digichem-core 7.0.3__py3-none-any.whl → 7.2.0__py3-none-any.whl

digichem/__init__.py

@@ -11,16 +11,7 @@ from digichem.datas import get_resource
 ####################
 
 
-# # Version information.
-# major_version = 6
-# minor_version = 0
-# revision = 0
-# prerelease = 1
-# # Whether this is a development version.
-# 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__ = "7.0.3"
+__version__ = "7.2.0"
 _v_parts = __version__.split("-")[0].split(".")
 major_version = int(_v_parts[0])
 minor_version = int(_v_parts[1])
@@ -39,7 +30,7 @@ __author__ = [
 ]
 
 # Program date (when we were last updated). This is changed automatically.
-_last_updated_string = "13/11/2025"
+_last_updated_string = "18/12/2025"
 last_updated = datetime.strptime(_last_updated_string, "%d/%m/%Y")
 
 # The sys attribute 'frozen' is our flag, '_MEIPASS' is the dir location.

digichem/config/base.py

@@ -249,7 +249,7 @@ To disable the maximum width, set to null.""", type = int, default = 1500),
     
     nmr = Options(help = "Options for controlling simulated NMR spectra",
         enable_rendering = Option(help = "Set to False to disable image rendering.", type = bool, default = True),
-        coupling_filter = Option(help = "Discard J coupling that is below this threshold (in Hz)", type = float, default = 1),
+        coupling_filter = Option(help = "Discard J coupling that is below this threshold (in Hz)", type = float, default = 0.1),
         fwhm = Option(help = "The full-width at half-maximum; changes how wide the drawn peaks are. Note that the choice of peak width is essentially arbitrary; only the peak height is given by calculation. Units are ppm.", type = float, default = 0.01),
         y_filter = Option(help = "The minimum y value to simulate using the Gaussian function (y values below this are discarded)", type = float, default = 1e-6),
         gaussian_cutoff = Option(help = "The minimum y value to plot using the Gaussian function (controls how close to the x axis we draw the gaussian) as a fraction of the max peak height.", type = float, default = 0.001),
@@ -271,7 +271,7 @@ To disable the maximum width, set to null.""", type = int, default = 1500),
         isotopes = Option(help = "Isotope specific options. Each key should consist of a tuple of (proton_number, isotope).", type = Nested_dict_type, default = Nested_dict_type({
             # Resonance frequencies calculated at 9.3947 T.
             # 1H, increase fidelity to see more detail.
-            "1H": {"frequency": 400, "fwhm": 0.005, "gaussian_resolution": 0.0005, "coupling_filter": 0.001, "pre_merge": 0.0005},
+            "1H": {"frequency": 400, "fwhm": 0.0015, "gaussian_resolution": 0.0001, "coupling_filter": 0.001, "pre_merge": 0.0005},
             # 11B.
             "11B": {"frequency": 128.3},
             # 13C.

digichem/image/spectroscopy.py

@@ -435,7 +435,7 @@ class NMR_graph_maker_abc(Spectroscopy_graph_maker):
             label = r"$\mathdefault{{{{{}}}_{{{}}}}}$ ({})".format(atom_group.element, atom_group.index, mult_string)
             #label += "\n" + r"$\int$ = {}{}".format(len(atom_group.atoms), atom_group.element.symbol)
             #label += "\n{:.2f} ppm".format(x_coord) + r", $\int$ = {}{}".format(len(atom_group.atoms), atom_group.element.symbol)
-            label += "\n{:.2f} ppm".format(x_coord) + r", {}{}".format(len(atom_group.atoms), atom_group.element.symbol)
+            label += "\n{:.2f} ppm".format(x_coord) + r", ∫ = {}{}".format(len(atom_group.atoms), atom_group.element.symbol)
         
         else:
             label = r"$\mathdefault{{{{{}}}_{{{}}}}}$".format(atom_group.element, atom_group.index)
@@ -572,9 +572,13 @@ class NMR_graph_maker(NMR_graph_maker_abc):
         # We always want to make sure that zero is shown however.
         #
         # NMR is also typically shown on a reversed scale.
+
+        # First, work out how wide our graph will be.
+        min_x = min(min(visible_x_values), 0)
+        max_x = max(max(visible_x_values), 0)
               
         x_padding = (
-            max(visible_x_values) - min(visible_x_values)
+            max_x - min_x
         ) * self.x_padding_percent
         
         # If we have no negative shifts, set zero as the end of one scale.
@@ -634,7 +638,7 @@ class NMR_graph_zoom_maker(NMR_graph_maker_abc):
         self.focus = focus
         
         self.x_padding = None
-        self.x_padding_percent = 1.0
+        self.x_padding_percent = 0.5
         
         self.target_width = 3.5
         
@@ -668,10 +672,11 @@ class NMR_graph_zoom_maker(NMR_graph_maker_abc):
         
         # We need to get a list of all peaks that are above our cutoff point.
         # First determine our highest point.
-        highest_point = max(self.transpose(graph.coordinates)[1])
+        coords = graph.plot_cumulative_gaussian()
+        highest_point = max(self.transpose(coords)[1])
         
