biotite 0.41.1__cp312-cp312-macosx_10_16_x86_64.whl

biotite/structure/io/mol/mol.py

@@ -0,0 +1,193 @@
+# 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"
+__all__ = ["MOLFile"]
+
+from ....file import TextFile, InvalidFileError
+from .ctab import read_structure_from_ctab, write_structure_to_ctab
+from .header import Header
+from ...bonds import BondType
+
+
+# Number of header lines
+N_HEADER = 3
+
+
+class MOLFile(TextFile):
+    """
+    This class represents a file in MOL format, that is used to store
+    structure information for small molecules.
+    :footcite:`Dalby1992`
+
+    Since its use is intended for single small molecules, it stores
+    less atom annotation information than the macromolecular structure
+    formats:
+    Only the atom positions, charges, elements and bonds can be read
+    from the file, chain and and residue information is missing.
+
+    This class can also be used to parse the first structure from an SDF
+    file, as the SDF format extends the MOL format.
+
+    Attributes
+    ----------
+    header : Header
+        The header of the MOL file.
+
+    References
+    ----------
+
+    .. footbibliography::
+
+    Examples
+    --------
+
+    >>> from os.path import join
+    >>> mol_file = MOLFile.read(join(path_to_structures, "molecules", "TYR.sdf"))
+    >>> atom_array = mol_file.get_structure()
+    >>> print(atom_array)
+                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
+    """
+
+    def __init__(self):
+        super().__init__()
+        # empty header lines
+        self.lines = [""] * N_HEADER
+        self._header = None
+
+
+    @classmethod
+    def read(cls, file):
+        mol_file = super().read(file)
+        mol_file._header = None
+        return mol_file
+
+
+    @property
+    def header(self):
+        if self._header is None:
+            self._header = Header.deserialize("\n".join(self.lines[0:3]) + "\n")
+        return self._header
+
+
+    @header.setter
+    def header(self, header):
+        self._header = header
+        self.lines[0:3] = self._header.serialize().splitlines()
+
+
+    def get_header(self):
+        """
+        Get the header from the MOL file.
+
+        DEPRECATED: Use the :attr:`header` property instead.
+
+        Returns
+        -------
+        header_attributes
+            See :class:`Header`.
+        """
+        header = self.header
+        return (
+            header.mol_name,
+            header.initials,
+            header.program,
+            header.time,
+            header.dimensions,
+            header.scaling_factors,
+            header.energy,
+            header.registry_number,
+            header.comments
+        )
+
+
+    def set_header(self, *args, **kwargs):
+        """
+        Set the header for the MOL file.
+
+        DEPRECATED: Use the :attr:`header` property instead.
+
+        Parameters
+        ----------
+        **args, **kwars
+            See :class:`Header`.
+        """
+        self.header = Header(*args, **kwargs)
+
+
+    def get_structure(self):
+        """
+        Get an :class:`AtomArray` from the MOL file.
+
+        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 = _get_ctab_lines(self.lines)
+        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 :class:`AtomArray` for the file.
+
+        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.lines = self.lines[:N_HEADER] + write_structure_to_ctab(
+            atoms, default_bond_type, version
+        )
+
+
+
+def _get_ctab_lines(lines):
+    for i, line in enumerate(lines):
+        if line.startswith("M  END"):
+            return lines[N_HEADER:i+1]
+    return lines[N_HEADER:]