biotite 1.3.0__cp312-cp312-macosx_10_13_x86_64.whl

biotite/structure/bonds.pyx

@@ -0,0 +1,1975 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+This module allows efficient search of atoms in a defined radius around
+a location.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["BondList", "BondType",
+           "connect_via_distances", "connect_via_residue_names",
+           "find_connected", "find_rotatable_bonds"]
+
+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
+import networkx as nx
+import numpy as np
+from .error import BadStructureError
+from ..copyable import Copyable
+
+ctypedef np.uint64_t ptr
+ctypedef np.uint8_t  uint8
+ctypedef np.uint16_t uint16
+ctypedef np.uint32_t uint32
+ctypedef np.uint64_t uint64
+ctypedef np.int8_t   int8
+ctypedef np.int16_t  int16
+ctypedef np.int32_t  int32
+ctypedef np.int64_t  int64
+
+
+ctypedef fused IndexType:
+    uint8
+    uint16
+    uint32
+    uint64
+    int8
+    int16
+    int32
+    int64
+
+
+class BondType(IntEnum):
+    """
+    This enum type represents the type of a chemical bond.
+
+        - `ANY` - Used if the actual type is unknown
+        - `SINGLE` - Single bond
+        - `DOUBLE` - Double bond
+        - `TRIPLE` - Triple bond
+        - `QUADRUPLE` - A quadruple bond
+        - `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
+    DOUBLE = 2
+    TRIPLE = 3
+    QUADRUPLE = 4
+    AROMATIC_SINGLE = 5
+    AROMATIC_DOUBLE = 6
+    AROMATIC_TRIPLE = 7
+    COORDINATION = 8
+    AROMATIC = 9
+
+
+    def without_aromaticity(self):
+        """
+        Remove aromaticity from the bond type.
+
+        :attr:`BondType.AROMATIC_{ORDER}` is converted into
+        :attr:`BondType.{ORDER}`.
+
+        Returns
+        -------
+        new_bond_type : BondType
+            The :class:`BondType` without aromaticity.
+
+        Examples
+        --------
+
+        >>> print(BondType.AROMATIC_DOUBLE.without_aromaticity().name)
+        DOUBLE
+        """
+        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
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+class BondList(Copyable):
+    """
+    __init__(atom_count, bonds=None)
+
+    A bond list stores indices of atoms
+    (usually of an :class:`AtomArray` or :class:`AtomArrayStack`)
+    that form chemical bonds together with the type (or order) of the
+    bond.
+
+    Internally the bonds are stored as *n x 3* :class:`ndarray`.
+    For each row, the first column specifies the index of the first
+    atom, the second column the index of the second atom involved in the
+    bond.
+    The third column stores an integer that is interpreted as member
+    of the the :class:`BondType` enum, that specifies the order of the
+    bond.
+
+    When indexing a :class:`BondList`, the index is not forwarded to the
+    internal :class:`ndarray`. Instead the indexing behavior is
+    consistent with indexing an :class:`AtomArray` or
+    :class:`AtomArrayStack`:
+    Bonds with at least one atom index that is not covered by the index
+    are removed, atom indices that occur after an uncovered atom index
+    move up.
+    Effectively, this means that after indexing an :class:`AtomArray`
+    and a :class:`BondList` with the same index, the atom indices in the
+    :class:`BondList` will still point to the same atoms in the
+    :class:`AtomArray`.
+    Indexing a :class:`BondList` with a single integer is equivalent
+    to calling :func:`get_bonds()`.
+
+    The same consistency applies to adding :class:`BondList` instances
+    via the '+' operator:
+    The atom indices of the second :class:`BondList` are increased by
+    the atom count of the first :class:`BondList` and then both
+    :class:`BondList` objects are merged.
+
+    Parameters
+    ----------
+    atom_count : int
+        A positive integer, that specifies the number of atoms the
+        :class:`BondList` refers to
+        (usually the length of an atom array (stack)).
+        Effectively, this value is the exclusive maximum for the indices
+        stored in the :class:`BondList`.
+    bonds : ndarray, shape=(n,2) or shape=(n,3), dtype=int, optional
+        This array contains the indices of atoms which are bonded:
+        For each row, the first column specifies the first atom,
+        the second row the second atom involved in a chemical bond.
+        If an *n x 3* array is provided, the additional column
+        specifies a :class:`BondType` instead of :attr:`BondType.ANY`.
+        By default, the created :class:`BondList` is empty.
+
+    Notes
+    -----
+    When initially providing the bonds as :class:`ndarray`, the input is
+    sanitized: Redundant bonds are removed, and each bond entry is
+    sorted so that the lower one of the two atom indices is in the first
+    column.
+    If a bond appears multiple times with different bond types, the
+    first bond takes precedence.
+
+    Examples
+    --------
+
+    Construct a :class:`BondList`, where a central atom (index 1) is
+    connected to three other atoms (index 0, 3 and 4):
+
+    >>> bond_list = BondList(5, np.array([(1,0),(1,3),(1,4)]))
+    >>> print(bond_list)
+    [[0 1 0]
+     [1 3 0]
+     [1 4 0]]
+
+    Remove the first atom (index 0) via indexing:
+    The bond containing index 0 is removed, since the corresponding atom
+    does not exist anymore. Since all other atoms move up in their
+    position, the indices in the bond list are decreased by one:
+
+    >>> bond_list = bond_list[1:]
+    >>> print(bond_list)
+    [[0 2 0]
+     [0 3 0]]
+
+    :class:`BondList` objects can be associated to an :class:`AtomArray`
+    or :class:`AtomArrayStack`.
+    The following snippet shows this for a benzene molecule:
+
+    >>> benzene = AtomArray(12)
+    >>> # Omit filling most required annotation categories for brevity
+    >>> benzene.atom_name = np.array(
+    ...     ["C1", "C2", "C3", "C4", "C5", "C6", "H1", "H2", "H3", "H4", "H5", "H6"]
+    ... )
+    >>> benzene.bonds = BondList(
+    ...     benzene.array_length(),
+    ...     np.array([
+    ...         # Bonds between carbon atoms in the ring
+    ...         (0,  1, BondType.AROMATIC_SINGLE),
+    ...         (1,  2, BondType.AROMATIC_DOUBLE),
+    ...         (2,  3, BondType.AROMATIC_SINGLE),
+    ...         (3,  4, BondType.AROMATIC_DOUBLE),
+    ...         (4,  5, BondType.AROMATIC_SINGLE),
+    ...         (5,  0, BondType.AROMATIC_DOUBLE),
+    ...         # Bonds between carbon and hydrogen
+    ...         (0,  6, BondType.SINGLE),
+    ...         (1,  7, BondType.SINGLE),
+    ...         (2,  8, BondType.SINGLE),
+    ...         (3,  9, BondType.SINGLE),
+    ...         (4, 10, BondType.SINGLE),
+    ...         (5, 11, BondType.SINGLE),
+    ...     ])
+    ... )
+    >>> for i, j, bond_type in benzene.bonds.as_array():
+    ...     print(
+    ...         f"{BondType(bond_type).name} bond between "
+    ...         f"{benzene.atom_name[i]} and {benzene.atom_name[j]}"
+    ...     )
+    AROMATIC_SINGLE bond between C1 and C2
+    AROMATIC_DOUBLE bond between C2 and C3
+    AROMATIC_SINGLE bond between C3 and C4
+    AROMATIC_DOUBLE bond between C4 and C5
+    AROMATIC_SINGLE bond between C5 and C6
+    AROMATIC_DOUBLE bond between C1 and C6
+    SINGLE bond between C1 and H1
+    SINGLE bond between C2 and H2
+    SINGLE bond between C3 and H3
+    SINGLE bond between C4 and H4
+    SINGLE bond between C5 and H5
+    SINGLE bond between C6 and H6
+
+    Obtain the bonded atoms for the :math:`C_1`:
+
+    >>> bonds, types = benzene.bonds.get_bonds(0)
+    >>> print(bonds)
+    [1 5 6]
+    >>> print(types)
+    [5 6 1]
+    >>> print(f"C1 is bonded to {', '.join(benzene.atom_name[bonds])}")
+    C1 is bonded to C2, C6, H1
+
+    Cut the benzene molecule in half.
