biotite 0.41.1__cp310-cp310-macosx_10_16_x86_64.whl

biotite/structure/io/mol/sdf.py

@@ -0,0 +1,916 @@
+# 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.mol"
+__author__ = "Patrick Kunzmann, Benjamin Mayer"
+__all__ = ["SDFile", "SDRecord", "Metadata"]
+
+import re
+import warnings
+from dataclasses import dataclass
+from collections.abc import MutableMapping, Mapping
+import numpy as np
+from ....file import File, InvalidFileError, is_open_compatible, is_text, \
+                     DeserializationError, SerializationError
+from .ctab import read_structure_from_ctab, write_structure_to_ctab
+from .header import Header
+from ...atoms import AtomArray
+from ...bonds import BondList, BondType
+
+
+_N_HEADER = 3
+# Number of header lines
+_RECORD_DELIMITER = "$$$$"
+
+
+class Metadata(MutableMapping):
+    r"""
+    Additional nonstructural data in an SD record.
+
+    The metadata is stored as key-value pairs.
+    As SDF allows multiple different identifiers for keys,
+    the keys are represented by :class:`Metadata.Key`.
+
+    Parameters
+    ----------
+    metadata : dict, optional
+        The metadata as key-value pairs.
+        Keys are instances of :class:`Metadata.Key`.
+        Alternatively, keys can be given as strings, in which case the
+        string is used as the :attr:`Metadata.Key.name`.
+        Values are strings.
+        Line breaks in values are allowed.
+
+    Notes
+    -----
+    Key names may only contain alphanumeric characters, underscores and
+    periods.
+
+    Examples
+    --------
+
+    >>> metadata = Metadata({
+    ...     "foo": "Lorem ipsum",
+    ...     Metadata.Key(number=42, name="bar"): "dolor sit amet,\nconsectetur"
+    ... })
+    >>> print(metadata)
+    > <foo>
+    Lorem ipsum
+    <BLANKLINE>
+    > DT42 <bar>
+    dolor sit amet,
+    consectetur
+    <BLANKLINE>
+    >>> print(metadata["foo"])
+    Lorem ipsum
+    >>> # Strings can be only used for access, if the key contains only a name
+    >>> print("bar" in metadata)
+    False
+    >>> print(metadata[Metadata.Key(number=42, name="bar")])
+    dolor sit amet,
+    consectetur
+
+    """
+
+    @dataclass(frozen=True, kw_only=True)
+    class Key:
+        """
+        A metadata key.
+
+        Parameters
+        ----------
+        number : int, optional
+            number of the field in the database.
+        name : str, optional
+            Name of the field.
+            May only contain alphanumeric characters, underscores and
+            periods.
+        registry_internal : int, optional
+            Internal registry number.
+        registry_external : str, optional
+            External registry number.
+
+        Attributes
+        ----------
+        number, name, registry_internal, registry_external
+            The same as the parameters.
+        """
+        # The characters that can be given as input to `name`
+        # First character must be alphanumeric,
+        # following characters may include underscores and periods
+        # Although the V3000 specification forbids the use of periods,
+        # they are still used in practice and therefore allowed here
+        _NAME_INPUT_REGEX = re.compile(r"^[a-zA-Z0-9][\w.]*$")
+        # These regexes are used to parse the key from a line
+        _COMPONENT_REGEX =  {
+            "number": re.compile(r"^DT(\d+)$"),
+            "name": re.compile(r"^<([a-zA-Z0-9][\w.]*)>$"),
+            "registry_internal": re.compile(r"^(\d+)$"),
+            "registry_external": re.compile(r"^\(([\w.-]*)\)$"),
+        }
+
+        number: ... = None
+        name: ... = None
+        registry_internal: ... = None
+        registry_external: ... = None
+
+        def __post_init__(self):
+            if self.name is None and self.number is None:
+                raise ValueError("At least the field number or name must be set")
+            if self.name is not None:
+                if not Metadata.Key._NAME_INPUT_REGEX.match(self.name):
+                    raise ValueError(
+                        f"Invalid name '{self.name}', must only contains "
+                        "alphanumeric characters, underscores and periods"
+                    )
+            if self.number is not None:
+                # Cannot set field directly as 'frozen=True'
+                object.__setattr__(self, "number", int(self.number))
+            if self.registry_internal is not None:
+                object.__setattr__(
+                    self, "registry_internal", int(self.registry_internal)
+                )
+
+        @staticmethod
+        def deserialize(text):
+            """
+            Create an object by deserializing the given text content.
