digichem-core 6.10.3__py3-none-any.whl → 7.0.1__py3-none-any.whl

digichem/result/nmr.py

@@ -22,7 +22,7 @@ class NMR_spectrometer(Result_object):
     A class for generating NMR spectra on-demand.
     """
     
-    def __init__(self, nmr_results, frequency = 300, fwhm = 0.001, resolution = 0.001, cutoff = 0.01, coupling_filter = 0.1, pre_merge = 0.01, post_merge = None, isotope_options = None):
+    def __init__(self, nmr_results, frequency = 300, fwhm = 0.001, resolution = 0.001, cutoff = 0.01, y_filter = 1e-6, coupling_filter = 0.1, pre_merge = 0.01, post_merge = None, isotope_options = None):
         """
         Constructor for NMR_spectrometer.
         
@@ -39,6 +39,7 @@ class NMR_spectrometer(Result_object):
         self.fwhm = fwhm
         self.gaussian_resolution = resolution
         self.gaussian_cutoff = cutoff
+        self.y_filter = y_filter
         self.coupling_filter = coupling_filter
         self._isotope_options = isotope_options if isotope_options is not None else {}
         
@@ -48,6 +49,7 @@ class NMR_spectrometer(Result_object):
             "pre_merge": self.pre_merge,
             "post_merge": self.post_merge,
             "fwhm": self.fwhm,
+            "y_filter": self.y_filter,
             "gaussian_resolution": self.gaussian_resolution,
             "coupling_filter": self.coupling_filter,
             "gaussian_cutoff": self.gaussian_cutoff,
@@ -66,6 +68,7 @@ class NMR_spectrometer(Result_object):
             fwhm = options['nmr']['fwhm'],
             resolution = options['nmr']['gaussian_resolution'],
             cutoff = options['nmr']['gaussian_cutoff'],
+            y_filter = options['nmr']['y_filter'],
             coupling_filter = options['nmr']['coupling_filter'],
             pre_merge = options['nmr']['pre_merge'],
             post_merge = options['nmr']['post_merge'],
@@ -160,6 +163,9 @@ class NMR_spectrometer(Result_object):
         
         return False
     
+    def __iter__(self):
+        return iter(self.available.keys())
+    
     def __getitem__(self, item):
         """
         Generate a spectrum for a given shortcode.
@@ -170,7 +176,7 @@ class NMR_spectrometer(Result_object):
         # match the interface.
         return lambda digichem_options: self.spectrum(*self.parse_shortcode(item))
     
-    def generate_for_dump(self):
+    def _get_dump_(self):
         """
         Method used to get a dictionary used to generate on-demand values for dumping.
         
@@ -180,7 +186,7 @@ class NMR_spectrometer(Result_object):
         """
         return self
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         # Return a list of possible spectra we can generate.
         return {
             "codes": list(self.available.keys()),
@@ -208,7 +214,7 @@ class NMR_spectrometer(Result_object):
         
         # The total spectrum takes all simulated peaks.
         # These are grouped by atom_group, flatten this list before passing to spectroscopy.
-        graph = Combined_graph.from_nmr(grouped_peaks, isotope_options['fwhm'], isotope_options['gaussian_resolution'], isotope_options['gaussian_cutoff'])
+        graph = Combined_graph.from_nmr(grouped_peaks, isotope_options['fwhm'], isotope_options['gaussian_resolution'], isotope_options['gaussian_cutoff'], filter = isotope_options['y_filter'])
         
         return graph
     
@@ -489,6 +495,8 @@ class NMR_list(Result_container):
         self.options = options
         self.groups = self.group()
         self.spectrometer = NMR_spectrometer.from_options(self.groups, options = options)
+        # This is used as part of the dump mechanic.
+        self.spectrum = self.spectrometer
     
     @classmethod
     def from_parser(self, parser):
@@ -599,14 +607,15 @@ class NMR_list(Result_container):
         
         return nmr_object_groups
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Dump this list of NMR results to a list of primitive types.
         """
         grouping = self.groups
         dump_dict = {
-            "values": super().dump(digichem_options),
-            "groups": {group_id.label: group.dump(digichem_options) for group_id, group in grouping.items()},
+            "values": super()._dump_(digichem_options, all),
+            "groups": {group_id.label: group.dump(digichem_options, all) for group_id, group in grouping.items()},
+            "spectrum": self.spectrometer.dump(digichem_options, all)
         }
         return dump_dict
     
@@ -620,17 +629,17 @@ class NMR_list(Result_container):
         """
         return self(NMR.list_from_dump(data['values'], result_set, options), atoms = result_set.atoms, options = options)
     
-    def generate_for_dump(self):
-        """
-        Method used to get a dictionary used to generate on-demand values for dumping.
+    # def _get_dump_(self):
+    #     """
+    #     Method used to get a dictionary used to generate on-demand values for dumping.
          
