biotite 0.41.2__cp312-cp312-win_amd64.whl → 1.0.0__cp312-cp312-win_amd64.whl

biotite/structure/io/pdbx/legacy.py

@@ -1,267 +0,0 @@
-# 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.pdbx"
-__author__ = "Patrick Kunzmann"
-__all__ = ["PDBxFile"]
-
-import copy
-from collections.abc import MutableMapping
-import warnings
-from .cif import CIFFile, CIFBlock, CIFCategory, CIFColumn
-from ....file import File, InvalidFileError
-
-
-class PDBxFile(File, MutableMapping):
-    """
-    This class represents the legacy interface to CIF files.
-
-    The categories of the file can be accessed using the
-    :meth:`get_category()`/:meth:`set_category()` methods.
-    The content of each category is represented by a dictionary.
-    The dictionary contains the entry
-    (e.g. *label_entity_id* in *atom_site*) as key.
-    The corresponding values are either strings in *non-looped*
-    categories, or 1-D numpy arrays of string objects in case of
-    *looped* categories.
-
-    A category can be changed or added using :meth:`set_category()`:
-    If a string-valued dictionary is provided, a *non-looped* category
-    will be created; if an array-valued dictionary is given, a
-    *looped* category will be created. In case of arrays, it is
-    important that all arrays have the same size.
-
-    Alternatively, The content of this file can also be read/write
-    accessed using dictionary-like indexing:
-    You can either provide a data block and a category or only a
-    category, in which case the first data block is taken.
-
-    DEPRECATED: Use :class:`CIFFile` instead.
-
-    Notes
-    -----
-    This class is also able to detect and parse multiline entries in the
-    file. However, when writing a category no multiline values are used.
-    This could lead to long lines.
-
-    This class uses a lazy category dictionary creation: When reading
-    the file only the line positions of all categories are checked. The
-    time consuming task of dictionary creation is done when
-    :meth:`get_category()` is called.
-
-    Examples
-    --------
-    Read the file and get author names:
-
-    >>> import os.path
-    >>> file = PDBxFile.read(os.path.join(path_to_structures, "1l2y.cif"))
-    >>> author_dict = file.get_category("citation_author", block="1L2Y")
-    >>> print(author_dict["name"])
-    ['Neidigh, J.W.' 'Fesinmeyer, R.M.' 'Andersen, N.H.']
-
-    Dictionary style indexing, no specification of data block:
-
-    >>> print(file["citation_author"]["name"])
-    ['Neidigh, J.W.' 'Fesinmeyer, R.M.' 'Andersen, N.H.']
-
-    Get the structure from the file:
-
-    >>> arr = get_structure(file)
-    >>> print(type(arr).__name__)
-    AtomArrayStack
-    >>> arr = get_structure(file, model=1)
-    >>> print(type(arr).__name__)
-    AtomArray
-
-    Modify atom array and write it back into the file:
-
-    >>> arr_mod = rotate(arr, [1,2,3])
-    >>> set_structure(file, arr_mod)
-    >>> file.write(os.path.join(path_to_directory, "1l2y_mod.cif"))
-    """
-
-    def __init__(self):
-        warnings.warn(
-            "'PDBxFile' is deprecated, use 'CIFFile' instead",
-            DeprecationWarning
-        )
-        super().__init__()
-        self._cif_file = CIFFile()
-
-    @property
-    def cif_file(self):
-        return self._cif_file
-
-    @property
-    def lines(self):
-        return self._cif_file.lines
-
-    @classmethod
-    def read(cls, file):
-        """
-        Read a PDBx/mmCIF file.
-
-        Parameters
-        ----------
-        file : file-like object or str
-            The file to be read.
-            Alternatively a file path can be supplied.
-
-        Returns
-        -------
-        file_object : PDBxFile
-            The parsed file.
-        """
-        pdbx_file = PDBxFile()
-        pdbx_file._cif_file = CIFFile.read(file)
-        return pdbx_file
-
-    def write(self, file):
-        self._cif_file.write(file)
-
-
-    def get_block_names(self):
-        """
-        Get the names of all data blocks in the file.
-
-        Returns
-        -------
-        blocks : list
-            List of data block names.
-        """
-        return sorted(self._cif_file.keys())
-
-    def get_category(self, category, block=None, expect_looped=False):
-        """
-        Get the dictionary for a given category.
-
-        Parameters
-        ----------
-        category : string
-            The name of the category. The leading underscore is omitted.
-        block : string, optional
-            The name of the data block. Default is the first
-            (and most times only) data block of the file.
-        expect_looped : bool, optional
-            If set to true, the returned dictionary will always contain
-            arrays (only if the category exists):
-            If the category is *non-looped*, each array will contain
-            only one element.
-
-        Returns
-        -------
-        category_dict : dict of (str or ndarray, dtype=str) or None
-            A entry keyed dictionary. The corresponding values are
-            strings or array of strings for *non-looped* and
-            *looped* categories, respectively.
-            Returns None, if the data block does not contain the given
-            category.
-        """
-        if block is None:
-            try:
-                block = self.get_block_names()[0]
-            except IndexError:
-                raise InvalidFileError("File is empty")
-
-        if category not in self._cif_file[block]:
-            return None
-
-        category_dict = {}
-        for column_name, column in self._cif_file[block][category].items():
-            if not expect_looped and len(column) == 1:
-                category_dict[column_name] = column.as_item()
-            else:
-                category_dict[column_name] = column.as_array()
-        return category_dict
-
-    def set_category(self, category, category_dict, block=None):
-        """
-        Set the content of a category.
-
-        If the category is already existing, all lines corresponding
-        to the category are replaced. Otherwise a new category is
-        created and the lines are appended at the end of the data block.
-
-        Parameters
-        ----------
-        category : string
-            The name of the category. The leading underscore is omitted.
-        category_dict : dict
-            The category content. The dictionary must have strings
-            (subcategories) as keys and strings or :class:`ndarray`
-            objects as values.
-        block : string, optional
-            The name of the data block. Default is the first
-            (and most times only) data block of the file. If the
-            block is not contained in the file yet, a new block is
-            appended at the end of the file.
-        """
-        if block is None:
-            try:
-                block = self.get_block_names()[0]
-            except IndexError:
-                raise InvalidFileError(
-                    "File is empty, give an explicit data block"
-                )
-
-        if block not in self._cif_file:
-            self._cif_file = CIFBlock()
-        self._cif_file[block][category] = CIFCategory({
-            column_name: CIFColumn(array)
-            for column_name, array in category_dict.items()
-        })
-
-    def __copy_fill__(self, clone):
-        super().__copy_fill__(clone)
-        clone._cif_file = copy.deepcopy(self._cif_file)
-
-    def __setitem__(self, index, item):
-        block, category_name = self._full_index(index)
-        self.set_category(category_name, item, block=block)
-
-    def __getitem__(self, index):
-        block, category_name = self._full_index(index)
-        return self.get_category(category_name, block=block)
-
-    def __delitem__(self, index):
-        block, category_name = self._full_index(index)
-        del self._cif_file[block][category_name]
-
-    def __contains__(self, index):
-        block, category_name = self._full_index(index)
-        return (block, category_name) in self._categories
-
-    def __iter__(self):
-        try:
-            block = self.get_block_names()[0]
-        except IndexError:
-            raise InvalidFileError(
-                "File is empty, give an explicit data block"
-            )
-
-        return iter(self._cif_file[block])
-
-    def __len__(self):
-        try:
-            block = self.get_block_names()[0]
-        except IndexError:
-            raise InvalidFileError(
-                "File is empty, give an explicit data block"
-            )
-
-        return len(self._cif_file[block])
-
-    def _full_index(self, index):
-        """
-        Converts a an integer or tuple index into a block and a category
-        name.
-        """
-        if isinstance(index, tuple):
-            return index[0], index[1]
-        elif isinstance(index, str):
-            return self.get_block_names()[0], index
-        else:
-            raise TypeError(
-                f"'{type(index).__name__}' is an invalid index type"
-            )

