biotite 1.5.0__cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/structure/spacegroups.license

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+The transformations in 'spacegroups.json' are adapted from
+'molstar/src/mol-math/geometry/spacegroup/tables.ts' from the Mol* project
+(https://github.com/molstar/molstar) governed by the following license:
+
+
+The MIT License
+
+    Copyright (c) 2017 - now, Mol* contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

biotite/structure/sse.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 allows estimation of secondary structure elements in protein
+structures.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["annotate_sse"]
+
+import numpy as np
+from biotite.structure.celllist import CellList
+from biotite.structure.filter import filter_amino_acids
+from biotite.structure.geometry import angle, dihedral, distance
+from biotite.structure.integrity import check_res_id_continuity
+from biotite.structure.residues import get_residue_starts
+
+_r_helix = (np.deg2rad(89 - 12), np.deg2rad(89 + 12))
+_a_helix = (np.deg2rad(50 - 20), np.deg2rad(50 + 20))
+_d2_helix = ((5.5 - 0.5), (5.5 + 0.5))  # Not used in the algorithm description
+_d3_helix = ((5.3 - 0.5), (5.3 + 0.5))
+_d4_helix = ((6.4 - 0.6), (6.4 + 0.6))
+
+_r_strand = (np.deg2rad(124 - 14), np.deg2rad(124 + 14))
+_a_strand = (np.deg2rad(-180), np.deg2rad(-125), np.deg2rad(145), np.deg2rad(180))
+_d2_strand = ((6.7 - 0.6), (6.7 + 0.6))
+_d3_strand = ((9.9 - 0.9), (9.9 + 0.9))
+_d4_strand = ((12.4 - 1.1), (12.4 + 1.1))
+
+
+def annotate_sse(atom_array):
+    r"""
+    Calculate the secondary structure elements (SSEs) of a
+    peptide chain based on the `P-SEA` algorithm.
+    :footcite:`Labesse1997`
+
+    The annotation is based CA coordinates only, specifically
+    distances and dihedral angles.
+    Discontinuities between chains are detected by residue ID.
+
+    Parameters
+    ----------
+    atom_array : AtomArray
+        The atom array to annotate for.
+        Non-peptide residues are also allowed and obtain a ``''``
+        SSE.
+
+    Returns
+    -------
+    sse : ndarray
+        An array containing the secondary structure elements,
+        where the index corresponds to a residue of  `atom_array`
+        (see e.g. :func:`get_residues()`).
+        ``'a'`` means :math:`{\alpha}`-helix, ``'b'`` means
+        :math:`{\beta}`-strand/sheet, ``'c'`` means coil.
+        ``''`` indicates that a residue is not an amino acid or it
+        comprises no ``CA`` atom.
+
+    Notes
+    -----
+    Although this function is based on the original `P-SEA` algorithm,
+    there are deviations compared to the official `P-SEA` software in
+    some cases.
+    Do not rely on getting the exact same results.
+
+    References
+    ----------
+
+    .. footbibliography::
+
+    Examples
+    --------
+
+    SSE of PDB 1L2Y:
+
+    >>> sse = annotate_sse(atom_array)
+    >>> print(sse)
+    ['c' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'a' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c' 'c'
+     'c' 'c']
+    """
+    residue_starts = get_residue_starts(atom_array)
+    # Sort CA coord into the coord array at the respective residue index
+    # If a residue has no CA, e.g. because it is not an amino acid,
+    # the coordinates for that residue remain NaN
+    ca_coord = np.full((len(residue_starts), 3), np.nan, dtype=np.float32)
+    ca_indices = np.where(
+        filter_amino_acids(atom_array) & (atom_array.atom_name == "CA")
+    )[0]
+    ca_coord[np.searchsorted(residue_starts, ca_indices, "right") - 1] = (
+        atom_array.coord[ca_indices]
+    )
+
+    if len(ca_coord) <= 5:
+        # The number of atoms is too small #
+        # to measure the distances/angles
+        # -> Return an SSE array where each amino acid is 'coil'
+        sse = np.full(len(ca_coord), "c", dtype="U1")