         # Now filter by a fraction of that amount.
-        visible_x_values = [x for x, y in graph.plot_cumulative_gaussian() if y >= (highest_point * self.peak_cutoff)]
+        visible_x_values = [x for x, y in coords if y >= (highest_point * self.peak_cutoff)]
         
         x_padding = (
             max(visible_x_values) -min(visible_x_values)
@@ -721,9 +726,11 @@ class NMR_graph_zoom_maker(NMR_graph_maker_abc):
         
         
         highest_point = max(spectrum[1])
+
+        height = highest_point * 1.3
         
         # Clamp to 0 -> pos.
-        self.axes.set_ylim(0, highest_point * 1.3)
+        self.axes.set_ylim(0 - height * 0.025, height)
         
     def plot_lines(self):
         """
@@ -796,8 +803,8 @@ class NMR_graph_zoom_maker(NMR_graph_maker_abc):
         if len(couplings) > 0 and mult[0]["number"] != 1:
             # Only show couplings for peaks we can actually distinguish.
             for (coupling_group, coupling_isotope), coupling in list(couplings.items())[:len(mult)]:
-            #for (coupling_group, coupling_isotope), coupling in [isotope_coupling for atom_dict in couplings.values() for isotope_coupling in atom_dict.items()][:len(mult)]:
-                label += "\n" + r"J = {:.2f} Hz ($\mathdefault{{^{{{}}}{}_{{{}}}}}$, {}{})".format(
+                label += "\n" + r"$\mathdefault{{^{{{}}}}}$J = {:.2f} Hz ($\mathdefault{{^{{{}}}{}_{{{}}}}}$, {}{})".format(
+                    coupling.distance if coupling.distance is not None else "",
                     coupling.total,
                     coupling_isotope,
                     coupling_group.element,

digichem/input/gaussian.py

@@ -130,11 +130,51 @@ class Gaussian_input_parser():
         
         # And anything else.
         self.additional_sections = sections[3:]
+    
+    def geometry_with_iso(self, isotopes = {}):
+        """
+        Get the geometry of this gaussian input file with specific isotopes.
+
+        :param isotopes: Isotope information. Each key should be an atomic index, or an element symbol, and each value the corresponding isotope (as an integer).
+        """
+        lines = []
+        for index, line in enumerate(self.geometry.split("\n")):
+            split_line = line.split()
+            atom = split_line[0]
+            if "(" in atom and ")" in atom:
+                atom = atom[atom.find("("):]
+
+            iso = None
+            if index in isotopes:
+                iso = isotopes[index]
+            
+            elif atom in isotopes:
+                iso = isotopes[atom]
+            
+            if iso is not None:
+                atom = "{}(iso={})".format(atom, iso)
+            
+
+            lines.append("    ".join(
+                [atom, *split_line[1:]]
+            ))
+        
+        return "\n".join(lines)
+
         
     @property
     def xyz(self):
         """
         Get the geometry of this gaussian input file in XYZ format.
         """
-        return "{}\n\n{}".format(len(self.geometry.split("\n")), self.geometry)
+        lines = []
+        for line in self.geometry.split("\n"):
+            split_line = line.split()
+            atom = split_line[0]
+            if "(" in atom and ")" in atom:
+                atom = atom[atom.find("("):]
+            lines.append("    ".join(
+                [atom, *split_line[1:]]
+            ))
+        return "{}\n\n{}".format(len(self.geometry.split("\n")), "\n".join(lines))
 

digichem/misc/base.py

@@ -1,4 +1,5 @@
 from itertools import chain, combinations
+import math
 
 def powerset(iterable):
     "powerset([1,2,3]) --> () (1,) (2,) (3,) (1,2) (1,3) (2,3) (1,2,3)"
@@ -26,6 +27,17 @@ def regular_range(median, number, spacing):
             peaks.append(median - magnitude * spacing)
         
     return sorted(peaks)
+
+def round_sig(number, sig_figs):
+    """Round a number to a given number of significant figures."""
+    try:
+        return round(number, sig_figs-int(math.floor(math.log10(abs(number))))-1)
+
+    except ValueError:
+        if number == 0:
+            return 0
+        else:
+            raise
     
 
 def dict_list_index(dictionary, item):

digichem/parse/base.py

@@ -32,7 +32,7 @@ custom_parsing_formats = [
 class Parser_abc():
     """ABC for all parsers."""
 
-    def __init__(self, *, raw_data = None, options, **kwargs):
+    def __init__(self, *, raw_data = None, options, metadata_defaults = None, **kwargs):
         """
         Top level constructor for calculation parsers.
         """
@@ -44,6 +44,9 @@ class Parser_abc():
 
         # Config options.
         self.options = options
+
+        # Manually provided overrides.
+        self.metadata_defaults = metadata_defaults if metadata_defaults is not None else {}
         
         # Parse (if we haven't already).
         try:
@@ -102,6 +105,11 @@ class Parser_abc():
         # Add current username.
         # TODO: It would probably be better if we used the name of the user who owns the output file, rather than the current user...
         self.data.metadata['user'] = self.get_current_username()
+
+        # Add any user supplied defaults.
+        metadata = self.metadata_defaults.copy()
+        metadata.update(self.data.metadata)
+        self.data.metadata = metadata
             
     def process_all(self):
         """
@@ -181,7 +189,7 @@ class Parser_abc():
 class File_parser_abc(Parser_abc):
     """ABC for all parsers."""
     
-    def __init__(self, *log_files, raw_data = None, **kwargs):
+    def __init__(self, *log_files, raw_data = None, metadata_defaults = None, **kwargs):
         """
         Top level constructor for calculation parsers.
         
@@ -194,7 +202,7 @@ class File_parser_abc(Parser_abc):
         if len(self.log_file_paths) == 0:
             raise Digichem_exception("Cannot parse calculation output; no available log files. Are you sure the given path is a log file or directory containing log files?")
         
-        super().__init__(raw_data=raw_data, **kwargs)
+        super().__init__(raw_data=raw_data, metadata_defaults = metadata_defaults, **kwargs)
 
     @classmethod
     def from_logs(self, *log_files, **kwargs):

digichem/parse/cclib.py

@@ -22,7 +22,7 @@ class Cclib_parser(File_parser_abc):
     # A dictionary of recognised auxiliary file types.
     INPUT_FILE_TYPES = {}
     
-    def __init__(self, *log_files, options, **auxiliary_files):
+    def __init__(self, *log_files, options, metadata_defaults = None, **auxiliary_files):
         """
         Top level constructor for calculation parsers.
         
