biotite 0.41.1__cp311-cp311-macosx_10_16_arm64.whl

biotite/structure/io/trr/__init__.py

@@ -0,0 +1,13 @@
+# 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 subpackage is used for reading and writing trajectories in the
+uncompressed *Gromacs* TRR format.
+"""
+
+__name__ = "biotite.structure.io.trr"
+__author__ = "Patrick Kunzmann"
+
+from .file import *

biotite/structure/io/trr/file.py

@@ -0,0 +1,46 @@
+# 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.
+
+__name__ = "biotite.structure.io.trr"
+__author__ = "Patrick Kunzmann"
+__all__ = ["TRRFile"]
+
+import numpy as np
+from ..trajfile import TrajectoryFile
+
+
+class TRRFile(TrajectoryFile):
+    """
+    This file class represents a TRR trajectory file.
+    """
+    
+    @classmethod
+    def traj_type(cls):
+        import mdtraj.formats as traj
+        return traj.TRRTrajectoryFile
+    
+    @classmethod
+    def process_read_values(cls, read_values):
+        # nm to Angstrom
+        coord = read_values[0] * 10
+        box = read_values[3]
+        if box is not None:
+            box *= 10
+        time = read_values[1]
+        return coord, box, time
+    
+    @classmethod
+    def prepare_write_values(cls, coord, box, time):
+        # Angstrom to nm
+        xyz = np.divide(coord, 10, dtype=np.float32) \
+              if coord is not None else None
+        time = time.astype(np.float32, copy=False) \
+               if time is not None else None
+        box = np.divide(box, 10, dtype=np.float32) \
+              if box is not None else None
+        return {
+            "xyz"  : xyz,
+            "box"  : box,
+            "time" : time,
+        }

biotite/structure/io/xtc/__init__.py

@@ -0,0 +1,13 @@
+# 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 subpackage is used for reading and writing trajectories in the
+compressed *Gromacs* XTC format.
+"""
+
+__name__ = "biotite.structure.io.xtc"
+__author__ = "Patrick Kunzmann"
+
+from .file import *

biotite/structure/io/xtc/file.py

@@ -0,0 +1,46 @@
+# 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.
+
+__name__ = "biotite.structure.io.xtc"
+__author__ = "Patrick Kunzmann"
+__all__ = ["XTCFile"]
+
+import numpy as np
+from ..trajfile import TrajectoryFile
+
+
+class XTCFile(TrajectoryFile):
+    """
+    This file class represents a XTC trajectory file.
+    """
+    
+    @classmethod
+    def traj_type(cls):
+        import mdtraj.formats as traj
+        return traj.XTCTrajectoryFile
+
+    @classmethod
+    def process_read_values(cls, read_values):
+        # nm to Angstrom
+        coord = read_values[0] * 10
+        box = read_values[3]
+        if box is not None:
+            box *= 10
+        time = read_values[1]
+        return coord, box, time
+    
+    @classmethod
+    def prepare_write_values(cls, coord, box, time):
+        # Angstrom to nm
+        xyz = np.divide(coord, 10, dtype=np.float32) \
+              if coord is not None else None
+        time = time.astype(np.float32, copy=False) \
+               if time is not None else None
+        box = np.divide(box, 10, dtype=np.float32) \
+              if box is not None else None
+        return {
+            "xyz"  : xyz,
+            "box"  : box,
+            "time" : time,
+        }

