biotite 1.3.0__cp312-cp312-macosx_10_13_x86_64.whl

biotite/structure/rings.py

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+# 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 provides functions related to aromatic rings.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["find_aromatic_rings", "find_stacking_interactions", "PiStacking"]
+
+
+from enum import IntEnum
+import networkx as nx
+import numpy as np
+from biotite.structure.bonds import BondType
+from biotite.structure.error import BadStructureError
+from biotite.structure.geometry import displacement
+from biotite.structure.util import norm_vector, vector_dot
+
+
+class PiStacking(IntEnum):
+    """
+    The type of pi-stacking interaction.
+
+    - ``PARALLEL``: parallel pi-stacking (also called *staggered* or *Sandwich*)
+    - ``PERPENDICULAR``: perpendicular pi-stacking (also called *T-shaped*)
+    """
+
+    PARALLEL = 0
+    PERPENDICULAR = 1
+
+
+def find_aromatic_rings(atoms):
+    """
+    Find (anti-)aromatic rings in a structure.
+
+    Parameters
+    ----------
+    atoms : AtomArray or AtomArrayStack
+        The atoms to be searched for aromatic rings.
+        Requires an associated :class:`BondList`.
+
+    Returns
+    -------
+    rings : list of ndarray
+        The indices of the atoms that form aromatic rings.
+        Each ring is represented by a list of indices.
+        Only rings with minimum size are returned, i.e. two connected rings
+        (e.g. in tryptophan) are reported as separate rings.
+
+    Notes
+    -----
+    This function does not distinguish between aromatic and antiaromatic rings.
+    All cycles containing atoms that are completely connected by aromatic bonds
+    are considered aromatic rings.
+
+    The PDB *Chemical Component Dictionary* (CCD) does not identify aromatic rings in
+    all compounds as such.
+    Prominent examples are the nucleobases, where the 6-membered rings are not
+    flagged as aromatic.
+
+    Examples
+    --------
+
+    >>> nad = residue("NAD")
+    >>> rings = find_aromatic_rings(nad)
+    >>> print(rings)
+    [array([41, 37, 36, 35, 43, 42]), array([19, 18, 16, 15, 21, 20]), array([12, 13, 14, 15, 21])]
+    >>> for atom_indices in rings:
+    ...     print(np.sort(nad.atom_name[atom_indices]))
+    ['C2N' 'C3N' 'C4N' 'C5N' 'C6N' 'N1N']
+    ['C2A' 'C4A' 'C5A' 'C6A' 'N1A' 'N3A']
+    ['C4A' 'C5A' 'C8A' 'N7A' 'N9A']
+    """
+    if atoms.bonds is None:
+        raise BadStructureError("Structure must have an associated BondList")
+    bond_array = atoms.bonds.as_array()
+    # To detect aromatic rings, only keep bonds that are aromatic
+    aromatic_bond_array = bond_array[
+        np.isin(
+            bond_array[:, 2],
+            [
+                BondType.AROMATIC,
+                BondType.AROMATIC_SINGLE,
+                BondType.AROMATIC_DOUBLE,
+                BondType.AROMATIC_TRIPLE,
+            ],
+        ),
+        # We can omit the bond type now
+        :2,
+    ]
+    aromatic_bond_graph = nx.from_edgelist(aromatic_bond_array.tolist())
+    # Find the cycles with minimum size -> cycle basis
+    rings = nx.cycle_basis(aromatic_bond_graph)
+    return [np.array(ring, dtype=int) for ring in rings]
+
+
+def find_stacking_interactions(
+    atoms,
+    centroid_cutoff=6.5,
+    plane_angle_tol=np.deg2rad(30.0),
+    shift_angle_tol=np.deg2rad(30.0),
+):
+    """
+    Find pi-stacking interactions between aromatic rings.
+
+    Parameters
+    ----------
+    atoms : AtomArray
+        The atoms to be searched for aromatic rings.
+        Requires an associated :class:`BondList`.
+    centroid_cutoff : float
+        The cutoff distance for ring centroids.
+    plane_angle_tol : float
+        The tolerance for the angle between ring planes that must be either
+        parallel or perpendicular.
+        Given in radians.
+    shift_angle_tol : float
+        The tolerance for the angle between the ring plane normals and the
+        centroid difference vector.
