Fix numpydoc lints

src/biotite/structure/io/trajfile.py

@@ -189,7 +189,9 @@ def read_iter(
 
         See Also
         --------
-        read_iter_structure
+        read_iter_structure :
+            Get an :class:`AtomArray` for each frame or an :class:`AtomArrayStack`
+            for each chunk of frames instead.
 
         Notes
         -----
@@ -317,7 +319,8 @@ def read_iter_structure(
 
         See Also
         --------
-        read_iter
+        read_iter :
+            Get an the raw data for each frame or for each chunk of frames instead.
 
         Notes
         -----
@@ -480,7 +483,7 @@ def set_box(self, box):
 
         Parameters
         ----------
-        time : ndarray, dtype=float, shape=(m,3,3)
+        box : ndarray, dtype=float, shape=(m,3,3)
             The box vectors to be set.
         """
         self._check_model_count(box)

src/biotite/structure/mechanics.py

@@ -30,7 +30,6 @@ def gyration_radius(array, masses=None):
         Must have the same length as `array`. By default, the standard
         atomic mass for each element is taken.
 
-
     Returns
     -------
     masses : float or ndarray, dtype=float

src/biotite/structure/molecules.py

@@ -39,11 +39,6 @@ def get_molecule_indices(array):
         Consequently, the length of this list is equal to the number of
         molecules in the input `array`.
 
-    See Also
-    --------
-    get_molecule_masks
-    molecule_iter
-
     Examples
     --------
     Get an :class:`AtomArray` for ATP and show that it is a single
@@ -157,11 +152,6 @@ def get_molecule_masks(array):
         Consequently, the length of this list is equal to the number of
         molecules in the input `array`.
 
-    See Also
-    --------
-    get_molecule_indices
-    molecule_iter
-
     Examples
     --------
     Get an :class:`AtomArray` for ATP and show that it is a single
@@ -270,11 +260,6 @@ def molecule_iter(array):
     molecule : AtomArray or AtomArrayStack
         A single molecule of the input `array`.
 
-    See Also
-    --------
-    get_molecule_indices
-    get_molecule_masks
-
     Examples
     --------
     Get an :class:`AtomArray` for ATP and break it into two molecules

src/biotite/structure/pseudoknots.py

@@ -69,6 +69,11 @@ def pseudoknots(base_pairs, scores=None, max_pseudoknot_order=None):
     Therefore, there are no pseudoknots between base pairs with the same
     pseudoknot order.
 
+    References
+    ----------
+
+    .. footbibliography::
+
     Examples
     --------
     Remove the pseudoknotted base pair for the sequence *ABCbac*, where
@@ -102,17 +107,6 @@ def pseudoknots(base_pairs, scores=None, max_pseudoknot_order=None):
     [[0 0 1]]
     >>> print(dot_bracket(basepairs, 6)[0])
     (([))]
-
-    See Also
-    --------
-    base_pairs
-    dot_bracket
-
-    References
-    ----------
-
-    .. footbibliography::
-
     """
     if len(base_pairs) == 0:
         # No base pairs -> empty pseudoknot order array
@@ -149,9 +143,9 @@ class _Region:
 
     Parameters
     ----------
-    base_pairs: ndarray, shape=(n,2), dtype=int
+    base_pairs : ndarray, shape=(n,2), dtype=int
         All base pairs of the structure the region is a subset for.
-    region_pairs: ndarray, dtype=int
+    region_pairs : ndarray, dtype=int
         The indices of the base pairs in ``base_pairs`` that are part of
         the region.
     scores : ndarray, dtype=int, shape=(n,) (default: None)

src/biotite/structure/repair.py

@@ -48,7 +48,6 @@ def create_continuous_res_ids(atoms, restart_each_chain=True):
     >>> res_ids, _ = get_residues(atom_array)
     >>> print(res_ids)
     [ 1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19]
-
     """
     res_ids_diff = np.zeros(atoms.array_length(), dtype=int)
     res_starts = get_residue_starts(atoms)
@@ -80,7 +79,7 @@ def infer_elements(atoms):
 
     See Also
     --------
-    create_atoms_names : The opposite of this function
+    create_atoms_names : The opposite of this function.
 
     Examples
     --------
@@ -89,7 +88,6 @@ def infer_elements(atoms):
     ['N' 'C' 'C' 'O' 'C' 'C' 'O' 'N' 'H' 'H']
     >>> print(infer_elements(["CA", "C", "C1", "OD1", "HD21", "1H", "FE"]))
     ['C' 'C' 'C' 'O' 'H' 'H' 'FE']
-
     """
     if isinstance(atoms, (AtomArray, AtomArrayStack)):
         atom_names = atoms.atom_name
@@ -117,7 +115,7 @@ def create_atom_names(atoms):
 
     See Also
     --------
-    infer_elements : The opposite of this function
+    infer_elements : The opposite of this function.
 
     Notes
     -----

src/biotite/structure/residues.py

@@ -126,9 +126,8 @@ def apply_residue_wise(array, data, function, axis=None):
     Returns
     -------
     processed_data : ndarray
-        Residue-wise evaluation of `data` by `function`. The size of the
-        first dimension of this array is equal to the amount of
-        residues.
+        Residue-wise evaluation of `data` by `function`. The size of the first dimension
+        of this array is equal to the amount of residues.
 
     Examples
     --------
@@ -196,14 +195,15 @@ def spread_residue_wise(array, input_data):
     array : AtomArray or AtomArrayStack
         The atom array (stack) to determine the residues from.
     input_data : ndarray
-        The data to be spread. The length of axis=0 must be equal to
-        the amount of different residue IDs in `array`.
+        The data to be spread.
+        The length of the 0-th axis must be equal to the amount of different residue IDs
+        in `array`.
 
