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VisualizeUtils

unpickle 

unpickle(file_name: AnyStr)

Unpickle (deserialize) and return a python object located at filename

Source code in symdesign/visualization/VisualizeUtils.py 
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def unpickle(file_name: AnyStr):  # , protocol=pickle.HIGHEST_PROTOCOL):
    """Unpickle (deserialize) and return a python object located at filename"""
    if '.pkl' not in file_name and '.pickle' not in file_name:
        file_name = f'{file_name}.pkl'
    try:
        with open(file_name, 'rb') as serial_f:
            new_object = load(serial_f)
    except EOFError as ex:
        raise ValueError(f"The object serialized at location {file_name} couldn't be accessed. No data present!")

    return new_object

get_all_file_paths 

get_all_file_paths(dir: str, suffix: str = '', extension: str = None, sort: bool = True) -> list[str]

Return all files in a directory with specified extensions and suffixes

Parameters:

  • dir (str) –

    The directory to retrieve filepaths from

  • suffix (str, default: '' ) –

    If a suffix should be appended to the files in the dir

  • extension (str, default: None ) –

    If a particular extension should be used to search for files

  • sort (bool, default: True ) –

    Whether to return the files in alphanumerically sorted order

Source code in symdesign/visualization/VisualizeUtils.py 
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def get_all_file_paths(dir: str, suffix: str = '', extension: str = None, sort: bool = True) -> list[str]:
    """Return all files in a directory with specified extensions and suffixes

    Args:
        dir: The directory to retrieve filepaths from
        suffix: If a suffix should be appended to the files in the dir
        extension: If a particular extension should be used to search for files
        sort: Whether to return the files in alphanumerically sorted order
    """
    if not extension:
        extension = '.pdb'
    if sort:
        return [os.path.join(os.path.abspath(dir), file)
                for file in sorted(glob(os.path.join(os.path.abspath(dir), '*%s*%s' % (suffix, extension))))]
    else:
        return [os.path.join(os.path.abspath(dir), file)
                for file in glob(os.path.join(os.path.abspath(dir), '*%s*%s' % (suffix, extension)))]

save_group 

save_group(group: str = 'all', one_file: bool = True, out_dir: str = os.getcwd()) -> None

Save all files inside a group to either one file or a list of files. Assumes the groups were generated using 'expand'

Parameters:

  • group (str, default: 'all' ) –

    name of the group to save

  • one_file (bool, default: True ) –

    Saves each protein in the group to one file, if False, then saves all members individually

  • out_dir (str, default: getcwd() ) –

    The directory location to save the files to

Returns:

  • None –

    None

Source code in symdesign/visualization/VisualizeUtils.py 
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def save_group(group: str = 'all', one_file: bool = True, out_dir: str = os.getcwd()) -> None:
    """Save all files inside a group to either one file or a list of files.
    Assumes the groups were generated using 'expand'

    Args:
        group: name of the group to save
        one_file: Saves each protein in the group to one file, if False, then saves all members individually
        out_dir: The directory location to save the files to

    Returns:
        None
    """
    if group == 'all':
        # remove appended symmetry mate number '_#' from the group instances and take the set of structures
        expanded_group = set('_'.join(name.split('_')[:-1]) for name in cmd.get_names('group_objects', enabled_only=1))
        groups = ['%s_expanded' % group for group in expanded_group]
    elif cmd.get_type(group) == 'object:group':
        groups = [group]
    else:
        print('Error: please provide a group name to save.')
        return None

    if one_file:
        for group in groups:
            cmd.save(os.path.join(out_dir, '%s.pdb' % group), group)
    else:
        for group in groups:
            stored.models = set()
            cmd.iterate(group, 'stored.models.add(model)')
            for model in stored.models:
                cmd.save(os.path.join(out_dir, '%s.pdb' % model), model)