@@ -36,7 +36,7 @@ class Cclib_parser(File_parser_abc):
         # Also have a look for a profile.csv file that we can us for performance metrics.
         self.profile_file = Path(log_files[0].parent, "../Logs/profile.csv")
         
-        super().__init__(*log_files, options = options)
+        super().__init__(*log_files, options = options, metadata_defaults = metadata_defaults)
         
     @classmethod
     def from_logs(self, *log_files, hints = None, options, **kwargs):

digichem/parse/gaussian.py

@@ -29,9 +29,9 @@ class Gaussian_parser(Cclib_parser):
     CPU_TIME_HEADER = "Job cpu time:"
     CPU_HEADER = "Will use up to"
 
-    def __init__(self, *log_files, rwfdump = "rwfdump", options, **auxiliary_files):
+    def __init__(self, *log_files, rwfdump = "rwfdump", options, metadata_defaults = None, **auxiliary_files):
         self.rwfdump = rwfdump
-        super().__init__(*log_files, options = options, **auxiliary_files)
+        super().__init__(*log_files, options = options, metadata_defaults = metadata_defaults, **auxiliary_files)
     
     def parse_metadata(self):
         """

digichem/parse/pyscf.py

@@ -18,11 +18,23 @@ class Pyscf_parser(Parser_abc):
         super().__init__(**kwargs)
 
     def _parse(self):
+        """
+        Extract results from our output files.
+        """
         self.data = cclibfrommethods(**self.methods)
-        
+    
+    def post_parse(self):
+        """
+        Perform any required operations after line-by-line parsing.
+        """ 
+        super().post_parse()
+        # Set some metadata objects.
+        self.data.metadata['name'] = self.mol_name
+        self.data._aux = {'methods': self.methods}
+
         try:
             # Try to generate a checksum from metadata.
-            self.data._id = hashlib.sha1(json.dumps(self.data.metadata, sort_keys = True).encode('utf-8')).hexdigest()
+            self.data._id = hashlib.sha1(json.dumps(self.data.metadata, sort_keys = True, default = str).encode('utf-8')).hexdigest()
 
         except Exception:
             # No luck, something in metadata must be unhashable.
@@ -30,6 +42,4 @@ class Pyscf_parser(Parser_abc):
             # TODO: Think of a better way to do this.
             self.data._id = hashlib.sha1(uuid4().hex.encode('utf-8')).hexdigest()
         
-        self.data.metadata['name'] = self.mol_name
-        self.data._aux = {'methods': self.methods}
             

digichem/result/atom.py

@@ -255,6 +255,14 @@ class Atom_list(Result_container, Unmergeable_container_mixin, Molecule_mixin):
             
         return self._groups
     
+    @property
+    def bond_matrix(self):
+        """
+        Get the bond distance matrix for this molecule, which indicates how many bonds separate each atom in the molecule.
+        """
+        from rdkit import Chem
+        return Chem.rdmolops.GetDistanceMatrix(self.to_rdkit_molecule())
+    
     def find(self, criteria = None, *, label = None, index = None):
         """
         Find an atom that matches a given criteria

digichem/result/excited_state.py

@@ -386,12 +386,12 @@ class Excited_state_transition(Result_object):
         }
         
     @classmethod
-    def list_from_parser(self, parser, threshold = 1e-4):
+    def list_from_parser(self, parser, threshold = 1e-3):
         """
         Create a list of excited state transitions from an output file parser.
         
         :param parser: An output file parser.
-        :param threshold: The threshold below which transitions will be discarded.
+        :param threshold: The probability threshold below which transitions will be discarded.
         :return: A list of Excited_state_transition objects.
         """
         try:

digichem/result/nmr.py

@@ -5,6 +5,7 @@ from fractions import Fraction
 import re
 import statistics
 import math
+from configurables.misc import is_int
 
 from digichem.misc.base import regular_range, powerset
 from digichem.exception.base import Result_unavailable_error
@@ -545,6 +546,9 @@ class NMR_list(Result_container):
         # First, decide which atoms are actually equivalent.
         # We can do this by comparing canonical SMILES groupings.
         atom_groups = self.atoms.groups
+
+        # Also get the bond distance matrix for the molecule, so we can work out which couplings are actually equivalent.
+        bond_matrix = self.atoms.bond_matrix
         
         nmr_groups = {}
         # Next, assemble group objects.
@@ -565,12 +569,34 @@ class NMR_list(Result_container):
         # We need to do this after initial group assembly in order to discard self coupling.
         # Get unique couplings (so we don't consider any twice).
         group_couplings = {}
-        unique_couplings = {(coupling.atoms, coupling.isotopes): coupling for group in nmr_groups.values() for coupling in group['couplings']}.values()        
+        unique_couplings = list({(coupling.atoms, coupling.isotopes): coupling for group in nmr_groups.values() for coupling in group['couplings']}.values())
         for coupling in unique_couplings:
             # Find the group numbers that correspond to the two atoms in the coupling.
-            coupling_groups = tuple([atom_group.id for atom_group in atom_groups.values() if atom in atom_group.atoms][0] for atom in coupling.atoms)
-            
-            isotopes = coupling.isotopes
+            coupling_groups = tuple(
+                [atom_group.id for atom_group in atom_groups.values() if atom in atom_group.atoms][0] for atom in coupling.atoms
+            )
+
+            # We need to ensure that coupling_groups is a unique representation of the coupling,
+            # the ordering should be fixed.
+            indices = [
+                int(coupling_groups[0] >= coupling_groups[1]),
+                int(coupling_groups[0] < coupling_groups[1])
+            ]
+            coupling_groups = (
+                coupling_groups[indices[0]],
+                coupling_groups[indices[1]]
+            )
+            isotopes = (
+                coupling.isotopes[indices[0]],
+                coupling.isotopes[indices[1]]
+            )
+
+            # The group key contains the two atom groups, and the distance between them.
+            coupling_groups = (
+                coupling_groups[0],
+                coupling_groups[1],
+                float(bond_matrix[coupling.atoms[0].index -1][coupling.atoms[1].index -1])
+            )
             
