biotite 1.5.0__cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

biotite/structure/io/pdbx/__init__.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 subpackage provides support for the the modern PDBx file formats.
+The :class:`CIFFile` class provides dictionary-like access to
+every field in text-based *mmCIF* files.
+:class:`BinaryCIFFile` provides analogous functionality for the
+*BinaryCIF* format.
+Additional utility functions allow reading and writing structures
+from/to these files.
+"""
+
+__name__ = "biotite.structure.io.pdbx"
+__author__ = "Patrick Kunzmann"
+
+from .bcif import *
+from .cif import *
+from .component import *
+from .compress import *
+from .convert import *
+from .encoding import *

biotite/structure/io/pdbx/bcif.py

@@ -0,0 +1,674 @@
+# 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__ = [
+    "BinaryCIFFile",
+    "BinaryCIFBlock",
+    "BinaryCIFCategory",
+    "BinaryCIFColumn",
+    "BinaryCIFData",
+]
+
+from collections.abc import Sequence
+import msgpack
+import numpy as np
+from biotite.file import File, SerializationError, is_binary, is_open_compatible
+from biotite.structure.io.pdbx.component import (
+    MaskValue,
+    _Component,
+    _HierarchicalContainer,
+)
+from biotite.structure.io.pdbx.encoding import (
+    create_uncompressed_encoding,
+    decode_stepwise,
+    deserialize_encoding,
+    encode_stepwise,
+)
+
+
+class BinaryCIFData(_Component):
+    r"""
+    This class represents the data in a :class:`BinaryCIFColumn`.
+
+    Parameters
+    ----------
+    array : array_like or int or float or str
+        The data array to be stored.
+        If a single item is given, it is converted into an array.
+    encoding : list of Encoding , optional
+        The encoding steps that are successively applied to the data.
+        By default, the data is stored uncompressed directly as bytes.
+
+    Attributes
+    ----------
+    array : ndarray
+        The stored data array.
+    encoding : list of Encoding
+        The encoding steps.
+
+    Examples
+    --------
+
+    >>> data = BinaryCIFData([1, 2, 3])
+    >>> print(data.array)
+    [1 2 3]
+    >>> print(len(data))
+    3
+    >>> # A single item is converted into an array
+    >>> data = BinaryCIFData("apple")
+    >>> print(data.array)
+    ['apple']
+
+    A well-chosen encoding can significantly reduce the serialized data
+    size:
+
+    >>> # Default uncompressed encoding
+    >>> array = np.arange(100)
+    >>> uncompressed_bytes = BinaryCIFData(array).serialize()["data"]
+    >>> print(len(uncompressed_bytes))
+    400
+    >>> # Delta encoding followed by run-length encoding
+    >>> # [0, 1, 2, ...] -> [0, 1, 1, ...] -> [0, 1, 1, 99]
+    >>> compressed_bytes = BinaryCIFData(
+    ...     array,
+    ...     encoding = [
+    ...         # [0, 1, 2, ...] -> [0, 1, 1, ...]
+    ...         DeltaEncoding(),
+    ...         # [0, 1, 1, ...] -> [0, 1, 1, 99]
+    ...         RunLengthEncoding(),
+    ...         # [0, 1, 1, 99] -> b"\x00\x00..."
+    ...         ByteArrayEncoding()
+    ...     ]
+    ... ).serialize()["data"]
+    >>> print(len(compressed_bytes))
+    16
+    """
+
+    def __init__(self, array, encoding=None):
+        if not isinstance(array, (Sequence, np.ndarray)) or isinstance(array, str):
+            array = [array]
+        array = np.asarray(array)
+        if np.issubdtype(array.dtype, np.object_):
+            raise ValueError("Object arrays are not supported")
+
+        self._array = array
+        if encoding is None:
+            self._encoding = create_uncompressed_encoding(array)
+        else:
+            self._encoding = list(encoding)
+
+    @property
+    def array(self):
+        return self._array
+
+    @property
+    def encoding(self):
+        return self._encoding
+
+    @staticmethod
+    def subcomponent_class():
+        return None
+
+    @staticmethod
+    def supercomponent_class():
+        return BinaryCIFColumn
+
+    @staticmethod
+    def deserialize(content):
+        encoding = [deserialize_encoding(enc) for enc in content["encoding"]]
+        return BinaryCIFData(decode_stepwise(content["data"], encoding), encoding)
+
+    def serialize(self):
+        serialized_data = encode_stepwise(self._array, self._encoding)
+        if not isinstance(serialized_data, bytes):
+            raise SerializationError("Final encoding must return 'bytes'")
+        serialized_encoding = [enc.serialize() for enc in self._encoding]
+        return {"data": serialized_data, "encoding": serialized_encoding}
+
+    def __len__(self):
+        return len(self._array)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if not np.array_equal(self._array, other._array):
+            return False
+        if self._encoding != other._encoding:
+            return False
+        return True
+
+
+class BinaryCIFColumn(_Component):
+    """
+    This class represents a single column in a :class:`CIFCategory`.
