Update docstrings

cosymlib/molecule/__init__.py

@@ -15,17 +15,19 @@ def wrapper(*args, **kwargs):
 
 class Molecule:
     """
-    Molecule class 2
+    Main molecule class
+
+    :param geometry: The geometry
+    :type geometry: Geometry
+    :param electronic_structure: The electronic structure
+    :type electronic_structure: ElectronicStructure
+    :param name: Molecule name
+    :type name: str
+
     """
     def __init__(self, geometry,
                  electronic_structure=None,
                  name=None):
-        """
-
-        :param geometry:
-        :param electronic_structure:
-        :param name:
-        """
 
         if not geometry:
             raise Exception('No geometry found in the input file, check out input file for possible errors')

cosymlib/molecule/electronic_structure/__init__.py

@@ -1,4 +1,23 @@
 class ElectronicStructure:
+    """
+    Main Electronic structure class
+
+    :param charge: The charge
+    :type charge: int
+    :param multiplicity: The multiplicity
+    :type multiplicity: int
+    :param basis: The basis set
+    :type basis: list
+    :param orbital_coefficients: Molecular orbital coefficients
+    :type orbital_coefficients: list
+    :param mo_energies: Molecular orbital energies
+    :type mo_energies: list
+    :param alpha_electrons: Number of alpha electrons
+    :type alpha_electrons: int
+    :param beta_electrons: Number of beta electrons
+    :type beta_electrons: int
+
+    """
     def __init__(self,
                  charge=0,
                  multiplicity=1,

cosymlib/molecule/geometry/__init__.py

@@ -14,7 +14,30 @@ def wrapper(*args, **kwargs):
 
 class Geometry:
     """
-    Geometry class
+    Main geometry class
+
+    :param positions: Cartesian coordinates
+    :type positions: list
+    :param symbols: Atomic elements symbols
+    :type symbols: list
+    :param name: Geometry name
+    :type name: str
+    :param connectivity: Connectivity list
+    :type connectivity: list
+    :param connectivity_thresh: Connectivity threshold
+    :type connectivity_thresh: float
+
+    :example:
+
+    .. code-block:: python
+
+        water = Geometry(positions=[[0.0, 0.0, 0.0],
+                                    [0.0, 1.0, 0.0],
+                                    [0.0, 0.0, 1.0],
+                         symbols=['O', 'H', 'H'],
+                         name='water molecule',
+                         connectivity=[[1, 2], [1, 3]])
+
 
     """
     def __init__(self,

cosymlib/shape/__init__.py

@@ -24,6 +24,7 @@ class Shape:
     Shape main class
 
     :param structure: a geometry, molecule or array type object
+    :type structure: list
     """
     def __init__(self, structure):
 
@@ -48,10 +49,14 @@ def measure(self, reference, central_atom=0, fix_permutation=False):
         """
         Get shape measure
 
-        :param reference: reference shape label or Geometry object
-        :param central_atom: central atom position
-        :param fix_permutation: do not permute atoms during shape calculations
-        :return: the measure
+        :param reference: Reference shape label or Geometry object
+        :type reference: str
+        :param central_atom: Central atom position
+        :type central_atom: int
+        :param fix_permutation: Do not permute atoms during shape calculations
+        :type fix_permutation: bool
+        :return: The measure
+        :rtype: float
         """
         key = _get_key(central_atom, reference, fix_permutation=fix_permutation)
         if key not in self._measures:
@@ -75,10 +80,14 @@ def structure(self, reference, central_atom=0, fix_permutation=False):
         """
         Get the nearest structure to reference
 
-        :param reference: reference shape label or Geometry object
-        :param central_atom: central atom position
-        :param fix_permutation: do not permute atoms during shape calculations
-        :return: the structure
+        :param reference: Reference shape label or Geometry object
+        :type reference: str, Geometry
+        :param central_atom: Central atom position
+        :type central_atom: int, Geometry
+        :param fix_permutation: Do not permute atoms during shape calculations
+        :type fix_permutation: bool
+        :return: The structure
+        :rtype: Structure
         """
         key = _get_key(central_atom, reference, fix_permutation=fix_permutation)
         if key not in self._structures:
@@ -107,10 +116,14 @@ def path_deviation(self, shape_label1, shape_label2, central_atom=0):
         """
         Get the path deviation
 
-        :param shape_label1: first shape reference label or Geometry object
-        :param shape_label2: second shape reference label or Geometry object
-        :param central_atom: central atom position
-        :return: the path deviation
+        :param shape_label1: First shape reference label or Geometry object
+        :type shape_label1: str, Geometry
+        :param shape_label2: Second shape reference label or Geometry object
+        :type shape_label2: str, Geometry
+        :param central_atom: Central atom position
+        :type central_atom: int
+        :return: The path deviation
+        :rtype: float
         """
         # TODO: Someone improve the description of this function
 