             # Append the isotropic coupling constant to the group.
             if coupling_groups not in group_couplings:
@@ -582,12 +608,14 @@ class NMR_list(Result_container):
             group_couplings[coupling_groups][isotopes].append(coupling)
             
         # Average each 'equivalent' coupling.
-        group_couplings = {
+        average_couplings = {
             group_key: {
                 isotope_key: NMR_group_spin_coupling(
-                    groups = [atom_groups[group_sub_key] for group_sub_key in group_key],
+                    # TODO: Add in bond distance.
+                    groups = [atom_groups[group_sub_key] for group_sub_key in group_key[:2]],
                     isotopes = isotope_key,
-                    couplings = isotope_couplings
+                    couplings = isotope_couplings,
+                    distance = group_key[2]
                 ) for isotope_key, isotope_couplings in  isotopes.items()}
             for group_key, isotopes in group_couplings.items()
         }
@@ -599,11 +627,11 @@ class NMR_list(Result_container):
             
             coupling = [
                 isotope_coupling
-                for group_key, group_coupling in group_couplings.items()
+                for group_key, group_coupling in average_couplings.items()
                     for isotope_coupling in group_coupling.values()
-                        if group_id in group_key
+                        if group_id in group_key[:2]
             ]
-            nmr_object_groups[raw_group['group']] = (NMR_group(raw_group['group'], raw_group['shieldings'], coupling))
+            nmr_object_groups[raw_group['group']] = NMR_group(raw_group['group'], raw_group['shieldings'], coupling)
         
         return nmr_object_groups
     
@@ -650,7 +678,10 @@ class NMR_group(Result_object, Floatable_mixin):
     def __init__(self, group, shieldings, couplings):
         self.group = group
         self.shieldings = shieldings
-        self.couplings = couplings
+        self.couplings = sorted(
+            couplings,
+            key = lambda coupling: abs(coupling.total)
+        )
         
         # Calculate average shieldings and couplings.
         self.shielding = float(sum([shielding.isotropic("total") for shielding in shieldings]) / len(shieldings))
@@ -678,15 +709,17 @@ class NMR_group_spin_coupling(Result_object):
     A result object containing the average coupling between two different groups of nuclei.
     """
     
-    def __init__(self, groups, isotopes, couplings):
+    def __init__(self, groups, isotopes, couplings, distance = None):
         """
         :param groups: The two atom groups that this coupling is between.
         :param isotopes: The isotopes of the two groups (the order should match that of groups).
         :param couplings: A list of individual coupling constants between the atoms of these two groups.
+        :param distance: The bond distance between the two atoms.
         """
         self.groups = groups
         self.isotopes = isotopes
         self.couplings = couplings
+        self.distance = int(distance) if distance is not None and is_int(distance) else distance
         
     @property
     def total(self):
@@ -705,6 +738,10 @@ class NMR_group_spin_coupling(Result_object):
             "total": {
                 "units": "Hz",
                 "value": float(self.total),
+            },
+            "distance": {
+                "units": "bonds",
+                "value": self.distance
             }
             #"couplings": [coupling.dump(digichem_options, all) for coupling in self.couplings]
         }
@@ -721,7 +758,19 @@ class NMR_group_spin_coupling(Result_object):
         """
         Calculate the number of atoms one of the atom groups is coupled to.
         """
-        second_index = self.other(atom_group)
+        # second_index = self.other(atom_group)
+
+        # if [group.label for group in self.groups] == ["H9", "H10"] or [group.label for group in self.groups] == ["H10", "H9"]:
+        #     print()
+
+        # atoms = []
+        # for coupling in self.couplings:
+        #     for atom in coupling.atoms:
+        #         if atom not in atom_group.atoms:
+        #             atoms.append(atom)
+        
+        # return len(list(set(atoms)))
+
         return int(len(self.couplings) / len(atom_group.atoms))
         
     def multiplicity(self, atom_group):
@@ -845,11 +894,11 @@ class NMR_tensor_ABC(Result_object):
     tensor_names = ()
     units = ""
     
-    def __init__(self, tensors):
+    def __init__(self, tensors, total_isotropic = None):
         self.tensors = tensors
         
         # This is unused.
-        #self.total_isotropic = total_isotropic
+        self.total_isotropic = total_isotropic
     
     def eigenvalues(self, tensor = "total", real_only = True):
         """
@@ -862,10 +911,10 @@ class NMR_tensor_ABC(Result_object):
         
         except KeyError:
             if tensor not in self.tensor_names:
-                raise ValueError("The tensor '{}' is not recognised") from None
+                raise ValueError("The tensor '{}' is not recognised".format(tensor)) from None
             
             elif tensor not in self.tensors:
-                raise ValueError("The tensor '{}' is not available") from None
+                raise ValueError("The tensor '{}' is not available".format(tensor)) from None
         
     def isotropic(self, tensor = "total"):
         """
@@ -873,8 +922,17 @@ class NMR_tensor_ABC(Result_object):
         