+
+    Parameters
+    ----------
+    data : BinaryCIFData or array_like or int or float or str
+        The data to be stored.
+        If no :class:`BinaryCIFData` is given, the passed argument is
+        coerced into such an object.
+    mask : BinaryCIFData or array_like, dtype=int or int
+        The mask to be stored.
+        If given, the mask indicates whether the `data` is
+        inapplicable (``.``) or missing (``?``) in some rows.
+        The data presence is indicated by values from the
+        :class:`MaskValue` enum.
+        If no :class:`BinaryCIFData` is given, the passed argument is
+        coerced into such an object.
+        By default, no mask is created.
+
+    Attributes
+    ----------
+    data : BinaryCIFData
+        The stored data.
+    mask : BinaryCIFData
+        The mask that indicates whether certain data elements are
+        inapplicable or missing.
+        If no mask is present, this attribute is ``None``.
+
+    Examples
+    --------
+
+    >>> print(BinaryCIFColumn([1, 2, 3]).as_array())
+    [1 2 3]
+    >>> mask = [MaskValue.PRESENT, MaskValue.INAPPLICABLE, MaskValue.MISSING]
+    >>> # Mask values are only inserted into string arrays
+    >>> print(BinaryCIFColumn([1, 2, 3], mask).as_array(int))
+    [1 2 3]
+    >>> print(BinaryCIFColumn([1, 2, 3], mask).as_array(str))
+    ['1' '.' '?']
+    >>> print(BinaryCIFColumn([1]).as_item())
+    1
+    >>> print(BinaryCIFColumn([1], mask=[MaskValue.MISSING]).as_item())
+    ?
+    """
+
+    def __init__(self, data, mask=None):
+        if not isinstance(data, BinaryCIFData):
+            data = BinaryCIFData(data)
+        if mask is not None:
+            if not isinstance(mask, BinaryCIFData):
+                mask = BinaryCIFData(mask)
+            if len(data) != len(mask):
+                raise IndexError(
+                    f"Data has length {len(data)}, but mask has length {len(mask)}"
+                )
+        self._data = data
+        self._mask = mask
+
+    @property
+    def data(self):
+        return self._data
+
+    @property
+    def mask(self):
+        return self._mask
+
+    @staticmethod
+    def subcomponent_class():
+        return BinaryCIFData
+
+    @staticmethod
+    def supercomponent_class():
+        return BinaryCIFCategory
+
+    def as_item(self):
+        """
+        Get the only item in the data of this column.
+
+        If the data is masked as inapplicable or missing, ``'.'`` or
+        ``'?'`` is returned, respectively.
+        If the data contains more than one item, an exception is raised.
+
+        Returns
+        -------
+        item : str or int or float
+            The item in the data.
+        """
+        if self._mask is None:
+            return self._data.array.item()
+        mask = self._mask.array.item()
+        if mask is None or mask == MaskValue.PRESENT:
+            return self._data.array.item()
+        elif mask == MaskValue.INAPPLICABLE:
+            return "."
+        elif mask == MaskValue.MISSING:
+            return "?"
+
+    def as_array(self, dtype=None, masked_value=None):
+        """
+        Get the data of this column as an :class:`ndarray`.
+
+        This is a shortcut to get ``BinaryCIFColumn.data.array``.
+        Furthermore, the mask is applied to the data.
+
+        Parameters
+        ----------
+        dtype : dtype-like, optional
+            The data type the array should be converted to.
+            By default, the original type is used.
+        masked_value : str or int or float, optional
+            The value that should be used for masked elements, i.e.
