protein

Classes:

• Protein –

  A helper tool for the protein file. It calculates the number of ions needed to neutralise it

Protein

Protein(filename=None, config=None)

A helper tool for the protein file. It calculates the number of ions needed to neutralise it (using ambertools for now).

:param filename: filepath to the protein :type filename: string :param config: Optional configuration for the protein :type config: :class:Config

Methods:

• get_path –

  Get a path to the protein.

Source code in ties/protein.py

def __init__(self, filename=None, config=None):
    if filename is None and config is None:
        raise Exception('Protein filename is not passed and the config file is missing. ')

    self.config = Config() if config is None else config

    if filename is None:
        if config.protein is None:
            raise Exception('Could not find the protein in the config object. ')
        self.file = config.protein
    elif filename is not None:
        self.file = filename
        # update the config
        config.protein = filename

    # fixme - check if the file exists at this point, throw an exception otherwise

    # calculate the charges of the protein (using ambertools)
    # fixme - turn this into a method? stage2: use propka or some other tool, not this workaround
    self.protein_net_charge = ties.generator.get_protein_net_charge(config.workdir, config.protein.absolute(),
                                                               config.ambertools_tleap, config.tleap_check_protein,
                                                               config.protein_ff)

    logger.info(f'Protein net charge: {self.protein_net_charge}')

get_path

get_path()

Get a path to the protein.

:return: the protein filename :rtype: string

Source code in ties/protein.py

def get_path(self):
    """
    Get a path to the protein.

    :return: the protein filename
    :rtype: string
    """
    return self.file