Module deeporigin.src.utilities.conversions

Functions

def convert_block(source_type, source, destination_type, add_hydrogens=False)

Expand source code

def convert_block(source_type, source, destination_type, add_hydrogens=False):
    """
    Convert molecular structure formats between different file types.

    This function takes a molecular structure in one format and converts it to another format
    using temporary files for the conversion process.

    Args:
        source_type (str): The file format of the input structure (e.g., 'pdb', 'mol2', 'sdf')
        source (str): The molecular structure content as a string in the source format
        destination_type (str): The desired output file format
        add_hydrogens (bool, optional): Whether to add hydrogen atoms during conversion. Defaults to False

    Returns:
        str: The converted molecular structure as a string in the destination format

    Raises:
        Any exceptions from the underlying convert_file function may be propagated

    Note:
        This function creates temporary files during the conversion process.
        The temporary files are automatically cleaned up by the system.
    """
    source_file = tempfile.mktemp()
    with open(source_file, 'w') as f:
        f.write(source)

    destination_file = convert_file(source_type, source_file, destination_type, add_hydrogens=add_hydrogens)

    with open(destination_file, 'r') as f:
        return f.read()

Convert molecular structure formats between different file types.

This function takes a molecular structure in one format and converts it to another format using temporary files for the conversion process.

Args

source_type : str

The file format of the input structure (e.g., 'pdb', 'mol2', 'sdf')

source : str

The molecular structure content as a string in the source format

destination_type : str

The desired output file format

add_hydrogens : bool, optional

Whether to add hydrogen atoms during conversion. Defaults to False

Returns

str

The converted molecular structure as a string in the destination format

Raises

Any exceptions from the underlying convert_file function may be propagated

Note

This function creates temporary files during the conversion process. The temporary files are automatically cleaned up by the system.

def convert_file(source_type, source, destination_type, destination=None, add_hydrogens=False)

Expand source code

def convert_file(source_type, source, destination_type, destination=None, add_hydrogens=False):
    """
    Converts a chemical structure file from one format to another.

    This function uses OpenBabel via Pybel to convert between different molecular file formats.
    If no destination path is specified, it creates a temporary file.

    Args:
        source_type (str): Input file format (e.g., 'pdb', 'mol2', 'sdf')
        source (str): Path to the input file
        destination_type (str): Output file format (e.g., 'pdb', 'mol2', 'sdf')
        destination (str, optional): Path for the output file. If None, creates a temp file. Defaults to None.
        add_hydrogens (bool, optional): Whether to add hydrogen atoms to the molecule. Defaults to False.

    Returns:
        str: Path to the converted file

    Raises:
        IOError: If the source file cannot be read or destination cannot be written
        ValueError: If the file formats are not supported by OpenBabel
    """
    mol_pb_gen = pybel.readfile(str(source_type), source)

    if not destination:
        destination = tempfile.mktemp()

    out_file = pybel.Outputfile(str(destination_type), destination, overwrite=True)

    for mol_pb in mol_pb_gen:
        if add_hydrogens:
            mol_pb.addh()
        out_file.write(mol_pb)

    out_file.close()
    return destination

Converts a chemical structure file from one format to another.

This function uses OpenBabel via Pybel to convert between different molecular file formats. If no destination path is specified, it creates a temporary file.

Args

source_type : str

Input file format (e.g., 'pdb', 'mol2', 'sdf')

source : str

Path to the input file

destination_type : str

Output file format (e.g., 'pdb', 'mol2', 'sdf')

destination : str, optional

Path for the output file. If None, creates a temp file. Defaults to None.

add_hydrogens : bool, optional

Whether to add hydrogen atoms to the molecule. Defaults to False.

Returns

str

Path to the converted file

Raises

IOError

If the source file cannot be read or destination cannot be written

ValueError

If the file formats are not supported by OpenBabel