biotite/structure/mechanics.py

@@ -0,0 +1,75 @@
+# 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 for calculation of mechanical or
+mass-related properties of a molecular structure.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["mass_center", "gyration_radius"]
+
+import numpy as np
+from .atoms import Atom, AtomArray, AtomArrayStack, coord
+from .util import vector_dot, norm_vector
+from .error import BadStructureError
+from .geometry import distance
+from .info.masses import mass
+
+
+def gyration_radius(array, masses=None):
+    """
+    Compute the radius/radii of gyration of an atom array or stack.
+    
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The array or stack to calculate the radius/radii of gyration
+        for.
+    masses : ndarray, optional
+        The masses to use for each atom in the input `array`.
+        Must have the same length as `array`. By default, the standard
+        atomic mass for each element is taken.
+
+    
+    Returns
+    -------
+    masses : float or ndarray, dtype=float
+        If `array` is an :class:`AtomArray`, the radius of gyration is
+        returned as single float.
+        If `array` is an :class:`AtomArrayStack`, a :class:`ndarray`
+        containing the radii of gyration for every model is returned.
+    """
+    if masses is None:
+        masses = np.array([mass(element) for element in array.element])
+    center = mass_center(array, masses)
+    radii = distance(array, center[..., np.newaxis, :])
+    inertia_moment = np.sum(masses * radii*radii, axis=-1)
+    return np.sqrt(inertia_moment / np.sum(masses))
+
+def mass_center(array, masses=None):
+    """
+    Calculate the center(s) of mass of an atom array or stack.
+    
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The array or stack to calculate the center(s) of mass for.
+    masses : ndarray, optional
+        The masses to use for each atom in the input `array`.
+        Must have the same length as `array`. By default, the standard
+        atomic mass for each element is taken.
+    
+    Returns
+    -------
+    radius : ndarray, ndarray, dtype=float
+        Array containing the the coordinates of the center of mass.
+        If `array` is an :class:`AtomArray`, this will be an length 3
+        :class:`ndarray`; if it is an :class:`AtomArrayStack` with *n* models,
+        a (*n x 3*) :class:`ndarray` is returned.
+    """
+    if masses is None:
+        masses = np.array([mass(element) for element in array.element])
+    return np.sum(masses[:,np.newaxis] * array.coord, axis=-2) / np.sum(masses)

