turns out the datatype is called np.ndarray, not np.array

cctk/array.py

@@ -3,7 +3,7 @@
 
 class OneIndexedArray(np.ndarray):
     """
-    Wrapper for ``np.array`` that's indexed from one, not zero, to store atomic numbers and geometries.
+    Wrapper for ``np.ndarray`` that's indexed from one, not zero, to store atomic numbers and geometries.
     This only works on 1D or 2D arrays. Additionally, only the first index of a 2D array will be 1-indexed.
 
     Note that ``enumerate(one_indexed_array)`` will throw ``IndexError`` -- instead, use ``enumerate(one_indexed_array, start=1)``.

cctk/ensemble.py

@@ -15,8 +15,8 @@ class Ensemble:
 
     Attributes:
         name (str): name, for identification
-        molecules (np.array): list of `Molecule` objects
-        energies (np.array): list of energies
+        molecules (np.ndarray): list of `Molecule` objects
+        energies (np.ndarray): list of energies
     """
 
     def __init__(self, name=None, **kwargs):

cctk/helper_functions.py

@@ -188,7 +188,7 @@ def compute_rotation_matrix(axis, theta):
     Adapted from user "unutbu" on StackExchange.
 
     Args:
-        axis (vector): the vector to rotate about
+        axis (np.ndarray): the vector to rotate about
         theta (float): how much to rotate (in degrees)
 
     Returns:
@@ -270,7 +270,14 @@ def compute_RMSD(geometry1, geometry2):
 
 def get_isotopic_distribution(z):
     """
-    For an element with number ``z``, returns two ``np.array`` objects containing that element's weights and relative abundances.
+    For an element with number ``z``, returns two ``np.ndarray`` objects containing that element's weights and relative abundances.
+
+    Args:
+        z (int): atomic number
+
+    Returns:
+        masses (np.ndarray): list of isotope masses
+        weights (np.ndarray): list of weights (relative to 1.00 for largest)
     """
     z = str(z)
     masses = list(ISOTOPE_DICTIONARY[z].keys())

cctk/mae_file.py

@@ -62,8 +62,8 @@ def _read_mae(
             print_status_messages (Bool):
 
         Returns:
-            geometries (np.array): array of 3-tuples of geometries
-            symbols (np.array): array of atom symbols (str)
+            geometries (np.ndarray): array of 3-tuples of geometries
+            symbols (np.ndarray): array of atom symbols (str)
             bonds (nx.Graph): ``NetworkX`` graph of bond information
             property_names:
             property_values:

cctk/mol2_file.py

@@ -67,17 +67,17 @@ def _read_mol2(
             save_memory_for_conformers (bool): if True, the first dimension (geometry number) will be
                                             dropped from the symbols and bonds to prevent
                                             the storage of redundant information.  Thus,
-                                            symbols will be a one-dimensional :obj:`np.array` of
-                                            :obj:`str` and bonds will be a single :obj:`nx.Graph`.
+                                            symbols will be a one-dimensional ``np.ndarray`` of
+                                            ``str`` and bonds will be a single ``nx.Graph``.
 
             print_status_messages (bool): if True, update the progerss of the parsing operation to stdout.
 
         Returns:
             all_geometries, all_clean_symbols, all_symbols, all_bonds, contains_conformers
 
-            all_geometries: np.array(geometry number, atom number, xyz) -> position (float)
-            all_clean_symbols: np.array(geometry number, atom number) -> atom symbol (:obj:`str`)
-            all_symbols: np.array(geometry number, atom number) -> atom symbol (:obj:`str`)
+            all_geometries: np.ndarray(geometry number, atom number, xyz) -> position (float)
+            all_clean_symbols: np.ndarray(geometry number, atom number) -> atom symbol (:obj:`str`)
+            all_symbols: np.ndarray(geometry number, atom number) -> atom symbol (:obj:`str`)
             all_bonds: list(geometry_number) -> bond connectivity (:obj:`nx.Graph`)
             contains_conformers: bool (True if the geometries correspond to conformers.)
         """

cctk/molecule.py

@@ -631,9 +631,9 @@ def _recurse_through_formula(self, formula, masses, weights, cutoff=0.0000001, m
         The default values should work nicely for low-res MS applications.
 
         Args:
-            formula (np.array, dtype=np.int8): vector containing atoms left to incorporate
-            masses (np.array): list of mass fragments at current iteration
-            weights (np.array): relative weights at current iteration
+            formula (np.ndarray, dtype=np.int8): vector containing atoms left to incorporate
+            masses (np.ndarray): list of mass fragments at current iteration
+            weights (np.ndarray): relative weights at current iteration
             cutoff (float): cutoff for similarity (masses within ``cutoff`` will be combined)
             mass_precision (int): number of decimal places to store for mass
             weight_precision (int): number of decimal places to store for weight