biotite 1.0.1__cp311-cp311-win_amd64.whl → 1.2.0__cp311-cp311-win_amd64.whl

biotite/structure/basepairs.py

@@ -338,8 +338,8 @@ def base_pairs_edge(atom_array, base_pairs):
 
     See Also
     --------
-    base_pairs
-    base_pairs_glycosidic_bond
+    base_pairs : Get the base pairs required for this function.
+    base_pairs_glycosidic_bond : Determine the orientation for each base pair.
 
     Notes
     -----
@@ -351,6 +351,11 @@ def base_pairs_edge(atom_array, base_pairs):
     The edge returned always corresponds to the edge with the most
     hydrogen bonding interactions.
 
+    References
+    ----------
+
+    .. footbibliography::
+
     Examples
     --------
     Compute the interacting base edges for the dna helix with the PDB
@@ -392,11 +397,6 @@ def base_pairs_edge(atom_array, base_pairs):
     WATSON_CRICK to WATSON_CRICK
     WATSON_CRICK to WATSON_CRICK
     WATSON_CRICK to WATSON_CRICK
-
-    References
-    ----------
-
-    .. footbibliography::
     """
     # Result-``ndarray`` matches the dimensions of the input array
     results = np.zeros_like(base_pairs, dtype="uint8")
@@ -494,7 +494,7 @@ def base_pairs_glycosidic_bond(atom_array, base_pairs):
 
     Returns
     -------
-    results : ndarray, dtype=edge, shape=(n,)
+    results : ndarray, dtype=int, shape=(n,)
         The ``ndarray`` has the same dimensions as ``base_pairs``. Each
         cell corresponds to the interacting edge of the referenced base
         in ``base_pairs``.
@@ -504,15 +504,20 @@ def base_pairs_glycosidic_bond(atom_array, base_pairs):
 
     See Also
     --------
-    base_pairs
-    base_pairs_edge
-    GlycosidicBond
+    base_pairs : Get the base pairs required for this function.
+    base_pairs_edge : Determine the interacting edge for each base pair.
+    GlycosidicBond : The Enum type for interpretation of the return value.
 
     Notes
     -----
     The orientation is found using the geometric centers of the bases
     and the glycosidic bonds as described in :footcite:`Yang2003`.
 
+    References
+    ----------
+
+    .. footbibliography::
+
     Examples
     --------
     Compute the glycosidic bond orientations for the dna helix with the
@@ -544,11 +549,6 @@ def base_pairs_glycosidic_bond(atom_array, base_pairs):
     CIS
     CIS
     CIS
-
-    References
-    ----------
-
-    .. footbibliography::
     """
     results = np.zeros(len(base_pairs), dtype="uint8")
 
@@ -654,6 +654,11 @@ def base_stacking(atom_array, min_atoms_per_base=3):
     Please note that ring normal vectors are assumed to be equal to the
     base normal vectors.
 
+    References
+    ----------
+
+    .. footbibliography::
+
     Examples
     --------
     Compute the stacking interactions for a DNA-double-helix (PDB ID
@@ -685,11 +690,6 @@ def base_stacking(atom_array, min_atoms_per_base=3):
      [21 22]
      [22 23]
      [23 24]]
-
-    References
-    ----------
-
-    .. footbibliography::
     """
     # Get the stacking candidates according to a cutoff distance, where
     # each base is identified as the first index of its respective
@@ -833,6 +833,11 @@ def base_pairs(atom_array, min_atoms_per_base=3, unique=True):
     1.00Å and 0.96Å respectively. Thus, including some buffer, a 3.6Å
     cutoff should cover all hydrogen bonds.
 