+        # Residues where coord are NaN do not belong to amino acids
+        # (or at least they have no CA)
+        sse[np.isnan(ca_coord).any(axis=-1)] = ""
+        return sse
+
+    # Add virtual residues w/o CA coord at chain discontinuity indices
+    # This ensures that such discontinuities are recognized for the
+    # purpose of geometric measurements
+    # -> the distances/angles spanning discontinuities are NaN
+    discont_indices = check_res_id_continuity(atom_array)
+    discont_res_indices = np.searchsorted(residue_starts, discont_indices, "right") - 1
+    ca_coord = np.insert(
+        ca_coord,
+        discont_res_indices,
+        np.full((len(discont_res_indices), 3), np.nan),
+        axis=0,
+    )
+    # Later the SSE for virtual residues are removed again
+    # via this mask
+    no_virtual_mask = np.ones(len(residue_starts), dtype=bool)
+    no_virtual_mask = np.insert(no_virtual_mask, discont_res_indices, False)
+
+    length = len(ca_coord)
+
+    # The distances and angles are not defined for the entire interval,
+    # therefore the indices do not have the full range
+    # Values that are not defined are NaN
+    d2i = np.full(length, np.nan)
+    d3i = np.full(length, np.nan)
+    d4i = np.full(length, np.nan)
+    ri = np.full(length, np.nan)
+    ai = np.full(length, np.nan)
+
+    d2i[1 : length - 1] = distance(ca_coord[0 : length - 2], ca_coord[2:length])
+    d3i[1 : length - 2] = distance(ca_coord[0 : length - 3], ca_coord[3:length])
+    d4i[1 : length - 3] = distance(ca_coord[0 : length - 4], ca_coord[4:length])
+    ri[1 : length - 1] = angle(
+        ca_coord[0 : length - 2], ca_coord[1 : length - 1], ca_coord[2:length]
+    )
+    ai[1 : length - 2] = dihedral(
+        ca_coord[0 : length - 3],
+        ca_coord[1 : length - 2],
+        ca_coord[2 : length - 1],
+        ca_coord[3 : length - 0],
+    )
+
+    # Find CA that meet criteria for potential helices and strands
+    relaxed_helix = ((d3i >= _d3_helix[0]) & (d3i <= _d3_helix[1])) | (
+        (ri >= _r_helix[0]) & (ri <= _r_helix[1])
+    )
+    strict_helix = (
+        (d3i >= _d3_helix[0])
+        & (d3i <= _d3_helix[1])
+        & (d4i >= _d4_helix[0])
+        & (d4i <= _d4_helix[1])
+    ) | (
+        (ri >= _r_helix[0])
+        & (ri <= _r_helix[1])
+        & (ai >= _a_helix[0])
+        & (ai <= _a_helix[1])
+    )
+
+    relaxed_strand = (d3i >= _d3_strand[0]) & (d3i <= _d3_strand[1])
+    strict_strand = (
+        (d2i >= _d2_strand[0])
+        & (d2i <= _d2_strand[1])
+        & (d3i >= _d3_strand[0])
+        & (d3i <= _d3_strand[1])
+        & (d4i >= _d4_strand[0])
+        & (d4i <= _d4_strand[1])
+    ) | (
+        (ri >= _r_strand[0])
+        & (ri <= _r_strand[1])
+        & (
+            # Account for periodic boundary of dihedral angle
+            ((ai >= _a_strand[0]) & (ai <= _a_strand[1]))
+            | ((ai >= _a_strand[2]) & (ai <= _a_strand[3]))
+        )
+    )
+
+    helix_mask = _mask_consecutive(strict_helix, 5)
+    helix_mask = _extend_region(helix_mask, relaxed_helix)
+
+    strand_mask = _mask_consecutive(strict_strand, 4)
+    short_strand_mask = _mask_regions_with_contacts(
+        ca_coord,
+        _mask_consecutive(strict_strand, 3),
+        min_contacts=5,
+        min_distance=4.2,
+        max_distance=5.2,
+    )
+    strand_mask = _extend_region(strand_mask | short_strand_mask, relaxed_strand)
+
+    sse = np.full(length, "c", dtype="U1")
+    sse[helix_mask] = "a"
+    sse[strand_mask] = "b"
+    # Residues where coord are NaN do not belong to amino acids
+    # (or at least they have no CA)
+    sse[np.isnan(ca_coord).any(axis=-1)] = ""
+    # Remove SSE for virtual atoms and return
+    return sse[no_virtual_mask]
+
+
+def _mask_consecutive(mask, number):
+    """
+    Find all regions in a mask with `number` consecutive ``True``
+    values.
