biotite 1.5.0__cp314-cp314-macosx_10_13_x86_64.whl

biotite/structure/io/pdbx/cif.py

@@ -0,0 +1,1091 @@
+# 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__ = ["CIFFile", "CIFBlock", "CIFCategory", "CIFColumn", "CIFData"]
+
+import itertools
+from collections.abc import MutableMapping, Sequence
+import numpy as np
+from biotite.file import (
+    DeserializationError,
+    File,
+    SerializationError,
+    is_open_compatible,
+    is_text,
+)
+from biotite.structure.io.pdbx.component import MaskValue, _Component
+
+UNICODE_CHAR_SIZE = 4
+
+
+# Small class without much functionality
+# It exists merely for consistency with BinaryCIFFile
+class CIFData:
+    """
+    This class represents the data in a :class:`CIFColumn`.
+
+    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.
+    dtype : dtype-like, optional
+        If given, the *dtype* the stored array should be converted to.
+
+    Attributes
+    ----------
+    array : ndarray
+        The stored data array.
+
+    Notes
+    -----
+    When a :class:`CIFFile` is written, the data type is automatically
+    converted to string.
+    The other way around, when a :class:`CIFFile` is read, the data type
+    is always a string type.
+
+    Examples
+    --------
+
+    >>> data = CIFData([1, 2, 3])
+    >>> print(data.array)
+    [1 2 3]
+    >>> print(len(data))
+    3
+    >>> # A single item is converted into an array
+    >>> data = CIFData("apple")
+    >>> print(data.array)
+    ['apple']
+    """
+
+    def __init__(self, array, dtype=None):
+        self._array = _arrayfy(array)
+        if np.issubdtype(self._array.dtype, np.object_):
+            raise ValueError("Object arrays are not supported")
+        if dtype is not None:
+            self._array = self._array.astype(dtype)
+
+    @property
+    def array(self):
+        return self._array
+
+    @staticmethod
+    def subcomponent_class():
+        return None
+
+    @staticmethod
+    def supercomponent_class():
+        return CIFColumn
+
+    def __len__(self):
+        return len(self._array)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        return np.array_equal(self._array, other._array)
+
+
+class CIFColumn:
+    """
+    This class represents a single column in a :class:`CIFCategory`.
+
+    Parameters
+    ----------
+    data : CIFData or array_like or int or float or str
+        The data to be stored.
+        If no :class:`CIFData` is given, the passed argument is
+        coerced into such an object.
+    mask : CIFData 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:`CIFData` is given, the passed argument is
+        coerced into such an object.
+        By default, no mask is created.
+
+    Attributes
+    ----------
+    data : CIFData
+        The stored data.
+    mask : CIFData
+        The mask that indicates whether certain data elements are
+        inapplicable or missing.
+        If no mask is present, this attribute is ``None``.
+
+    Examples
+    --------
+
+    >>> print(CIFColumn([1, 2, 3]).as_array())
+    ['1' '2' '3']
+    >>> mask = [MaskValue.PRESENT, MaskValue.INAPPLICABLE, MaskValue.MISSING]
+    >>> print(CIFColumn([1, 2, 3], mask).as_array())
+    ['1' '.' '?']
+    >>> print(CIFColumn([1]).as_item())
+    1
+    >>> print(CIFColumn([1], mask=[MaskValue.MISSING]).as_item())
+    ?
+    """
+
+    def __init__(self, data, mask=None):
+        if not isinstance(data, CIFData):
+            data = CIFData(data, str)
+        if mask is None:
+            mask = np.full(len(data), MaskValue.PRESENT, dtype=np.uint8)
+            mask[data.array == "."] = MaskValue.INAPPLICABLE
+            mask[data.array == "?"] = MaskValue.MISSING
+            if np.all(mask == MaskValue.PRESENT):
+                # No mask required
+                mask = None
+            else:
+                mask = CIFData(mask)
+        else:
+            if not isinstance(mask, CIFData):
+                mask = CIFData(mask, np.uint8)
+            if len(mask) != len(data):
+                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 CIFData
+
+    @staticmethod
+    def supercomponent_class():
+        return CIFCategory
+
+    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
+            The item in the data.