+        Given in radians.
+
+    Returns
+    -------
+    interactions : list of tuple(ndarray, ndarray, PiStacking)
+        The stacking interactions between aromatic rings.
+        Each element in the list represents one stacking interaction.
+        The first two elements of each tuple represent atom indices of the stacked
+        rings.
+        The third element of each tuple is the type of stacking interaction.
+
+    See Also
+    --------
+    find_aromatic_rings : Used for finding the aromatic rings in this function.
+
+    Notes
+    -----
+    This function does not distinguish between aromatic and antiaromatic rings.
+    Furthermore, it does not distinguish between repulsive and attractive stacking:
+    Usually, stacking two rings directly above each other is repulsive, as the pi
+    orbitals above the rings repel each other, so a slight horizontal shift is
+    usually required to make the interaction attractive.
+    However, in details this is strongly dependent on heteroatoms and the exact
+    orientation of the rings.
+    Hence, this function aggregates all stacking interactions to simplify the
+    conditions for pi-stacking.
+
+    The conditions for pi-stacking are :footcite:`Wojcikowski2015` :
+
+        - The ring centroids must be within cutoff `centroid_cutoff` distance.
+          While :footcite:`Wojcikowski2015` uses a cutoff of 5.0 Å, 6.5 Å was
+          adopted from :footcite:`Bouysset2021` to better identify perpendicular
+          stacking interactions.
+        - The planes must be parallel or perpendicular to each other within a default
+          tolerance of 30°.
+        - The angle between the plane normals and the centroid difference vector must be
+          be either 0° or 90° within a default tolerance of 30°, to check for lateral
+          shifts.
+
+    References
+    ----------
+
+    .. footbibliography::
+
+    Examples
+    --------
+
+    Detect base stacking interactions in a DNA helix
+
+    >>> from os.path import join
+    >>> dna_helix = load_structure(
+    ...     join(path_to_structures, "base_pairs", "1qxb.cif"), include_bonds=True
+    ... )
+    >>> interactions = find_stacking_interactions(dna_helix)
+    >>> for ring_atom_indices_1, ring_atom_indices_2, stacking_type in interactions:
+    ...     print(
+    ...         dna_helix.res_id[ring_atom_indices_1[0]],
+    ...         dna_helix.res_id[ring_atom_indices_2[0]],
+    ...         PiStacking(stacking_type).name
+    ...     )
+    17 18 PARALLEL
+    17 18 PARALLEL
+    5 6 PARALLEL
+    5 6 PARALLEL
+    5 6 PARALLEL
+    """
+    rings = find_aromatic_rings(atoms)
+    if len(rings) == 0:
+        return []
+
+    ring_centroids = np.array(
+        [atoms.coord[atom_indices].mean(axis=0) for atom_indices in rings]
+    )
+    ring_normals = np.array(
+        [_get_ring_normal(atoms.coord[atom_indices]) for atom_indices in rings]
+    )
+
+    # Create an index array that contains the Cartesian product of all rings
+    indices = np.stack(
+        [
+            np.repeat(np.arange(len(rings)), len(rings)),
+            np.tile(np.arange(len(rings)), len(rings)),
+        ],
+        axis=-1,
+    )
+    # Do not include duplicate pairs
+    indices = indices[indices[:, 0] > indices[:, 1]]
+
+    ## Condition 1: Ring centroids are close enough to each other
+    diff = displacement(ring_centroids[indices[:, 0]], ring_centroids[indices[:, 1]])
+    # Use squared distance to avoid time consuming sqrt computation
+    sq_distance = vector_dot(diff, diff)
+    is_interacting = sq_distance < centroid_cutoff**2
+    indices = indices[is_interacting]
+
+    ## Condition 2: Ring planes are parallel or perpendicular
+    plane_angles = _minimum_angle(
+        ring_normals[indices[:, 0]], ring_normals[indices[:, 1]]
+    )
+    is_parallel = _is_within_tolerance(plane_angles, 0, plane_angle_tol)
+    is_perpendicular = _is_within_tolerance(plane_angles, np.pi / 2, plane_angle_tol)
+    is_interacting = is_parallel | is_perpendicular
+    indices = indices[is_interacting]
+    # Keep in sync with the shape of the filtered indices,
+    # i.e. after filtering, `is_parallel==False` means a perpendicular interaction
+    is_parallel = is_parallel[is_interacting]
+
+    ## Condition 3: The ring centroids are not shifted too much
+    ## (in terms of normal-centroid angle)
