Conform code to consistent implementation philosophy

Removal of global logic, inplace, update_structure etc
Ensure __copy__ methods work as intended
Unify `to_xyz` and `to_xyzblock`
Remove `downgrade_to_xyz`

isicle/adducts.py

@@ -301,7 +301,7 @@ def set_charge(self):
         '''
 
         if self.geom.__dict__.get('charge') is None:
-            self.geom.__dict__.update(charge=self.geom.get_formal_charge())
+            self.geom.__dict__.update(charge=self.geom.get_charge())
 
     def _set_ions(self, ion_path=None, ion_list=None):
         '''
@@ -472,7 +472,7 @@ def _update_geometry_charge(self, geom):
         '''
         '''
 
-        geom.__dict__.update(charge=geom.get_formal_charge())
+        geom.__dict__.update(charge=geom.get_charge())
 
     def _add_ion(self, init_mol, base_atom_idx, ion_atomic_num, sanitize, forcefield, ff_iter):
         '''
@@ -983,9 +983,9 @@ def set_charge(self):
             if self.geom.load.get('filetype') == '.xyz':
                 # self.geom.__dict__.update(charge=charge)
                 raise ValueError(
-                    'Must first run geom.set_formal_charge for an xyz structure')
+                    'Must first run geom.set_charge for an xyz structure')
             else:
-                self.geom.__dict__.update(charge=self.geom.get_formal_charge())
+                self.geom.__dict__.update(charge=self.geom.get_charge())
 
     def _set_ions(self, ion_path=None, ion_list=None):
         cations, anions, complex = _parse_ions(

isicle/conformers.py

@@ -379,7 +379,9 @@ def __init__(self, *args):
         ----------
         *args
             Objects to comprise the conformational ensemble.
+
         '''
+
         super().__init__((Geometry, XYZGeometry), *args)
 
     def _check_attributes(self, attr):
@@ -395,7 +397,9 @@ def _check_attributes(self, attr):
         ------
         AttributeError
             If all members do not have `attr`.
+
         '''
+
         value = [x.get___dict__() for x in self]
         for key in safelist(attr):
             if not all(key in x for x in value):
@@ -421,7 +425,9 @@ def reduce(self, attr, func='boltzmann', **kwargs):
         -------
         :obj:`~pandas.DataFrame`
             Result of reduction operation.
+
         '''
+
         # Select reduction function
         f = _function_selector(func)
 
@@ -493,7 +499,9 @@ def _apply_method(self, method, **kwargs):
         -------
         :obj:`~isicle.conformers.ConformationalEnsemble` or list
             Result of operation, type depends on `method` return type.
+
         '''
+
         # Check for attribute
         if not all(hasattr(x, method) for x in self):
             raise AttributeError('"{}" not found for all conformational '
@@ -525,7 +533,9 @@ def _apply_function(self, func, **kwargs):
         -------
         :obj:`~isicle.conformers.ConformationalEnsemble` or list
             Result of operation, type depends on `func` return type.
+
         '''
+
         # Apply method to collection
         result = [func(x, **kwargs) for x in self]
 
@@ -560,7 +570,9 @@ def apply(self, func=None, method=None, **kwargs):
         ------
         ValueError
             If neither `func` nor `method` is supplied.
+
         '''
+
         # Apply function
         if func is not None:
             return self._apply_function(func, **kwargs)
@@ -579,7 +591,9 @@ def get_structures(self):
         -------
         :obj:`~isicle.conformers.ConformationalEnsemble`
             Conformational ensemble.
+
         '''
+
         # Check for geom attribute
         self._check_attributes('geom')