-        This functionality is useful for hiding expense properties from the normal dump process, while still exposing them when specifically requested.
+    #     This functionality is useful for hiding expense properties from the normal dump process, while still exposing them when specifically requested.
          
-        Each key in the returned dict is the name of a dumpable item, each value is a function to call with digichem_options as its only param.
-        """
-        return {
-            "spectrum": lambda digichem_options: self.spectrometer
-        }
+    #     Each key in the returned dict is the name of a dumpable item, each value is a function to call with digichem_options as its only param.
+    #     """
+    #     return {
+    #         "spectrum": lambda digichem_options: self.spectrometer
+    #     }
 
 
 class NMR_group(Result_object, Floatable_mixin):
@@ -649,7 +658,7 @@ class NMR_group(Result_object, Floatable_mixin):
     def __float__(self):
         return float(self.shielding)
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -661,7 +670,7 @@ class NMR_group(Result_object, Floatable_mixin):
                 "value": self.shielding
             },
             #"couplings": [{"groups": [group.label for group in coupling['groups']], "isotopes": list(coupling["isotopes"]), "total": coupling["total"]} for coupling in self.couplings],
-            "couplings": [coupling.dump(digichem_options) for coupling in self.couplings]
+            "couplings": [coupling.dump(digichem_options, all) for coupling in self.couplings]
         }
         
 class NMR_group_spin_coupling(Result_object):
@@ -686,7 +695,7 @@ class NMR_group_spin_coupling(Result_object):
         """
         return sum([coupling.isotropic('total') for coupling in self.couplings]) / len(self.couplings)
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -697,7 +706,7 @@ class NMR_group_spin_coupling(Result_object):
                 "units": "Hz",
                 "value": float(self.total),
             }
-            #"couplings": [coupling.dump(digichem_options) for coupling in self.couplings]
+            #"couplings": [coupling.dump(digichem_options, all) for coupling in self.couplings]
         }
         
     def other(self, atom_group):
@@ -819,14 +828,14 @@ class NMR(Result_object, Floatable_mixin):
         ]
         
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
         return {
             "atom": self.atom.label,
-            "shielding": self.shielding.dump(digichem_options),
-            "couplings": self.couplings.dump(digichem_options)
+            "shielding": self.shielding.dump(digichem_options, all),
+            "couplings": self.couplings.dump(digichem_options, all)
         }
         
 
@@ -867,7 +876,7 @@ class NMR_tensor_ABC(Result_object):
         eigenvalues = self.eigenvalues(tensor)
         return sum(eigenvalues) / len(eigenvalues)
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -931,7 +940,7 @@ class NMR_shielding(NMR_tensor_ABC):
         
         return shieldings
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -939,7 +948,7 @@ class NMR_shielding(NMR_tensor_ABC):
             "reference": self.reference,
         }
         
-        dump_dic.update(super().dump(digichem_options))
+        dump_dic.update(super()._dump_(digichem_options, all))
         return dump_dic
     
     @classmethod
@@ -1073,7 +1082,7 @@ class NMR_spin_coupling(NMR_tensor_ABC):
             in data
         ]
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -1082,5 +1091,5 @@ class NMR_spin_coupling(NMR_tensor_ABC):
             "isotopes": (self.isotopes[0], self.isotopes[1]),
         }
         
-        dump_dic.update(super().dump(digichem_options))
+        dump_dic.update(super()._dump_(digichem_options, all))
         return dump_dic

digichem/result/orbital.py

@@ -238,7 +238,7 @@ class Molecular_orbital_list(Result_container):
         
         return self(cls.list_from_dump(data['values'], result_set, options))
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -249,7 +249,7 @@ class Molecular_orbital_list(Result_container):
             },
             "num_occupied": len(self.occupied),
             "num_virtual": len(self.virtual),
-            "values": super().dump(digichem_options),
+            "values": super()._dump_(digichem_options, all),
             "spin_type": self.safe_get("spin_type")
         }
 #         # Add HOMO and LUMO
@@ -498,7 +498,7 @@ class Molecular_orbital(Result_object, Floatable_mixin):
     # The index used to access data from cclib (which always has two lists, one for alpha one for beta).
     ccdata_index = 0
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """

digichem/result/result.py

@@ -221,7 +221,7 @@ class Result_set(Result_object):
             # No S1 available.
             return None
         