+    diff = displacement(ring_centroids[indices[:, 0]], ring_centroids[indices[:, 1]])
+    norm_vector(diff)
+    angles = np.stack(
+        [_minimum_angle(ring_normals[indices[:, i]], diff) for i in range(2)]
+    )
+    is_interacting = (
+        # For parallel stacking, the lateral shift may not exceed the tolerance
+        (is_parallel & np.any(_is_within_tolerance(angles, 0, shift_angle_tol), axis=0))
+        # For perpendicular stacking, one ring must be above the other,
+        # but from the perspective of the other ring, the first ring is approximately
+        # in the same plane
+        | (
+            ~is_parallel
+            & (
+                (
+                    _is_within_tolerance(angles[0], 0, shift_angle_tol)
+                    & _is_within_tolerance(angles[1], np.pi / 2, shift_angle_tol)
+                )
+                | (
+                    _is_within_tolerance(angles[0], np.pi / 2, shift_angle_tol)
+                    & _is_within_tolerance(angles[1], 0, shift_angle_tol)
+                )
+            )
+        )
+    )
+    indices = indices[is_interacting]
+    is_parallel = is_parallel[is_interacting]
+
+    # Only return pairs of rings where all conditions were fulfilled
+    return [
+        (
+            rings[ring_i],
+            rings[ring_j],
+            PiStacking.PARALLEL if is_parallel[i] else PiStacking.PERPENDICULAR,
+        )
+        for i, (ring_i, ring_j) in enumerate(indices)
+    ]
+
+
+def _get_ring_normal(ring_coord):
+    """
+    Get the normal vector perpendicular to the ring plane.
+
+    Parameters
+    ----------
+    ring_coord : ndarray
+        The coordinates of the atoms in the ring.
+
+    Returns
+    -------
+    normal : ndarray
+        The normal vector of the ring plane.
+    """
+    # Simply use any three atoms in the ring to calculate the normal vector
+    # We can also safely assume that there are at least three atoms in the ring,
+    # as otherwise it would not be a ring
+    normal = np.cross(ring_coord[1] - ring_coord[0], ring_coord[2] - ring_coord[0])
+    norm_vector(normal)
+    return normal
+
+
+def _minimum_angle(v1, v2):
+    """
+    Get the minimum angle between two vectors, i.e. the possible angle range is
+    ``[0, pi/2]``.
+
+    Parameters
+    ----------
+    v1, v2 : ndarray, shape=(n,3), dtype=float
+        The vectors to measure the angle between.
+
+    Returns
+    -------
+    angle : ndarray, shape=(n,), dtype=float
+        The minimum angle between the two vectors.
+
+    Notes
+    -----
+    This restriction is added here as the normal vectors of the ring planes
+    have no 'preferred side'.
+    """
+    # Do not distinguish between the 'sides' of the rings -> take absolute of cosine
+    return np.arccos(np.abs(vector_dot(v1, v2)))
+
+
+def _is_within_tolerance(angles, expected_angle, tolerance):
+    """
+    Check if the angles are within a certain tolerance.
+
+    Parameters
+    ----------
+    angles : ndarray, shape=x, dtype=float
+        The angles to check.
+    expected_angle : float
+        The expected angle.
+    tolerance : float
+        The tolerance.
+
+    Returns
+    -------
+    is_within_tolerance : ndarray, shape=x, dtype=bool
+        True if the angles are within the tolerance, False otherwise.
+    """
+    return np.abs(angles - expected_angle) < tolerance

biotite/structure/sasa.pyx

@@ -0,0 +1,322 @@
+# 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.
+
+"""
+Use this module to calculate the Solvent Accessible Surface Area (SASA) of
+a protein or single atoms.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["sasa"]
+
+cimport cython
+cimport numpy as np
+from libc.stdlib cimport malloc, free
+
+import numpy as np
+from .celllist import CellList
+from .filter import filter_solvent, filter_monoatomic_ions
+from .info.radii import vdw_radius_protor, vdw_radius_single
+
+ctypedef np.uint8_t np_bool
+ctypedef np.int64_t int64
+ctypedef np.float32_t float32
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
+         bint ignore_ions=True, int point_number=1000,
+         point_distr="Fibonacci", vdw_radii="ProtOr"):
+    """
+    sasa(array, probe_radius=1.4, atom_filter=None, ignore_ions=True,
+         point_number=1000, point_distr="Fibonacci", vdw_radii="ProtOr")
+
+    Calculate the Solvent Accessible Surface Area (SASA) of a protein.
