biotite 1.2.0__cp312-cp312-macosx_11_0_arm64.whl → 1.4.0__cp312-cp312-macosx_11_0_arm64.whl

biotite/structure/spacegroups.license

@@ -0,0 +1,26 @@
+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/superimpose.py

@@ -12,7 +12,6 @@ __all__ = [
     "superimpose",
     "superimpose_homologs",
     "superimpose_without_outliers",
-    "AffineTransformation",
 ]
 
 
@@ -27,186 +26,7 @@ from biotite.structure.chains import chain_iter
 from biotite.structure.filter import filter_amino_acids, filter_nucleotides
 from biotite.structure.geometry import centroid, distance
 from biotite.structure.sequence import to_sequence
-
-
-class AffineTransformation:
-    """
-    An affine transformation, consisting of translations and a rotation.
-
-    Parameters
-    ----------
-    center_translation : ndarray, shape=(3,) or shape=(m,3), dtype=float
-        The translation vector for moving the centroid into the
-        origin.
-    rotation : ndarray, shape=(3,3) or shape=(m,3,3), dtype=float
-        The rotation matrix.
-    target_translation : ndarray, shape=(m,3), dtype=float
-        The translation vector for moving the structure onto the
-        fixed one.
-
-    Attributes
-    ----------
-    center_translation, rotation, target_translation : ndarray
-        Same as the parameters.
-        The dimensions are always expanded to *(m,3)* or *(m,3,3)*,
-        respectively.
-    """
-
-    def __init__(self, center_translation, rotation, target_translation):
-        self.center_translation = _expand_dims(center_translation, 2)
-        self.rotation = _expand_dims(rotation, 3)
-        self.target_translation = _expand_dims(target_translation, 2)
-
-    def apply(self, atoms):
-        """
-        Apply this transformation on the given structure.
-
-        Parameters
-        ----------
-        atoms : AtomArray or AtomArrayStack or ndarray, shape(n,), dtype=float or ndarray, shape(m,n), dtype=float
-            The structure to apply the transformation on.
-
-        Returns
-        -------
-        transformed : AtomArray or AtomArrayStack or ndarray, shape(n,), dtype=float or ndarray, shape(m,n), dtype=float
-            A copy of the `atoms` structure,
-            with transformations applied.
-            Only coordinates are returned, if coordinates were given in
-            `atoms`.
-
-        Examples
-        --------
-
-        >>> coord = np.arange(15).reshape(5,3)
-        >>> print(coord)
-        [[ 0  1  2]
-         [ 3  4  5]
-         [ 6  7  8]
-         [ 9 10 11]
-         [12 13 14]]
-        >>> # Rotates 90 degrees around the z-axis
-        >>> transform = AffineTransformation(
-        ...     center_translation=np.array([0,0,0]),
-        ...     rotation=np.array([
-        ...         [0, -1,  0],
-        ...         [1,  0,  0],
-        ...         [0,  0,  1]
-        ...     ]),
-        ...     target_translation=np.array([0,0,0])
-        ... )
-        >>> print(transform.apply(coord))
-        [[ -1.   0.   2.]
-         [ -4.   3.   5.]
-         [ -7.   6.   8.]
-         [-10.   9.  11.]
-         [-13.  12.  14.]]
-        """
-        mobile_coord = coord(atoms)
-        original_shape = mobile_coord.shape
-        mobile_coord = _reshape_to_3d(mobile_coord)
-        if mobile_coord.shape[0] != self.rotation.shape[0]:
-            raise IndexError(
-                f"Number of transformations is {self.rotation.shape[0]}, "
-                f"but number of structure models is {mobile_coord.shape[0]}"
-            )
-
-        superimposed_coord = mobile_coord.copy()
-        superimposed_coord += self.center_translation[:, np.newaxis, :]
-        superimposed_coord = _multi_matmul(self.rotation, superimposed_coord)
-        superimposed_coord += self.target_translation[:, np.newaxis, :]
-
-        superimposed_coord = superimposed_coord.reshape(original_shape)
-        if isinstance(atoms, np.ndarray):
-            return superimposed_coord
-        else:
-            superimposed = atoms.copy()
-            superimposed.coord = superimposed_coord
-            return superimposed
-
-    def as_matrix(self):
-        """
-        Get the translations and rotation as a combined 4x4
-        transformation matrix.
-
-        Multiplying this matrix with coordinates in the form
-        *(x, y, z, 1)* will apply the same transformation as
-        :meth:`apply()` to coordinates in the form *(x, y, z)*.
-
-        Returns
-        -------
-        transformation_matrix : ndarray, shape=(m,4,4), dtype=float
-            The transformation matrix.
-            *m* is the number of models in the transformation.
-
-        Examples
-        --------
-
-        >>> coord = np.arange(15).reshape(5,3)
-        >>> print(coord)
-        [[ 0  1  2]
-         [ 3  4  5]
-         [ 6  7  8]
-         [ 9 10 11]
-         [12 13 14]]
-        >>> # Rotates 90 degrees around the z-axis
-        >>> transform = AffineTransformation(
-        ...     center_translation=np.array([0,0,0]),
-        ...     rotation=np.array([
-        ...         [0, -1,  0],
-        ...         [1,  0,  0],
-        ...         [0,  0,  1]
-        ...     ]),
-        ...     target_translation=np.array([0,0,0])
-        ... )
-        >>> print(transform.apply(coord))
-        [[ -1.   0.   2.]
-         [ -4.   3.   5.]
-         [ -7.   6.   8.]
-         [-10.   9.  11.]
-         [-13.  12.  14.]]
-        >>> # Use a 4x4 matrix for transformation as alternative
-        >>> coord_4 = np.concatenate([coord, np.ones((len(coord), 1))], axis=-1)
-        >>> print(coord_4)
-        [[ 0.  1.  2.  1.]
-         [ 3.  4.  5.  1.]
-         [ 6.  7.  8.  1.]
-         [ 9. 10. 11.  1.]
-         [12. 13. 14.  1.]]
-        >>> print((transform.as_matrix()[0] @ coord_4.T).T)
-        [[ -1.   0.   2.   1.]
-         [ -4.   3.   5.   1.]
-         [ -7.   6.   8.   1.]
-         [-10.   9.  11.   1.]
-         [-13.  12.  14.   1.]]
-        """
-        n_models = self.rotation.shape[0]
-        rotation_mat = _3d_identity(n_models, 4)
-        rotation_mat[:, :3, :3] = self.rotation
-        center_translation_mat = _3d_identity(n_models, 4)
-        center_translation_mat[:, :3, 3] = self.center_translation
-        target_translation_mat = _3d_identity(n_models, 4)
-        target_translation_mat[:, :3, 3] = self.target_translation
-        return target_translation_mat @ rotation_mat @ center_translation_mat
-
-
-def _expand_dims(array, n_dims):
-    """
-    Expand the dimensions of an `ndarray` to a certain number of
-    dimensions.
-    """
-    while array.ndim < n_dims:
-        array = array[np.newaxis, ...]
-    return array
-
-
-def _3d_identity(m, n):
-    """
-    Create an array of *m* identity matrices of shape *(n, n)*
-    """
-    matrices = np.zeros((m, n, n), dtype=float)
-    indices = np.arange(n)
-    matrices[:, indices, indices] = 1
-    return matrices
+from biotite.structure.transform import AffineTransformation
 