+        """
+        if self._mask is None:
+            return self._data.array.item()
+        mask = self._mask.array.item()
+        if self._mask is None or mask == MaskValue.PRESENT:
+            item = self._data.array.item()
+            # Limit float precision to 3 decimals
+            if isinstance(item, float):
+                return f"{item:.3f}"
+            else:
+                return str(item)
+        elif mask == MaskValue.INAPPLICABLE:
+            return "."
+        elif mask == MaskValue.MISSING:
+            return "?"
+
+    def as_array(self, dtype=str, masked_value=None):
+        """
+        Get the data of this column as an :class:`ndarray`.
+
+        This is a shortcut to get ``CIFColumn.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, a string type is used.
+        masked_value : str, 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 self._mask is None:
+            return self._data.array.astype(dtype, copy=False)
+
+        elif np.issubdtype(dtype, np.str_):
+            # Limit float precision to 3 decimals
+            if np.issubdtype(self._data.array.dtype, np.floating):
+                array = np.array([f"{e:.3f}" for e in self._data.array], type=dtype)
+            else:
+                # 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
+
+        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
+
+    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 CIFCategory(_Component, MutableMapping):
+    """
+    This class represents a category in a :class:`CIFBlock`.
+
+    Columns can be accessed and modified like a dictionary.
+    The values are :class:`CIFColumn` objects.
+
+    Parameters
+    ----------
+    columns : dict, optional
+        The columns of the category.
+        The keys are the column names and the values are the
+        :class:`CIFColumn` objects (or objects that can be coerced into
+        a :class:`CIFColumn`).
+        By default, an empty category is created.
+        Each column must have the same length.
+    name : str, optional
+        The name of the category.
+        This is only used for serialization and is automatically set,
+        when the :class:`CIFCategory` is added to a :class:`CIFBlock`.
+        It only needs to be set manually, when the category is directly
+        serialized.
+
+    Attributes
+    ----------
+    name : str
+        The name of the category.
+    row_count : int
+        The number of rows in the category, i.e. the length of each
+        column.
+
+    Notes
+    -----
+    When a column containing strings with line breaks are added, these
+    strings are written as multiline strings to the CIF file.
+
+    Examples
+    --------
+
+    >>> # Add column on creation
+    >>> category = CIFCategory({"fruit": ["apple", "banana"]}, name="fruits")
+    >>> # Add column later on
+    >>> category["taste"] = ["delicious", "tasty"]
+    >>> # Add column the formal way
+    >>> category["color"] = CIFColumn(CIFData(["red", "yellow"]))
+    >>> # Access a column
+    >>> print(category["fruit"].as_array())
+    ['apple' 'banana']
+    >>> print(category.serialize())
+    loop_
+    _fruits.fruit
+    _fruits.taste
+    _fruits.color
+    apple  delicious red
+    banana tasty     yellow
+    """
+
+    def __init__(self, columns=None, name=None):
+        self._name = name
+        if columns is None:
+            columns = {}
+        else:
+            columns = {
+                key: CIFColumn(col) if not isinstance(col, CIFColumn) else col
+                for key, col in columns.items()
+            }
+
+        self._row_count = None
+        self._columns = columns
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+
+    @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 CIFColumn
+
+    @staticmethod
+    def supercomponent_class():
+        return CIFBlock
+
+    @staticmethod
+    def deserialize(text):
+        lines = [line.strip() for line in text.splitlines() if not _is_empty(line)]
+
+        if _is_loop_start(lines[0]):
+            is_looped = True
+            lines.pop(0)
+        else:
+            is_looped = False
+
+        category_name = _parse_category_name(lines[0])
+        if category_name is None:
+            raise DeserializationError("Failed to parse category name")
+
+        lines = _to_single(lines)
+        if is_looped:
+            category_dict = CIFCategory._deserialize_looped(lines)
+        else:
+            category_dict = CIFCategory._deserialize_single(lines)
+        return CIFCategory(category_dict, category_name)
+
+    def serialize(self):