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         "Dump the data contained in this result set, serialising it to a hierarchy of dicts that can be saved in various formats."
         # Start with our DB ID if we have one.
         dump_dic = {}
@@ -229,19 +229,19 @@ class Result_set(Result_object):
             dump_dic['_id'] = self._id
             
         dump_dic.update({
-            "metadata": self.metadata.dump(digichem_options),
-            "ground_state": self.ground_state.dump(digichem_options) if self.ground_state is not None else None,
-            "energies": self.energies.dump(digichem_options),
-            "atoms": self.atoms.dump(digichem_options),
-            "raw_atoms": self.raw_atoms.dump(digichem_options),
-            "orbitals": self.orbitals.dump(digichem_options),
-            "beta_orbitals": self.beta_orbitals.dump(digichem_options),
-            "pdm": self.pdm.dump(digichem_options) if self.pdm is not None else None,
-            "excited_states": self.excited_states.dump(digichem_options),
-            "soc": self.soc.dump(digichem_options),
-            "vibrations": self.vibrations.dump(digichem_options),
-            "nmr": self.nmr.dump(digichem_options),
-            "emission": self.emission.dump(digichem_options)
+            "metadata": self.metadata.dump(digichem_options, all),
+            "ground_state": self.ground_state.dump(digichem_options, all) if self.ground_state is not None else None,
+            "energies": self.energies.dump(digichem_options, all),
+            "atoms": self.atoms.dump(digichem_options, all),
+            "raw_atoms": self.raw_atoms.dump(digichem_options, all),
+            "orbitals": self.orbitals.dump(digichem_options, all),
+            "beta_orbitals": self.beta_orbitals.dump(digichem_options, all),
+            "pdm": self.pdm.dump(digichem_options, all) if self.pdm is not None else None,
+            "excited_states": self.excited_states.dump(digichem_options, all),
+            "soc": self.soc.dump(digichem_options, all),
+            "vibrations": self.vibrations.dump(digichem_options, all),
+            "nmr": self.nmr.dump(digichem_options, all),
+            "emission": self.emission.dump(digichem_options, all)
         })
         
         return dump_dic

digichem/result/soc.py

@@ -104,7 +104,7 @@ class Spin_orbit_coupling(Result_object, Floatable_mixin):
         self.zero = zero
         self.negative_one = negative_one
         
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
@@ -235,11 +235,11 @@ class Total_spin_orbit_coupling(Spin_orbit_coupling):
         """
         return "<{}|Hso|{}> (cm-1): {:10.5f}".format(self.singlet_state.state_symbol, self.triplet_state.state_symbol, self.root_sum_square)
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
-        dump_dic = super().dump(digichem_options)
+        dump_dic = super()._dump_(digichem_options, all)
         # Remove elements.
         del(dump_dic['soc'])
         return dump_dic

digichem/result/spectroscopy.py

@@ -112,7 +112,7 @@ class Spectroscopy_graph(Spectroscopy_graph_abc):
     For generating pictures of these graphs, see digichem.image.spectroscopy
     """
     
-    def __init__(self, coordinates, fwhm, resolution = 1, cutoff = 0.01, adjust_zero = False):
+    def __init__(self, coordinates, fwhm, resolution = 1, cutoff = 0.01, filter = 1e-6, adjust_zero = False):
         """
         Constructor for Spectroscopy_graph objects
         
@@ -137,6 +137,7 @@ class Spectroscopy_graph(Spectroscopy_graph_abc):
         self.fwhm = fwhm
         self.resolution = resolution
         self.cutoff = cutoff
+        self.filter = filter
         
         # Caches
         self._gaussians = []
@@ -187,7 +188,7 @@ class Spectroscopy_graph(Spectroscopy_graph_abc):
         # Next, determine the limits in which we'll plot.
         limits = self.gaussian_limits()
         
-        # Apply rounding to nearest resolution step cover up floating-point errors.
+        # Apply rounding to nearest resolution step to cover up floating-point errors.
         points = [self.resolution *round(point / self.resolution) for point in numpy.linspace(*limits)]
         
