
+            silico_version = None,
             solvent = None,
             num_cpu = None,
             memory_available = None,
@@ -221,6 +222,8 @@ class Metadata(Result_object):
         self.pressure = pressure
         self.orbital_spin_type = orbital_spin_type
         # TOOD: Ideally this would be parsed from the calculation output somehow, but this is fine for now.
+        if silico_version:
+            self.digichem_version = silico_version
         self.digichem_version = digichem.__version__ if digichem_version is None else digichem_version
         self.solvent = solvent
         self.num_cpu = num_cpu

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/test/test_translate.py

@@ -99,7 +99,7 @@ def test_grid_points():
     
     assert default.translate("gaussian")    == 0
     assert default.translate("orca")        == 100
-    assert default.translate("turbomole")   == 100
+    assert default.translate("turbomole")   == "m3"
     
     # Check the named values.
     for name, value in [("Tiny", 25), ("Small", 50), ("Medium", 100), ("Large", 200), ("Huge", 500)]:

{digichem_core-6.0.0rc1 → digichem_core-6.0.1}/digichem/translate.py

@@ -146,7 +146,7 @@ class Basis_set(Translate):
                 basis_set["turbomole"] = basis_set['name'][:-5] + "**"
                 
             # Gaussian has a strange, contracted style naming scheme for Karlsruhe,
-            # and a misleading/incorrect name for def2-SVP(P).
+            # and a misleading/incorrect name for def2-SV(P).
             #print(basis_set['name'])
             if basis_set['name'] == "def2-SV(P)":
                 basis_set['gaussian'] = "def2SVPP"
@@ -452,12 +452,12 @@ class Cube_grid_points(Translate):
     """A class for converting between cube grid sizes."""
     
     table = [
-        {"name": "Default",     "points": 100,      "gaussian": 0,       "turbomole": 100,      "orca": 100},   # Default depends on the calc program. Gaussian uses a special value of 'zero' to select a default algorithm.
-        {"name": "Tiny",        "points": 25},
-        {"name": "Small",       "points": 50},
-        {"name": "Medium",      "points": 100},
-        {"name": "Large",       "points": 200},
-        {"name": "Huge",        "points": 500},
+        {"name": "Default",     "points": 100,      "gaussian": 0,       "turbomole": "m3",      "orca": 100},   # Default depends on the calc program. Gaussian uses a special value of 'zero' to select a default algorithm.
+        {"name": "Tiny",        "points": 25,                            "turbomole": "1",                  },
+        {"name": "Small",       "points": 50,                            "turbomole": "2",                  },
+        {"name": "Medium",      "points": 100,                           "turbomole": "3",                  },
+        {"name": "Large",       "points": 200,                           "turbomole": "4",                  },
+        {"name": "Huge",        "points": 500,                           "turbomole": "5",                  },
         
     ]