+        if self._name is None:
+            raise SerializationError("Category name is required")
+        if not self._columns:
+            raise ValueError("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}"
+                )
+
+        if self._row_count == 0:
+            raise ValueError("At least one row is required")
+        elif self._row_count == 1:
+            lines = self._serialize_single()
+        else:
+            lines = self._serialize_looped()
+        # Enforce terminal line break
+        lines.append("")
+        return "\n".join(lines)
+
+    def __getitem__(self, key):
+        return self._columns[key]
+
+    def __setitem__(self, key, column):
+        if not isinstance(column, CIFColumn):
+            column = CIFColumn(column)
+        self._columns[key] = column
+
+    def __delitem__(self, key):
+        if len(self._columns) == 1:
+            raise ValueError("At least one column must remain")
+        del self._columns[key]
+
+    def __contains__(self, key):
+        return key in self._columns
+
+    def __iter__(self):
+        return iter(self._columns)
+
+    def __len__(self):
+        return len(self._columns)
+
+    def __eq__(self, other):
+        # Row count can be omitted here, as it is based on the columns
+        if not isinstance(other, type(self)):
+            return False
+        if set(self.keys()) != set(other.keys()):
+            return False
+        for col_name in self.keys():
+            if self[col_name] != other[col_name]:
+                return False
+        return True
+
+    @staticmethod
+    def _deserialize_single(lines):
+        """
+        Process a category where each field has a single value.
+        """
+        category_dict = {}
+        line_i = 0
+        while line_i < len(lines):
+            line = lines[line_i]
+            parts = list(_split_one_line(line))
+            if len(parts) == 2:
+                # Standard case -> name and value in one line
+                name_part, value_part = parts
+                line_i += 1
+            elif len(parts) == 1:
+                # Value is a multiline value on the next line
+                name_part = parts[0]
+                parts = list(_split_one_line(lines[line_i + 1]))
+                if len(parts) == 1:
+                    value_part = parts[0]
+                else:
+                    raise DeserializationError(f"Failed to parse line '{line}'")
+                line_i += 2
+            elif len(parts) == 0:
+                raise DeserializationError("Empty line within category")
+            else:
+                raise DeserializationError(f"Failed to parse line '{line}'")
+            category_dict[name_part.split(".")[1]] = CIFColumn(value_part)
+        return category_dict
+
+    @staticmethod
+    def _deserialize_looped(lines):
+        """
+        Process a category where each field has multiple values
+        (category is a table).
+        """
+        category_dict = {}
+        column_names = []
+        i = 0
+        for key_line in lines:
+            if key_line[0] == "_":
+                # Key line
+                key = key_line.split(".")[1]
+                column_names.append(key)
+                category_dict[key] = []
+                i += 1
+            else:
+                break
+
+        data_lines = lines[i:]
+        # Rows may be split over multiple lines -> do not rely on
+        # row-line-alignment at all and simply cycle through columns
+        column_indices = itertools.cycle(range(len(column_names)))
+        for data_line in data_lines:
+            values = _split_one_line(data_line)
+            for val in values:
+                column_index = next(column_indices)
+                column_name = column_names[column_index]
+                category_dict[column_name].append(val)
+
+        # Check if all columns have the same length
+        # Otherwise, this would indicate a parsing error or an invalid CIF file
+        column_index = next(column_indices)
+        if column_index != 0:
+            raise DeserializationError(
+                "Category contains columns with different lengths"
+            )
+
+        return category_dict
+
+    def _serialize_single(self):
+        keys = ["_" + self._name + "." + name for name in self.keys()]
+        max_len = max(len(key) for key in keys)
+        # "+3" Because of three whitespace chars after longest key
+        req_len = max_len + 3
+        return [
+            # Remove potential terminal newlines from multiline values