+            ``MaskValue.INAPPLICABLE`` or ``MaskValue.MISSING``.
+            By default, masked elements are converted to ``'.'`` or
+            ``'?'`` depending on the :class:`MaskValue`.
+
+        Returns
+        -------
+        array : ndarray
+            The column data as array.
+        """
+        if dtype is None:
+            dtype = self._data.array.dtype
+
+        if self._mask is None:
+            return self._data.array.astype(dtype, copy=False)
+
+        elif np.issubdtype(dtype, np.str_):
+            # Copy, as otherwise original data would be overwritten
+            # with mask values
+            array = self._data.array.astype(dtype, copy=True)
+            if masked_value is None:
+                array[self._mask.array == MaskValue.INAPPLICABLE] = "."
+                array[self._mask.array == MaskValue.MISSING] = "?"
+            else:
+                array[self._mask.array == MaskValue.INAPPLICABLE] = masked_value
+                array[self._mask.array == MaskValue.MISSING] = masked_value
+            return array
+
+        elif np.dtype(dtype).kind == self._data.array.dtype.kind:
+            if masked_value is None:
+                return self._data.array.astype(dtype, copy=False)
+            else:
+                array = self._data.array.astype(dtype, copy=True)
+                array[self._mask.array == MaskValue.INAPPLICABLE] = masked_value
+                array[self._mask.array == MaskValue.MISSING] = masked_value
+                return array
+
+        else:
+            # Array needs to be converted, but masked values are
+            # not necessarily convertible
+            # (e.g. '.' cannot be converted to int)
+            if masked_value is None:
+                array = np.zeros(len(self._data), dtype=dtype)
+            else:
+                array = np.full(len(self._data), masked_value, dtype=dtype)
+
+            present_mask = self._mask.array == MaskValue.PRESENT
+            array[present_mask] = self._data.array[present_mask].astype(dtype)
+            return array
+
+    @staticmethod
+    def deserialize(content):
+        return BinaryCIFColumn(
+            BinaryCIFData.deserialize(content["data"]),
+            BinaryCIFData.deserialize(content["mask"])
+            if content["mask"] is not None
+            else None,
+        )
+
+    def serialize(self):
+        return {
+            "data": self._data.serialize(),
+            "mask": self._mask.serialize() if self._mask is not None else None,
+        }
+
+    def __len__(self):
+        return len(self._data)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if self._data != other._data:
+            return False
+        if self._mask != other._mask:
+            return False
+        return True
+
+
+class BinaryCIFCategory(_HierarchicalContainer):
+    """
+    This class represents a category in a :class:`BinaryCIFBlock`.
+
+    Columns can be accessed and modified like a dictionary.
+    The values are :class:`BinaryCIFColumn` objects.
+
+    Parameters
+    ----------
+    columns : dict, optional
+        The columns of the category.
+        The keys are the column names and the values are the
+        :class:`BinaryCIFColumn` objects (or objects that can be coerced
+        into a :class:`BinaryCIFColumn`).
+        By default, an empty category is created.
+        Each column must have the same length.
+    row_count : int, optional
+        The number of rows in the category.
+
+    Attributes
+    ----------
+    row_count : int
+        The number of rows in the category, i.e. the length of each
+        column.
+        By default, the row count is determined when the first column is added.