+    Although the first half of the atoms are missing the indices of
+    the cropped :class:`BondList` still represents the bonds of the
+    remaining atoms:
+
+    >>> half_benzene = benzene[
+    ...     np.isin(benzene.atom_name, ["C4", "C5", "C6", "H4", "H5", "H6"])
+    ... ]
+    >>> for i, j, bond_type in half_benzene.bonds.as_array():
+    ...     print(
+    ...         f"{BondType(bond_type).name} bond between "
+    ...         f"{half_benzene.atom_name[i]} and {half_benzene.atom_name[j]}"
+    ...     )
+    AROMATIC_DOUBLE bond between C4 and C5
+    AROMATIC_SINGLE bond between C5 and C6
+    SINGLE bond between C4 and H4
+    SINGLE bond between C5 and H5
+    SINGLE bond between C6 and H6
+    """
+
+    def __init__(self, uint32 atom_count, np.ndarray bonds=None):
+        self._atom_count = atom_count
+
+        if bonds is not None and len(bonds) > 0:
+            if bonds.ndim != 2:
+                raise ValueError("Expected a 2D-ndarray for input bonds")
+
+            self._bonds = np.zeros((bonds.shape[0], 3), dtype=np.uint32)
+            if bonds.shape[1] == 3:
+                # Input contains bonds (index 0 and 1)
+                # including the bond type value (index 2)
+                # Bond indices:
+                self._bonds[:,:2] = np.sort(
+                    # Indices are sorted per bond
+                    # so that the lower index is at the first position
+                    _to_positive_index_array(bonds[:,:2], atom_count), axis=1
+                )
+                # Bond type:
+                if (bonds[:, 2] >= len(BondType)).any():
+                    raise ValueError(
+                        f"BondType {np.max(bonds[:, 2])} is invalid"
+                    )
+                self._bonds[:,2] = bonds[:, 2]
+
+                # Indices are sorted per bond
+                # so that the lower index is at the first position
+            elif bonds.shape[1] == 2:
+                # Input contains the bonds without bond type
+                # -> Default: Set bond type ANY (0)
+                self._bonds[:,:2] = np.sort(
+                    # Indices are sorted per bond
+                    # so that the lower index is at the first position
+                    _to_positive_index_array(bonds[:,:2], atom_count), axis=1
+                )
+            else:
+                raise ValueError(
+                    "Input array containing bonds must be either of shape "
+                    "(n,2) or (n,3)"
+                )
+            self._remove_redundant_bonds()
+            self._max_bonds_per_atom = self._get_max_bonds_per_atom()
+
+        else:
+            # Create empty bond list
+            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
+        # and calculation of maximum bonds per atom
+        return BondList(self._atom_count)
+
+    def __copy_fill__(self, clone):
+        # The bonds are added here
+        clone._bonds = self._bonds.copy()
+        clone._max_bonds_per_atom = self._max_bonds_per_atom
+
+    def offset_indices(self, int offset):
+        """
+        offset_indices(offset)
+
+        Increase all atom indices in the :class:`BondList` by the given
+        offset.
+
+        Implicitly this increases the atom count.
+
+        Parameters
+        ----------
+        offset : int
+            The atom indices are increased by this value.
+            Must be positive.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(5, np.array([(1,0),(1,3),(1,4)]))
+        >>> print(bond_list)
+        [[0 1 0]
+         [1 3 0]
+         [1 4 0]]
+        >>> bond_list.offset_indices(2)
+        >>> print(bond_list)
+        [[2 3 0]
+         [3 5 0]
+         [3 6 0]]
+        """
+        if offset < 0:
+            raise ValueError("Offest must be positive")
+        self._bonds[:,:2] += offset
+        self._atom_count += offset
+
+    def as_array(self):
+        """
+        as_array()
+
+        Obtain a copy of the internal :class:`ndarray`.
+
+        Returns
+        -------
+        array : ndarray, shape=(n,3), dtype=np.uint32
+            Copy of the internal :class:`ndarray`.
+            For each row, the first column specifies the index of the
+            first atom, the second column the index of the second atom
+            involved in the bond.
+            The third column stores the :class:`BondType`.
+        """
+        return self._bonds.copy()
+
+    def as_set(self):
+        """
+        as_set()
+
+        Obtain a set representation of the :class:`BondList`.
+
+        Returns
+        -------
+        bond_set : set of tuple(int, int, int)
+            A set of tuples.
+            Each tuple represents one bond:
+            The first integer represents the first atom,
+            the second integer represents the second atom,
+            the third integer represents the :class:`BondType`.
+        """
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        cdef int i
+        cdef set bond_set = set()
+        for i in range(all_bonds_v.shape[0]):
+            bond_set.add(
+                (all_bonds_v[i,0], all_bonds_v[i,1], all_bonds_v[i,2])
+            )
+        return bond_set
+
+    def as_graph(self):
+        """
+        as_graph()
+
+        Obtain a graph representation of the :class:`BondList`.
+
+        Returns
+        -------
+        bond_set : Graph
+            A *NetworkX* :class:`Graph`.
+            The atom indices are nodes, the bonds are edges.
+            Each edge has a ``"bond_type"`` attribute containing the
+            :class:`BondType`.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(5, np.array([(1,0,2), (1,3,1), (1,4,1)]))
+        >>> graph = bond_list.as_graph()
+        >>> print(graph.nodes)
+        [0, 1, 3, 4]
+        >>> print(graph.edges)
+        [(0, 1), (1, 3), (1, 4)]
+        >>> for i, j in graph.edges:
+        ...     print(i, j, graph.get_edge_data(i, j))
+        0 1 {'bond_type': <BondType.DOUBLE: 2>}
+        1 3 {'bond_type': <BondType.SINGLE: 1>}
+        1 4 {'bond_type': <BondType.SINGLE: 1>}
+        """
+        cdef int i
+
+        cdef uint32[:,:] all_bonds_v = self._bonds
+
+        g = nx.Graph()
+        cdef list edges = [None] * all_bonds_v.shape[0]
+        for i in range(all_bonds_v.shape[0]):
+            edges[i] = (
+                all_bonds_v[i,0], all_bonds_v[i,1],
+                {"bond_type": BondType(all_bonds_v[i,2])}
+            )
+        g.add_edges_from(edges)
+        return g
+
+    def remove_aromaticity(self):
+        """
+        Remove aromaticity from the bond types.
+
+        :attr:`BondType.AROMATIC_{ORDER}` is converted into
+        :attr:`BondType.{ORDER}`.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(3)
+        >>> bond_list.add_bond(0, 1, BondType.AROMATIC_SINGLE)
+        >>> bond_list.add_bond(1, 2, BondType.AROMATIC_DOUBLE)
+        >>> bond_list.remove_aromaticity()
+        >>> for i, j, bond_type in bond_list.as_array():
+        ...     print(i, j, BondType(bond_type).name)
+        0 1 SINGLE
+        1 2 DOUBLE
+        """
+        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):
+        """
+        Convert all bonds to :attr:`BondType.ANY`.
+        """
+        self._bonds[:,2] = BondType.ANY
+
+    def get_atom_count(self):
+        """
+        get_atom_count()
+
+        Get the atom count.
+
+        Returns
+        -------
+        atom_count : int
+            The atom count.
+        """
+        return self._atom_count
+
+    def get_bond_count(self):
+        """
+        get_bond_count()
+
+        Get the amount of bonds.
+
+        Returns
+        -------
+        bond_count : int
+            The amount of bonds. This is equal to the length of the
+            internal :class:`ndarray` containing the bonds.
+        """
+        return len(self._bonds)
+
+    def get_bonds(self, int32 atom_index):
+        """
+        get_bonds(atom_index)
+
+        Obtain the indices of the atoms bonded to the atom with the
+        given index as well as the corresponding bond types.
+
+        Parameters
+        ----------
+        atom_index : int
+            The index of the atom to get the bonds for.
+
+        Returns
+        -------
+        bonds : np.ndarray, dtype=np.uint32, shape=(k,)
+            The indices of connected atoms.
+        bond_types : np.ndarray, dtype=np.uint8, shape=(k,)
+            Array of integers, interpreted as :class:`BondType`
+            instances.
+            This array specifies the type (or order) of the bonds to
+            the connected atoms.
+
+        Examples
+        --------
+
+        >>> bond_list = BondList(5, np.array([(1,0),(1,3),(1,4)]))
+        >>> bonds, types = bond_list.get_bonds(1)
+        >>> print(bonds)
+        [0 3 4]
+        """
+        cdef int i=0, j=0
+
+        cdef uint32 index = _to_positive_index(atom_index, self._atom_count)
+
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # Pessimistic array allocation:
+        # assume size is equal to the atom with most bonds
+        cdef np.ndarray bonds = np.zeros(self._max_bonds_per_atom,
+                                         dtype=np.uint32)
+        cdef uint32[:] bonds_v = bonds
+        cdef np.ndarray bond_types = np.zeros(self._max_bonds_per_atom,
+                                              dtype=np.uint8)
+        cdef uint8[:] bond_types_v = bond_types
+
+        for i in range(all_bonds_v.shape[0]):
+            # If a bond is found for the desired atom index
+            # at the first or second position of the bond,
+            # then append the index of the respective other position
+            if all_bonds_v[i,0] == index:
+                bonds_v[j] = all_bonds_v[i,1]
+                bond_types_v[j] = all_bonds_v[i,2]
+                j += 1
+            elif all_bonds_v[i,1] == index:
+                bonds_v[j] = all_bonds_v[i,0]
+                bond_types_v[j] = all_bonds_v[i,2]
+                j += 1
+
+        # Trim to correct size
+        bonds = bonds[:j]
+        bond_types = bond_types[:j]
+
+        return bonds, bond_types
+
+
+    def get_all_bonds(self):
+        """
+        get_all_bonds()
+
+        For each atom index, give the indices of the atoms bonded to
+        this atom as well as the corresponding bond types.