+
+            Parameters
+            ----------
+            content : str
+                The content to be deserialized.
+            """
+            # Omit the leading '>'
+            key_components = text[1:].split()
+            parsed_component_dict = {}
+            for component in key_components:
+                # For each component in each the key,
+                # try to match it with each of the regexes
+                for attr_name, regex in Metadata.Key._COMPONENT_REGEX.items():
+                    pattern_match = regex.match(component)
+                    if pattern_match is None:
+                        # Try next pattern
+                        continue
+                    if attr_name in parsed_component_dict:
+                        raise DeserializationError(
+                            f"Duplicate key component for '{attr_name}'"
+                        )
+                    value = pattern_match.group(1)
+                    parsed_component_dict[attr_name] = value
+                    break
+                else:
+                    # There is no matching pattern
+                    raise DeserializationError(
+                        f"Invalid key component '{component}'"
+                    )
+            return Metadata.Key(**parsed_component_dict)
+
+        def serialize(self):
+            """
+            Convert this object into text content.
+
+            Returns
+            -------
+            content : str
+                The serialized content.
+            """
+            key_string = "> "
+            if self.number is not None:
+                key_string += f"DT{self.number} "
+            if self.name is not None:
+                key_string += f"<{self.name}> "
+            if self.registry_internal is not None:
+                key_string += f"{self.registry_internal} "
+            if self.registry_external is not None:
+                key_string += f"({self.registry_external}) "
+            return key_string
+
+        def __str__(self):
+            return self.serialize()
+
+
+    def __init__(self, metadata=None):
+        if metadata is None:
+            metadata = {}
+        self._metadata = {}
+        for key, value in metadata.items():
+            self._metadata[_to_metadata_key(key)] = value
+
+    @staticmethod
+    def deserialize(text):
+        """
+        Create an object by deserializing the given text content.
+
+        Parameters
+        ----------
+        content : str
+            The content to be deserialized.
+        """
+        metadata = {}
+        current_key = None
+        current_value = None
+        for line in text.splitlines():
+            line = line.strip()
+            if len(line) == 0:
+                # Skip empty lines
+                continue
+            if line.startswith(">"):
+                _add_key_value_pair(metadata, current_key, current_value)
+                current_key = Metadata.Key.deserialize(line)
+                current_value = None
+            else:
+                if current_key is None:
+                    raise DeserializationError(
+                        "Value found before metadata key"
+                    )
+                if current_value is None:
+                    current_value = line
+                else:
+                    current_value += "\n" + line
+        # Add final pair
+        _add_key_value_pair(metadata, current_key, current_value)
+        return Metadata(metadata)
+
+    def serialize(self):
+        """
+        Convert this object into text content.
+
+        Returns
+        -------
+        content : str
+            The serialized content.
+        """
+        text_blocks = []
+        for key, value in self._metadata.items():
+            text_blocks.append(key.serialize())
+            # Add empty line after value
+            text_blocks.append(value + "\n")
+        return _join_with_terminal_newline(text_blocks)
+
+    def __getitem__(self, key):
+        return self._metadata[_to_metadata_key(key)]
+
+    def __setitem__(self, key, value):
+        if len(value) == 0:
+            raise ValueError("Metadata value must not be empty")
+        self._metadata[_to_metadata_key(key)] = value
+
+    def __delitem__(self, key):
+        del self._metadata[_to_metadata_key(key)]
+
+    def __iter__(self):
+        return iter(self._metadata)
+
+    def __len__(self):
+        return len(self._metadata)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if set(self.keys()) != set(other.keys()):
+            return False
+        for key in self.keys():
+            if self[key] != other[key]:
+                return False
+        return True
+
+    def __str__(self):
+        return self.serialize()
+
+
+class SDRecord:
+    """
+    A record in a SD file.