 
 def superimpose(fixed, mobile, atom_mask=None):
@@ -624,16 +444,6 @@ def _get_rotation_matrices(fixed, mobile):
     return matrices
 
 
-def _multi_matmul(matrices, vectors):
-    """
-    Calculate the matrix multiplication of m matrices
-    with m x n vectors.
-    """
-    return np.transpose(
-        np.matmul(matrices, np.transpose(vectors, axes=(0, 2, 1))), axes=(0, 2, 1)
-    )
-
-
 def _get_backbone_anchor_indices(atoms):
     """
     Select one representative anchor atom for each amino acid and

biotite/structure/transform.py

@@ -10,6 +10,7 @@ that can be applied on structures.
 __name__ = "biotite.structure"
 __author__ = "Patrick Kunzmann", "Claude J. Rogers"
 __all__ = [
+    "AffineTransformation",
     "translate",
     "rotate",
     "rotate_centered",
@@ -20,10 +21,215 @@ __all__ = [
 
 import numpy as np
 from biotite.structure.atoms import Atom, AtomArray, AtomArrayStack, coord
-from biotite.structure.geometry import centroid
 from biotite.structure.util import matrix_rotate, norm_vector, vector_dot
 
 
+class AffineTransformation:
+    """
+    An affine transformation, consisting of translations and a rotation.
+
+    Parameters
+    ----------
+    center_translation : ndarray, shape=(3,) or shape=(m,3), dtype=float
+        The translation vector for moving the centroid into the
+        origin.
+    rotation : ndarray, shape=(3,3) or shape=(m,3,3), dtype=float
+        The rotation matrix.
+    target_translation : ndarray, shape=(m,3), dtype=float
+        The translation vector for moving the structure onto the
+        fixed one.
+
+    Attributes
+    ----------
+    center_translation, rotation, target_translation : ndarray
+        Same as the parameters.
+        The dimensions are always expanded to *(m,3)* or *(m,3,3)*,
+        respectively.
+    """
+
+    def __init__(self, center_translation, rotation, target_translation):
+        self.center_translation = _expand_dims(center_translation, 2)
+        self.rotation = _expand_dims(rotation, 3)
+        self.target_translation = _expand_dims(target_translation, 2)
+
+    def apply(self, atoms):
+        """
+        Apply this transformation on the given structure.
+
+        Parameters
+        ----------
+        atoms : AtomArray or AtomArrayStack or ndarray, shape(n,), dtype=float or ndarray, shape(m,n), dtype=float
+            The structure to apply the transformation on.
+
+        Returns
+        -------
+        transformed : AtomArray or AtomArrayStack or ndarray, shape(n,), dtype=float or ndarray, shape(m,n), dtype=float
+            A copy of the `atoms` structure, with transformations applied.
+            Only coordinates are returned, if coordinates were given in `atoms`.
+
+        Examples
+        --------
+
+        >>> coord = np.arange(15).reshape(5,3)
+        >>> print(coord)
+        [[ 0  1  2]
+         [ 3  4  5]
+         [ 6  7  8]
+         [ 9 10 11]
+         [12 13 14]]
+        >>> # Rotates 90 degrees around the z-axis
+        >>> transform = AffineTransformation(
+        ...     center_translation=np.array([0,0,0]),
+        ...     rotation=np.array([
+        ...         [0, -1,  0],
+        ...         [1,  0,  0],
+        ...         [0,  0,  1]
+        ...     ]),
+        ...     target_translation=np.array([0,0,0])
+        ... )
+        >>> print(transform.apply(coord))
+        [[ -1.   0.   2.]
+         [ -4.   3.   5.]
+         [ -7.   6.   8.]
+         [-10.   9.  11.]
+         [-13.  12.  14.]]
+        """
+        mobile_coord = coord(atoms)
+        original_shape = mobile_coord.shape
+        mobile_coord = _reshape_to_3d(mobile_coord)
+        if (
+            self.rotation.shape[0] != 1
+            and mobile_coord.shape[0] != self.rotation.shape[0]
+        ):
+            raise IndexError(
+                f"Number of transformations is {self.rotation.shape[0]}, "
+                f"but number of structure models is {mobile_coord.shape[0]}"
+            )
+
+        superimposed_coord = mobile_coord.copy()
+        superimposed_coord += self.center_translation[:, np.newaxis, :]
+        superimposed_coord = _multi_matmul(self.rotation, superimposed_coord)
+        superimposed_coord += self.target_translation[:, np.newaxis, :]
+
+        superimposed_coord = superimposed_coord.reshape(original_shape)
+        if isinstance(atoms, np.ndarray):
+            return superimposed_coord
+        else:
+            superimposed = atoms.copy()
+            superimposed.coord = superimposed_coord
+            return superimposed