+            (key.ljust(req_len) + _escape(column.as_item())).strip()
+            for key, column in zip(keys, self.values())
+        ]
+
+    def _serialize_looped(self):
+        key_lines = ["_" + self._name + "." + key + " " for key in self.keys()]
+
+        column_arrays = []
+        for column in self.values():
+            array = column.as_array(str)
+            # Quote before measuring the number of chars,
+            # as the quote characters modify the length
+            array = np.array([_escape(element) for element in array])
+            column_arrays.append(array)
+
+        # Number of characters the longest string in the column needs
+        # This can be deduced from the dtype
+        # The "+1" is for the small whitespace column
+        column_n_chars = [
+            array.dtype.itemsize // UNICODE_CHAR_SIZE + 1 for array in column_arrays
+        ]
+        value_lines = [""] * self._row_count
+        for i in range(self._row_count):
+            for j, array in enumerate(column_arrays):
+                value_lines[i] += array[i].ljust(column_n_chars[j])
+            # Remove trailing justification of last column
+            # and potential terminal newlines from multiline values
+            value_lines[i] = value_lines[i].strip()
+
+        return ["loop_"] + key_lines + value_lines
+
+
+class CIFBlock(_Component, MutableMapping):
+    """
+    This class represents a block in a :class:`CIFFile`.
+
+    Categories can be accessed and modified like a dictionary.
+    The values are :class:`CIFCategory` objects.
+
+    Parameters
+    ----------
+    categories : dict, optional
+        The categories of the block.
+        The keys are the category names and the values are the
+        :class:`CIFCategory` objects.
+        By default, an empty block is created.
+    name : str, optional
+        The name of the block.
+        This is only used for serialization and is automatically set,
+        when the :class:`CIFBlock` is added to a :class:`CIFFile`.
+        It only needs to be set manually, when the block is directly
+        serialized.
+
+    Attributes
+    ----------
+    name : str
+        The name of the block.
+
+    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 = CIFBlock({"foo": CIFCategory({"some_column": 1})}, name="baz")
+    >>> # Add category later on
+    >>> block["bar"] = CIFCategory({"another_column": [2, 3]})
+    >>> # Access a column
+    >>> print(block["bar"]["another_column"].as_array())
+    ['2' '3']
+    >>> print(block.serialize())
+    data_baz
+    #
+    _foo.some_column   1
+    #
+    loop_
+    _bar.another_column
+    2
+    3
+    #
+    """
+
+    def __init__(self, categories=None, name=None):
+        self._name = name
+        if categories is None:
+            categories = {}
+        self._categories = categories
+
+    @property
+    def name(self):
+        return self._name
+
+    @name.setter
+    def name(self, name):
+        self._name = name
+
+    @staticmethod
+    def subcomponent_class():
+        return CIFCategory
+
+    @staticmethod
+    def supercomponent_class():
+        return CIFFile
+
+    @staticmethod
+    def deserialize(text):
+        lines = text.splitlines()
+        current_category_name = None
+        category_starts = []
+        category_names = []
+        for i, line in enumerate(lines):
+            if not _is_empty(line):
+                is_loop_in_line = _is_loop_start(line)
+                category_name_in_line = _parse_category_name(line)
+                if is_loop_in_line or (
+                    category_name_in_line != current_category_name
+                    and category_name_in_line is not None
+                ):
+                    # Track the new category
+                    if is_loop_in_line:
+                        # In case of lines with "loop_" the category is
+                        # in the next line
+                        category_name_in_line = _parse_category_name(lines[i + 1])
+                    current_category_name = category_name_in_line
+                    category_starts.append(i)
+                    category_names.append(current_category_name)
+        return CIFBlock(_create_element_dict(lines, category_names, category_starts))
+
+    def serialize(self):
+        if self._name is None:
+            raise SerializationError("Block name is required")
+        # The block starts with the black name line followed by a comment line
+        text_blocks = ["data_" + self._name + "\n#\n"]
+        for category_name, category in self._categories.items():
+            if isinstance(category, str):