     Returns
     -------
     output_data : ndarray
-        Residue-wise spread `input_data`. Length is the same as
-        `array_length()` of `array`.
+        Residue-wise spread `input_data`.
+        Length is the same as `array_length()` of `array`.
 
     Examples
     --------
@@ -263,11 +263,6 @@ def get_residue_masks(array, indices):
         Each array masks the atoms that belong to the same residue as
         the atom at the given index.
 
-    See Also
-    --------
-    get_residue_starts_for
-    get_residue_positions
-
     Examples
     --------
 
@@ -341,11 +336,6 @@ def get_residue_starts_for(array, indices):
         The indices that point to the residue starts for the input
         `indices`.
 
-    See Also
-    --------
-    get_residue_masks
-    get_residue_positions
-
     Examples
     --------
 
@@ -385,14 +375,9 @@ def get_residue_positions(array, indices):
 
     Returns
     -------
-    start_indices : ndarray, dtype=int, shape=(k,)
+    residue_indices : ndarray, dtype=int, shape=(k,)
         The indices that point to the position of the residues.
 
-    See Also
-    --------
-    get_residue_masks
-    get_residue_starts_for
-
     Examples
     --------
     >>> atom_index = [5, 42]
@@ -572,4 +557,5 @@ def residue_iter(array):
     """
     # The exclusive stop is appended to the residue starts
     starts = get_residue_starts(array, add_exclusive_stop=True)
-    return segment_iter(array, starts)
+    for residue in segment_iter(array, starts):
+        yield residue

src/biotite/structure/segments.py

@@ -27,6 +27,22 @@ def apply_segment_wise(starts, data, function, axis=None):
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+    data : ndarray
+        The data, whose intervals are the parameter for `function`.
+        Must have same length as `array`.
+    function : function
+        The `function` must have either the form *f(data)* or
+        *f(data, axis)* in case `axis` is given. Every `function` call
+        must return a value with the same shape and data type.
+    axis : int, optional
+        This value is given to the `axis` parameter of `function`.
+
+    Returns
+    -------
+    processed_data : ndarray
+        Segment-wise evaluation of `data` by `function`.
+        The size of the first dimension of this array is equal to the amount of
+        residues.
     """
     # The result array
     processed_data = None
@@ -65,6 +81,16 @@ def spread_segment_wise(starts, input_data):
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+    input_data : ndarray
+        The data to be spread.
+        The length of the 0-th axis must be equal to the amount of different residue IDs
+        in `array`.
+
+    Returns
+    -------
+    output_data : ndarray
+        Segment-wise spread `input_data`.
+        Length is the same as `array_length()` of `array`.
     """
     output_data = np.zeros(starts[-1], dtype=input_data.dtype)
     for i in range(len(starts) - 1):
@@ -85,6 +111,17 @@ def get_segment_masks(starts, indices):
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+    indices : ndarray, dtype=int, shape=(k,)
+        These indices indicate the atoms to get the corresponding
+        segments for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    residues_masks : ndarray, dtype=bool, shape=(k,n)
+        Multiple boolean masks, one for each given index in `indices`.
+        Each array masks the atoms that belong to the same segment as
+        the atom at the given index.
     """
     indices = np.asarray(indices)
     length = starts[-1]
@@ -116,6 +153,16 @@ def get_segment_starts_for(starts, indices):
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+    indices : ndarray, dtype=int, shape=(k,)
+        These indices point to the atoms to get the corresponding
+        segment starts for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    start_indices : ndarray, dtype=int, shape=(k,)
+        The indices that point to the segment starts for the input
+        `indices`.
     """
     indices = np.asarray(indices)
     length = starts[-1]
@@ -145,6 +192,15 @@ def get_segment_positions(starts, indices):
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+    indices : ndarray, shape=(k,)
+        These indices point to the atoms to get the corresponding
+        residue positions for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    segment_indices : ndarray, shape=(k,)
+        The indices that point to the position of the segments.
     """
     indices = np.asarray(indices)
     length = starts[-1]
@@ -169,10 +225,17 @@ def segment_iter(array, starts):
 
     Parameters
     ----------
+    array : AtomArray or AtomArrayStack
+        The structure to iterate over.
     starts : ndarray, dtype=int
         The sorted start indices of segments.
         Includes exclusive stop, i.e. the length of the corresponding
         atom array.
+
+    Yields
+    ------
+    segment : AtomArray or AtomArrayStack
+       Each residue or chain of the structure.
     """
     for i in range(len(starts) - 1):
         yield array[..., starts[i] : starts[i + 1]]

src/biotite/structure/sequence.py

@@ -58,7 +58,6 @@ def to_sequence(atoms, allow_hetero=False):
     >>> sequences, chain_starts = to_sequence(atom_array)
     >>> print(sequences)
     [ProteinSequence("NLYIQWLKDGGPSSGRPPPS")]
-
     """
     sequences = []
     chain_start_indices = get_chain_starts(atoms, add_exclusive_stop=True)

src/biotite/structure/sse.py

@@ -48,7 +48,6 @@ def annotate_sse(atom_array):
         Non-peptide residues are also allowed and obtain a ``''``
         SSE.
 
-
     Returns
     -------
     sse : ndarray
@@ -81,7 +80,6 @@ def annotate_sse(atom_array):
     >>> print(sse)
     ['c' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c'
      'c' 'c']
-
     """
     residue_starts = get_residue_starts(atom_array)
     # Sort CA coord into the coord array at the respective residue index