+    Return a mask that is ``True`` for all indices in such a region and
+    ``False`` otherwise.
+    """
+    # An element is in a consecutive region,
+    # if it and the following `number-1` elements are True
+    # The elements `mask[-(number-1):]` cannot have the sufficient count
+    # by this definition, as they are at the end of the array
+    counts = np.zeros(len(mask) - (number - 1), dtype=int)
+    for i in range(number):
+        counts[mask[i : i + len(counts)]] += 1
+    consecutive_seed = counts == number
+
+    # Not only that element, but also the
+    # following `number-1` elements are in a consecutive region
+    consecutive_mask = np.zeros(len(mask), dtype=bool)
+    for i in range(number):
+        consecutive_mask[i : i + len(consecutive_seed)] |= consecutive_seed
+
+    return consecutive_mask
+
+
+def _extend_region(base_condition_mask, extension_condition_mask):
+    """
+    Extend a ``True`` region in `base_condition_mask` by at maximum of
+    one element at each side, if such element fulfills
+    `extension_condition_mask.`
+    """
+    # This mask always marks the start
+    # of either a 'True' or 'False' region
+    # Prepend absent region to the start to capture the event,
+    # that the first element is already the start of a region
+    region_change_mask = np.diff(np.append([False], base_condition_mask))
+
+    # These masks point to the first `False` element
+    # left and right of a 'True' region
+    # The left end is the element before the first element of a 'True' region
+    left_end_mask = region_change_mask & base_condition_mask
+    # Therefore the mask needs to be shifted to the left
+    left_end_mask = np.append(left_end_mask[1:], [False])
+    # The right end is first element of a 'False' region
+    right_end_mask = region_change_mask & ~base_condition_mask
+
+    # The 'base_condition_mask' gets additional 'True' elements
+    # at left or right ends, which meet the extension criterion
+    return base_condition_mask | (
+        (left_end_mask | right_end_mask) & extension_condition_mask
+    )
+
+
+def _mask_regions_with_contacts(
+    coord, candidate_mask, min_contacts, min_distance, max_distance
+):
+    """
+    Mask regions of `candidate_mask` that have at least `min_contacts`
+    contacts with `coord` in the range `min_distance` to `max_distance`.
+    """
+    potential_contact_coord = coord[~np.isnan(coord).any(axis=-1)]
+    if len(potential_contact_coord) == 0:
+        # No potential contacts -> no contacts
+        # -> no residue can satisfy 'min_contacts'
+        return np.zeros(len(candidate_mask), dtype=bool)
+
+    cell_list = CellList(potential_contact_coord, max_distance)
+    # For each candidate position,
+    # get all contacts within maximum distance
+    all_within_max_dist_indices = cell_list.get_atoms(
+        coord[candidate_mask], max_distance
+    )
+
+    contacts = np.zeros(len(coord), dtype=int)
+    for i, atom_index in enumerate(np.where(candidate_mask)[0]):
+        within_max_dist_indices = all_within_max_dist_indices[i]
+        # Remove padding values
+        within_max_dist_indices = within_max_dist_indices[within_max_dist_indices != -1]
+        # Now count all contacts within maximum distance
+        # that also satisfy the minimum distance
+        contacts[atom_index] = np.count_nonzero(
+            distance(
+                coord[atom_index], potential_contact_coord[within_max_dist_indices]
+            )
+            > min_distance
+        )
+
+    # Count the number of contacts per region
+    # These indices mark the start of either a 'True' or 'False' region
+    # Prepend absent region to the start to capture the event,
+    # that the first element is already the start of a region
+    region_change_indices = np.where(np.diff(np.append([False], candidate_mask)))[0]
+    # Add exclusive stop
+    region_change_indices = np.append(region_change_indices, [len(coord)])
+    output_mask = np.zeros(len(candidate_mask), dtype=bool)
+    for i in range(len(region_change_indices) - 1):
+        start = region_change_indices[i]
+        stop = region_change_indices[i + 1]
+        total_contacts = np.sum(contacts[start:stop])
+        if total_contacts >= min_contacts:
+            output_mask[start:stop] = True
+
+    return output_mask