biotite/structure/molecules.py

@@ -0,0 +1,353 @@
+# 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 utility for separating structures into single
+molecules.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["get_molecule_indices", "get_molecule_masks", "molecule_iter"]
+
+import numpy as np
+from .atoms import AtomArray, AtomArrayStack
+from .bonds import BondList, find_connected
+
+
+def get_molecule_indices(array):
+    """
+    Get an index array for each molecule in the given structure.
+
+    A molecule is defined as a group of atoms that are directly or
+    indirectly connected via covalent bonds.
+    In this function a single atom, that has no connection to any other
+    atom (e.g. an ion), also qualifies as a molecule.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack or BondList
+        The input structure with an associated :class:`BondList`.
+        Alternatively, the :class:`BondList` can be directly supplied.
+
+    Returns
+    -------
+    indices : list of ndarray, dtype=int
+        Each element in the list is an index array referring to the
+        atoms of a single molecule.
+        Consequently, the length of this list is equal to the number of
+        molecules in the input `array`.
+
+    See also
+    --------
+    get_molecule_masks
+    molecule_iter
+
+    Examples
+    --------
+    Get an :class:`AtomArray` for ATP and show that it is a single
+    molecule:
+
+    >>> atp = residue("ATP")
+    >>> indices = get_molecule_indices(atp)
+    >>> print(len(indices))
+    1
+
+    Separate ATP into two molecules by breaking the glycosidic bond
+    to the triphosphate:
+
+    >>> i, j = np.where(np.isin(atp.atom_name, ("O5'", "PA")))[0]
+    >>> atp.bonds.remove_bond(i, j)
+    >>> indices = get_molecule_indices(atp)
+    >>> print(len(indices))
+    2
+    >>> print(atp[indices[0]])
+    HET         0  ATP PG     P         1.200   -0.230   -6.850
+    HET         0  ATP O1G    O         1.740    1.140   -6.670
+    HET         0  ATP O2G    O         2.120   -1.040   -7.890
+    HET         0  ATP O3G    O        -0.300   -0.140   -7.420
+    HET         0  ATP PB     P         0.260   -0.130   -4.450
+    HET         0  ATP O1B    O         0.810    1.230   -4.300
+    HET         0  ATP O2B    O        -1.230   -0.040   -5.060
+    HET         0  ATP O3B    O         1.190   -0.990   -5.430
+    HET         0  ATP PA     P        -0.740    0.070   -2.070
+    HET         0  ATP O1A    O        -2.100    0.140   -2.670
+    HET         0  ATP O2A    O        -0.120    1.550   -1.960
+    HET         0  ATP O3A    O         0.200   -0.840   -3.000
+    HET         0  ATP HOG2   H         2.100   -0.550   -8.730
+    HET         0  ATP HOG3   H        -0.620   -1.050   -7.520
+    HET         0  ATP HOB2   H        -1.550   -0.950   -5.130
+    HET         0  ATP HOA2   H         0.750    1.460   -1.560
+    >>> print(atp[indices[1]])
+    HET         0  ATP O5'    O        -0.840   -0.590   -0.600
+    HET         0  ATP C5'    C        -1.690    0.260    0.170
+    HET         0  ATP C4'    C        -1.830   -0.310    1.580
+    HET         0  ATP O4'    O        -0.540   -0.360    2.230
+    HET         0  ATP C3'    C        -2.680    0.630    2.460
+    HET         0  ATP O3'    O        -4.030    0.160    2.530
+    HET         0  ATP C2'    C        -2.010    0.560    3.860
+    HET         0  ATP O2'    O        -2.930    0.040    4.830
+    HET         0  ATP C1'    C        -0.830   -0.420    3.650
+    HET         0  ATP N9     N         0.330    0.020    4.430
+    HET         0  ATP C8     C         1.300    0.880    4.010
+    HET         0  ATP N7     N         2.180    1.040    4.960
+    HET         0  ATP C5     C         1.830    0.300    6.030
+    HET         0  ATP C6     C         2.390    0.080    7.300
+    HET         0  ATP N6     N         3.560    0.710    7.680
+    HET         0  ATP N1     N         1.760   -0.750    8.140
+    HET         0  ATP C2     C         0.640   -1.350    7.780
+    HET         0  ATP N3     N         0.090   -1.180    6.600
+    HET         0  ATP C4     C         0.640   -0.370    5.700
+    HET         0  ATP H5'1   H        -2.680    0.310   -0.300
+    HET         0  ATP H5'2   H        -1.260    1.260    0.220
+    HET         0  ATP H4'    H        -2.280   -1.300    1.550
+    HET         0  ATP H3'    H        -2.650    1.650    2.080
+    HET         0  ATP HO3'   H        -4.520    0.790    3.090
+    HET         0  ATP H2'    H        -1.650    1.540    4.160
+    HET         0  ATP HO2'   H        -3.670    0.660    4.870
+    HET         0  ATP H1'    H        -1.120   -1.430    3.930
+    HET         0  ATP H8     H         1.330    1.360    3.040
+    HET         0  ATP HN61   H         3.940    0.550    8.560
+    HET         0  ATP HN62   H         4.020    1.300    7.060
+    HET         0  ATP H2     H         0.170   -2.010    8.490
+    """
+    if isinstance(array, BondList):
+        bonds = array
+    elif isinstance(array, (AtomArray, AtomArrayStack)):
+        if array.bonds is None:
+            raise ValueError("An associated BondList is required")
+        bonds = array.bonds
+    else:
+        raise TypeError(
+            f"Expected a 'BondList', 'AtomArray' or 'AtomArrayStack', "
+            f"not '{type(array).__name__}'"
+        )
+
+    molecule_indices = []
+    visited_mask = np.zeros(bonds.get_atom_count(), dtype=bool)
+    while not visited_mask.all():
+        root = np.argmin(visited_mask)
+        connected = find_connected(bonds, root)
+        visited_mask[connected] = True
+        molecule_indices.append(connected)
+    return molecule_indices
+
+
+def get_molecule_masks(array):
+    """
+    Get a boolean mask for each molecule in the given structure.
+
+    A molecule is defined as a group of atoms that are directly or
+    indirectly connected via covalent bonds.
+    In this function a single atom, that has no connection to any other
+    atom (e.g. an ion), also qualifies as a molecule.
+
+    Parameters
+    ----------
+    array : AtomArray, shape=(n,) or AtomArrayStack, shape=(m,n) or BondList
+        The input structure with an associated :class:`BondList`.
+        Alternatively, the :class:`BondList` can be directly supplied.
+
+    Returns
+    -------
+    masks : ndarray, shape=(k,n), dtype=bool,
+        Each element in the array is a boolean mask referring to the
+        atoms of a single molecule.
+        Consequently, the length of this list is equal to the number of
+        molecules in the input `array`.
+
+    See also
+    --------
+    get_molecule_indices
+    molecule_iter
+
+    Examples
+    --------
+    Get an :class:`AtomArray` for ATP and show that it is a single
+    molecule:
+
+    >>> atp = residue("ATP")
+    >>> masks = get_molecule_masks(atp)
+    >>> print(len(masks))
+    1
+
+    Separate ATP into two molecules by breaking the glycosidic bond
+    to the triphosphate:
+
+    >>> i, j = np.where(np.isin(atp.atom_name, ("O5'", "PA")))[0]
+    >>> atp.bonds.remove_bond(i, j)
+    >>> masks = get_molecule_masks(atp)
+    >>> print(len(masks))
+    2
+    >>> print(atp[masks[0]])
+    HET         0  ATP PG     P         1.200   -0.230   -6.850
+    HET         0  ATP O1G    O         1.740    1.140   -6.670
+    HET         0  ATP O2G    O         2.120   -1.040   -7.890
+    HET         0  ATP O3G    O        -0.300   -0.140   -7.420
+    HET         0  ATP PB     P         0.260   -0.130   -4.450
+    HET         0  ATP O1B    O         0.810    1.230   -4.300
+    HET         0  ATP O2B    O        -1.230   -0.040   -5.060
+    HET         0  ATP O3B    O         1.190   -0.990   -5.430
+    HET         0  ATP PA     P        -0.740    0.070   -2.070
+    HET         0  ATP O1A    O        -2.100    0.140   -2.670
+    HET         0  ATP O2A    O        -0.120    1.550   -1.960
+    HET         0  ATP O3A    O         0.200   -0.840   -3.000
+    HET         0  ATP HOG2   H         2.100   -0.550   -8.730
+    HET         0  ATP HOG3   H        -0.620   -1.050   -7.520
+    HET         0  ATP HOB2   H        -1.550   -0.950   -5.130
+    HET         0  ATP HOA2   H         0.750    1.460   -1.560
+    >>> print(atp[masks[1]])
+    HET         0  ATP O5'    O        -0.840   -0.590   -0.600
+    HET         0  ATP C5'    C        -1.690    0.260    0.170
+    HET         0  ATP C4'    C        -1.830   -0.310    1.580
+    HET         0  ATP O4'    O        -0.540   -0.360    2.230
+    HET         0  ATP C3'    C        -2.680    0.630    2.460
+    HET         0  ATP O3'    O        -4.030    0.160    2.530
+    HET         0  ATP C2'    C        -2.010    0.560    3.860
+    HET         0  ATP O2'    O        -2.930    0.040    4.830
+    HET         0  ATP C1'    C        -0.830   -0.420    3.650
+    HET         0  ATP N9     N         0.330    0.020    4.430
+    HET         0  ATP C8     C         1.300    0.880    4.010
+    HET         0  ATP N7     N         2.180    1.040    4.960
+    HET         0  ATP C5     C         1.830    0.300    6.030
+    HET         0  ATP C6     C         2.390    0.080    7.300
+    HET         0  ATP N6     N         3.560    0.710    7.680
+    HET         0  ATP N1     N         1.760   -0.750    8.140
+    HET         0  ATP C2     C         0.640   -1.350    7.780
+    HET         0  ATP N3     N         0.090   -1.180    6.600
+    HET         0  ATP C4     C         0.640   -0.370    5.700
+    HET         0  ATP H5'1   H        -2.680    0.310   -0.300
+    HET         0  ATP H5'2   H        -1.260    1.260    0.220
+    HET         0  ATP H4'    H        -2.280   -1.300    1.550
+    HET         0  ATP H3'    H        -2.650    1.650    2.080
+    HET         0  ATP HO3'   H        -4.520    0.790    3.090
+    HET         0  ATP H2'    H        -1.650    1.540    4.160
+    HET         0  ATP HO2'   H        -3.670    0.660    4.870
+    HET         0  ATP H1'    H        -1.120   -1.430    3.930
+    HET         0  ATP H8     H         1.330    1.360    3.040
+    HET         0  ATP HN61   H         3.940    0.550    8.560
+    HET         0  ATP HN62   H         4.020    1.300    7.060
+    HET         0  ATP H2     H         0.170   -2.010    8.490
+    """
+    if isinstance(array, BondList):
+        bonds = array
+    elif isinstance(array, (AtomArray, AtomArrayStack)):
+        if array.bonds is None:
+            raise ValueError("An associated BondList is required")
+        bonds = array.bonds
+    else:
+        raise TypeError(
+            f"Expected a 'BondList', 'AtomArray' or 'AtomArrayStack', "
+            f"not '{type(array).__name__}'"
+        )
+
+    molecule_indices = get_molecule_indices(bonds)
+    molecule_masks = np.zeros(
+        (len(molecule_indices), bonds.get_atom_count()),
+        dtype=bool
+    )
+    for i in range(len(molecule_indices)):
+        molecule_masks[i, molecule_indices[i]] = True
+    return molecule_masks
+
+
+def molecule_iter(array):
+    """
+    Iterate over each molecule in a input structure.
+
+    A molecule is defined as a group of atoms that are directly or
+    indirectly connected via covalent bonds.
+    In this function a single atom, that has no connection to any other
+    atom (e.g. an ion), also qualifies as a molecule.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The input structure with an associated :class:`BondList`.
+
+    Yields
+    ------
+    molecule : AtomArray or AtomArrayStack
+        A single molecule of the input `array`.
+
+    See also
+    --------
+    get_molecule_indices
+    get_molecule_masks
+
+    Examples
+    --------
+    Get an :class:`AtomArray` for ATP and break it into two molecules
+    at the glycosidic bond to the triphosphate:
+
+    >>> atp = residue("ATP")
+    >>> i, j = np.where(np.isin(atp.atom_name, ("O5'", "PA")))[0]
+    >>> atp.bonds.remove_bond(i, j)
+    >>> for molecule in molecule_iter(atp):
+    ...     print("New molecule")
+    ...     print(molecule)
+    ...     print()
+    New molecule
+    HET         0  ATP PG     P         1.200   -0.230   -6.850
+    HET         0  ATP O1G    O         1.740    1.140   -6.670
+    HET         0  ATP O2G    O         2.120   -1.040   -7.890
+    HET         0  ATP O3G    O        -0.300   -0.140   -7.420
+    HET         0  ATP PB     P         0.260   -0.130   -4.450
+    HET         0  ATP O1B    O         0.810    1.230   -4.300
+    HET         0  ATP O2B    O        -1.230   -0.040   -5.060
+    HET         0  ATP O3B    O         1.190   -0.990   -5.430
+    HET         0  ATP PA     P        -0.740    0.070   -2.070
+    HET         0  ATP O1A    O        -2.100    0.140   -2.670
+    HET         0  ATP O2A    O        -0.120    1.550   -1.960
+    HET         0  ATP O3A    O         0.200   -0.840   -3.000
+    HET         0  ATP HOG2   H         2.100   -0.550   -8.730
+    HET         0  ATP HOG3   H        -0.620   -1.050   -7.520
+    HET         0  ATP HOB2   H        -1.550   -0.950   -5.130
+    HET         0  ATP HOA2   H         0.750    1.460   -1.560
+    <BLANKLINE>
+    New molecule
+    HET         0  ATP O5'    O        -0.840   -0.590   -0.600
+    HET         0  ATP C5'    C        -1.690    0.260    0.170
+    HET         0  ATP C4'    C        -1.830   -0.310    1.580
+    HET         0  ATP O4'    O        -0.540   -0.360    2.230
+    HET         0  ATP C3'    C        -2.680    0.630    2.460
+    HET         0  ATP O3'    O        -4.030    0.160    2.530
+    HET         0  ATP C2'    C        -2.010    0.560    3.860
+    HET         0  ATP O2'    O        -2.930    0.040    4.830
+    HET         0  ATP C1'    C        -0.830   -0.420    3.650
+    HET         0  ATP N9     N         0.330    0.020    4.430
+    HET         0  ATP C8     C         1.300    0.880    4.010
+    HET         0  ATP N7     N         2.180    1.040    4.960
+    HET         0  ATP C5     C         1.830    0.300    6.030
+    HET         0  ATP C6     C         2.390    0.080    7.300
+    HET         0  ATP N6     N         3.560    0.710    7.680
+    HET         0  ATP N1     N         1.760   -0.750    8.140
+    HET         0  ATP C2     C         0.640   -1.350    7.780
+    HET         0  ATP N3     N         0.090   -1.180    6.600
+    HET         0  ATP C4     C         0.640   -0.370    5.700
+    HET         0  ATP H5'1   H        -2.680    0.310   -0.300
+    HET         0  ATP H5'2   H        -1.260    1.260    0.220
+    HET         0  ATP H4'    H        -2.280   -1.300    1.550
+    HET         0  ATP H3'    H        -2.650    1.650    2.080
+    HET         0  ATP HO3'   H        -4.520    0.790    3.090
+    HET         0  ATP H2'    H        -1.650    1.540    4.160
+    HET         0  ATP HO2'   H        -3.670    0.660    4.870
+    HET         0  ATP H1'    H        -1.120   -1.430    3.930
+    HET         0  ATP H8     H         1.330    1.360    3.040
+    HET         0  ATP HN61   H         3.940    0.550    8.560
+    HET         0  ATP HN62   H         4.020    1.300    7.060
+    HET         0  ATP H2     H         0.170   -2.010    8.490
+    <BLANKLINE>
+    """
+    if array.bonds is None:
+        raise ValueError("An associated BondList is required")
+    bonds = array.bonds
+
+    visited_mask = np.zeros(bonds.get_atom_count(), dtype=bool)
+    while not visited_mask.all():
+        # Take the first atom that has not been considered yet as root
+        root = np.argmin(visited_mask)
+        connected = find_connected(bonds, root)
+        visited_mask[connected] = True
+        yield array[..., connected]