+    References
+    ----------
+
+    .. footbibliography::
+
     Examples
     --------
     Compute the base pairs for the structure with the PDB ID 1QXB:
@@ -855,11 +860,6 @@ def base_pairs(atom_array, min_atoms_per_base=3, unique=True):
      ['DG' 'DC']
      ['DC' 'DG']
      ['DG' 'DC']]
-
-    References
-    ----------
-
-    .. footbibliography::
     """
 
     # Get the nucleotides for the given atom_array

biotite/structure/bonds.pyx

@@ -17,6 +17,7 @@ cimport cython
 cimport numpy as np
 from libc.stdlib cimport free, realloc
 
+from collections.abc import Sequence
 import itertools
 import numbers
 from enum import IntEnum
@@ -59,6 +60,8 @@ class BondType(IntEnum):
         - `AROMATIC_SINGLE` - Aromatic bond with a single formal bond
         - `AROMATIC_DOUBLE` - Aromatic bond with a double formal bond
         - `AROMATIC_TRIPLE` - Aromatic bond with a triple formal bond
+        - `AROMATIC` - Aromatic bond without specification of the formal bond
+        - `COORDINATION` - Coordination complex involving a metal atom
     """
     ANY = 0
     SINGLE = 1
@@ -68,6 +71,8 @@ class BondType(IntEnum):
     AROMATIC_SINGLE = 5
     AROMATIC_DOUBLE = 6
     AROMATIC_TRIPLE = 7
+    COORDINATION = 8
+    AROMATIC = 9
 
 
     def without_aromaticity(self):
@@ -88,10 +93,14 @@ class BondType(IntEnum):
         >>> print(BondType.AROMATIC_DOUBLE.without_aromaticity().name)
         DOUBLE
         """
-        difference = BondType.AROMATIC_SINGLE - BondType.SINGLE
-        if self >= BondType.AROMATIC_SINGLE:
-            difference = BondType.AROMATIC_SINGLE - BondType.SINGLE
-            return BondType(self - difference)
+        if self == BondType.AROMATIC_SINGLE:
+            return BondType.SINGLE
+        elif self == BondType.AROMATIC_DOUBLE:
+            return BondType.DOUBLE
+        elif self == BondType.AROMATIC_TRIPLE:
+            return BondType.TRIPLE
+        elif self == BondType.AROMATIC:
+            return BondType.ANY
         else:
             return self
 
@@ -305,6 +314,61 @@ class BondList(Copyable):
             self._bonds = np.zeros((0, 3), dtype=np.uint32)
             self._max_bonds_per_atom = 0
 
+    @staticmethod
+    def concatenate(bonds_lists):
+        """
+        Concatenate multiple :class:`BondList` objects into a single
+        :class:`BondList`, respectively.
+
+        Parameters
+        ----------
+        bonds_lists : iterable object of BondList
+            The bond lists to be concatenated.
+
+        Returns
+        -------
+        concatenated_bonds : BondList
+            The concatenated bond lists.
+
+        Examples
+        --------
+
+        >>> bonds1 = BondList(2, np.array([(0, 1)]))
+        >>> bonds2 = BondList(3, np.array([(0, 1), (0, 2)]))
+        >>> merged_bonds = BondList.concatenate([bonds1, bonds2])
+        >>> print(merged_bonds.get_atom_count())
+        5
+        >>> print(merged_bonds.as_array()[:, :2])
+        [[0 1]
+         [2 3]
+         [2 4]]
+        """
+        # Ensure that the bonds_lists can be iterated over multiple times
+        if not isinstance(bonds_lists, Sequence):
+            bonds_lists = list(bonds_lists)
+
+        cdef np.ndarray merged_bonds = np.concatenate(
+            [bond_list._bonds for bond_list in bonds_lists]
+        )
+        # Offset the indices of appended bonds list
+        # (consistent with addition of AtomArray)
+        cdef int start = 0, stop = 0
+        cdef int cum_atom_count = 0
+        for bond_list in bonds_lists:
+            stop = start + bond_list._bonds.shape[0]
+            merged_bonds[start : stop, :2] += cum_atom_count
+            cum_atom_count += bond_list._atom_count
+            start = stop
+
+        cdef merged_bond_list = BondList(cum_atom_count)
+        # Array is not used in constructor to prevent unnecessary
+        # maximum and redundant bond calculation
+        merged_bond_list._bonds = merged_bonds
+        merged_bond_list._max_bonds_per_atom = max(
+            [bond_list._max_bonds_per_atom for bond_list in bonds_lists]
+        )
+        return merged_bond_list
+
     def __copy_create__(self):
         # Create empty bond list to prevent
         # unnecessary removal of redundant atoms
@@ -453,9 +517,14 @@ class BondList(Copyable):
         0 1 SINGLE
         1 2 DOUBLE
         """
-        bonds = self._bonds
-        difference = BondType.AROMATIC_SINGLE - BondType.SINGLE
-        bonds[bonds[:, 2] >= BondType.AROMATIC_SINGLE, 2] -= difference
+        bond_types = self._bonds[:,2]
+        for aromatic_type, non_aromatic_type in [
+            (BondType.AROMATIC_SINGLE, BondType.SINGLE),
+            (BondType.AROMATIC_DOUBLE, BondType.DOUBLE),
+            (BondType.AROMATIC_TRIPLE, BondType.TRIPLE),
+            (BondType.AROMATIC, BondType.ANY),
+        ]:
+            bond_types[bond_types == aromatic_type] = non_aromatic_type
 