+
+        Returns
+        -------
+        bonds : np.ndarray, dtype=np.uint32, shape=(n,k)
+            The indices of connected atoms.
+            The first dimension represents the atoms,
+            the second dimension represents the indices of atoms bonded
+            to the respective atom.
+            Atoms can have have different numbers of atoms bonded to
+            them.
+            Therefore, the length of the second dimension *k* is equal
+            to the maximum number of bonds for an atom in this
+            :class:`BondList`.
+            For atoms with less bonds, the corresponding entry in the
+            array is padded with ``-1`` values.
+        bond_types : np.ndarray, dtype=np.uint32, shape=(n,k)
+            Array of integers, interpreted as :class:`BondType`
+            instances.
+            This array specifies the bond type (or order) corresponding
+            to the returned `bonds`.
+            It uses the same ``-1``-padding.
+
+        Examples
+        --------
+
+        >>> # BondList for benzene
+        >>> bond_list = BondList(
+        ...     12,
+        ...     np.array([
+        ...         # Bonds between the carbon atoms in the ring
+        ...         (0,  1, BondType.AROMATIC_SINGLE),
+        ...         (1,  2, BondType.AROMATIC_DOUBLE),
+        ...         (2,  3, BondType.AROMATIC_SINGLE),
+        ...         (3,  4, BondType.AROMATIC_DOUBLE),
+        ...         (4,  5, BondType.AROMATIC_SINGLE),
+        ...         (5,  0, BondType.AROMATIC_DOUBLE),
+        ...         # Bonds between carbon and hydrogen
+        ...         (0,  6, BondType.SINGLE),
+        ...         (1,  7, BondType.SINGLE),
+        ...         (2,  8, BondType.SINGLE),
+        ...         (3,  9, BondType.SINGLE),
+        ...         (4, 10, BondType.SINGLE),
+        ...         (5, 11, BondType.SINGLE),
+        ...     ])
+        ... )
+        >>> bonds, types = bond_list.get_all_bonds()
+        >>> print(bonds)
+        [[ 1  5  6]
+         [ 0  2  7]
+         [ 1  3  8]
+         [ 2  4  9]
+         [ 3  5 10]
+         [ 4  0 11]
+         [ 0 -1 -1]
+         [ 1 -1 -1]
+         [ 2 -1 -1]
+         [ 3 -1 -1]
+         [ 4 -1 -1]
+         [ 5 -1 -1]]
+        >>> print(types)
+        [[ 5  6  1]
+         [ 5  6  1]
+         [ 6  5  1]
+         [ 5  6  1]
+         [ 6  5  1]
+         [ 5  6  1]
+         [ 1 -1 -1]
+         [ 1 -1 -1]
+         [ 1 -1 -1]
+         [ 1 -1 -1]
+         [ 1 -1 -1]
+         [ 1 -1 -1]]
+        >>> for i in range(bond_list.get_atom_count()):
+        ...     bonds_for_atom = bonds[i]
+        ...     # Remove trailing '-1' values
+        ...     bonds_for_atom = bonds_for_atom[bonds_for_atom != -1]
+        ...     print(f"{i}: {bonds_for_atom}")
+        0: [1 5 6]
+        1: [0 2 7]
+        2: [1 3 8]
+        3: [2 4 9]
+        4: [ 3  5 10]
+        5: [ 4  0 11]
+        6: [0]
+        7: [1]
+        8: [2]
+        9: [3]
+        10: [4]
+        11: [5]
+        """
+        cdef int i=0
+        cdef uint32 atom_index_i, atom_index_j, bond_type
+
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # The size of 2nd dimension is equal to the atom with most bonds
+        # Since each atom can have an individual number of bonded atoms,
+        # The arrays are padded with '-1'
+        cdef np.ndarray bonds = np.full(
+            (self._atom_count, self._max_bonds_per_atom), -1, dtype=np.int32
+        )
+        cdef int32[:,:] bonds_v = bonds
+        cdef np.ndarray bond_types = np.full(
+            (self._atom_count, self._max_bonds_per_atom), -1, dtype=np.int8
+        )
+        cdef int8[:,:] bond_types_v = bond_types
+        # Track the number of already found bonds for each given index
+        cdef np.ndarray lengths = np.zeros(self._atom_count, dtype=np.uint32)
+        cdef uint32[:] lengths_v = lengths
+
+        for i in range(all_bonds_v.shape[0]):
+            atom_index_i = all_bonds_v[i,0]
+            atom_index_j = all_bonds_v[i,1]
+            bond_type = all_bonds_v[i,2]
+            # Add second bonded atom for the first bonded atom
+            # and vice versa
+            # Use 'lengths' variable to append the value
+            bonds_v[atom_index_i, lengths_v[atom_index_i]] = atom_index_j
+            bonds_v[atom_index_j, lengths_v[atom_index_j]] = atom_index_i
+            bond_types_v[atom_index_i, lengths_v[atom_index_i]] = bond_type
+            bond_types_v[atom_index_j, lengths_v[atom_index_j]] = bond_type
+            # Increment lengths
+            lengths_v[atom_index_i] += 1
+            lengths_v[atom_index_j] += 1
+
+        return bonds, bond_types
+
+
+    def adjacency_matrix(self):
+        r"""
+        adjacency_matrix(bond_list)
+
+        Represent this :class:`BondList` as adjacency matrix.
+
+        The adjacency matrix is a quadratic matrix with boolean values
+        according to
+
+        .. math::
+
+            M_{i,j} =
+            \begin{cases}
+                \text{True},  & \text{if } \text{Atom}_i \text{ and } \text{Atom}_j \text{ form a bond} \\
+                \text{False}, & \text{otherwise}
+            \end{cases}.
+
+        Returns
+        -------
+        matrix : ndarray, dtype=bool, shape=(n,n)
+            The created adjacency matrix.
+
+        Examples
+        --------
+
+        >>> # BondList for formaldehyde
+        >>> bond_list = BondList(
+        ...     4,
+        ...     np.array([
+        ...         # Bond between carbon and oxygen
+        ...         (0,  1, BondType.DOUBLE),
+        ...         # Bonds between carbon and hydrogen
+        ...         (0,  2, BondType.SINGLE),
+        ...         (0,  3, BondType.SINGLE),
+        ...     ])
+        ... )
+        >>> print(bond_list.adjacency_matrix())
+        [[False  True  True  True]
+         [ True False False False]
+         [ True False False False]
+         [ True False False False]]
+        """
+        matrix = np.zeros(
+            (self._atom_count, self._atom_count), dtype=bool
+        )
+        matrix[self._bonds[:,0], self._bonds[:,1]] = True
+        matrix[self._bonds[:,1], self._bonds[:,0]] = True
+        return matrix
+
+
+    def bond_type_matrix(self):
+        r"""
+        adjacency_matrix(bond_list)
+
+        Represent this :class:`BondList` as a matrix depicting the bond
+        type.
+
+        The matrix is a quadratic matrix:
+
+        .. math::
+
+            M_{i,j} =
+            \begin{cases}
+                \text{BondType}_{ij},  & \text{if } \text{Atom}_i \text{ and } \text{Atom}_j \text{ form a bond} \\
+                -1,                    & \text{otherwise}
+            \end{cases}.
+
+        Returns
+        -------
+        matrix : ndarray, dtype=bool, shape=(n,n)
+            The created bond type matrix.