+
+    This function uses the Shrake-Rupley ("rolling probe")
+    algorithm :footcite:`Shrake1973`:
+    Every atom is occupied by a evenly distributed point mesh. The
+    points that can be reached by the "rolling probe", are surface
+    accessible.
+
+    Parameters
+    ----------
+    array : AtomArray
+        The protein model to calculate the SASA for.
+    probe_radius : float, optional
+        The VdW-radius of the solvent molecules.
+    atom_filter : ndarray, dtype=bool, optional
+        If this parameter is given, SASA is only calculated for the
+        filtered atoms.
+    ignore_ions : bool, optional
+        If true, all monoatomic ions are removed before SASA calculation.
+    point_number : int, optional
+        The number of points in the mesh occupying each atom for SASA
+        calculation.
+        The SASA calculation time is proportional to the amount of sphere points.
+    point_distr : str or function, optional
+        If a function is given, the function is used to calculate the
+        point distribution for the mesh (the function must take `float`
+        *n* as parameter and return a *(n x 3)* :class:`ndarray`).
+        Alternatively a string can be given to choose a built-in
+        distribution:
+
+            - **Fibonacci** - Distribute points using a golden section
+              spiral.
+
+        By default *Fibonacci* is used.
+    vdw_radii : str or ndarray, dtype=float, optional
+        Indicates the set of VdW radii to be used. If an `array`-length
+        :class:`ndarray` is given, each atom gets the radius at the
+        corresponding index. Radii given for atoms that are not used in
+        SASA calculation (e.g. solvent atoms) can have arbitrary values
+        (e.g. `NaN`). If instead a string is given, one of the
+        built-in sets is used:
+
+            - **ProtOr** - A set, which does not require hydrogen atoms
+              in the model. Suitable for crystal structures.
+              :footcite:`Tsai1999`
+            - **Single** - A set, which uses a defined VdW radius for
+              every single atom, therefore hydrogen atoms are required
+              in the model (e.g. NMR elucidated structures).
+              Values for main group elements are taken from :footcite:`Mantina2009`,
+              and for relevant transition metals from the :footcite:`RDKit`.
+
+        By default *ProtOr* is used.
+
+
+    Returns
+    -------
+    sasa : ndarray, dtype=bool, shape=(n,)
+        Atom-wise SASA. `NaN` for atoms where SASA has not been
+        calculated
+        (solvent atoms, hydrogen atoms (ProtOr), atoms not in `filter`).
+
+    References
+    ----------
+
+    .. footbibliography::
+
+    """
+    cdef int i=0, j=0, k=0, adj_atom_i=0, rel_atom_i=0
+
+    cdef np.ndarray sasa_filter
+    cdef np.ndarray occl_filter
+    if atom_filter is not None:
+        # Filter for all atoms to calculate SASA for
+        sasa_filter = np.array(atom_filter, dtype=bool)
+    else:
+        sasa_filter = np.ones(len(array), dtype=bool)
+    # Filter for all atoms that are considered for occlusion calculation
+    # sasa_filter is subfilter of occlusion_filter
+    occl_filter = np.ones(len(array), dtype=bool)
+    # Remove water residues, since it is the solvent
+    filter = ~filter_solvent(array)
+    sasa_filter = sasa_filter & filter
+    occl_filter = occl_filter & filter
+    if ignore_ions:
+        filter = ~filter_monoatomic_ions(array)
+        sasa_filter = sasa_filter & filter
+        occl_filter = occl_filter & filter
+
+    cdef np.ndarray sphere_points
+    if callable(point_distr):
+        sphere_points = point_distr(point_number)
+    elif point_distr == "Fibonacci":
+        sphere_points = _create_fibonacci_points(point_number)