     def remove_bond_order(self):
         """
@@ -874,7 +943,6 @@ class BondList(Copyable):
         ----------
         atom_index : int
             The index of the atom whose bonds should be removed.
-
         """
         cdef uint32 index = _to_positive_index(atom_index, self._atom_count)
 
@@ -994,20 +1062,7 @@ class BondList(Copyable):
         )
 
     def __add__(self, bond_list):
-        cdef np.ndarray merged_bonds \
-            = np.concatenate([self._bonds, bond_list._bonds])
-        # Offset the indices of appended bonds list
-        # (consistent with addition of AtomArray)
-        merged_bonds[len(self._bonds):, :2] += self._atom_count
-        cdef uint32 merged_count = self._atom_count + bond_list._atom_count
-        cdef merged_bond_list = BondList(merged_count)
-        # Array is not used in constructor to prevent unnecessary
-        # maximum and redundant bond calculation
-        merged_bond_list._bonds = merged_bonds
-        merged_bond_list._max_bonds_per_atom = max(
-            self._max_bonds_per_atom, bond_list._max_bonds_per_atom
-        )
-        return merged_bond_list
+        return BondList.concatenate([self, bond_list])
 
     def __getitem__(self, index):
         ## Variables for both, integer and boolean index arrays
@@ -1427,7 +1482,7 @@ def connect_via_distances(atoms, dict distance_range=None, bint inter_residue=Tr
     BondList
         The created bond list.
 
-    See also
+    See Also
     --------
     connect_via_residue_names
 
@@ -1566,7 +1621,7 @@ def connect_via_residue_names(atoms, bint inter_residue=True,
         No bonds are added for residues that are not found in
         ``components.cif``.
 
-    See also
+    See Also
     --------
     connect_via_distances
 
@@ -1608,7 +1663,6 @@ def connect_via_residue_names(atoms, bint inter_residue=True,
              ('OXT', 'HXT'): <BondType.SINGLE: 1>},
      'XYZ': {('A', 'B'): <BondType.SINGLE: 1>,
              ('B', 'C'): <BondType.SINGLE: 1>}}
-
     """
     from .info.bonds import bonds_in_residue
     from .residues import get_residue_starts

biotite/structure/box.py

@@ -45,10 +45,10 @@ def vectors_from_unitcell(len_a, len_b, len_c, alpha, beta, gamma):
     ----------
     len_a, len_b, len_c : float
         The lengths of the three box/unit cell vectors *a*, *b* and *c*.
-    alpha, beta, gamma:
+    alpha, beta, gamma : float
         The angles between the box vectors in radians.
         *alpha* is the angle between *b* and *c*,
-        *beta* between *a* and *c*, *gamma* between *a* and *b*
+        *beta* between *a* and *c*, *gamma* between *a* and *b*.
 