+                # Category is already stored as lines
+                text_blocks.append(category)
+            else:
+                try:
+                    category.name = category_name
+                    text_blocks.append(category.serialize())
+                except Exception:
+                    raise SerializationError(
+                        f"Failed to serialize category '{category_name}'"
+                    )
+                # A comment line is set after each category
+                text_blocks.append("#\n")
+        return "".join(text_blocks)
+
+    def __getitem__(self, key):
+        category = self._categories[key]
+        if isinstance(category, str):
+            # Element is stored in serialized form
+            # -> must be deserialized first
+            try:
+                category = CIFCategory.deserialize(category)
+            except Exception:
+                raise DeserializationError(f"Failed to deserialize category '{key}'")
+            # Update with deserialized object
+            self._categories[key] = category
+        return category
+
+    def __setitem__(self, key, category):
+        if not isinstance(category, CIFCategory):
+            raise TypeError(
+                f"Expected 'CIFCategory', but got '{type(category).__name__}'"
+            )
+        category.name = key
+        self._categories[key] = category
+
+    def __delitem__(self, key):
+        del self._categories[key]
+
+    def __contains__(self, key):
+        return key in self._categories
+
+    def __iter__(self):
+        return iter(self._categories)
+
+    def __len__(self):
+        return len(self._categories)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if set(self.keys()) != set(other.keys()):
+            return False
+        for cat_name in self.keys():
+            if self[cat_name] != other[cat_name]:
+                return False
+        return True
+
+
+class CIFFile(_Component, File, MutableMapping):
+    """
+    This class represents a CIF file.
+
+    The categories of the file can be accessed and modified like a
+    dictionary.
+    The values are :class:`CIFBlock` objects.
+
+    To parse or write a structure from/to a :class:`CIFFile` object,
+    use the high-level :func:`get_structure()` or
+    :func:`set_structure()` function respectively.
+
+    Parameters
+    ----------
+    blocks : dict (str -> CIFBlock), optional
+        The initial blocks of the file.
+        Maps the block names to the corresponding :class:`CIFBlock` objects.
+        By default no initial blocks are added.
+
+    Attributes
+    ----------
+    block : CIFBlock
+        The sole block of the file.
+        If the file contains multiple blocks, an exception is raised.
+
+    Notes
+    -----
+    The content of CIF files are lazily deserialized:
+    When reading the file only the line positions of all blocks are
+    indexed.
+    The time consuming deserialization of a block/category is only
+    performed when accessed.
+    The deserialized :class:`CIFBlock`/:class:`CIFCategory` objects
+    are cached for subsequent accesses.
+
+    Examples
+    --------
+    Read a CIF file and access its content:
+
+    >>> import os.path
+    >>> file = CIFFile.read(os.path.join(path_to_structures, "1l2y.cif"))
+    >>> 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 CIF file and write it to disk:
+
+    >>> category = CIFCategory(
+    ...     {"some_column": "some_value", "another_column": "another_value"}
+    ... )
+    >>> block = CIFBlock({"some_category": category, "another_category": category})
+    >>> file = CIFFile({"some_block": block, "another_block": block})
+    >>> print(file.serialize())
+    data_some_block
+    #
+    _some_category.some_column      some_value
+    _some_category.another_column   another_value
+    #
+    _another_category.some_column      some_value
+    _another_category.another_column   another_value
+    #
+    data_another_block
+    #
+    _some_category.some_column      some_value
+    _some_category.another_column   another_value
+    #
+    _another_category.some_column      some_value
+    _another_category.another_column   another_value
+    #
+    >>> file.write(os.path.join(path_to_directory, "some_file.cif"))
+    """
+
+    def __init__(self, blocks=None):
+        if blocks is None:
+            blocks = {}
+        self._blocks = blocks
+
+    @property
+    def lines(self):
+        return self.serialize().splitlines()
+
+    @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 CIFBlock
+
+    @staticmethod