+
+    Parameters
+    ----------
+    header : Header, optional
+        The header of the record.
+        By default, an empty header is created.
+    ctab : str, optional
+        The connection table (atoms and bonds) in the record.
+        By default, an empty structure is created.
+    metadata : Metadata, Mapping or str, optional
+        The metadata of the record.
+        Can be given as dictionary mapping :attr:`Metadata.Key.name`
+        to the respective metadata value.
+        By default, no metadata is appended to the record.
+
+    Attributes
+    ----------
+    header, ctab, metadata
+        The same as the parameters.
+
+    Examples
+    --------
+
+    >>> atoms = residue("ALA")
+    >>> record = SDRecord(header=Header(mol_name="ALA", dimensions="3D"))
+    >>> record.set_structure(atoms)
+    >>> print(record.get_structure())
+            0             N        -0.970    0.490    1.500
+            0             C         0.260    0.420    0.690
+            0             C        -0.090    0.020   -0.720
+            0             O        -1.060   -0.680   -0.920
+            0             C         1.200   -0.620    1.300
+            0             O         0.660    0.440   -1.740
+            0             H        -1.380   -0.420    1.480
+            0             H        -0.680    0.660    2.450
+            0             H         0.750    1.390    0.680
+            0             H         1.460   -0.330    2.320
+            0             H         0.720   -1.590    1.310
+            0             H         2.110   -0.680    0.700
+            0             H         0.440    0.180   -2.650
+    >>> # Add the record to an SD file
+    >>> file = SDFile()
+    >>> file["ALA"] = record
+    >>> print(file)
+    ALA
+                        3D
+    <BLANKLINE>
+     13 12  0     0  0  0  0  0  0  1 V2000
+       -0.9700    0.4900    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
+        0.2600    0.4200    0.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0900    0.0200   -0.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.0600   -0.6800   -0.9200 O   0  0  0  0  0  0  0  0  0  0  0  0
+        1.2000   -0.6200    1.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.6600    0.4400   -1.7400 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3800   -0.4200    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.6800    0.6600    2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7500    1.3900    0.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.4600   -0.3300    2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7200   -1.5900    1.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
+        2.1100   -0.6800    0.7000 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4400    0.1800   -2.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
+      1  2  1  0  0  0  0
+      1  7  1  0  0  0  0
+      1  8  1  0  0  0  0
+      2  3  1  0  0  0  0
+      2  5  1  0  0  0  0
+      2  9  1  0  0  0  0
+      3  4  2  0  0  0  0
+      3  6  1  0  0  0  0
+      5 10  1  0  0  0  0
+      5 11  1  0  0  0  0
+      5 12  1  0  0  0  0
+      6 13  1  0  0  0  0
+    M  END
+    $$$$
+    """
+
+    def __init__(self, header=None, ctab=None, metadata=None):
+        if header is None:
+            self._header = Header()
+        else:
+            self._header = header
+
+        self._ctab = ctab
+
+        if metadata is None:
+            self._metadata = Metadata()
+        elif isinstance(metadata, Metadata):
+            self._metadata = metadata
+        elif isinstance(metadata, Mapping):
+            self._metadata = Metadata(metadata)
+        elif isinstance(metadata, str):
+            # Serialized form -> will be lazily deserialized
+            self._metadata = metadata
+        else:
+            raise TypeError(
+                "Expected 'Metadata', Mapping or str, "
+                f"but got '{type(metadata).__name__}'"
+            )
+
+    @property
+    def header(self):
+        if isinstance(self._header, str):
+            try:
+                self._header = Header.deserialize(self._header)
+            except:
+                raise DeserializationError("Failed to deserialize header")
+        return self._header
+
+    @header.setter
+    def header(self, header):
+        self._header = header
+
+    @property
+    def ctab(self):
+        # CTAB string cannot be changed directly -> no setter
+        return self._ctab
+
+    @property
+    def metadata(self):
+        if isinstance(self._metadata, str):
+            try:
+                self._metadata = Metadata.deserialize(self._metadata)
+            except:
+                raise DeserializationError("Failed to deserialize metadata")
+        return self._metadata
+
+    @metadata.setter
+    def metadata(self, metadata):
+        if isinstance(metadata, Metadata):
+            self._metadata = metadata
+        elif isinstance(metadata, Mapping):
+            self._metadata = Metadata(metadata)
+        else:
+            raise TypeError(
+                "Expected 'Metadata' or Mapping, "
+                f"but got '{type(metadata).__name__}'"
+            )
+
+    @staticmethod
+    def deserialize(text):
+        """
+        Create an object by deserializing the given text content.
