Merge pull request duartegroup#145 from duartegroup/v1.2.3

v1.2.3

.gitignore

@@ -16,6 +16,8 @@ tests/__pycache__/
 
 tests/*.xyz
 
+**/tmp.xyz
+
 autode/conformers/__pycache__/
 
 autode/transition_states/__pycache__/

README.md

@@ -57,7 +57,7 @@ additional documentation.
 ## Development
 
 There is a [slack workspace](https://autodeworkspace.slack.com) for development and discussion - please 
-[email](mailto:[email protected]?subject=autodE%20slack) to be added. Pull requests are 
+[email](mailto:[email protected]?subject=autodE%20slack) to be added. Pull requests are 
 very welcome but must pass all the unit tests prior to being merged. Please write code and tests!
 See the [todo list](https://github.com/duartegroup/autodE/projects/1) for features on the horizon. 
 Bugs and feature requests should be raised on the [issue page](https://github.com/duartegroup/autodE/issues). 

autode/__init__.py

@@ -33,7 +33,7 @@
   - Merge when tests pass
 """
 
-__version__ = '1.2.2'
+__version__ = '1.2.3'
 
 
 __all__ = [

autode/atoms.py

@@ -13,7 +13,8 @@ def __init__(self,
                  atomic_symbol: str,
                  x:             float = 0.0,
                  y:             float = 0.0,
-                 z:             float = 0.0):
+                 z:             float = 0.0,
+                 atom_class:    Optional[int] = None):
         """
         Atom class. Centered at the origin by default. Can be initialised from
         positional or keyword arguments:
@@ -32,17 +33,23 @@ def __init__(self,
 
         -----------------------------------------------------------------------
         Arguments:
-            atomic_symbol (str): Symbol of an element e.g. 'C' for carbon
+            atomic_symbol: Symbol of an element e.g. 'C' for carbon
 
-        Keyword Arguments:
-            x (float): x coordinate in 3D space (Å)
-            y (float): y coordinate in 3D space (Å)
-            z (float): z coordinate in 3D space (Å)
+            x: x coordinate in 3D space (Å)
+
+            y: y coordinate in 3D space (Å)
+
+            z: z coordinate in 3D space (Å)
+
+            atom_class: Fictitious additional labels to distinguish otherwise
+                        identical atoms. Useful in finding bond isomorphisms
+                        over identity reactions
         """
         assert atomic_symbol in elements
 
         self.label = atomic_symbol
         self._coord = Coordinate(float(x), float(y), float(z))
+        self.atom_class = atom_class
 
     def __repr__(self):
         """
@@ -471,6 +478,9 @@ def rotate(self,
 
         return None
 
+    def copy(self) -> 'Atom':
+        return deepcopy(self)
+
     # --- Method aliases ---
     coordinate = coord
 
@@ -733,7 +743,7 @@ class AtomCollection:
     def __init__(self,
                  atoms: Union[List[Atom], Atoms, None] = None):
         """
-        Collection of atoms, used as a a base class for a species, complex
+        Collection of atoms, used as a base class for a species, complex
         or transition state.
 
         -----------------------------------------------------------------------

autode/calculation.py

@@ -178,7 +178,7 @@ def is_identical():
         if not os.path.exists(register_name):
             logger.info('No calculations have been performed here yet')
             append_register()
-            return
+            return None
 
         # Populate a register of calculation names and their unique identifiers
         register = {}
@@ -189,13 +189,13 @@ def is_identical():
 
         if is_identical():
             logger.info('Calculation has already been run')
-            return
+            return None
 
         # If this calculation doesn't yet appear in the register add it
         if not exists():
             logger.info('This calculation has not yet been run')
             append_register()
-            return
+            return None
 
         # If we're here then this calculation - with these input - has not yet
         # been run. Therefore, add an integer to the calculation name until
@@ -209,7 +209,7 @@ def is_identical():
             logger.info(f'New calculation name is: {self.name}')
 
             if is_identical():
-                return
+                return None
 
             if not exists():
                 append_register()
@@ -339,6 +339,10 @@ def get_final_atoms(self) -> Atoms:
             raise ex.AtomsNotFound(f'Failed to get atoms from '
                                    f'{self.output.filename}')
 
+        # Atom classes are persistent when calculations are performed
+        for old_atom, new_atom in zip(self.molecule.atoms, atoms):
+            new_atom.atom_class = old_atom.atom_class
+
         return atoms
 
