biotite.structure.io.mol.MOLFile¶

class biotite.structure.io.mol.MOLFile[source]¶

Bases: TextFile

This class represents a file in MOL format, that is used to store structure information for small molecules. 1

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.

References

1: A. Dalby, J. G. Nourse, W. D. Hounshell, A. K. I. Gushurst, D. L. Grier, B. A. Leland, J. Laufer, “Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited,” Journal of Chemical Information and Computer Sciences, vol. 32, pp. 244–255, May 1992. doi: 10.1021/ci00007a012

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

copy()¶

Create a deep copy of this object.

Returns

copy: A copy of this object.

get_header()¶

Get the header from the MOL file.

Returns

mol_namestr: The name of the molecule.
initialsstr: The author’s initials.
programstr: The program name.
timedatetime: The time of file creation.
dimensionsstr: Dimensional codes.
scaling_factorsstr: Scaling factors.
energystr: Energy from modeling program.
registry_numberstr: MDL registry number.
commentsstr: Additional comments.

get_structure()¶

Get an AtomArray from the MOL file.

Returns

arrayAtomArray: This AtomArray contains the optional charge annotation and has an associated BondList. All other annotation categories, except element are empty.

classmethod read(file, *args, **kwargs)¶

Parse a file (or file-like object).

Parameters

filefile-like object or str: The file to be read. Alternatively a file path can be supplied.

Returns

file_objectFile: An instance from the respective File subclass representing the parsed file.

static read_iter(file)¶

Create an iterator over each line of the given text file.

Parameters

filefile-like object or str: The file to be read. Alternatively a file path can be supplied.

Yields

linestr: The current line in the file.

set_header(mol_name, initials='', program='', time=None, dimensions='', scaling_factors='', energy='', registry_number='', comments='')¶

Set the header for the MOL file.

Parameters

mol_namestr: The name of the molecule.
initialsstr, optional: The author’s initials. Maximum length is 2.
programstr, optional: The program name. Maximum length is 8.
timedatetime or date, optional: The time of file creation.
dimensionsstr, optional: Dimensional codes. Maximum length is 2.
scaling_factorsstr, optional: Scaling factors. Maximum length is 12.
energystr, optional: Energy from modeling program. Maximum length is 12.
registry_numberstr, optional: MDL registry number. Maximum length is 6.
commentsstr, optional: Additional comments.

set_structure(atoms, default_bond_type=BondType.ANY)¶

Set the AtomArray for the file.

Parameters

arrayAtomArray: The array to be saved into this file. Must have an associated BondList.
default_bond_typeBondType: Bond type fallback in the Bond block if a bond has no bond_type defined in atoms array. By default, each bond is treated as BondType.ANY.

write(file)¶

Write the contents of this object into a file (or file-like object).

Parameters

filefile-like object or str: The file to be written to. Alternatively a file path can be supplied.

static write_iter(file, lines)¶

Iterate over the given lines of text and write each line into the specified file.

In contrast to write(), each line of text is not stored in an intermediate TextFile, but is directly written to the file. Hence, this static method may save a large amount of memory if a large file should be written, especially if the lines are provided as generator.

Parameters

filefile-like object or str: The file to be written to. Alternatively a file path can be supplied.
linesgenerator or array-like of str: The lines of text to be written. Must not include line break characters.