+
+        Parameters
+        ----------
+        content : str
+            The content to be deserialized.
+        """
+        lines = text.splitlines()
+        ctab_end = _get_ctab_stop(lines)
+
+        header = _join_with_terminal_newline(lines[:_N_HEADER])
+        ctab = _join_with_terminal_newline(lines[_N_HEADER:ctab_end])
+        metadata = _join_with_terminal_newline(lines[ctab_end:])
+        return SDRecord(header, ctab, metadata)
+
+    def serialize(self):
+        """
+        Convert this object into text content.
+
+        Returns
+        -------
+        content : str
+            The serialized content.
+        """
+        if isinstance(self._header, str):
+            header_string = self._header
+        else:
+            header_string = self._header.serialize()
+
+        if self._ctab is None:
+            ctab_string = _empty_ctab()
+        else:
+            ctab_string = self._ctab
+
+        if isinstance(self._metadata, str):
+            metadata_string = self._metadata
+        else:
+            metadata_string = self._metadata.serialize()
+
+        return header_string + ctab_string + metadata_string
+
+    def get_structure(self):
+        """
+        Parse the structural data in the SD record.
+
+        Returns
+        -------
+        array : AtomArray
+            This :class:`AtomArray` contains the optional ``charge``
+            annotation and has an associated :class:`BondList`.
+            All other annotation categories, except ``element`` are
+            empty.
+        """
+        ctab_lines = self._ctab.splitlines()
+        if len(ctab_lines) == 0:
+            raise InvalidFileError("File does not contain structure data")
+        return read_structure_from_ctab(ctab_lines)
+
+    def set_structure(self, atoms, default_bond_type=BondType.ANY,
+                      version=None):
+        """
+        Set the structural data in the SD record.
+
+        Parameters
+        ----------
+        array : AtomArray
+            The array to be saved into this file.
+            Must have an associated :class:`BondList`.
+        default_bond_type : BondType, optional
+            Bond type fallback for the *Bond block*, if a
+            :class:`BondType` has no CTAB counterpart.
+            By default, each such bond is treated as
+            :attr:`BondType.ANY`.
+        version : {"V2000", "V3000"}, optional
+            The version of the CTAB format.
+            ``"V2000"`` uses the *Atom* and *Bond* block, while
+            ``"V3000"`` uses the *Properties* block.
+            By default, ``"V2000"`` is used, unless the number of atoms
+            or bonds exceeds 999, in which case ``"V3000"`` is used.
+        """
+        self._ctab = _join_with_terminal_newline(write_structure_to_ctab(
+            atoms, default_bond_type, version
+        ))
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if not self.header == other.header:
+            return False
+        if not self.ctab == other.ctab:
+            return False
+        if not self.metadata == other.metadata:
+            return False
+        return True
+
+    def __str__(self):
+        return self.serialize()
+
+
+class SDFile(File, MutableMapping):
+    """
+    This class represents an SD file for storing small molecule
+    structures.
+
+    The records for each molecule in the file can be accessed and
+    modified like a dictionary.
+    The structures can be parsed and written from/to each
+    :class:`SDRecord` object via :func:`get_structure()` or
+    :func:`set_structure()`, respectively.
+
+    Attributes
+    ----------
+    record : CIFBlock
+        The sole record of the file.
+        If the file contains multiple blocks, an exception is raised.