biotite/structure/io/tng/__init__.py

@@ -1,13 +0,0 @@
-# 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* TNG format.
-"""
-
-__name__ = "biotite.structure.io.tng"
-__author__ = "Patrick Kunzmann"
-
-from .file import *

biotite/structure/io/tng/file.py

@@ -1,46 +0,0 @@
-# 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.tng"
-__author__ = "Patrick Kunzmann"
-__all__ = ["TNGFile"]
-
-import numpy as np
-from ..trajfile import TrajectoryFile
-
-
-class TNGFile(TrajectoryFile):
-    """
-    This file class represents a TNG trajectory file.
-    """
-    
-    @classmethod
-    def traj_type(cls):
-        import mdtraj.formats as traj
-        return traj.TNGTrajectoryFile
-    
-    @classmethod
-    def process_read_values(cls, read_values):
-        # nm to Angstrom
-        coord = read_values[0] * 10
-        box = read_values[2]
-        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/temp.py

@@ -1,86 +0,0 @@
-# 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"
-__author__ = "Patrick Kunzmann"
-__all__ = ["temp_file", "temp_dir"]
-
-import shutil
-import atexit
-import os
-import tempfile
-import warnings
-
-
-_temp_dir = ""
-
-def _create_temp_dir():
-    global _temp_dir
-    if _temp_dir == "":
-        cwd = os.getcwd()
-        _temp_dir = os.path.join(cwd, ".biotitetemp")
-        if not os.path.isdir(_temp_dir):
-            os.makedirs(_temp_dir)
-        atexit.register(_delete_temp)
-
-
-def _delete_temp():
-    global _temp_dir
-    # Condition only for savety reasons
-    if ".biotitetemp" in _temp_dir: 
-        shutil.rmtree(_temp_dir)
-
-
-def temp_file(suffix=""):
-    """
-    Get a file path to a temporary file.
-    
-    All temporary files will be deleted after script execution.
-
-    DEPRECATED: Please use the :mod:`tempfile` module from the
-    standard library.
-    
-    Parameters
-    ----------
-    suffix : str
-        Suffix of the file.
-        By default no suffix will be appended.
-    
-    Returns
-    -------
-    temp_file_name : str
-        a file name in the temporary directory.
-    """
-    global _temp_dir
-    warnings.warn(
-        "Please use the :mod:`tempfile` module from the standard library",
-        DeprecationWarning
-    )
-    _create_temp_dir()
-    if suffix != "" and not suffix.startswith("."):
-        suffix = "." + suffix
-    return tempfile.mktemp(suffix=suffix, dir=_temp_dir)
-     
-
-def temp_dir():
-    """
-    Get the temporary directory path.
-    
-    The temporary directory will be deleted after script execution.
-
-    DEPRECATED: Please use the :mod:`tempfile` module from the
-    standard library.
-    
-    Returns
-    -------
-    temp_dir : str
-        Path of the temporary directory.
-    """
-    global _temp_dir
-    warnings.warn(
-        "Please use the :mod:`tempfile` module from the standard library",
-        DeprecationWarning
-    )
-    _create_temp_dir()
-    return _temp_dir