+
+        Examples
+        --------
+
+        >>> # BondList for formaldehyde
+        >>> bond_list = BondList(
+        ...     4,
+        ...     np.array([
+        ...         # Bond between carbon and oxygen
+        ...         (0,  1, BondType.DOUBLE),
+        ...         # Bonds between carbon and hydrogen
+        ...         (0,  2, BondType.SINGLE),
+        ...         (0,  3, BondType.SINGLE),
+        ...     ])
+        ... )
+        >>> print(bond_list.bond_type_matrix())
+        [[-1  2  1  1]
+         [ 2 -1 -1 -1]
+         [ 1 -1 -1 -1]
+         [ 1 -1 -1 -1]]
+        """
+        matrix = np.full(
+            (self._atom_count, self._atom_count), -1, dtype=np.int8
+        )
+        matrix[self._bonds[:,0], self._bonds[:,1]] = self._bonds[:,2]
+        matrix[self._bonds[:,1], self._bonds[:,0]] = self._bonds[:,2]
+        return matrix
+
+
+    def add_bond(self, int32 atom_index1, int32 atom_index2,
+                 bond_type=BondType.ANY):
+        """
+        add_bond(atom_index1, atom_index2, bond_type=BondType.ANY)
+
+        Add a bond to the :class:`BondList`.
+
+        If the bond is already existent, only the bond type is updated.
+
+        Parameters
+        ----------
+        atom_index1, atom_index2 : int
+            The indices of the atoms to create a bond for.
+        bond_type : BondType or int, optional
+            The type of the bond. Default is :attr:`BondType.ANY`.
+        """
+        if bond_type >= len(BondType):
+            raise ValueError(f"BondType {bond_type} is invalid")
+
+        cdef uint32 index1 = _to_positive_index(atom_index1, self._atom_count)
+        cdef uint32 index2 = _to_positive_index(atom_index2, self._atom_count)
+        _sort(&index1, &index2)
+
+        cdef int i
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # Check if bond is already existent in list
+        cdef bint in_list = False
+        for i in range(all_bonds_v.shape[0]):
+            # Since the bonds have the atom indices sorted
+            # the reverse check is omitted
+            if (all_bonds_v[i,0] == index1 and all_bonds_v[i,1] == index2):
+                in_list = True
+                # If in list, update bond type
+                all_bonds_v[i,2] = int(bond_type)
+                break
+        if not in_list:
+            self._bonds = np.append(
+                self._bonds,
+                np.array(
+                    [(index1, index2, int(bond_type))], dtype=np.uint32
+                ),
+                axis=0
+            )
+            self._max_bonds_per_atom = self._get_max_bonds_per_atom()
+
+    def remove_bond(self, int32 atom_index1, int32 atom_index2):
+        """
+        remove_bond(atom_index1, atom_index2)
+
+        Remove a bond from the :class:`BondList`.
+
+        If the bond is not existent in the :class:`BondList`, nothing happens.
+
+        Parameters
+        ----------
+        atom_index1, atom_index2 : int
+            The indices of the atoms whose bond should be removed.
+        """
+        cdef uint32 index1 = _to_positive_index(atom_index1, self._atom_count)
+        cdef uint32 index2 = _to_positive_index(atom_index2, self._atom_count)
+        _sort(&index1, &index2)
+
+        # Find the bond in bond list
+        cdef int i
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        for i in range(all_bonds_v.shape[0]):
+            # Since the bonds have the atom indices sorted
+            # the reverse check is omitted
+            if (all_bonds_v[i,0] == index1 and all_bonds_v[i,1] == index2):
+                self._bonds = np.delete(self._bonds, i, axis=0)
+        # The maximum bonds per atom is not recalculated,
+        # as the value can only be decreased on bond removal
+        # Since this value is only used for pessimistic array allocation
+        # in 'get_bonds()', the slightly larger memory usage is a better
+        # option than the repetitive call of _get_max_bonds_per_atom()
+
+    def remove_bonds_to(self, int32 atom_index):
+        """
+        remove_bonds_to(self, atom_index)
+
+        Remove all bonds from the :class:`BondList` where the given atom
+        is involved.
+
+        Parameters
+        ----------
+        atom_index : int
+            The index of the atom whose bonds should be removed.
+        """
+        cdef uint32 index = _to_positive_index(atom_index, self._atom_count)
+
+        cdef np.ndarray mask = np.ones(len(self._bonds), dtype=np.uint8)
+        cdef uint8[:] mask_v = mask
+
+        # Find the bond in bond list
+        cdef int i
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        for i in range(all_bonds_v.shape[0]):
+            if (all_bonds_v[i,0] == index or all_bonds_v[i,1] == index):
+                mask_v[i] = False
+        # Remove the bonds
+        self._bonds = self._bonds[mask.astype(bool, copy=False)]
+        # The maximum bonds per atom is not recalculated
+        # (see 'remove_bond()')
+
+    def remove_bonds(self, bond_list):
+        """
+        remove_bonds(bond_list)
+
+        Remove multiple bonds from the :class:`BondList`.
+
+        All bonds present in `bond_list` are removed from this instance.
+        If a bond is not existent in this instance, nothing happens.
+        Only the bond indices, not the bond types, are relevant for
+        this.
+
+        Parameters
+        ----------
+        bond_list : BondList
+            The bonds in `bond_list` are removed from this instance.
+        """
+        cdef int i=0, j=0
+
+        # All bonds in the own BondList
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # The bonds that should be removed
+        cdef uint32[:,:] rem_bonds_v = bond_list._bonds
+        cdef np.ndarray mask = np.ones(all_bonds_v.shape[0], dtype=np.uint8)
+        cdef uint8[:] mask_v = mask
+        for i in range(all_bonds_v.shape[0]):
+            for j in range(rem_bonds_v.shape[0]):
+                if      all_bonds_v[i,0] == rem_bonds_v[j,0] \
+                    and all_bonds_v[i,1] == rem_bonds_v[j,1]:
+                        mask_v[i] = False
+
+        # Remove the bonds
+        self._bonds = self._bonds[mask.astype(bool, copy=False)]
+        # The maximum bonds per atom is not recalculated
+        # (see 'remove_bond()')
+
+    def merge(self, bond_list):
+        """
+        merge(bond_list)
+
+        Merge another :class:`BondList` with this instance into a new
+        object.
+        If a bond appears in both :class:`BondList`'s, the
+        :class:`BondType` from the given `bond_list` takes precedence.
+
+        The internal :class:`ndarray` instances containg the bonds are
+        simply concatenated and the new atom count is the maximum of
+        both bond lists.
+
+        Parameters
+        ----------
+        bond_list : BondList
+            This bond list is merged with this instance.
+
+        Returns
+        -------
+        bond_list : BondList
+            The merged :class:`BondList`.
+
+        Notes
+        -----
+        This is not equal to using the `+` operator.