+
+    Examples
+    --------
+    Read a SD file and parse the molecular structure:
+
+    >>> import os.path
+    >>> file = SDFile.read(os.path.join(path_to_structures, "molecules", "TYR.sdf"))
+    >>> molecule = file.record.get_structure()
+    >>> print(molecule)
+            0             N         1.320    0.952    1.428
+            0             C        -0.018    0.429    1.734
+            0             C        -0.103    0.094    3.201
+            0             O         0.886   -0.254    3.799
+            0             C        -0.274   -0.831    0.907
+            0             C        -0.189   -0.496   -0.559
+            0             C         1.022   -0.589   -1.219
+            0             C        -1.324   -0.102   -1.244
+            0             C         1.103   -0.282   -2.563
+            0             C        -1.247    0.210   -2.587
+            0             C        -0.032    0.118   -3.252
+            0             O         0.044    0.420   -4.574
+            0             O        -1.279    0.184    3.842
+            0             H         1.977    0.225    1.669
+            0             H         1.365    1.063    0.426
+            0             H        -0.767    1.183    1.489
+            0             H         0.473   -1.585    1.152
+            0             H        -1.268   -1.219    1.134
+            0             H         1.905   -0.902   -0.683
+            0             H        -2.269   -0.031   -0.727
+            0             H         2.049   -0.354   -3.078
+            0             H        -2.132    0.523   -3.121
+            0             H        -0.123   -0.399   -5.059
+            0             H        -1.333   -0.030    4.784
+
+    Note that important atom annotations may be missing.
+    These can be set afterwards:
+
+    >>> molecule.res_name[:] = "TYR"
+    >>> molecule.atom_name[:] = create_atom_names(molecule)
+    >>> print(molecule)
+            0  TYR N1     N         1.320    0.952    1.428
+            0  TYR C1     C        -0.018    0.429    1.734
+            0  TYR C2     C        -0.103    0.094    3.201
+            0  TYR O1     O         0.886   -0.254    3.799
+            0  TYR C3     C        -0.274   -0.831    0.907
+            0  TYR C4     C        -0.189   -0.496   -0.559
+            0  TYR C5     C         1.022   -0.589   -1.219
+            0  TYR C6     C        -1.324   -0.102   -1.244
+            0  TYR C7     C         1.103   -0.282   -2.563
+            0  TYR C8     C        -1.247    0.210   -2.587
+            0  TYR C9     C        -0.032    0.118   -3.252
+            0  TYR O2     O         0.044    0.420   -4.574
+            0  TYR O3     O        -1.279    0.184    3.842
+            0  TYR H1     H         1.977    0.225    1.669
+            0  TYR H2     H         1.365    1.063    0.426
+            0  TYR H3     H        -0.767    1.183    1.489
+            0  TYR H4     H         0.473   -1.585    1.152
+            0  TYR H5     H        -1.268   -1.219    1.134
+            0  TYR H6     H         1.905   -0.902   -0.683
+            0  TYR H7     H        -2.269   -0.031   -0.727
+            0  TYR H8     H         2.049   -0.354   -3.078
+            0  TYR H9     H        -2.132    0.523   -3.121
+            0  TYR H10    H        -0.123   -0.399   -5.059
+            0  TYR H11    H        -1.333   -0.030    4.784
+
+    Create a SD file and write it to disk:
+
+    >>> another_molecule = residue("ALA")
+    >>> file = SDFile()
+    >>> record = SDRecord()
+    >>> record.set_structure(molecule)
+    >>> file["TYR"] = record
+    >>> record = SDRecord()
+    >>> record.set_structure(another_molecule)
+    >>> file["ALA"] = record
+    >>> file.write(os.path.join(path_to_directory, "some_file.cif"))
+    >>> print(file)
+    TYR
+    <BLANKLINE>
+    <BLANKLINE>
+     24 24  0     0  0  0  0  0  0  1 V2000
+        1.3200    0.9520    1.4280 N   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0180    0.4290    1.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.1030    0.0940    3.2010 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.8860   -0.2540    3.7990 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.2740   -0.8310    0.9070 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.1890   -0.4960   -0.5590 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1.0220   -0.5890   -1.2190 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3240   -0.1020   -1.2440 C   0  0  0  0  0  0  0  0  0  0  0  0