         :param tensor: The name of a tensor to calculate for (see tensor_names). Use 'total' for the total tensor.
         """
-        eigenvalues = self.eigenvalues(tensor)
-        return sum(eigenvalues) / len(eigenvalues)
+        try:
+            eigenvalues = self.eigenvalues(tensor)
+            return sum(eigenvalues) / len(eigenvalues)
+
+        except ValueError:
+            if tensor == "total" and self.total_isotropic is not None:
+                # Use the fallback.
+                return self.total_isotropic
+
+            else:
+                raise
     
     def _dump_(self, digichem_options, all):
         """
@@ -895,12 +953,12 @@ class NMR_shielding(NMR_tensor_ABC):
     tensor_names = ("paramagnetic", "diamagnetic", "total")
     units = "ppm"
     
-    def __init__(self, tensors, reference = None):
+    def __init__(self, tensors, reference = None, total_isotropic = None):
         """
         :param tensors: A dictionary of tensors.
         :param reference: An optional reference isotropic value to correct this shielding by.
         """
-        super().__init__(tensors)
+        super().__init__(tensors, total_isotropic)
         self.reference = reference
         
     def isotropic(self, tensor = "total", correct = True):
@@ -910,8 +968,18 @@ class NMR_shielding(NMR_tensor_ABC):
         :param tensor: The name of a tensor to calculate for (see tensor_names). Use 'total' for the total tensor.
         :param correct: Whether to correct this shielding value by the reference.
         """
-        eigenvalues = self.eigenvalues(tensor)
-        absolute = sum(eigenvalues) / len(eigenvalues)
+        try:
+            eigenvalues = self.eigenvalues(tensor)
+            absolute = sum(eigenvalues) / len(eigenvalues)
+        
+        except ValueError:
+            if tensor == "total" and self.total_isotropic is not None:
+                # Use the fallback.
+                absolute = self.total_isotropic
+            
+            else:
+                raise None
+
         if correct and self.reference is not None:
             return self.reference - absolute
         else:
@@ -932,7 +1000,8 @@ class NMR_shielding(NMR_tensor_ABC):
                 total_isotropic = tensors.pop("isotropic")
                 shieldings[parser.results.atoms[atom_index]] = self(
                     tensors,
-                    reference = parser.options['nmr']['standards'].get(parser.results.atoms[atom_index].element.symbol, None)
+                    reference = parser.options['nmr']['standards'].get(parser.results.atoms[atom_index].element.symbol, None),
+                    total_isotropic = total_isotropic
                 )
         
         except AttributeError:
@@ -1036,13 +1105,13 @@ class NMR_spin_coupling(NMR_tensor_ABC):
     tensor_names = ("paramagnetic", "diamagnetic", "fermi", "spin-dipolar", "spin-dipolar-fermi", "total")
     units = "Hz"
     
-    def __init__(self, atoms, isotopes, tensors):
+    def __init__(self, atoms, isotopes, tensors, total_isotropic = None):
         """
         :param atoms: Tuple of atoms that this coupling is between.
         :param isotopes: Tuple of the specific isotopes of atoms.
         :param tensors: A dictionary of tensors.
         """
-        super().__init__(tensors)
+        super().__init__(tensors, total_isotropic = total_isotropic)
         self.atoms = atoms
         self.isotopes = isotopes
         
@@ -1059,7 +1128,14 @@ class NMR_spin_coupling(NMR_tensor_ABC):
             for atom_tuple, isotopes in parser.data.nmrcouplingtensors.items():
                 for isotope_tuple, tensors in isotopes.items():
                     total_isotropic = tensors.pop("isotropic")
-                    couplings.append(self((parser.results.atoms[atom_tuple[0]], parser.results.atoms[atom_tuple[1]]), isotope_tuple, tensors))
+                    couplings.append(
+                        self(
+                            (parser.results.atoms[atom_tuple[0]], parser.results.atoms[atom_tuple[1]]),
+                            isotope_tuple,
+                            tensors,
+                            total_isotropic = total_isotropic
+                        )
+                    )
         
         except AttributeError:
             return []

digichem/result/spectroscopy.py

@@ -420,7 +420,7 @@ class NMR_graph(Spectroscopy_graph):
     For plotting an entire spectrum, use a Combined_graph of NMR_graph objects.
     """
     
-    def multiplicity(self, atom_group, coupling, satellite_threshold = 0.02):
+    def multiplicity(self, atom_group, coupling, satellite_threshold = 0.05):
         """
         Determine the multiplicity of this peak.
         
@@ -456,7 +456,7 @@ class NMR_graph(Spectroscopy_graph):
         # For atoms in which the majority of the abundance is already accounted for (1H, for example),
         # exclude the residual peak.
         residual_isotope_peaks = set(
-            [atom_group for atom_group, isotopes in coupling.items() if sum((atom_group.element[isotope].abundance for isotope in isotopes.keys())) / 100 > satellite_threshold]
+            [a_group for a_group, isotopes in coupling.items() if sum((a_group.element[isotope].abundance for isotope in isotopes.keys())) / 100 > satellite_threshold]
         )
         
         # We will keep requesting more splitting until we are able to account for all the peaks we can see.

digichem/test/test_input.py

@@ -4,7 +4,7 @@ import pytest
 from pathlib import Path
 
 from digichem.test.util import pyridine_si_v2, pyridine_si_v1, pyridine_cml,\
-    result_files, ethane_xyz, benzene_cdx, cyclopentane_com
+    result_files, ethane_xyz, benzene_cdx, cyclopentane_com, cyclopentane_iso_com
 from digichem.input.digichem_input import si_from_file
 
 @pytest.mark.parametrize("file_path", [
@@ -66,6 +66,7 @@ def test_si_history(file_path, sha):
 