+    def supercomponent_class():
+        return None
+
+    @staticmethod
+    def deserialize(text):
+        lines = text.splitlines()
+        block_starts = []
+        block_names = []
+        for i, line in enumerate(lines):
+            if not _is_empty(line):
+                data_block_name = _parse_data_block_name(line)
+                if data_block_name is not None:
+                    block_starts.append(i)
+                    block_names.append(data_block_name)
+        return CIFFile(_create_element_dict(lines, block_names, block_starts))
+
+    def serialize(self):
+        text_blocks = []
+        for block_name, block in self._blocks.items():
+            if isinstance(block, str):
+                # Block is already stored as text
+                text_blocks.append(block)
+            else:
+                try:
+                    block.name = block_name
+                    text_blocks.append(block.serialize())
+                except Exception:
+                    raise SerializationError(
+                        f"Failed to serialize block '{block_name}'"
+                    )
+        # Enforce terminal line break
+        text_blocks.append("")
+        return "".join(text_blocks)
+
+    @classmethod
+    def read(cls, file):
+        """
+        Read a CIF file.
+
+        Parameters
+        ----------
+        file : file-like object or str
+            The file to be read.
+            Alternatively a file path can be supplied.
+
+        Returns
+        -------
+        file_object : CIFFile
+            The parsed file.
+        """
+        # File name
+        if is_open_compatible(file):
+            with open(file, "r") as f:
+                text = f.read()
+        # File object
+        else:
+            if not is_text(file):
+                raise TypeError("A file opened in 'text' mode is required")
+            text = file.read()
+        return CIFFile.deserialize(text)
+
+    def write(self, file):
+        """
+        Write the contents of this object into a CIF file.
+
+        Parameters
+        ----------
+        file : file-like object or str
+            The file to be written to.
+            Alternatively a file path can be supplied.
+        """
+        if is_open_compatible(file):
+            with open(file, "w") as f:
+                f.write(self.serialize())
+        else:
+            if not is_text(file):
+                raise TypeError("A file opened in 'text' mode is required")
+            file.write(self.serialize())
+
+    def __getitem__(self, key):
+        block = self._blocks[key]
+        if isinstance(block, str):
+            # Element is stored in serialized form
+            # -> must be deserialized first
+            try:
+                block = CIFBlock.deserialize(block)
+            except Exception:
+                raise DeserializationError(f"Failed to deserialize block '{key}'")
+            block.name = key
+            # Update with deserialized object
+            self._blocks[key] = block
+        return block
+
+    def __setitem__(self, key, block):
+        if not isinstance(block, CIFBlock):
+            raise TypeError(f"Expected 'CIFBlock', but got '{type(block).__name__}'")
+        block.name = key
+        self._blocks[key] = block
+
+    def __delitem__(self, key):
+        del self._blocks[key]
+
+    def __contains__(self, key):
+        return key in self._blocks
+
+    def __iter__(self):
+        return iter(self._blocks)
+
+    def __len__(self):
+        return len(self._blocks)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if set(self.keys()) != set(other.keys()):
+            return False
+        for block_name in self.keys():
+            if self[block_name] != other[block_name]:
+                return False
+        return True
+
+
+def _is_empty(line):
+    return len(line.strip()) == 0 or line[0] == "#"
+
+
+def _create_element_dict(lines, element_names, element_starts):
+    """
+    Create a dict mapping the `element_names` to the corresponding
+    `lines`, which are located between ``element_starts[i]`` and
+    ``element_starts[i+1]``.
+    """
+    # Add exclusive stop to indices for easier slicing
+    element_starts.append(len(lines))
+    # Lazy deserialization
+    # -> keep as text for now and deserialize later if needed
+    return {
+        element_name: "\n".join(lines[element_starts[i] : element_starts[i + 1]]) + "\n"
+        for i, element_name in enumerate(element_names)
+    }
+
+
+def _parse_data_block_name(line):
+    """
+    If the line defines a data block, return this name.