+
+    def as_matrix(self):
+        """
+        Get the translations and rotation as a combined 4x4
+        transformation matrix.
+
+        Multiplying this matrix with coordinates in the form
+        *(x, y, z, 1)* will apply the same transformation as
+        :meth:`apply()` to coordinates in the form *(x, y, z)*.
+
+        Returns
+        -------
+        transformation_matrix : ndarray, shape=(m,4,4), dtype=float
+            The transformation matrix.
+            *m* is the number of models in the transformation.
+
+        Examples
+        --------
+
+        >>> coord = np.arange(15).reshape(5,3)
+        >>> print(coord)
+        [[ 0  1  2]
+         [ 3  4  5]
+         [ 6  7  8]
+         [ 9 10 11]
+         [12 13 14]]
+        >>> # Rotates 90 degrees around the z-axis
+        >>> transform = AffineTransformation(
+        ...     center_translation=np.array([0,0,0]),
+        ...     rotation=np.array([
+        ...         [0, -1,  0],
+        ...         [1,  0,  0],
+        ...         [0,  0,  1]
+        ...     ]),
+        ...     target_translation=np.array([0,0,0])
+        ... )
+        >>> print(transform.apply(coord))
+        [[ -1.   0.   2.]
+         [ -4.   3.   5.]
+         [ -7.   6.   8.]
+         [-10.   9.  11.]
+         [-13.  12.  14.]]
+        >>> # Use a 4x4 matrix for transformation as alternative
+        >>> coord_4 = np.concatenate([coord, np.ones((len(coord), 1))], axis=-1)
+        >>> print(coord_4)
+        [[ 0.  1.  2.  1.]
+         [ 3.  4.  5.  1.]
+         [ 6.  7.  8.  1.]
+         [ 9. 10. 11.  1.]
+         [12. 13. 14.  1.]]
+        >>> print((transform.as_matrix()[0] @ coord_4.T).T)
+        [[ -1.   0.   2.   1.]
+         [ -4.   3.   5.   1.]
+         [ -7.   6.   8.   1.]
+         [-10.   9.  11.   1.]
+         [-13.  12.  14.   1.]]
+        """
+        n_models = self.rotation.shape[0]
+        rotation_mat = _3d_identity(n_models, 4)
+        rotation_mat[:, :3, :3] = self.rotation
+        center_translation_mat = _3d_identity(n_models, 4)
+        center_translation_mat[:, :3, 3] = self.center_translation
+        target_translation_mat = _3d_identity(n_models, 4)
+        target_translation_mat[:, :3, 3] = self.target_translation
+        return target_translation_mat @ rotation_mat @ center_translation_mat
+
+    def __eq__(self, other):
+        if not isinstance(other, AffineTransformation):
+            return False
+        if not np.array_equal(self.center_translation, other.center_translation):
+            return False
+        if not np.array_equal(self.rotation, other.rotation):
+            return False
+        if not np.array_equal(self.target_translation, other.target_translation):
+            return False
+        return True
+
+
+def _expand_dims(array, n_dims):
+    """
+    Expand the dimensions of an `ndarray` to a certain number of
+    dimensions.
+    """
+    while array.ndim < n_dims:
+        array = array[np.newaxis, ...]
+    return array
+
+
+def _3d_identity(m, n):
+    """
+    Create an array of *m* identity matrices of shape *(n, n)*
+    """
+    matrices = np.zeros((m, n, n), dtype=float)
+    indices = np.arange(n)
+    matrices[:, indices, indices] = 1
+    return matrices
+
+
+def _reshape_to_3d(coord):
+    """
+    Reshape the coordinate array to 3D, if it is 2D.
+    """
+    if coord.ndim < 2:
+        raise ValueError("Coordinates must be at least two-dimensional")
+    if coord.ndim == 2:
+        return coord[np.newaxis, ...]
+    elif coord.ndim == 3:
+        return coord
+    else:
+        raise ValueError("Coordinates must be at most three-dimensional")
+
+
 def translate(atoms, vector):
     """
     Translate the given atoms or coordinates by a given vector.
@@ -150,6 +356,9 @@ def rotate_centered(atoms, angles):
     rotate : Rotate atoms about the origin.
     rotate_about_axis : Rotate atoms about a given axis.
     """
+    # Avoid circular import
+    from biotite.structure.geometry import centroid
+
     if len(coord(atoms).shape) == 1:
         # Single value -> centered rotation does not change coordinates
         return atoms.copy()
@@ -515,3 +724,13 @@ def _put_back(input_atoms, transformed):
         return moved_atoms
     else:
         return transformed
+
+
+def _multi_matmul(matrices, vectors):
+    """
+    Calculate the matrix multiplication of m matrices
+    with m x n vectors.
+    """
+    return np.transpose(
+        np.matmul(matrices, np.transpose(vectors, axes=(0, 2, 1))), axes=(0, 2, 1)
+    )