         # Plot and return.
@@ -202,7 +203,7 @@ class Spectroscopy_graph(Spectroscopy_graph_abc):
             )
         )
         gaussians = [
-            [(x, self.gaussian(a, b, c, x)) for x in points]
+            [(x, y) for x in points if (y  := self.gaussian(a, b, c, x)) >= self.filter]
             for b, a in self.base_coordinates
         ]
         
@@ -232,7 +233,7 @@ class Spectroscopy_graph(Spectroscopy_graph_abc):
         # Plot and return.
         digichem.log.get_logger().debug("Plotting cumulative gaussian peaks from {:0.2f} to {:0.2f} with a step size of {} ({} total points) for {} peaks ({} total iterations)".format(limits[0], limits[1], self.resolution, limits[2], len(self.base_coordinates), len(self.base_coordinates) * limits[2]))
         gaussian = [
-            (x, sum((self.gaussian(a, b, c, x) for b, a in self.base_coordinates))) for x in points
+            (x, y) for x in points if ( y := sum((self.gaussian(a, b, c, x) for b, a in self.base_coordinates))) > self.filter
         ]
         
         return gaussian

digichem/result/tdm.py

@@ -42,12 +42,12 @@ class Transition_dipole_moment_ABC(Dipole_moment_ABC):
             atoms = result_set.atoms
             )
         
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
         data = {'state_level': self.state_level}
-        data.update(super().dump(digichem_options))
+        data.update(super()._dump_(digichem_options, all))
         return data
     
     @property
@@ -221,13 +221,13 @@ class Transition_dipole_moment(Result_object):
         
         return self(electric = electric, magnetic = magnetic)
         
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """
         return {
-            "electric": self.electric.dump(digichem_options) if self.electric is not None else None,
-            "magnetic": self.magnetic.dump(digichem_options) if self.magnetic is not None else None,
+            "electric": self.electric.dump(digichem_options, all) if self.electric is not None else None,
+            "magnetic": self.magnetic.dump(digichem_options, all) if self.magnetic is not None else None,
             "angle": {
                 "value": float(self.angle().angle) if self.electric is not None and self.magnetic is not None else None,
                 "units": self.angle().units if self.electric is not None and self.magnetic is not None else None,

digichem/result/vibration.py

@@ -43,7 +43,7 @@ class Vibrations_list(Result_container, Unmergeable_container_mixin):
         """
         return self(Vibration.list_from_parser(parser))
     
-    def generate_for_dump(self):
+    def _get_dump_(self):
         """
         Method used to get a dictionary used to generate on-demand values for dumping.
         
@@ -51,7 +51,9 @@ class Vibrations_list(Result_container, Unmergeable_container_mixin):
         
         Each key in the returned dict is the name of a dumpable item, each value is a function to call with digichem_options as its only param.
         """
-        return {"spectrum": self.generate_spectrum}
+        return {
+            "spectrum": self.generate_spectrum,
+        }
     
     def generate_spectrum(self, digichem_options):
         """
@@ -65,7 +67,14 @@ class Vibrations_list(Result_container, Unmergeable_container_mixin):
         from digichem.result.spectroscopy import Spectroscopy_graph
         
         
-        spectrum = Spectroscopy_graph.from_vibrations(self, digichem_options['IR_spectrum']['fwhm'], digichem_options['IR_spectrum']['gaussian_resolution'], digichem_options['IR_spectrum']['gaussian_cutoff'])
+        spectrum = Spectroscopy_graph.from_vibrations(
+            self,
+            fwhm = digichem_options['IR_spectrum']['fwhm'],
+            resolution = digichem_options['IR_spectrum']['gaussian_resolution'],
+            cutoff = digichem_options['IR_spectrum']['gaussian_cutoff'],
+            filter = digichem_options['IR_spectrum']['y_filter'],
+        )
+        
         
         try:
             spectrum_data = spectrum.plot_cumulative_gaussian()
@@ -82,11 +91,11 @@ class Vibrations_list(Result_container, Unmergeable_container_mixin):
             "peaks": spectrum_peaks
         }
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         dump_dict = {
             "num_vibrations": len(self),
             "num_negative": len(self.negative),
-            "values": super().dump(digichem_options),
+            "values": super()._dump_(digichem_options, all),
         }
         return dump_dict
 
@@ -126,7 +135,7 @@ class Vibration(Result_object, Floatable_mixin):
         """
         return float(self.frequency)
     