 @pytest.mark.parametrize("file_path, format", [
     (cyclopentane_com, "mol"),
+    (cyclopentane_iso_com, "mol"),
     (ethane_xyz, "cml"),
     (benzene_cdx, "xyz"),
     (result_files['gaussian'][0], "com")

digichem/test/test_result.py

@@ -465,8 +465,8 @@ def test_nmr_h_isotope_options(orca_nmr_result):
     # Check we have the right options set for H.
     options = orca_nmr_result.nmr.spectrometer.isotope_options(1, 1)
     assert options['frequency'] == 400
-    assert options['fwhm'] == 0.005
-    assert options['gaussian_resolution'] == 0.0005
+    assert options['fwhm'] == 0.0015
+    assert options['gaussian_resolution'] == 0.0001
     assert options['coupling_filter'] == 0.001
     assert options['pre_merge'] == 0.0005
 

digichem/test/util.py

@@ -18,6 +18,7 @@ def data_directory():
 benzene_cdx = Path(data_directory(), "Input", "Benzene.cdx")
 pyridine_cml = Path(data_directory(), "Input", "Pyridine.cml")
 cyclopentane_com = Path(data_directory(), "Input", "Cyclopentane.com")
+cyclopentane_iso_com = Path(data_directory(), "Input", "Cyclopentane_iso.com")
 water_xyz = Path(data_directory(), "Input", "Water.xyz")
 ethane_xyz = Path(data_directory(), "Input", "Ethane.xyz")
 pyridine_si_v2 = Path(data_directory(), "Input/Pyridine.v2.si")

{digichem_core-7.0.3.dist-info → digichem_core-7.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: digichem-core
-Version: 7.0.3
+Version: 7.2.0
 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
@@ -52,7 +52,7 @@ Welcome to Digichem: the computational chemistry management suite!
 This is Digichem-core, the open-source library for Digichem. If you are looking to build your own computational workflows using the tools that Digichem has to offer, then you have come to the right place.
 
  - 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)
+ - If you'd like more information on the Digichem project, check out the [website](https://digi-chem.co.uk)
 