+
+        Examples
+        --------
+
+        >>> bond_list1 = BondList(3, np.array([(0,1),(1,2)]))
+        >>> bond_list2 = BondList(5, np.array([(2,3),(3,4)]))
+        >>> merged_list = bond_list2.merge(bond_list1)
+        >>> print(merged_list.get_atom_count())
+        5
+        >>> print(merged_list)
+        [[0 1 0]
+         [1 2 0]
+         [2 3 0]
+         [3 4 0]]
+
+        The BondList given as parameter takes precedence:
+
+        >>> # Specifiy bond type to see where a bond is taken from
+        >>> bond_list1 = BondList(4, np.array([
+        ...     (0, 1, BondType.SINGLE),
+        ...     (1, 2, BondType.SINGLE)
+        ... ]))
+        >>> bond_list2 = BondList(4, np.array([
+        ...     (1, 2, BondType.DOUBLE),    # This one is a duplicate
+        ...     (2, 3, BondType.DOUBLE)
+        ... ]))
+        >>> merged_list = bond_list2.merge(bond_list1)
+        >>> print(merged_list)
+        [[0 1 1]
+         [1 2 1]
+         [2 3 2]]
+        """
+        return BondList(
+            max(self._atom_count, bond_list._atom_count),
+            np.concatenate(
+                [bond_list.as_array(), self.as_array()],
+                axis=0
+            )
+        )
+
+    def __add__(self, bond_list):
+        return BondList.concatenate([self, bond_list])
+
+    def __getitem__(self, index):
+        ## Variables for both, integer and boolean index arrays
+        cdef uint32[:,:] all_bonds_v
+        cdef int i
+        cdef uint32* index1_ptr
+        cdef uint32* index2_ptr
+        cdef np.ndarray removal_filter
+        cdef uint8[:] removal_filter_v
+
+        ## Variables for integer arrays
+        cdef int32[:] inverse_index_v
+        cdef int32 new_index1, new_index2
+
+        ## Variables for boolean mask
+        # Boolean mask representation of the index
+        cdef np.ndarray mask
+        cdef uint8[:] mask_v
+        # Boolean mask for removal of bonds
+        cdef np.ndarray offsets
+        cdef uint32[:] offsets_v
+
+        if isinstance(index, numbers.Integral):
+            ## Handle single index
+            return self.get_bonds(index)
+
+        elif isinstance(index, np.ndarray) and index.dtype == bool:
+            ## Handle boolean masks
+            copy = self.copy()
+            all_bonds_v = copy._bonds
+            # Use 'uint8' instead of 'bool' for memory view
+            mask = np.frombuffer(index, dtype=np.uint8)
+
+            # Each time an atom is missing in the mask,
+            # the offset is increased by one
+            offsets = np.cumsum(
+                ~mask.astype(bool, copy=False), dtype=np.uint32
+            )
+            removal_filter = np.ones(all_bonds_v.shape[0], dtype=np.uint8)
+            removal_filter_v = removal_filter
+            mask_v = mask
+            offsets_v = offsets
+            # If an atom in a bond is not masked,
+            # the bond is removed from the list
+            # If an atom is masked,
+            # its index value is decreased by the respective offset
+            # The offset is neccessary, removing atoms in an AtomArray
+            # decreases the index of the following atoms
+            for i in range(all_bonds_v.shape[0]):
+                # Usage of pointer to increase performance
+                # as redundant indexing is avoided
+                index1_ptr = &all_bonds_v[i,0]
+                index2_ptr = &all_bonds_v[i,1]
+                if mask_v[index1_ptr[0]] and mask_v[index2_ptr[0]]:
+                    # Both atoms involved in bond are masked
+                    # -> decrease atom index by offset
+                    index1_ptr[0] -= offsets_v[index1_ptr[0]]
+                    index2_ptr[0] -= offsets_v[index2_ptr[0]]
+                else:
+                    # At least one atom involved in bond is not masked
+                    # -> remove bond
+                    removal_filter_v[i] = False
+            # Apply the bond removal filter
+            copy._bonds = copy._bonds[removal_filter.astype(bool, copy=False)]
+            copy._atom_count = len(np.nonzero(mask)[0])
+            copy._max_bonds_per_atom = copy._get_max_bonds_per_atom()
+            return copy
+
+        else:
+            ## Convert any other type of index into index array, as it preserves order
+            copy = self.copy()
+            all_bonds_v = copy._bonds
+            index = _to_index_array(index, self._atom_count)
+            index = _to_positive_index_array(index, self._atom_count)
+
+            # The inverse index is required to efficiently obtain
+            # the new index of an atom in case of an unsorted index
+            # array
+            inverse_index_v = _invert_index(index, self._atom_count)
+            removal_filter = np.ones(all_bonds_v.shape[0], dtype=np.uint8)
+            removal_filter_v = removal_filter
+            for i in range(all_bonds_v.shape[0]):
+                # Usage of pointer to increase performance
+                # as redundant indexing is avoided
+                index1_ptr = &all_bonds_v[i,0]
+                index2_ptr = &all_bonds_v[i,1]
+                new_index1 = inverse_index_v[index1_ptr[0]]
+                new_index2 = inverse_index_v[index2_ptr[0]]
+                if new_index1 != -1 and new_index2 != -1:
+                    # Both atoms involved in bond are included
+                    # by index array
+                    # -> assign new atom indices
+                    index1_ptr[0] = <int32>new_index1
+                    index2_ptr[0] = <int32>new_index2
+                else:
+                    # At least one atom in bond is not included
+                    # -> remove bond
+                    removal_filter_v[i] = False
+
+            copy._bonds = copy._bonds[
+                removal_filter.astype(bool, copy=False)
+            ]
+            # Again, sort indices per bond
+            # as the correct order is not guaranteed anymore
+            # for unsorted index arrays
+            copy._bonds[:,:2] = np.sort(copy._bonds[:,:2], axis=1)
+            copy._atom_count = len(index)
+            copy._max_bonds_per_atom = copy._get_max_bonds_per_atom()
+            return copy
+
+    def __iter__(self):
+        raise TypeError("'BondList' object is not iterable")
+
+    def __str__(self):
+        return str(self.as_array())
+
+    def __eq__(self, item):
+        if not isinstance(item, BondList):
+            return False
+        return (self._atom_count == item._atom_count and
+                self.as_set() == item.as_set())
+
+    def __contains__(self, item):
+        if not isinstance(item, tuple) and len(tuple) != 2:
+            raise TypeError("Expected a tuple of atom indices")
+
+        cdef int i=0
+
+        cdef uint32 match_index1, match_index2
+        # Sort indices for faster search in loop
+        cdef uint32 atom_index1 = min(item)
+        cdef uint32 atom_index2 = max(item)
+
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        for i in range(all_bonds_v.shape[0]):
+            match_index1 = all_bonds_v[i,0]
+            match_index2 = all_bonds_v[i,1]
+            if atom_index1 == match_index1 and atom_index2 == match_index2:
+                return True
+
+        return False
+
+
+    def _get_max_bonds_per_atom(self):
+        if self._atom_count == 0:
+            return 0
+
+        cdef int i
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # Create an array that counts number of occurences of each index
+        cdef np.ndarray index_count = np.zeros(self._atom_count,
+                                               dtype=np.uint32)
+        cdef uint32[:] index_count_v = index_count
+        for i in range(all_bonds_v.shape[0]):
+            # Increment count of both indices found in bond list at i
+            index_count_v[all_bonds_v[i,0]] += 1
+            index_count_v[all_bonds_v[i,1]] += 1
+        return np.max(index_count_v)
+
+    def _remove_redundant_bonds(self):
+        cdef int j
+        cdef uint32[:,:] all_bonds_v = self._bonds
+        # Boolean mask for final removal of redundant atoms
+        # Unfortunately views of boolean ndarrays are not supported
+        # -> use uint8 array
+        cdef np.ndarray redundancy_filter = np.ones(all_bonds_v.shape[0],
+                                                    dtype=np.uint8)
+        cdef uint8[:] redundancy_filter_v = redundancy_filter
+        # Array of pointers to C-arrays
+        # The array is indexed with the atom indices in the bond list
+        # The respective C-array contains the indices of bonded atoms
+        cdef ptr[:] ptrs_v = np.zeros(self._atom_count, dtype=np.uint64)
+        # Stores the length of the C-arrays
+        cdef int[:] array_len_v = np.zeros(self._atom_count, dtype=np.int32)
+        # Iterate over bond list:
+        # If bond is already listed in the array of pointers,
+        # set filter to false at that position
+        # Else add bond to array of pointers
+        cdef uint32 i1, i2
+        cdef uint32* array_ptr
+        cdef int length
+
+        try:
+            for j in range(all_bonds_v.shape[0]):
+                i1 = all_bonds_v[j,0]
+                i2 = all_bonds_v[j,1]
+                # Since the bonds have the atom indices sorted
+                # the reverse check is omitted
+                if _in_array(<uint32*>ptrs_v[i1], i2, array_len_v[i1]):
+                        redundancy_filter_v[j] = False
+                else:
+                    # Append bond in respective C-array
+                    # and update C-array length
+                    length = array_len_v[i1] +1
+                    array_ptr = <uint32*>ptrs_v[i1]
+                    array_ptr = <uint32*>realloc(
+                        array_ptr, length * sizeof(uint32)
+                    )
+                    if not array_ptr:
+                        raise MemoryError()
+                    array_ptr[length-1] = i2
+                    ptrs_v[i1] = <ptr>array_ptr
+                    array_len_v[i1] = length
+
+        finally:
+            # Free pointers
+            for i in range(ptrs_v.shape[0]):
+                free(<int*>ptrs_v[i])
+
+        # Eventually remove redundant bonds
+        self._bonds = self._bonds[redundancy_filter.astype(bool, copy=False)]
+
+
+cdef uint32 _to_positive_index(int32 index, uint32 array_length) except -1:
+    """
+    Convert a potentially negative index into a positive index.
+    """
+    cdef uint32 pos_index
+    if index < 0:
+        pos_index = <uint32> (array_length + index)
+        if pos_index < 0:
+            raise IndexError(
+                f"Index {index} is out of range "
+                f"for an atom count of {array_length}"
+            )
+        return pos_index
+    else:
+        if <uint32> index >= array_length:
+            raise IndexError(
+                f"Index {index} is out of range "
+                f"for an atom count of {array_length}"
+            )
+        return <uint32> index
+
+
+def _to_positive_index_array(index_array, length):
+    """
+    Convert potentially negative values in an array into positive
+    values and check for out-of-bounds values.
+    """
+    index_array = index_array.copy()
+    orig_shape = index_array.shape
+    index_array = index_array.flatten()
+    negatives = index_array < 0
+    index_array[negatives] = length + index_array[negatives]
+    if (index_array < 0).any():
+        raise IndexError(
+            f"Index {np.min(index_array)} is out of range "
+            f"for an atom count of {length}"
+        )
+    if (index_array >= length).any():
+        raise IndexError(
+            f"Index {np.max(index_array)} is out of range "
+            f"for an atom count of {length}"
+        )
+    return index_array.reshape(orig_shape)
+
+
+def _to_index_array(object index, uint32 length):
+    """
+    Convert an index of arbitrary type into an index array.