@@ -133,10 +146,13 @@ def generalized_coordinate(self, shape_label1, shape_label2, central_atom=0):
         """
         Get the generalized coordinate
 
-        :param shape_label1: first shape reference label or Geometry object
-        :param shape_label2: second shape reference label or Geometry object
-        :param central_atom: central atom position
-        :return:
+        :param shape_label1: First shape reference label or Geometry object
+        :type shape_label1: str, Geometry
+        :param shape_label2: Second shape reference label or Geometry object
+        :type shape_label2: str, Geometry
+        :param central_atom: Central atom position
+        :type central_atom: int
+        :return: The generalized coordinate
         """
 
         key = _get_key(central_atom, shape_label1, reference_2=shape_label2)

cosymlib/symmetry/__init__.py

@@ -29,12 +29,19 @@ class Symmetry:
     Symmetry main class
 
     :param structure: a geometry, molecule or array type object
+    :type structure: Geometry, Molecule, np.array
     :param central_atom: central atom position
-    :param center: center of symmetry. By default center is optimized
+    :type central_atom: int
+    :param center: center of symmetry in Cartesian coordinates. By default center is optimized
+    :type center: list
     :param connect_thresh: Connectivity threshold (Ionic radius is used as reference)
-    :param multi: number of symmetry axis to find
-    :param axis: main symmetry axis (If None, then optimize)
+    :type connect_thresh: float
+    :param multi: Number of symmetry axis to find
+    :type multi: int
+    :param axis: Main symmetry axis (If None, then optimize)
+    :type axis: list
     :param axis2: secondary symmetry axis (If None, then optimize)
+    :type axis2: list
     """
 
     def __init__(self,
@@ -84,7 +91,7 @@ def set_parameters(self, parameters_dict):
         Set symmetry calculation related parameters
 
         :param parameters_dict: parameters in dictionary
-        :return:
+        :type parameters_dict: dict
         """
         for name, value in parameters_dict.items():
             setattr(self, '_' + name, value)
@@ -146,17 +153,21 @@ def measure(self, label):
         """
         Get symmetry measure
 
-        :param label: point group label
-        :return: the measure
+        :param label: Point group label
+        :type label: str
+        :return: The measure
+        :rtype: float
         """
         return self._get_symgroup_results(label).csm
 
     def nearest_structure(self, label):
         """
         Get nearest structure
 
-        :param label: point group label
-        :return: the structure
+        :param label: Point group label
+        :type label: str
+        :return: The structure
+        :rtype: Structure
         """
         # TODO: Improve this docstring
 
@@ -166,8 +177,10 @@ def optimum_axis(self, label):
         """
         Get the optimum main symmetry axis
 
-        :param label: point group label
-        :return:
+        :param label: Point group label
+        :type label: str
+        :return: The axis
+        :rtype: list
         """
         return self._get_symgroup_results(label).optimum_axis
 
@@ -176,7 +189,8 @@ def optimum_permutation(self, label):
         Get the optimum atoms permutation
 
         :param label: point group label
-        :return:
+        :return: The permutation
+        :rtype: list
         """
         return self._get_symgroup_results(label).optimum_permutation
 
@@ -185,7 +199,9 @@ def reference_axis(self, label):
         Get reference axis
 
         :param label: point group label
-        :return:
+        :type label: str
+        :return: The axis
+        :rtype: list
         """
         return self._get_symgroup_results(label).reference_axis
 
@@ -194,8 +210,11 @@ def cms_multi(self, label, multi=1):
         Get symmetry measure of the optimum N axis
 
         :param label: point group label
+        :type label: str
         :param multi: number of axis
-        :return: list of measures
+        :type multi: int
+        :return: The measures
+        :rtype: list
         """
         self._multi = multi
         return self._get_symgroup_results(label).cms_multi
@@ -205,8 +224,11 @@ def axis_multi(self, label, multi=1):
         Get the optimum N axis
 
         :param label: point group label
+        :type label: str
         :param multi: number of axis
-        :return: list of axis
+        :type multi: int
+        :return: List of axis
+        :rtype: list
         """
         self._multi = multi
         return self._get_symgroup_results(label).axis_multi

docs/api.rst

@@ -27,3 +27,8 @@ Geometry
 .. automodule:: cosymlib.molecule.geometry
     :members: Geometry
 
+Electronic structure
+--------------------
+.. automodule:: cosymlib.molecule.electronic_structure
+    :members: ElectronicStructure
+