+    else:
+        raise ValueError(f"'{point_distr}' is not a valid point distribution")
+    sphere_points = sphere_points.astype(np.float32)
+
+    cdef np.ndarray radii
+    if isinstance(vdw_radii, np.ndarray):
+        radii = vdw_radii.astype(np.float32)
+        if len(radii) != array.array_length():
+            raise ValueError(
+                f"Amount VdW radii ({len(radii)}) and "
+                f"amount of atoms ({array.array_length()}) are not equal"
+            )
+    elif vdw_radii == "ProtOr":
+        filter = (array.element != "H")
+        sasa_filter = sasa_filter & filter
+        occl_filter = occl_filter & filter
+        radii = np.full(len(array), np.nan, dtype=np.float32)
+        for i in np.arange(len(radii))[occl_filter]:
+            rad = vdw_radius_protor(array.res_name[i], array.atom_name[i])
+            # 1.8 is default radius
+            radii[i] = rad if rad is not None else 1.8
+    elif vdw_radii == "Single":
+        radii = np.full(len(array), np.nan, dtype=np.float32)
+        for i in np.arange(len(radii))[occl_filter]:
+            rad = vdw_radius_single(array.element[i])
+            # 1.5 is default radius
+            radii[i] = rad if rad is not None else 1.8
+    else:
+        raise KeyError(f"'{vdw_radii}' is not a valid radii set")
+    # Increase atom radii by probe size ("rolling probe")
+    radii += probe_radius
+
+    # Memoryview for filter
+    # Problem with creating boolean memoryviews
+    # -> Type uint8 is used
+    cdef np_bool[:] sasa_filter_view = np.frombuffer(sasa_filter,
+                                                     dtype=np.uint8)
+
+    cdef np.ndarray occl_r = radii[occl_filter]
+    # Atom array containing occluding atoms
+    occl_array = array[occl_filter]
+
+    # Memoryviews for coordinates of entire (main) array
+    # and for coordinates of occluding atom array
+    cdef float32[:,:] main_coord = array.coord.astype(np.float32,
+                                                      copy=False)
+    cdef float32[:,:] occl_coord = occl_array.coord.astype(np.float32,
+                                                           copy=False)
+    # Memoryviews for sphere points
+    cdef float32[:,:] sphere_coord = sphere_points
+    # Check if any of these arrays are empty to prevent segfault
+    if     main_coord.shape[0]   == 0 \
+        or occl_coord.shape[0]   == 0 \
+        or sphere_coord.shape[0] == 0:
+            raise ValueError("Coordinates are empty")
+    # Memoryviews for radii of SASA and occluding atoms
+    # their squares and their sum of sqaures
+    cdef float32[:] atom_radii = radii
+    cdef float32[:] atom_radii_sq = radii * radii
+    cdef float32[:] occl_radii = occl_r
+    cdef float32[:] occl_radii_sq = occl_r * occl_r
+    # Memoryview for atomwise SASA
+    cdef float32[:] sasa = np.full(len(array), np.nan, dtype=np.float32)
+
+    # Area of a sphere point on a unit sphere
+    cdef float32 area_per_point = 4.0 * np.pi / point_number
+
+    # Define further statically typed variables
+    # that are needed for SASA calculation
+    cdef int n_accesible = 0
+    cdef float32 radius = 0
+    cdef float32 radius_sq = 0
+    cdef float32 adj_radius = 0
+    cdef float32 adj_radius_sq = 0
+    cdef float32 dist_sq = 0
+    cdef float32 point_x = 0
+    cdef float32 point_y = 0
+    cdef float32 point_z = 0
+    cdef float32 atom_x = 0
+    cdef float32 atom_y = 0
+    cdef float32 atom_z = 0
+    cdef float32 occl_x = 0
+    cdef float32 occl_y = 0
+    cdef float32 occl_z = 0
+    cdef float32[:,:] relevant_occl_coord = None
+
+    # Cell size is as large as the maximum distance,
+    # where two atom can intersect.
+    # Therefore intersecting atoms are always in the same or adjacent cell.