+    """
+    if isinstance(index, np.ndarray) and np.issubdtype(index.dtype, np.integer):
+        return index
+    else:
+        # Convert into index array
+        all_indices = np.arange(length, dtype=np.uint32)
+        return all_indices[index]
+
+
+cdef inline bint _in_array(uint32* array, uint32 atom_index, int array_length):
+    """
+    Test whether a value (`atom_index`) is in a C-array `array`.
+    """
+    cdef int i = 0
+    if array == NULL:
+        return False
+    for i in range(array_length):
+        if array[i] == atom_index:
+            return True
+    return False
+
+
+cdef inline void _sort(uint32* index1_ptr, uint32* index2_ptr):
+    cdef uint32 swap
+    if index1_ptr[0] > index2_ptr[0]:
+        # Swap indices
+        swap = index1_ptr[0]
+        index1_ptr[0] = index2_ptr[0]
+        index2_ptr[0] = swap
+
+
+@cython.wraparound(False)
+# Do bounds check, as the input indices may be out of bounds
+def _invert_index(IndexType[:] index_v, uint32 length):
+    """
+    Invert an input index array, so that
+    if *input[i] = j*, *output[j] = i*.
+    For all elements *j*, that are not in *input*, *output[j]* = -1.
+    """
+    cdef int32 i
+    cdef IndexType index_val
+    inverse_index = np.full(length, -1, dtype=np.int32)
+    cdef int32[:] inverse_index_v = inverse_index
+
+    for i in range(index_v.shape[0]):
+        index_val = index_v[i]
+        if inverse_index_v[index_val] != -1:
+            # One index can theoretically appear multiple times
+            # This is currently not supported
+            raise NotImplementedError(
+                f"Duplicate indices are not supported, "
+                f"but index {index_val} appeared multiple times"
+            )
+        inverse_index_v[index_val] = i
+
+
+    return inverse_index
+
+
+
+
+# fmt: off
+_DEFAULT_DISTANCE_RANGE = {
+    # Taken from Allen et al.
+    #               min   - 2*std     max   + 2*std
+    ("B",  "C" ) : (1.556 - 2*0.015,  1.556 + 2*0.015),
+    ("BR", "C" ) : (1.875 - 2*0.029,  1.966 + 2*0.029),
+    ("BR", "O" ) : (1.581 - 2*0.007,  1.581 + 2*0.007),
+    ("C",  "C" ) : (1.174 - 2*0.011,  1.588 + 2*0.025),
+    ("C",  "CL") : (1.713 - 2*0.011,  1.849 + 2*0.011),
+    ("C",  "F" ) : (1.320 - 2*0.009,  1.428 + 2*0.009),
+    ("C",  "H" ) : (1.059 - 2*0.030,  1.099 + 2*0.007),
+    ("C",  "I" ) : (2.095 - 2*0.015,  2.162 + 2*0.015),
+    ("C",  "N" ) : (1.325 - 2*0.009,  1.552 + 2*0.023),
+    ("C",  "O" ) : (1.187 - 2*0.011,  1.477 + 2*0.008),
+    ("C",  "P" ) : (1.791 - 2*0.006,  1.855 + 2*0.019),
+    ("C",  "S" ) : (1.630 - 2*0.014,  1.863 + 2*0.015),
+    ("C",  "SE") : (1.893 - 2*0.013,  1.970 + 2*0.032),
+    ("C",  "SI") : (1.837 - 2*0.012,  1.888 + 2*0.023),
+    ("CL", "O" ) : (1.414 - 2*0.026,  1.414 + 2*0.026),
+    ("CL", "P" ) : (1.997 - 2*0.035,  2.008 + 2*0.035),
+    ("CL", "S" ) : (2.072 - 2*0.023,  2.072 + 2*0.023),
+    ("CL", "SI") : (2.072 - 2*0.009,  2.072 + 2*0.009),
+    ("F",  "N" ) : (1.406 - 2*0.016,  1.406 + 2*0.016),
+    ("F",  "P" ) : (1.495 - 2*0.016,  1.579 + 2*0.025),
+    ("F",  "S" ) : (1.640 - 2*0.011,  1.640 + 2*0.011),
+    ("F",  "SI") : (1.588 - 2*0.014,  1.694 + 2*0.013),
+    ("H",  "N" ) : (1.009 - 2*0.022,  1.033 + 2*0.022),
+    ("H",  "O" ) : (0.967 - 2*0.010,  1.015 + 2*0.017),
+    ("I",  "O" ) : (2.144 - 2*0.028,  2.144 + 2*0.028),
+    ("N",  "N" ) : (1.124 - 2*0.015,  1.454 + 2*0.021),
+    ("N",  "O" ) : (1.210 - 2*0.011,  1.463 + 2*0.012),
+    ("N",  "P" ) : (1.571 - 2*0.013,  1.697 + 2*0.015),
+    ("N",  "S" ) : (1.541 - 2*0.022,  1.710 + 2*0.019),
+    ("N",  "SI") : (1.711 - 2*0.019,  1.748 + 2*0.022),
+    ("O",  "P" ) : (1.449 - 2*0.007,  1.689 + 2*0.024),
+    ("O",  "S" ) : (1.423 - 2*0.008,  1.580 + 2*0.015),
+    ("O",  "SI") : (1.622 - 2*0.014,  1.680 + 2*0.008),
+    ("P",  "P" ) : (2.214 - 2*0.022,  2.214 + 2*0.022),
+    ("P",  "S" ) : (1.913 - 2*0.014,  1.954 + 2*0.005),
+    ("P",  "SE") : (2.093 - 2*0.019,  2.093 + 2*0.019),
+    ("P",  "SI") : (2.264 - 2*0.019,  2.264 + 2*0.019),
+    ("S",  "S" ) : (1.897 - 2*0.012,  2.070 + 2*0.022),
+    ("S",  "SE") : (2.193 - 2*0.015,  2.193 + 2*0.015),
+    ("S",  "SI") : (2.145 - 2*0.020,  2.145 + 2*0.020),
+    ("SE", "SE") : (2.340 - 2*0.024,  2.340 + 2*0.024),
+    ("SI", "SE") : (2.359 - 2*0.012,  2.359 + 2*0.012),
+}
+# fmt: on
+
+def connect_via_distances(atoms, dict distance_range=None, bint inter_residue=True,
+                          default_bond_type=BondType.ANY, bint periodic=False):
+    """
+    connect_via_distances(atoms, distance_range=None, atom_mask=None,
+                          inter_residue=True, default_bond_type=BondType.ANY,
+                          periodic=False)
+
+    Create a :class:`BondList` for a given atom array, based on
+    pairwise atom distances.
+
+    A :attr:`BondType.ANY`, bond is created for two atoms within the
+    same residue, if the distance between them is within the expected
+    bond distance range.
+    Bonds between two adjacent residues are created for the atoms
+    expected to connect these residues, i.e. ``'C'`` and ``'N'`` for
+    peptides and ``"O3'"`` and ``'P'`` for nucleotides.
+
+    Parameters
+    ----------
+    atoms : AtomArray
+        The structure to create the :class:`BondList` for.
+    distance_range : dict of tuple(str, str) -> tuple(float, float), optional
+        Custom minimum and maximum bond distances.
+        The dictionary keys are tuples of chemical elements representing
+        the atoms to be potentially bonded.
+        The order of elements within each tuple does not matter.
+        The dictionary values are the minimum and maximum bond distance,
+        respectively, for the given combination of elements.
+        This parameter updates the default dictionary.
+        Hence, the default bond distances for missing element pairs are
+        still taken from the default dictionary.
+        The default bond distances are taken from :footcite:`Allen1987`.
+    inter_residue : bool, optional
+        If true, connections between consecutive amino acids and
+        nucleotides are also added.
+    default_bond_type : BondType or int, optional
+        By default, all created bonds have :attr:`BondType.ANY`.
+        An alternative :class:`BondType` can be given in this parameter.
+    periodic : bool, optional
+        If set to true, bonds can also be detected in periodic
+        boundary conditions.
+        The `box` attribute of `atoms` is required in this case.
+
+    Returns
+    -------
+    BondList
+        The created bond list.
+
+    See Also
+    --------
+    connect_via_residue_names
+
+    Notes
+    -----
+    This method might miss bonds, if the bond distance is unexpectedly
+    high or low, or it might create false bonds, if two atoms within a
+    residue are accidentally in the right distance.
+    A more accurate method for determining bonds is
+    :func:`connect_via_residue_names()`.