     Returns
     -------
@@ -58,9 +58,9 @@ def vectors_from_unitcell(len_a, len_b, len_c, alpha, beta, gamma):
         The value can be directly used as :attr:`box` attribute in an
         atom array.
 
-    See also
+    See Also
     --------
-    unitcell_from_vectors
+    unitcell_from_vectors : The reverse operation.
     """
     a_x = len_a
     b_x = len_b * np.cos(gamma)
@@ -87,7 +87,7 @@ def unitcell_from_vectors(box):
     Parameters
     ----------
     box : ndarray, shape=(3,3)
-        The box vectors
+        The box vectors.
 
     Returns
     -------
@@ -96,9 +96,9 @@ def unitcell_from_vectors(box):
     alpha, beta, gamma : float
         The angles between the box vectors in radians.
 
-    See also
+    See Also
     --------
-    vectors_from_unitcell
+    vectors_from_unitcell : The reverse operation.
     """
     a = box[0]
     b = box[1]
@@ -124,6 +124,7 @@ def box_volume(box):
     Returns
     -------
     volume : float or ndarray, shape=(m,)
+        The volume(s) of the given box(es).
     """
     # Using the triple product
     return np.abs(linalg.det(box))
@@ -164,9 +165,9 @@ def repeat_box(atoms, amount=1):
         Equal to
         ``numpy.tile(np.arange(atoms.array_length()), (1 + 2 * amount) ** 3)``.
 
-    See also
+    See Also
     --------
-    repeat_box_coord
+    repeat_box_coord : Variant that acts directly on coordinates.
 
     Examples
     --------
@@ -383,9 +384,9 @@ def remove_pbc(atoms, selection=None):
         The input structure with removed segmentation over periodic
         boundaries.
 
-    See also
+    See Also
     --------
-    remove_pbc_from_coord
+    remove_pbc_from_coord : Variant that acts directly on coordinates.
 
     Notes
     -----
@@ -430,8 +431,6 @@ def remove_pbc_from_coord(coord, box):
     is moved inside the box.
     All other coordinates are assembled relative to the origin by using
     the displacement coordinates in adjacent array positions.
-    Basically, this function performs the reverse action of
-    :func:`move_inside_box()`.
 
     Parameters
     ----------
@@ -447,10 +446,9 @@ def remove_pbc_from_coord(coord, box):
     sanitized_coord : ndarray, dtype=float, shape=(m,n,3) or shape=(n,3)
         The reassembled coordinates.
 
-    See also
+    See Also
     --------
-    remove_pbc_from_coord
-    move_inside_box
+    move_inside_box : The reverse operation.
 
     Notes
     -----
@@ -501,9 +499,9 @@ def coord_to_fraction(coord, box):
     fraction : ndarray, dtype=float, shape=(n,3) or shape=(m,n,3)
         The fractions of the box vectors.
 
-    See also
+    See Also
     --------
-    fraction_to_coord
+    fraction_to_coord : The reverse operation.
 
     Examples
     --------
@@ -548,9 +546,9 @@ def fraction_to_coord(fraction, box):
     coord : ndarray, dtype=float, shape=(n,3) or shape=(m,n,3)
         The coordinates.
 
-    See also
+    See Also
     --------
-    coord_to_fraction
+    coord_to_fraction : The reverse operation.
     """
     return np.matmul(fraction, box)
 
@@ -570,7 +568,7 @@ def is_orthogonal(box):
     Returns
     -------
     is_orthgonal : bool or ndarray, shape=(m,), dtype=bool
-        True, if the box vectors are orthogonal, false otherwise
+        True, if the box vectors are orthogonal, false otherwise.
 
     Notes
     -----