-    def dump(self, digichem_options):
+    def _dump_(self, digichem_options, all):
         """
         Get a representation of this result object in primitive format.
         """

digichem/test/test_input.py

@@ -4,14 +4,14 @@ import pytest
 from pathlib import Path
 
 from digichem.test.util import pyridine_si_v2, pyridine_si_v1, pyridine_cml,\
-    result_files
+    result_files, ethane_xyz, benzene_cdx, cyclopentane_com
 from digichem.input.digichem_input import si_from_file
 
 @pytest.mark.parametrize("file_path", [
         pyridine_si_v2,
         pyridine_si_v1
      ])
-def test_input_reading(file_path):
+def test_si_reading(file_path):
     """
     Test whether we can correctly read from an existing si file.
     """
@@ -51,7 +51,7 @@ def test_si_writing(tmp_path):
         [result_files['turbomole'][0], "60a8ebd9e701b849cfccd9cbb41684519a7fdf0b"],
         [result_files['orca'][0], "e48e7f653f4e67c1bd4c5c4bb76405fad2d441d0"],
      ])
-def test_input_history(file_path, sha):
+def test_si_history(file_path, sha):
     """
     Test whether the history attribute is set properly.
     """
@@ -62,3 +62,17 @@ def test_input_history(file_path, sha):
     dump = si_file.dict
     
     assert dump['history'] == sha
+
+
+@pytest.mark.parametrize("file_path, format", [
+    (cyclopentane_com, "mol"),
+    (ethane_xyz, "cml"),
+    (benzene_cdx, "xyz"),
+    (result_files['gaussian'][0], "com")
+])
+def test_si_file_convert(file_path, format, tmp_path):
+    """
+    Test whether we can convert from arbitrary formats to another format.
+    """
+    si_file = si_from_file(file_path)
+    si_file.to_format(format, (tmp_path / "file").with_suffix("." + format))

digichem/test/test_parsing.py

@@ -144,3 +144,12 @@ def test_turbomole_archives(result_files, num_archives, digichem_options):
 
     finally:
         archive.cleanup()
+
+def test_profile_parsing(digichem_options):
+    """Can we parse profile data from profile.csv?"""
+    src = Path(data_directory(), 'Pyridine/Gaussian 16 Excited States TDA Optimised S(1) PBE1PBE (GD3BJ) Toluene 6-31G(d,p).tar.gz')
+
+    res = parse_calculation(src, options = digichem_options)
+
+    assert res.metadata.performance is not None
+

digichem/test/test_prattle.py

@@ -1,9 +1,9 @@
 """Tests for functioning of oprattle"""
+from pathlib import Path
 
 import pytest
 
 from digichem.file.prattle import Oprattle_formats, Openprattle_converter
-
 from digichem.test.util import ethane_xyz, benzene_cdx
 
 @pytest.mark.parametrize("readwrite", ["read", "write"])
@@ -14,14 +14,43 @@ def test_formats(readwrite):
     else:
         assert len(Oprattle_formats().write()) > 0
 
+
 @pytest.mark.parametrize("file_path", [
     ethane_xyz,
     benzene_cdx
 ])
-def test_convert(file_path):
+def test_from_path(file_path):
+    """
+    Can we convert a file found on the filesystem?
+    """
     Openprattle_converter(input_file_path = file_path).convert("com")
 
 
+@pytest.mark.parametrize("file_path, mode", [
+    (ethane_xyz, "r"),
+    (benzene_cdx, "rb")
+])
+def test_from_file(file_path, mode):
+    """
+    Can we convert from an open file?
+    """
+    with open(file_path, mode) as input_file:
+        Openprattle_converter(input_file = input_file, input_file_type = Path(file_path).suffix[1:]).convert("com")
+
+
+@pytest.mark.parametrize("file_path, mode", [
+    (ethane_xyz, "r"),
+    (benzene_cdx, "rb")
+])
+def test_from_buffer(file_path, mode):
+    """
+    Can we convert from an open file?
+    """
+    with open(file_path, mode) as input_file:
+        data = input_file.read()
+        Openprattle_converter(input_file_buffer = data, input_file_type = Path(file_path).suffix[1:]).convert("com")
+
+
 @pytest.mark.parametrize("file_path", [
     ethane_xyz,
     benzene_cdx

{digichem_core-6.10.3.dist-info → digichem_core-7.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: digichem-core
-Version: 6.10.3
+Version: 7.0.1
 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