 ## Documentation
 

{digichem_core-7.0.3.dist-info → digichem_core-7.2.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-digichem/__init__.py,sha256=B84Ts6PW2ZqvYT-BwIGGzLxtvueP4EqRsxu883KGKa4,2287
+digichem/__init__.py,sha256=ChTuRj6CsvNmgu2v8yY94WqAp_x78nVnyxhvEpo6XFU,1934
 digichem/basis.py,sha256=khzIS9A_w8QH2vsXctWr16Bw5TA84_9_Fo-vuveP_5w,4875
 digichem/datas.py,sha256=t2PuQFvPb55WO_qVF3Xz67XNodQDimqYD26VkRPEWLA,433
 digichem/log.py,sha256=tjl8Er16HUsAibBZGZMu8KyT0w53YM3u0Neh_l2jD9Q,6166
@@ -6,7 +6,7 @@ digichem/memory.py,sha256=_HJMwiElr0534lr3h17WwvXOi-DxCN-bAD1Ij8Lwg6U,5638
 digichem/translate.py,sha256=YKm7wko13A17zQJW8qOT52rzp9wDmR0GDzOepuzr75I,21326
 digichem/config/README,sha256=0y5sxYPAmpD3XNzgJrr-U8xmiQbheC8bz8lvnNmsNtc,180
 digichem/config/__init__.py,sha256=wXnmk1fuNZeHOKz06wBfTUkM8-XuW08F2H8QiHyS8Xs,227
-digichem/config/base.py,sha256=_ViUdljCObLGPzsqEFwqCKzbHRly3nPzALvRcJXW_U8,26036
+digichem/config/base.py,sha256=hJMeUMz1Y_D9aLMCQij7ccV6K85Y0ougAfqhqF6DSOA,26039
 digichem/config/locations.py,sha256=Jlvql0KJrJEIO_2U6BRS5bjHelKjGGIETR9hOuNe0K0,584
 digichem/config/parse.py,sha256=amJx89JXkkEyMMSYr5GvLFnLZO3hWahuZtNlx0F0PhA,2667
 digichem/config/util.py,sha256=E-5He3AbrwHNHFbBdfNMOimaDPXqtAi96l-4Acmn08o,4611
@@ -45,45 +45,45 @@ digichem/image/excited_states.py,sha256=1YUa8KYXTvh_Vwl2DSaRwpIh15FtW18KpjLlnD8V
 digichem/image/graph.py,sha256=3wcembS3gcI5Ejq1lv4Sw1g_7s-fubDpiho_85kzkks,10880
 digichem/image/orbitals.py,sha256=UcPnOm3tQOdTegsVm_a7AizVe7OpBCz_4sve6u7jAvA,9705
 digichem/image/render.py,sha256=fQu9QcuIolzoeMoaQPQo27Z-JEXUCQCWiSVWQgv2iG4,30470
-digichem/image/spectroscopy.py,sha256=fgrLGL1BSUHUmYMWpSSgAbNTu6uzmYxj5a9U94QL0fQ,33892
+digichem/image/spectroscopy.py,sha256=lB7O8QxeV0-B_jasr51XvBozfBjCOWwNgDW74HMxbqs,33998
 digichem/image/structure.py,sha256=gxgX5cXA3BaqBh5K7UPcVGWX-yG5kc6Robf5sWT1IYM,4900
 digichem/image/vmd.py,sha256=GGE35qypgBbpadHo1M929czuxM0U4NRICPkltKWEojE,39305
 digichem/input/__init__.py,sha256=DJMFLt-p2DZaTdvk2zIR6gdUepsa1n0e2_mk-BB45Sk,179
 digichem/input/base.py,sha256=9nxut3IlvKSYCjRUzpi7SdlaO_4MU8KWAecV-z3T1jo,3082
 digichem/input/digichem_input.py,sha256=kAoLmphdIHLB4RoxHTXohTcL-L5iaYSl8peIR3vJPx8,19628
-digichem/input/gaussian.py,sha256=ZwfCA0jgHcY8JVcyyKmnchU-OyQ26-8ynQJdeYtNT7A,5651
+digichem/input/gaussian.py,sha256=W3JqRdsfebs_2G3grlYRv_dR1FsTBbf8YrxCNGwSd0U,6963
 digichem/misc/__init__.py,sha256=gRlflbkXYyKvqeQ2KTnNAdJ00S6Vhmk-tzSVCBSiWgk,162
 digichem/misc/argparse.py,sha256=AG33L7MCi-ftb4XnvndQb4hKcorzJxESAVB0HIZRlcw,1371
-digichem/misc/base.py,sha256=ZaeeLJrRZnF66bhkGdPvhsVGgxzcV_pneESQ1ReDedc,1884
+digichem/misc/base.py,sha256=X75sM4X9aCQlzg8SrOnEr7GPFQkLBlaRXiE9tj8xj5o,2189
 digichem/misc/io.py,sha256=7Oqi7UQLwhCsVHdEN0n7Vubsbzk14fLSkAYXe4obPbQ,11007
 digichem/misc/layered_dict.py,sha256=Psf30UmHVHAE95RnFYiR2f7oaW05CsUhT4FtXhUtQcw,15561
 digichem/misc/text.py,sha256=FVcxf8ctt3D2yGFYgrZk3dpO48f_0aDhHiry_xGirD8,3673
 digichem/misc/time.py,sha256=Z7FWpkb8gqBHVMXdhFiBWn2VwmXuU9uaMxEKsfAH5Kw,2214
 digichem/parse/__init__.py,sha256=SIAj7do6mXRNuOEkN691Nh-je2YlZ3qL6fxnjsTE6QY,867
-digichem/parse/base.py,sha256=HV7dmHz2VqrVc2umlB93aZwe8thIqpWwrNuXKb7M0KI,8778
-digichem/parse/cclib.py,sha256=fwWtKPisNA9AYSgRnyC5D6A_CTIWf-2tGWdPzYwNg6o,10084
+digichem/parse/base.py,sha256=G7GULLX9YTSRote3o2MJk7nZ_wPrIKcG7Dyri5pyGCA,9175
+digichem/parse/cclib.py,sha256=g4a8r1IouVTz2N3Swmx8YVG5kZ5NnhBj6PoJpSP1eLY,10149
 digichem/parse/dump.py,sha256=PnVwas1sFZTG9dgjAn7VLxQ8gSzTNllE-tx_PXh51DI,9332
-digichem/parse/gaussian.py,sha256=TWrNIBrxm9bgKupX6J_9beAFp-4QL57hPOo3pPyjIRA,5279
+digichem/parse/gaussian.py,sha256=VaL0eotz2_b-OsWfzQioFU9JDDd3lYElrkXpLEy78fE,5344
 digichem/parse/orca.py,sha256=QahMQh-rZphDzyM8Kn6xEbEB9imCWpKUhUmlOxpDio0,4680
-digichem/parse/pyscf.py,sha256=Io13LOxnkSZ1lKFu1tSFzkDZKmFRqDyOVMBesiQIb7o,1197
+digichem/parse/pyscf.py,sha256=DFR9xvM4ewHMM9-CikdaYq9I3Q78Xe7XA73x0cnLiIM,1465
 digichem/parse/turbomole.py,sha256=dulO8Y5txEABnK4Ybbp97KwOmnCrJMVSJSI9427SVIo,9133
 digichem/parse/util.py,sha256=QSxrRN3HFllVlsWqzTC4EKjj9w7t4kFbXuvhsMTpLIY,28930
 digichem/result/__init__.py,sha256=FUNL2pc2bP3XNVFRrlyrTppVWEsPRHcThLiVytpsH84,222
