biotite 1.1.0__cp311-cp311-macosx_11_0_arm64.whl → 1.3.0__cp311-cp311-macosx_11_0_arm64.whl

biotite/structure/rings.py

@@ -0,0 +1,335 @@
+# 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

@@ -35,39 +35,38 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
          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 (default: 1.4).
+        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
-        (default: True).
+        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 (default: 100). The SASA calculation time is
-        proportional to the amount of sphere points.
+        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
@@ -76,33 +75,34 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
         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).
-              :footcite:`Bondi1964`
-              
+              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 
+        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:
@@ -121,7 +121,7 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
         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)
@@ -130,7 +130,7 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
     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)
@@ -158,17 +158,17 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
         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,
@@ -190,10 +190,10 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
     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
@@ -212,8 +212,8 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
     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, 
+
+    # 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)
@@ -226,7 +226,7 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
     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
@@ -236,7 +236,7 @@ def sasa(array, float probe_radius=1.4, np.ndarray atom_filter=None,
     # 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