     @_requires_set_output_filename
@@ -453,7 +457,7 @@ def clean_up(self,
 
         if Config.keep_input_files and not force:
             logger.info('Keeping input files')
-            return
+            return None
 
         filenames = self.input.filenames
         if everything:
@@ -500,7 +504,7 @@ def generate_input(self) -> None:
             if not hasattr(keyword, self.method.name):
                 err_str = (f'Keyword: {keyword} is not supported set '
                            f'{repr(keyword)}.{self.method.name} as a string')
-                raise ex.UnsuppportedCalculationInput(err_str)
+                raise ex.UnsupportedCalculationInput(err_str)
 
         self.method.generate_input(self, self.molecule)
 

autode/conformers/conformer.py

@@ -1,4 +1,7 @@
 from typing import Optional
+
+from autode.atoms import Atoms
+from autode.values import Coordinates
 from autode.exceptions import AtomsNotFound
 from autode.log import logger
 from autode.species.species import Species
@@ -22,16 +25,19 @@ def __init__(self,
         See Also:
             (autode.species.species.Species):
         """
-
         super().__init__(name, atoms, charge, mult, solvent_name=solvent_name)
+        self._parent_atoms = None
+        self._coordinates = None
 
         if species is not None:
+            self._parent_atoms = species.atoms
+            self._coordinates = species.coordinates.copy()
             self.charge = species.charge  # Require identical charge/mult/solv
             self.mult = species.mult
             self.solvent = species.solvent
 
-            if atoms is None:
-                self.atoms = species.atoms.copy()
+        if atoms is not None:  # Specified atoms overrides species
+            self.atoms = Atoms(atoms)
 
         self.constraints.update(distance=dist_consts)
 
@@ -94,3 +100,69 @@ def optimise(self,
             self.atoms = None
 
         return None
+
+    @property
+    def coordinates(self) -> Optional[Coordinates]:
+        """Coordinates of this conformer"""
+        return self._coordinates
+
+    @coordinates.setter
+    def coordinates(self, value: 'numpy.ndarray'):
+        """Set the coordinates of this conformer"""
+        if self._parent_atoms is None:
+            raise ValueError('Conformer has no parent atoms. Setting the '
+                            'coordinates will leave the atoms undefined')
+
+        self._coordinates = Coordinates(value)
+
+    @property
+    def atoms(self) -> Optional[Atoms]:
+        """
+        Atoms of this conformer are built from the parent atoms and the
+        coordinates that are unique to this conformer.
+        """
+
+        if self._parent_atoms is None or self._coordinates is None:
+            return None
+
+        atoms = Atoms()
+        for parent_atom, coord in zip(self._parent_atoms, self._coordinates):
+            atom = parent_atom.copy()
+            atom.coord = coord
+
+            atoms.append(atom)
+
+        return atoms
+
+    @atoms.setter
+    def atoms(self,
+              value: Optional[Atoms]):
+        """
+        Set the atoms of this conformer.
+
+        If None then set the corresponding coordinates of this conformer to
+        None (such that self.atoms is None). If this conformer has coordinates
+        then set those from the individual atomic coordinates otherwise
+        set the coordinates as a batch
+        """
+
+        if value is None:  # Clear the coordinates
+            self._coordinates = None
+            return None
+
+        if self._parent_atoms is None:
+            self._parent_atoms = value
+
+        if self._coordinates is None:
+            self._coordinates = value.coordinates
+            return
+
+        for i, atom in enumerate(value):
+
+            parent_atom = self._parent_atoms[i]
+            if atom.label != parent_atom.label:
+                raise ValueError('Cannot alter the atomic symbols of a '
+                                 'conformer. Parent molecule was different: '
+                                 f'{atom.label} != {parent_atom.label}')
+
+            self._coordinates[i] = atom.coord.copy()

autode/conformers/conformers.py

@@ -153,7 +153,7 @@ def prune_on_rmsd(self,
         if len(self) < 2:
             logger.info(f'Only have {len(self)} conformers. No need to prune '
                         f'on RMSD')
-            return
+            return None
 
         rmsd_tol = Config.rmsd_threshold if rmsd_tol is None else rmsd_tol
 
@@ -183,7 +183,7 @@ def prune_on_rmsd(self,
         return None
 
     def prune_diff_graph(self,
-                         graph: 'networkx.Graph'
+                         graph: 'autode.mol_graphs.MolecularGraph'
                          ) -> None:
         """
         Remove conformers with a different molecular graph to a defined
@@ -193,7 +193,7 @@ def prune_diff_graph(self,
         -----------------------------------------------------------------------
 
         Arguments:
-            graph (networkx.Graph): Reference graph
+            graph: Reference graph
         """
         n_prev_confs = len(self)
 
@@ -225,7 +225,7 @@ def _parallel_calc(self, calc_type, method, keywords):
         # TODO: Test efficiency + improve with dynamic load balancing
         if len(self) == 0:
             logger.error(f'Cannot run {calc_type} over 0 conformers')
-            return
+            return None
 
         n_cores_pp = max(Config.n_cores // len(self), 1)