+        1.1030   -0.2820   -2.5630 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.2470    0.2100   -2.5870 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0320    0.1180   -3.2520 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.0440    0.4200   -4.5740 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.2790    0.1840    3.8420 O   0  0  0  0  0  0  0  0  0  0  0  0
+        1.9770    0.2250    1.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.3650    1.0630    0.4260 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.7670    1.1830    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4730   -1.5850    1.1520 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.2680   -1.2190    1.1340 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.9050   -0.9020   -0.6830 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.2690   -0.0310   -0.7270 H   0  0  0  0  0  0  0  0  0  0  0  0
+        2.0490   -0.3540   -3.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -2.1320    0.5230   -3.1210 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.1230   -0.3990   -5.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3330   -0.0300    4.7840 H   0  0  0  0  0  0  0  0  0  0  0  0
+      1  2  1  0  0  0  0
+      1 14  1  0  0  0  0
+      1 15  1  0  0  0  0
+      2  3  1  0  0  0  0
+      2  5  1  0  0  0  0
+      2 16  1  0  0  0  0
+      3  4  2  0  0  0  0
+      3 13  1  0  0  0  0
+      5  6  1  0  0  0  0
+      5 17  1  0  0  0  0
+      5 18  1  0  0  0  0
+      6  7  2  0  0  0  0
+      6  8  1  0  0  0  0
+      7  9  1  0  0  0  0
+      7 19  1  0  0  0  0
+      8 10  2  0  0  0  0
+      8 20  1  0  0  0  0
+      9 11  2  0  0  0  0
+      9 21  1  0  0  0  0
+     10 11  1  0  0  0  0
+     10 22  1  0  0  0  0
+     11 12  1  0  0  0  0
+     12 23  1  0  0  0  0
+     13 24  1  0  0  0  0
+    M  END
+    $$$$
+    ALA
+    <BLANKLINE>
+    <BLANKLINE>
+     13 12  0     0  0  0  0  0  0  1 V2000
+       -0.9700    0.4900    1.5000 N   0  0  0  0  0  0  0  0  0  0  0  0
+        0.2600    0.4200    0.6900 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.0900    0.0200   -0.7200 C   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.0600   -0.6800   -0.9200 O   0  0  0  0  0  0  0  0  0  0  0  0
+        1.2000   -0.6200    1.3000 C   0  0  0  0  0  0  0  0  0  0  0  0
+        0.6600    0.4400   -1.7400 O   0  0  0  0  0  0  0  0  0  0  0  0
+       -1.3800   -0.4200    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
+       -0.6800    0.6600    2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7500    1.3900    0.6800 H   0  0  0  0  0  0  0  0  0  0  0  0
+        1.4600   -0.3300    2.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.7200   -1.5900    1.3100 H   0  0  0  0  0  0  0  0  0  0  0  0
+        2.1100   -0.6800    0.7000 H   0  0  0  0  0  0  0  0  0  0  0  0
+        0.4400    0.1800   -2.6500 H   0  0  0  0  0  0  0  0  0  0  0  0
+      1  2  1  0  0  0  0
+      1  7  1  0  0  0  0
+      1  8  1  0  0  0  0
+      2  3  1  0  0  0  0
+      2  5  1  0  0  0  0
+      2  9  1  0  0  0  0
+      3  4  2  0  0  0  0
+      3  6  1  0  0  0  0
+      5 10  1  0  0  0  0
+      5 11  1  0  0  0  0
+      5 12  1  0  0  0  0
+      6 13  1  0  0  0  0
+    M  END
+    $$$$
+    <BLANKLINE>
+    """
+
+    def __init__(self, records=None):
+        self._records = {}
+        if records is not None:
+            for mol_name, record in records.items():
+                if isinstance(record, SDRecord):
+                    record.header.mol_name = mol_name
+                self._records[mol_name] = record
+
+    @property
+    def lines(self):
+        return self.serialize().splitlines()
+
+    @property
+    def record(self):
+        if len(self) == 0:
+            raise ValueError("There are no records in the file")
+        if len(self) > 1:
+            raise ValueError("There are multiple records in the file")
+        return self[next(iter(self))]
+
+    @staticmethod
+    def deserialize(text):
+        """
+        Create an object by deserializing the given text content.
+
+        Parameters
+        ----------
+        content : str
+            The content to be deserialized.