 digichem/result/angle.py,sha256=jehU0dRN4nALvUFzIdkh4GGQORq4lgXre8ZfFQMzB94,5043
-digichem/result/atom.py,sha256=ZJqUj7kUAZGgzzt9P1CCjC-wyRBL26YJNzFDyOWD_gc,27990
+digichem/result/atom.py,sha256=TOlMiKYFe8vvBv9qCMBEJD1LYNzFtd7VePnUNCfCIbY,28287
 digichem/result/base.py,sha256=Lahahog9EHEQFP--DClyhiFIoJ0bRFJN37GH-Z2Nu2c,11615
 digichem/result/dipole_moment.py,sha256=1Z0qksmk7HYyov7318zWJQVXvteCo59DCCXd2rT2-hg,11082
 digichem/result/emission.py,sha256=XsyOgMtxV6wg9iBpPK-3WSbcIh6ohlZtGybMkuZaEbY,19785
 digichem/result/energy.py,sha256=iboiQF5Twa-TU9b_Utxg5B5U7RmL3LHtRp6XzmQHG0o,10899
-digichem/result/excited_state.py,sha256=oYE_kFIMX5yl3U9mANW8FpwLymOjsNEte6ZOEsyuhfM,34580
+digichem/result/excited_state.py,sha256=FtQuW3R6yMCJMXmqxutwIleyYWqzDBgQ6O36sjWCSq0,34592
 digichem/result/ground_state.py,sha256=B8lOalD90uNq_pMHy0JhwYYY3rlWpcFlOHPLSO5CjhQ,3804
 digichem/result/metadata.py,sha256=Aak2tviK2HXfbr2m97AbNW1myfWVsSBwgT1ISLRKG88,38602
 digichem/result/multi.py,sha256=IzupKHMcXTf6AReeUCjY9Szy2b4TdOHVtC2Tlb9xg0o,4330
-digichem/result/nmr.py,sha256=oVye1S0gmZmvoOBLyaUHe7k8Oiu7LjkaRcss__Fr5Qc,47784
+digichem/result/nmr.py,sha256=vvhfVQSsi3fQ1VU_5POAUvwsJuN7XFidLkpmZy4UBzQ,50659
 digichem/result/orbital.py,sha256=8oMAtYSi8hYWWsjXJC2z5UAA47h0axM24ALqIo7yxFY,28292
 digichem/result/result.py,sha256=92ZszBIHYOYAJx7s-bIggrUnPo5AgQjtT-bi-tp0Jq4,9861
 digichem/result/soc.py,sha256=bvz3qhpW5VjTM9c9fnLFX0XAggncT3osZxl_syxejSM,9942
-digichem/result/spectroscopy.py,sha256=Au3qMGgWPL3ZpfubFRBZuKEsYXA6kdQwBSWbgSf7P40,23080
+digichem/result/spectroscopy.py,sha256=XzJR2xF6QljXp0YNP0G8WjuN3JZjE1_ccrfcUeMxgh0,23071
 digichem/result/tdm.py,sha256=B5LEB_Rx-8z_5tjPfNj-Od1hu2QspLolqAJC1DLy0Fk,10809
 digichem/result/vibration.py,sha256=bKskcbis2L8mvs8xzzG9qBNXKIK8RN0-g_mpyw1Wric,6631
 digichem/result/alignment/AA.py,sha256=957GtXeaioyH1T6cBjK6Sf-W8a_3K9vR5fi8wttkKhk,4627
@@ -100,17 +100,17 @@ digichem/test/test_cube.py,sha256=y1Cr0cz00pwSWT-z-PgUQAzp41Ttsk_Ti_eQXagzO1Q,14
 digichem/test/test_exception.py,sha256=f-8XVQqq9gfJFpURjOoEfcC4pxieye8ZxvmguoN9QyY,530
 digichem/test/test_file.py,sha256=n2BJ55_AjNY7IGEjHjJJ-OhE4Lgn3pGyyyfnPIduges,3682
 digichem/test/test_image.py,sha256=bGb6xdn4k2VxZlVef0HI2HPrQdxx5XUTMyl97iYzzT8,13598
-digichem/test/test_input.py,sha256=wOxaym4Y64t-QDHZ88ne4BZjqLjwXOQM_PxTMeInJpk,2259
+digichem/test/test_input.py,sha256=TIYfWYAnVQ-Qo8EZakRK2DSZdHpDB3afIX3mFVuY244,2316
 digichem/test/test_memory.py,sha256=wKxAOtDm7d9aNbpgdgjacVPCBGdDUKx5f_3OGsGuWR0,582
 digichem/test/test_parsing.py,sha256=4cU8SJtGmF6WobVSYtFrG9DBNAxXBL-Xe_GKP1eg7kc,6656
 digichem/test/test_prattle.py,sha256=dlBd38vOcF4blfBqjr6uABc6aEWdLdTSdAc08XniWGs,1865
-digichem/test/test_result.py,sha256=DmaAdSTGV6UoHigiy6P38cT3y4ef57Ji6Ot4m2BZfLs,24327
+digichem/test/test_result.py,sha256=p71z2AxKr0mDI6hMSW4t3pXJQs53IutLXqVT0RNh95A,24328
 digichem/test/test_translate.py,sha256=_3FkYottqHZGxMSTJkbcE8dQXhQlrNlVS0FjMopIwl4,3575
-digichem/test/util.py,sha256=p7KgyR9VGPstD7y8FH0onIxgY4YCvSCmbtJ-kJggxeA,8798
+digichem/test/util.py,sha256=p1NfdSunB6WJM4BknyTDld7fGYWuvi2kHPu7pZcL9zE,8877
 digichem/test/mock/cubegen,sha256=h2HvmW8YbmYDqycnfCJYstZ2yO1uUxErbCWFKgzXaJ8,6781858
 digichem/test/mock/formchk,sha256=KZWhyJtaMXAGX1Xlx7Ikw9gbncOqLrpYkynz9IMYUlY,756867
-digichem_core-7.0.3.dist-info/METADATA,sha256=U8v1Q_XijfoHUIsIk6xen6LwW7EbTiQ1AK_kyvp4Fkk,4098
-digichem_core-7.0.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-digichem_core-7.0.3.dist-info/licenses/COPYING.md,sha256=d-yG6IJrlqLkuiuoOFe331YKzMRS05pnmk4e98gu9pQ,900
-digichem_core-7.0.3.dist-info/licenses/LICENSE,sha256=ZLlePQN2WLgdvmIGLEjjHtgIoneUGR2MgE9yjMg1JiY,1457
-digichem_core-7.0.3.dist-info/RECORD,,
+digichem_core-7.2.0.dist-info/METADATA,sha256=fB6uhPUZ02TY6dx1Uz-_mHDdsPiXPHpGUwMbN8N1ZcU,4094
+digichem_core-7.2.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+digichem_core-7.2.0.dist-info/licenses/COPYING.md,sha256=d-yG6IJrlqLkuiuoOFe331YKzMRS05pnmk4e98gu9pQ,900
+digichem_core-7.2.0.dist-info/licenses/LICENSE,sha256=ZLlePQN2WLgdvmIGLEjjHtgIoneUGR2MgE9yjMg1JiY,1457
+digichem_core-7.2.0.dist-info/RECORD,,

{digichem_core-7.0.3.dist-info → digichem_core-7.2.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any