+
+    Examples
+    --------
+
+    >>> # Add column on creation
+    >>> category = BinaryCIFCategory({"fruit": ["apple", "banana"]})
+    >>> # Add column later on
+    >>> category["taste"] = ["delicious", "tasty"]
+    >>> # Add column the formal way
+    >>> category["color"] = BinaryCIFColumn(BinaryCIFData(["red", "yellow"]))
+    >>> # Access a column
+    >>> print(category["fruit"].as_array())
+    ['apple' 'banana']
+    """
+
+    def __init__(self, columns=None, row_count=None):
+        if columns is None:
+            columns = {}
+        else:
+            columns = {
+                key: BinaryCIFColumn(col)
+                if not isinstance(col, (BinaryCIFColumn, dict))
+                else col
+                for key, col in columns.items()
+            }
+
+        self._row_count = row_count
+        super().__init__(columns)
+
+    @property
+    def row_count(self):
+        if self._row_count is None:
+            # Row count is not determined yet
+            # -> check the length of the first column
+            self._row_count = len(next(iter(self.values())))
+        return self._row_count
+
+    @staticmethod
+    def subcomponent_class():
+        return BinaryCIFColumn
+
+    @staticmethod
+    def supercomponent_class():
+        return BinaryCIFBlock
+
+    @staticmethod
+    def deserialize(content):
+        return BinaryCIFCategory(
+            BinaryCIFCategory._deserialize_elements(content["columns"], "name"),
+            content["rowCount"],
+        )
+
+    def serialize(self):
+        if len(self) == 0:
+            raise SerializationError("At least one column is required")
+
+        for column_name, column in self.items():
+            if self._row_count is None:
+                self._row_count = len(column)
+            elif len(column) != self._row_count:
+                raise SerializationError(
+                    f"All columns must have the same length, "
+                    f"but '{column_name}' has length {len(column)}, "
+                    f"while the first column has row_count {self._row_count}"
+                )
+
+        return {
+            "rowCount": self.row_count,
+            "columns": self._serialize_elements("name"),
+        }
+
+    def __setitem__(self, key, element):
+        if not isinstance(element, (BinaryCIFColumn, dict)):
+            element = BinaryCIFColumn(element)
+        super().__setitem__(key, element)
+
+
+class BinaryCIFBlock(_HierarchicalContainer):
+    """
+    This class represents a block in a :class:`BinaryCIFFile`.
+
+    Categories can be accessed and modified like a dictionary.
+    The values are :class:`BinaryCIFCategory` objects.
+
+    Parameters
+    ----------
+    categories : dict, optional
+        The categories of the block.
+        The keys are the category names and the values are the
+        :class:`BinaryCIFCategory` objects.
+        By default, an empty block is created.
+
+    Notes
+    -----
+    The category names do not include the leading underscore character.
+    This character is automatically added when the category is
+    serialized.
+
+    Examples
+    --------
+
+    >>> # Add category on creation
+    >>> block = BinaryCIFBlock({"foo": BinaryCIFCategory({"some_column": 1})})
+    >>> # Add category later on
+    >>> block["bar"] = BinaryCIFCategory({"another_column": [2, 3]})
+    >>> # Access a column
+    >>> print(block["bar"]["another_column"].as_array())
+    [2 3]
+    """
+
+    def __init__(self, categories=None):
+        if categories is None:
+            categories = {}
+        super().__init__(
+            # Actual bcif files use leading '_' as category names
+            {"_" + name: category for name, category in categories.items()}
+        )
+
+    @staticmethod
+    def subcomponent_class():
+        return BinaryCIFCategory
+
+    @staticmethod
+    def supercomponent_class():
+        return BinaryCIFFile
+
+    @staticmethod
+    def deserialize(content):
+        return BinaryCIFBlock(
+            {
+                # The superclass uses leading '_' in category names,
+                # but on the level of this class, the leading '_' is omitted
+                name.lstrip("_"): category
+                for name, category in BinaryCIFBlock._deserialize_elements(
+                    content["categories"], "name"
+                ).items()
+            }
+        )
+
+    def serialize(self):
+        return {"categories": self._serialize_elements("name")}
+
+    def __getitem__(self, key):
+        try:
+            return super().__getitem__("_" + key)
+        except KeyError:
+            raise KeyError(key)
+
+    def __setitem__(self, key, element):
+        try:
+            return super().__setitem__("_" + key, element)
+        except KeyError:
+            raise KeyError(key)
+
+    def __delitem__(self, key):
+        try:
+            return super().__delitem__("_" + key)
+        except KeyError:
+            raise KeyError(key)
+
+    def __iter__(self):
+        return (key.lstrip("_") for key in super().__iter__())
+
+    def __contains__(self, key):
+        return super().__contains__("_" + key)
+
+
+class BinaryCIFFile(File, _HierarchicalContainer):
+    """
+    This class represents a *BinaryCIF* file.
+
+    The categories of the file can be accessed and modified like a
+    dictionary.
+    The values are :class:`BinaryCIFBlock` objects.
+
+    To parse or write a structure from/to a :class:`BinaryCIFFile`
+    object, use the high-level :func:`get_structure()` or
+    :func:`set_structure()` function respectively.
+
+    Parameters
+    ----------
+    blocks : dict (str -> BinaryCIFBlock), optional
+        The initial blocks of the file.