biotite/version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.2.0'
-__version_tuple__ = version_tuple = (1, 2, 0)
+__version__ = version = '1.4.0'
+__version_tuple__ = version_tuple = (1, 4, 0)

{biotite-1.2.0.dist-info → biotite-1.4.0.dist-info}/METADATA

@@ -1,46 +1,16 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: biotite
-Version: 1.2.0
+Version: 1.4.0
 Summary: A comprehensive library for computational molecular biology
 Project-URL: homepage, https://www.biotite-python.org
 Project-URL: repository, https://github.com/biotite-dev/biotite
 Project-URL: documentation, https://www.biotite-python.org
 Author: The Biotite contributors
-License: BSD 3-Clause License
-        --------------------
-        
-        Copyright 2017, The Biotite contributors
-        All rights reserved.
-        
-        Redistribution and use in source and binary forms, with or without modification,
-        are permitted provided that the following conditions are met:
-        
-        1. Redistributions of source code must retain the above copyright notice, this
-        list of conditions and the following disclaimer.
-        
-        2. Redistributions in binary form must reproduce the above copyright notice,
-        this list of conditions and the following disclaimer in the documentation and/or
-        other materials provided with the distribution.
-        
-        3. Neither the name of the copyright holder nor the names of its contributors
-        may be used to endorse or promote products derived from this software without
-        specific prior written permission.
-        
-        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
-        ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-        WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
-        ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
-        (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
-        LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-        ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-        (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-Expression: BSD-3-Clause
 License-File: LICENSE.rst
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: Microsoft :: Windows
@@ -48,7 +18,7 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Requires-Dist: biotraj<2.0,>=1.0
 Requires-Dist: msgpack>=0.5.6
 Requires-Dist: networkx>=2.0