+    cell_list = CellList(occl_array, np.max(radii[occl_filter])*2)
+    cdef np.ndarray cell_indices
+    cdef int[:,:] cell_indices_view
+    cdef int length
+    cdef int max_adj_list_length = 0
+    cdef int array_length = array.array_length()
+
+    cell_indices = cell_list.get_atoms_in_cells(array.coord)
+    cell_indices_view = cell_indices
+    max_adj_list_length = cell_indices.shape[0]
+
+    # Later on, this array stores coordinates for actual
+    # occluding atoms for a certain atom to calculate the
+    # SASA for
+    # The first three indices of the second axis
+    # are x, y and z, the last one is the squared radius
+    # This list is as long as the maximal length of a list of
+    # adjacent atoms
+    relevant_occl_coord = np.zeros((max_adj_list_length, 4),
+                                   dtype=np.float32)
+
+    # Actual SASA calculation
+    for i in range(array_length):
+        # First level: The atoms to calculate SASA for
+        if not sasa_filter_view[i]:
+            # SASA is not calculated for this atom
+            continue
+        n_accesible = point_number
+        atom_x = main_coord[i,0]
+        atom_y = main_coord[i,1]
+        atom_z = main_coord[i,2]
+        radius = atom_radii[i]
+        radius_sq = atom_radii_sq[i]
+        # Find occluding atoms from list of adjacent atoms
+        rel_atom_i = 0
+        for j in range(max_adj_list_length):
+            # Remove all atoms, where the distance to the relevant atom
+            # is larger than the sum of the radii,
+            # since those atoms do not touch
+            # If distance is 0, it is the same atom,
+            # and the atom is removed from the list as well
+            adj_atom_i = cell_indices_view[i,j]
+            if adj_atom_i == -1:
+                # -1 means end of list
+                break
+            occl_x = occl_coord[adj_atom_i,0]
+            occl_y = occl_coord[adj_atom_i,1]
+            occl_z = occl_coord[adj_atom_i,2]
+            adj_radius = occl_radii[adj_atom_i]
+            adj_radius_sq = occl_radii_sq[adj_atom_i]
+            dist_sq = distance_sq(atom_x, atom_y, atom_z,
+                                      occl_x, occl_y, occl_z)
+            if dist_sq != 0 \
+                and dist_sq < (adj_radius+radius) * (adj_radius+radius):
+                    relevant_occl_coord[rel_atom_i,0] = occl_x
+                    relevant_occl_coord[rel_atom_i,1] = occl_y
+                    relevant_occl_coord[rel_atom_i,2] = occl_z
+                    relevant_occl_coord[rel_atom_i,3] = adj_radius_sq
+                    rel_atom_i += 1
+        for j in range(sphere_coord.shape[0]):
+            # Second level: The sphere points for that atom
+            # Transform sphere point to sphere of current atom
+            point_x = sphere_coord[j,0] * radius + atom_x
+            point_y = sphere_coord[j,1] * radius + atom_y
+            point_z = sphere_coord[j,2] * radius + atom_z
+            for k in range(rel_atom_i):
+                # Third level: Compare point to occluding atoms
+                dist_sq = distance_sq(point_x, point_y, point_z,
+                                      relevant_occl_coord[k, 0],
+                                      relevant_occl_coord[k, 1],
+                                      relevant_occl_coord[k, 2])
+                # Compare squared distance
+                # to squared radius of occluding atom
+                # (Radius is relevant_occl_coord[3])
+                if dist_sq < relevant_occl_coord[k, 3]:
+                    # Point is occluded
+                    # -> Continue with next point
+                    n_accesible -= 1
+                    break
+        sasa[i] = area_per_point * n_accesible * radius_sq
+    return np.asarray(sasa)
+
+
+cdef inline float32 distance_sq(float32 x1, float32 y1, float32 z1,
+                        float32 x2, float32 y2, float32 z2):
+    cdef float32 dx = x2 - x1
+    cdef float32 dy = y2 - y1
+    cdef float32 dz = z2 - z1
+    return dx*dx + dy*dy + dz*dz
+
+
+def _create_fibonacci_points(n):
+    """
+    Get an array of approximately equidistant points on a sphere surface
+    using a golden section spiral.
+    """
+    phi = (3 - np.sqrt(5)) * np.pi * np.arange(n)
+    z = np.linspace(1 - 1.0/n, 1.0/n - 1, n)
+    radius = np.sqrt(1 - z*z)
+    coords = np.zeros((n, 3))
+    coords[:,0] = radius * np.cos(phi)
+    coords[:,1] = radius * np.sin(phi)
+    coords[:,2] = z
+    return coords