+
+    References
+    ----------
+
+    .. footbibliography::
+    """
+    from .atoms import AtomArray
+    from .geometry import distance
+    from .residues import get_residue_starts
+
+    cdef list bonds = []
+    cdef int i
+    cdef int curr_start_i, next_start_i
+    cdef np.ndarray coord = atoms.coord
+    cdef np.ndarray coord_in_res
+    cdef np.ndarray distances
+    cdef float dist
+    cdef np.ndarray elements = atoms.element
+    cdef np.ndarray elements_in_res
+    cdef int atom_index1, atom_index2
+    cdef dict dist_ranges = {}
+    cdef tuple dist_range
+    cdef float min_dist, max_dist
+
+    if not isinstance(atoms, AtomArray):
+        raise TypeError(f"Expected 'AtomArray', not '{type(atoms).__name__}'")
+    if periodic:
+        if atoms.box is None:
+            raise BadStructureError("Atom array has no box")
+        box = atoms.box
+    else:
+        box = None
+
+    # Prepare distance dictionary...
+    if distance_range is None:
+        distance_range = {}
+    # Merge default and custom entries
+    for key, val in itertools.chain(
+        _DEFAULT_DISTANCE_RANGE.items(), distance_range.items()
+    ):
+        element1, element2 = key
+        # Add entries for both element orders
+        dist_ranges[(element1.upper(), element2.upper())] = val
+        dist_ranges[(element2.upper(), element1.upper())] = val
+
+    residue_starts = get_residue_starts(atoms, add_exclusive_stop=True)
+    # Omit exclsive stop in 'residue_starts'
+    for i in range(len(residue_starts)-1):
+        curr_start_i = residue_starts[i]
+        next_start_i = residue_starts[i+1]
+
+        elements_in_res = elements[curr_start_i : next_start_i]
+        coord_in_res = coord[curr_start_i : next_start_i]
+        # Matrix containing all pairwise atom distances in the residue
+        distances = distance(
+            coord_in_res[:, np.newaxis, :],
+            coord_in_res[np.newaxis, :, :],
+            box
+        )
+        for atom_index1 in range(len(elements_in_res)):
+            for atom_index2 in range(atom_index1):
+                dist_range = dist_ranges.get((
+                    elements_in_res[atom_index1],
+                    elements_in_res[atom_index2]
+                ))
+                if dist_range is None:
+                    # No bond distance entry for this element
+                    # combination -> skip
+                    continue
+                else:
+                    min_dist, max_dist = dist_range
+                dist = distances[atom_index1, atom_index2]
+                if dist >= min_dist and dist <= max_dist:
+                    bonds.append((
+                        curr_start_i + atom_index1,
+                        curr_start_i + atom_index2,
+                        default_bond_type
+                    ))
+
+    bond_list = BondList(atoms.array_length(), np.array(bonds))
+
+    if inter_residue:
+        inter_bonds = _connect_inter_residue(atoms, residue_starts)
+        if default_bond_type == BondType.ANY:
+            # As all bonds should be of type ANY, convert also
+            # inter-residue bonds to ANY
+            inter_bonds.remove_bond_order()
+        return bond_list.merge(inter_bonds)
+    else:
+        return bond_list
+
+
+
+def connect_via_residue_names(atoms, bint inter_residue=True,
+                              dict custom_bond_dict=None):
+    """
+    connect_via_residue_names(atoms, atom_mask=None, inter_residue=True)
+
+    Create a :class:`BondList` for a given atom array (stack), based on
+    the deposited bonds for each residue in the RCSB ``components.cif``
+    dataset.
+
+    Bonds between two adjacent residues are created for the atoms
+    expected to connect these residues, i.e. ``'C'`` and ``'N'`` for
+    peptides and ``"O3'"`` and ``'P'`` for nucleotides.
+
+    Parameters
+    ----------
+    atoms : AtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)
+        The structure to create the :class:`BondList` for.
+    inter_residue : bool, optional
+        If true, connections between consecutive amino acids and
+        nucleotides are also added.
+    custom_bond_dict : dict (str -> dict ((str, str) -> int)), optional
+        A dictionary of dictionaries:
+        The outer dictionary maps residue names to inner dictionaries.
+        The inner dictionary maps tuples of two atom names to their
+        respective :class:`BondType` (represented as integer).
+        If given, these bonds are used instead of the bonds read from
+        ``components.cif``.
+
+    Returns
+    -------
+    BondList
+        The created bond list.
+        No bonds are added for residues that are not found in
+        ``components.cif``.
+
+    See Also
+    --------
+    connect_via_distances
+
+    Notes
+    -----
+    This method can only find bonds for residues in the RCSB
+    *Chemical Component Dictionary*, unless `custom_bond_dict` is set.
+    Although this includes most molecules one encounters, this will fail
+    for exotic molecules, e.g. specialized inhibitors.
+
+    .. currentmodule:: biotite.structure.info
+
+    To supplement `custom_bond_dict` with bonds for residues from the
+    *Chemical Component Dictionary*  you can use
+    :meth:`bonds_in_residue()`.
+
+    >>> import pprint
+    >>> custom_bond_dict = {
+    ...     "XYZ": {
+    ...         ("A", "B"): BondType.SINGLE,
+    ...         ("B", "C"): BondType.SINGLE
+    ...     }
+    ... }
+    >>> # Supplement with bonds for common residues
+    >>> custom_bond_dict["ALA"] = bonds_in_residue("ALA")
+    >>> pp = pprint.PrettyPrinter(width=40)
+    >>> pp.pprint(custom_bond_dict)
+    {'ALA': {('C', 'O'): <BondType.DOUBLE: 2>,
+             ('C', 'OXT'): <BondType.SINGLE: 1>,
+             ('CA', 'C'): <BondType.SINGLE: 1>,
+             ('CA', 'CB'): <BondType.SINGLE: 1>,
+             ('CA', 'HA'): <BondType.SINGLE: 1>,
+             ('CB', 'HB1'): <BondType.SINGLE: 1>,
+             ('CB', 'HB2'): <BondType.SINGLE: 1>,
+             ('CB', 'HB3'): <BondType.SINGLE: 1>,
+             ('N', 'CA'): <BondType.SINGLE: 1>,
+             ('N', 'H'): <BondType.SINGLE: 1>,
+             ('N', 'H2'): <BondType.SINGLE: 1>,
+             ('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
+
+    cdef list bonds = []
+    cdef int res_i
+    cdef int i, j
+    cdef int curr_start_i, next_start_i
+    cdef np.ndarray atom_names = atoms.atom_name
+    cdef np.ndarray atom_names_in_res
+    cdef np.ndarray res_names = atoms.res_name
+    cdef str atom_name1, atom_name2
+    cdef int64[:] atom_indices1, atom_indices2
+    cdef dict bond_dict_for_res
+
+    residue_starts = get_residue_starts(atoms, add_exclusive_stop=True)
+    # Omit exclsive stop in 'residue_starts'
+    for res_i in range(len(residue_starts)-1):
+        curr_start_i = residue_starts[res_i]
+        next_start_i = residue_starts[res_i+1]
+
+        if custom_bond_dict is None:
+            bond_dict_for_res = bonds_in_residue(res_names[curr_start_i])
+        else:
+            bond_dict_for_res = custom_bond_dict.get(
+                res_names[curr_start_i], {}
+            )
+
+        atom_names_in_res = atom_names[curr_start_i : next_start_i]
+        for (atom_name1, atom_name2), bond_type in bond_dict_for_res.items():
+            atom_indices1 = np.where(atom_names_in_res == atom_name1)[0] \
+                            .astype(np.int64, copy=False)
+            atom_indices2 = np.where(atom_names_in_res == atom_name2)[0] \
+                            .astype(np.int64, copy=False)
+            # In rare cases the same atom name may appear multiple times
+            # (e.g. in altlocs)
+            # -> create all possible bond combinations
+            for i in range(atom_indices1.shape[0]):
+                for j in range(atom_indices2.shape[0]):
+                    bonds.append((
+                        curr_start_i + atom_indices1[i],
+                        curr_start_i + atom_indices2[j],
+                        bond_type
+                    ))
+
+    bond_list = BondList(atoms.array_length(), np.array(bonds))
+
+    if inter_residue:
+        inter_bonds = _connect_inter_residue(atoms, residue_starts)
+        return bond_list.merge(inter_bonds)
+    else:
+        return bond_list
+
+
+
+_PEPTIDE_LINKS = ["PEPTIDE LINKING", "L-PEPTIDE LINKING", "D-PEPTIDE LINKING"]
+_NUCLEIC_LINKS = ["RNA LINKING", "DNA LINKING"]
+
+def _connect_inter_residue(atoms, residue_starts):
+    """
+    Create a :class:`BondList` containing the bonds between adjacent
+    amino acid or nucleotide residues.