+        """
+        lines = text.splitlines()
+        record_ends = np.array([
+            i for i, line in enumerate(lines)
+            if line.startswith(_RECORD_DELIMITER)
+        ], dtype=int)
+        if len(record_ends) == 0:
+            warnings.warn(
+                "Final record delimiter missing, "
+                "maybe this is a MOL file instead of a SD file"
+            )
+            record_ends = np.array([len(lines)-1], dtype=int)
+        # The first record starts at the first line and the last
+        # delimiter is at the end of the file
+        # Records in the middle start directly after the delimiter
+        record_starts = np.concatenate(([0], record_ends[:-1] + 1), dtype=int)
+        record_names = [lines[start].strip() for start in record_starts]
+        return SDFile({
+            # Do not include the delimiter
+            # -> stop at end (instead of end + 1)
+            name: _join_with_terminal_newline(lines[start : end])
+            for name, start, end
+            in zip(record_names, record_starts, record_ends)
+        })
+
+    def serialize(self):
+        """
+        Convert this object into text content.
+
+        Returns
+        -------
+        content : str
+            The serialized content.
+        """
+        text_blocks = []
+        for record_name, record in self._records.items():
+            if isinstance(record, str):
+                # Record is already stored as text
+                text_blocks.append(record)
+            else:
+                try:
+                    text_blocks.append(record.serialize())
+                except:
+                    raise SerializationError(
+                        f"Failed to serialize record '{record_name}'"
+                    )
+            text_blocks.append(_RECORD_DELIMITER + "\n")
+        return "".join(text_blocks)
+
+    @classmethod
+    def read(cls, file):
+        """
+        Read a SD file.
+
+        Parameters
+        ----------
+        file : file-like object or str
+            The file to be read.
+            Alternatively a file path can be supplied.
+
+        Returns
+        -------
+        file_object : SDFile
+            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 SDFile.deserialize(text)
+
+    def write(self, file):
+        """
+        Write the contents of this object into a SD 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):
+        record = self._records[key]
+        if isinstance(record, str):
+            # Element is stored in serialized form
+            # -> must be deserialized first
+            try:
+                record = SDRecord.deserialize(record)
+            except:
+                raise DeserializationError(
+                    f"Failed to deserialize record '{key}'"
+                )
+            # Update with deserialized object
+            self._records[key] = record
+        return record
+
+    def __setitem__(self, key, record):
+        if not isinstance(record, SDRecord):
+            raise TypeError(
+                f"Expected 'SDRecord', but got '{type(record).__name__}'"
+            )
+        # The molecule name in the header is unique across the file
+        record.header.mol_name = key
+        self._records[key] = record
+
+    def __delitem__(self, key):
+        del self._records[key]
+
+    def __iter__(self):
+        return iter(self._records)
+
+    def __len__(self):
+        return len(self._records)
+
+    def __eq__(self, other):
+        if not isinstance(other, type(self)):
+            return False
+        if set(self.keys()) != set(other.keys()):
+            return False
+        for record_name in self.keys():
+            if self[record_name] != other[record_name]:
+                return False
+        return True
+
+    def __str__(self):
+        return self.serialize()
+
+
+def _join_with_terminal_newline(text_blocks):
+    if len(text_blocks) == 0:
+        return ""
+    else:
+        return "\n".join(text_blocks) + "\n"
+
+
+def _empty_ctab():
+    empty_atoms = AtomArray(0)
+    empty_atoms.bonds = BondList(0)
+    return _join_with_terminal_newline(write_structure_to_ctab(empty_atoms))
+
+
+def _to_metadata_key(key):
+    if isinstance(key, Metadata.Key):
+        return key
+    elif isinstance(key, str):
+        return Metadata.Key(name=key)
+    else:
+        raise TypeError(
+            "Expected 'Metadata.Key' or str, "
+            f"but got '{type(key).__name__}'"
+        )
+
+
+def _add_key_value_pair(metadata, key, value):
+    if key is not None:
+        if value is None:
+            raise DeserializationError(
+                f"No value found for metadata key {key}"
+            )
+        metadata[key] = value
+
+
+def _get_ctab_stop(lines):
+    for i in range(_N_HEADER, len(lines)):
+        if lines[i].startswith("M  END"):
+            return i+1
+    return len(lines)