+        Maps the block names to the corresponding :class:`BinaryCIFBlock` objects.
+        By default no initial blocks are added.
+
+    Attributes
+    ----------
+    block : BinaryCIFBlock
+        The sole block of the file.
+        If the file contains multiple blocks, an exception is raised.
+
+    Notes
+    -----
+    The content of *BinaryCIF* files are lazily deserialized:
+    Only when a column is accessed, the time consuming data decoding
+    is performed.
+    The decoded :class:`BinaryCIFBlock`/:class:`BinaryCIFCategory`
+    objects are cached for subsequent accesses.
+
+    Examples
+    --------
+    Read a *BinaryCIF* file and access its content:
+
+    >>> import os.path
+    >>> file = BinaryCIFFile.read(os.path.join(path_to_structures, "1l2y.bcif"))
+    >>> print(file["1L2Y"]["citation_author"]["name"].as_array())
+    ['Neidigh, J.W.' 'Fesinmeyer, R.M.' 'Andersen, N.H.']
+    >>> # Access the only block in the file
+    >>> print(file.block["entity"]["pdbx_description"].as_item())
+    TC5b
+
+    Create a *BinaryCIF* file and write it to disk:
+
+    >>> category = BinaryCIFCategory({"some_column": "some_value"})
+    >>> block = BinaryCIFBlock({"some_category": category})
+    >>> file = BinaryCIFFile({"some_block": block})
+    >>> file.write(os.path.join(path_to_directory, "some_file.bcif"))
+    """
+
+    def __init__(self, blocks=None):
+        File.__init__(self)
+        _HierarchicalContainer.__init__(self, blocks)
+
+    @property
+    def block(self):
+        if len(self) == 0:
+            raise ValueError("There are no blocks in the file")
+        elif len(self) > 1:
+            raise ValueError("There are multiple blocks in the file")
+        else:
+            return self[next(iter(self))]
+
+    @staticmethod
+    def subcomponent_class():
+        return BinaryCIFBlock
+
+    @staticmethod
+    def supercomponent_class():
+        return None
+
+    @staticmethod
+    def deserialize(content):
+        return BinaryCIFFile(
+            BinaryCIFFile._deserialize_elements(content["dataBlocks"], "header")
+        )
+
+    def serialize(self):
+        return {"dataBlocks": self._serialize_elements("header")}
+
+    @classmethod
+    def read(cls, file):
+        """
+        Read a *BinaryCIF* file.
+
+        Parameters
+        ----------
+        file : file-like object or str
+            The file to be read.
+            Alternatively a file path can be supplied.
+
+        Returns
+        -------
+        file_object : BinaryCIFFile
+            The parsed file.
+        """
+        # File name
+        if is_open_compatible(file):
+            with open(file, "rb") as f:
+                return BinaryCIFFile.deserialize(
+                    msgpack.unpackb(f.read(), use_list=True, raw=False)
+                )
+        # File object
+        else:
+            if not is_binary(file):
+                raise TypeError("A file opened in 'binary' mode is required")
+            return BinaryCIFFile.deserialize(
+                msgpack.unpackb(file.read(), use_list=True, raw=False)
+            )
+
+    def write(self, file):
+        """
+        Write contents into a *BinaryCIF* file.
+
+        Parameters
+        ----------
+        file : file-like object or str
+            The file to be written to.
+            Alternatively, a file path can be supplied.
+        """
+        serialized_content = self.serialize()
+        serialized_content["encoder"] = "biotite"
+        serialized_content["version"] = "0.3.0"
+        packed_bytes = msgpack.packb(
+            serialized_content, use_bin_type=True, default=_encode_numpy
+        )
+        if is_open_compatible(file):
+            with open(file, "wb") as f:
+                f.write(packed_bytes)
+        else:
+            if not is_binary(file):
+                raise TypeError("A file opened in 'binary' mode is required")
+            file.write(packed_bytes)
+
+
+def _encode_numpy(item):
+    """
+    Convert NumPy scalar types to native Python types,
+    as *Msgpack* cannot handle NumPy types (e.g. float32).
+
+    The function is given to the Msgpack packer as value for the
+    `default` parameter.
+    """
+    if isinstance(item, np.generic):
+        return item.item()
+    else:
+        raise TypeError(f"can not serialize '{type(item).__name__}' object")