+    Return ``None`` otherwise.
+    """
+    if line.startswith("data_"):
+        return line[5:]
+    else:
+        return None
+
+
+def _parse_category_name(line):
+    """
+    If the line defines a category, return this name.
+    Return ``None`` otherwise.
+    """
+    if line[0] != "_":
+        return None
+    else:
+        return line[1 : line.find(".")]
+
+
+def _is_loop_start(line):
+    """
+    Return whether the line starts a looped category.
+    """
+    return line.startswith("loop_")
+
+
+def _to_single(lines):
+    r"""
+    Convert multiline values into singleline values
+    (in terms of 'lines' list elements).
+    Linebreaks are preserved as ``'\n'`` characters within a list element.
+    The initial ``';'`` character is also preserved, while the final ``';'`` character
+    is removed.
+    """
+    processed_lines = []
+    in_multi_line = False
+    mutli_line_value = []
+    for line in lines:
+        # Multiline value are enclosed by ';' at the start of the beginning and end line
+        if line[0] == ";":
+            if not in_multi_line:
+                # Start of multiline value
+                in_multi_line = True
+                mutli_line_value.append(line)
+            else:
+                # End of multiline value
+                in_multi_line = False
+                # The current line contains only the end character ';'
+                # Hence this line is not added to the processed lines
+                processed_lines.append("\n".join(mutli_line_value))
+                mutli_line_value = []
+        else:
+            if in_multi_line:
+                mutli_line_value.append(line)
+            else:
+                processed_lines.append(line)
+    return processed_lines
+
+
+def _escape(value):
+    """
+    Escape special characters in a value to make it compatible with CIF.
+    """
+    if "\n" in value:
+        # A value with linebreaks must be represented as multiline value
+        return _multiline(value)
+    elif "'" in value and '"' in value:
+        # If both quote types are present, you cannot use them for escaping
+        return _multiline(value)
+    elif len(value) == 0:
+        return "''"
+    elif value[0] == "_":
+        return "'" + value + "'"
+    elif "'" in value:
+        return '"' + value + '"'
+    elif '"' in value:
+        return "'" + value + "'"
+    elif " " in value:
+        return "'" + value + "'"
+    elif "\t" in value:
+        return "'" + value + "'"
+    else:
+        return value
+
+
+def _multiline(value):
+    """
+    Convert a string that may contain linebreaks into CIF-compatible
+    multiline string.
+    """
+    return "\n;" + value + "\n;\n"
+
+
+def _split_one_line(line):
+    """
+    Split a line into its fields.
+    Supporting embedded quotes (' or "), like `'a dog's life'` to  `a dog's life`
+    """
+    # Special case of multiline value, where the line starts with ';'
+    if line[0] == ";":
+        yield line[1:]
+    elif "'" in line or '"' in line:
+        # Quoted values in the line
+        while line:
+            # Strip leading whitespace(s)
+            stripped_line = line.lstrip()
+            # Split the line on whitespace
+            word, _, line = stripped_line.partition(" ")
+            # Handle the case where the word start with a quote
+            if word.startswith(("'", '"')):
+                # Set the separator to the quote found
+                separator = word[0]
+                # Handle the case of a quoted word without space
+                if word.endswith(separator) and len(word) > 1:
+                    # Yield the word without the opening and closing quotes
+                    yield word[1:-1]
+                    continue
+                # split the word on the separator
+                word, _, line = stripped_line[1:].partition(separator)
+
+            yield word
+    else:
+        # No quoted values in the line -> simple whitespace split
+        for line in line.split():
+            yield line
+
+
+def _arrayfy(data):
+    if not isinstance(data, (Sequence, np.ndarray)) or isinstance(data, str):
+        data = [data]
+    elif len(data) == 0:
+        raise ValueError("Array must contain at least one element")
+    return np.asarray(data)