+
+    Parameters
+    ----------
+    atoms : AtomArray or AtomArrayStack
+        The structure to create the :class:`BondList` for.
+    residue_starts : ndarray, dtype=int
+        Return value of
+        ``get_residue_starts(atoms, add_exclusive_stop=True)``.
+
+    Returns
+    -------
+    BondList
+        A bond list containing all inter residue bonds.
+    """
+    from .info.misc import link_type
+
+    cdef list bonds = []
+    cdef int i
+    cdef np.ndarray atom_names = atoms.atom_name
+    cdef np.ndarray res_names = atoms.res_name
+    cdef np.ndarray res_ids = atoms.res_id
+    cdef np.ndarray chain_ids = atoms.chain_id
+    cdef int curr_start_i, next_start_i, after_next_start_i
+    cdef str curr_connect_atom_name, next_connect_atom_name
+    cdef np.ndarray curr_connect_indices, next_connect_indices
+
+    # Iterate over all starts excluding:
+    #   - the last residue and
+    #   - exclusive end index of 'atoms'
+    for i in range(len(residue_starts)-2):
+        curr_start_i = residue_starts[i]
+        next_start_i = residue_starts[i+1]
+        after_next_start_i = residue_starts[i+2]
+
+        # Check if the current and next residue is in the same chain
+        if chain_ids[next_start_i] != chain_ids[curr_start_i]:
+            continue
+        # Check if the current and next residue
+        # have consecutive residue IDs
+        # (Same residue ID is also possible if insertion code is used)
+        if res_ids[next_start_i] - res_ids[curr_start_i] > 1:
+            continue
+
+        # Get link type for this residue from RCSB components.cif
+        curr_link = link_type(res_names[curr_start_i])
+        next_link = link_type(res_names[next_start_i])
+
+        if curr_link in _PEPTIDE_LINKS and next_link in _PEPTIDE_LINKS:
+            curr_connect_atom_name = "C"
+            next_connect_atom_name = "N"
+        elif curr_link in _NUCLEIC_LINKS and next_link in _NUCLEIC_LINKS:
+            curr_connect_atom_name = "O3'"
+            next_connect_atom_name = "P"
+        else:
+            # Create no bond if the connection types of consecutive
+            # residues are not compatible
+            continue
+
+        # Index in atom array for atom name in current residue
+        # Addition of 'curr_start_i' is necessary, as only a slice of
+        # 'atom_names' is taken, beginning at 'curr_start_i'
+        curr_connect_indices = curr_start_i + np.where(
+            atom_names[curr_start_i : next_start_i]
+            == curr_connect_atom_name
+        )[0]
+        # Index in atom array for atom name in next residue
+        next_connect_indices = next_start_i + np.where(
+            atom_names[next_start_i : after_next_start_i]
+            == next_connect_atom_name
+        )[0]
+        if len(curr_connect_indices) == 0 or len(next_connect_indices) == 0:
+            # The connector atoms are not found in the adjacent residues
+            # -> skip this bond
+            continue
+
+        bonds.append((
+            curr_connect_indices[0],
+            next_connect_indices[0],
+            BondType.SINGLE
+        ))
+
+    return BondList(atoms.array_length(), np.array(bonds, dtype=np.uint32))
+
+
+
+def find_connected(bond_list, uint32 root, bint as_mask=False):
+    """
+    find_connected(bond_list, root, as_mask=False)
+
+    Get indices to all atoms that are directly or inderectly connected
+    to the root atom indicated by the given index.
+
+    An atom is *connected* to the `root` atom, if that atom is reachable
+    by traversing an arbitrary number of bonds, starting from the
+    `root`.
+    Effectively, this means that all atoms are *connected* to `root`,
+    that are in the same molecule as `root`.
+    Per definition `root` is also *connected* to itself.
+
+    Parameters
+    ----------
+    bond_list : BondList
+        The reference bond list.
+    root : int
+        The index of the root atom.
+    as_mask : bool, optional
+        If true, the connected atom indices are returned as boolean
+        mask.
+        By default, the connected atom indices are returned as integer
+        array.
+
+    Returns
+    -------
+    connected : ndarray, dtype=int or ndarray, dtype=bool
+        Either a boolean mask or an integer array, representing the
+        connected atoms.
+        In case of a boolean mask: ``connected[i] == True``, if the atom
+        with index ``i`` is connected.
+
+    Examples
+    --------
+    Consider a system with 4 atoms, where only the last atom is not
+    bonded with the other ones (``0-1-2 3``):
+
+    >>> bonds = BondList(4)
+    >>> bonds.add_bond(0, 1)
+    >>> bonds.add_bond(1, 2)
+    >>> print(find_connected(bonds, 0))
+    [0 1 2]
+    >>> print(find_connected(bonds, 1))
+    [0 1 2]
+    >>> print(find_connected(bonds, 2))
+    [0 1 2]
+    >>> print(find_connected(bonds, 3))
+    [3]
+    """
+    all_bonds, _ = bond_list.get_all_bonds()
+
+    if root >= bond_list.get_atom_count():
+        raise ValueError(
+            f"Root atom index {root} is out of bounds for bond list "
+            f"representing {bond_list.get_atom_count()} atoms"
+        )
+
+    cdef uint8[:] is_connected_mask = np.zeros(
+        bond_list.get_atom_count(), dtype=np.uint8
+    )
+    # Find connections in a recursive way,
+    # by visiting all atoms that are reachable by a bond
+    _find_connected(bond_list, root, is_connected_mask, all_bonds)
+    if as_mask:
+        return is_connected_mask
+    else:
+        return np.where(np.asarray(is_connected_mask))[0]
+
+
+cdef _find_connected(bond_list,
+                     int32 index,
+                     uint8[:] is_connected_mask,
+                     int32[:,:] all_bonds):
+    if is_connected_mask[index]:
+        # This atom has already been visited
+        # -> exit condition
+        return
+    is_connected_mask[index] = True
+
+    cdef int32 j
+    cdef int32 connected_index
+    for j in range(all_bonds.shape[1]):
+        connected_index = all_bonds[index, j]
+        if connected_index == -1:
+            # Ignore padding values
+            continue
+        _find_connected(
+            bond_list, connected_index, is_connected_mask, all_bonds
+        )
+
+
+def find_rotatable_bonds(bonds):
+    """
+    find_rotatable_bonds(bonds)
+
+    Find all rotatable bonds in a given :class:`BondList`.
+
+    The following conditions must be true for a bond to be counted as
+    rotatable:
+
+        1. The bond must be a single bond (``BondType.SINGLE``)
+        2. The connected atoms must not be within the same cycle/ring
+        3. Both connected atoms must not be terminal, e.g. not a *C-H*
+           bond, as rotation about such bonds would not change any
+           coordinates
+
+    Parameters
+    ----------
+    bonds : BondList
+        The bonds to find the rotatable bonds in.
+
+    Returns
+    -------
+    rotatable_bonds : BondList
+        The subset of the input `bonds` that contains only rotatable
+        bonds.
+
+    Examples
+    --------
+
+    >>> molecule = residue("TYR")
+    >>> for i, j, _ in find_rotatable_bonds(molecule.bonds).as_array():
+    ...     print(molecule.atom_name[i], molecule.atom_name[j])
+    N CA
+    CA C
+    CA CB
+    C OXT
+    CB CG
+    CZ OH
+    """
+    cdef uint32 i, j
+    cdef uint32 bond_type
+    cdef uint32 SINGLE = int(BondType.SINGLE)
+    cdef bint in_same_cycle
+
+    bond_graph = bonds.as_graph()
+    cycles = nx.algorithms.cycles.cycle_basis(bond_graph)
+
+    cdef int64[:] number_of_partners_v = np.count_nonzero(
+        bonds.get_all_bonds()[0] != -1,
+        axis=1
+    ).astype(np.int64, copy=False)
+
+    rotatable_bonds = []
+    cdef uint32[:,:] bonds_v = bonds.as_array()
+    for i, j, bond_type in bonds_v:
+        # Can only rotate about single bonds
+        # Furthermore, it makes no sense to rotate about a bond,
+        # that leads to a single atom
+        if bond_type == BondType.SINGLE \
+            and number_of_partners_v[i] > 1 \
+            and number_of_partners_v[j] > 1:
+                # Cannot rotate about a bond, if the two connected atoms
+                # are in a cycle
+                in_same_cycle = False
+                for cycle in cycles:
+                    if i in cycle and j in cycle:
+                        in_same_cycle = True
+                if not in_same_cycle:
+                    rotatable_bonds.append((i,j, bond_type))
+    return BondList(bonds.get_atom_count(), np.array(rotatable_bonds))