amd.cli.main()

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7

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Total Lines	104
Code Lines	71

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"""Command line interface for :func:`amd.compare() <.compare.compare>`.
def main():
    """Entry point for command line interface for
    :func:`amd.compare() <.compare.compare>.
    """

    desc = "Compare crystals by PDD or AMD from the command line. Given one " \
           "or two paths to cifs/folders, lists of CSD refcodes or periodic " \
           "sets, compare them and return a DataFrame of the distance " \
           "matrix. Default is to comapre by AMD with k = 100. Accepts most " \
           "keyword arguments accepted by amd's CIF/CSD readers and " \
           "comparison functions."

    parser = argparse.ArgumentParser(description=desc)

    parser.add_argument('paths_or_refcodes', type=str, nargs='+',
        help='(str) One or two paths to files or folders, or a collection ' \
             'of CSD refcodes if csd-python-api is installed.')
    parser.add_argument('--outpath', '-o', type=str,
        help='(str) Path of the output file.')
    parser.add_argument('--format', '-f', type=str, default='csv', 
        help='(str) Format of the output file, default csv.')

    # amd.compare args 
    parser.add_argument(
        '--by', '-b', type=str, default='AMD', choices=['AMD', 'PDD'],
        help='(str) Use AMD or PDD to compare crystals.')
    parser.add_argument('--k', '-k', type=int, default=100,
        help='(int) Number of neighbour atoms to use for AMD/PDD.')
    parser.add_argument('--nearest', '-n', type=int, default=None,
        help='(int) Find n nearest neighbours instead of a full distance ' \
             'matrix between crystals.')

    # Reading args
    parser.add_argument(
        '--supress_warnings', default=False, action='store_true',
        help='(flag) Do not show warnings encountered during reading.')
    parser.add_argument('--reader', '-r', type=str, default='ase',
        choices=['ase', 'pycodcif', 'ccdc', 'pymatgen', 'gemmi'],
        help='(str) Backend package used to parse files, default ase.')
    parser.add_argument('--remove_hydrogens', default=False,
        action='store_true', help='(flag) Remove Hydrogen atoms.')
    parser.add_argument('--disorder', type=str, default='skip',
        choices=['skip', 'ordered_sites', 'all_sites'],
        help='(str) Control how disordered structures are handled.')
    parser.add_argument(
        '--heaviest_component', default=False, action='store_true',
        help='(flag) (csd-python-api only) Keep only the heaviest part of ' \
             'the asymmetric unit, intended for removing solvents.')
    parser.add_argument(
        '--molecular_centres', default=False, action='store_true',
        help='(flag) (csd-python-api only) Uses the centres of molecules ' \
             'for comparisons instead of atoms.')
    parser.add_argument('--families', default=False, action='store_true',
        help='(flag) (csd-python-api only) Interpret path_or_refcodes as ' \
             'refcode families.')

    # PDD args
    parser.add_argument('--collapse_tol', type=float, default=1e-4,
        help='(float) Tolerance for collapsing rows of PDDs.')

    # compare args
    parser.add_argument('--metric', type=str, default='chebyshev',
        help='(str) Metric used to compare AMDs/rows of PDDs, default chebyshev.')
    parser.add_argument('--n_jobs', type=int, default=1,
        help='(int) Number of cores to use for multiprocessing when comparing PDDs.')
    parser.add_argument('--verbose', type=int, default=1,
        help='(int) Print an ETA to the terminal when comparing PDDs. Passed to joblib.Parallel if using multiprocessing.')
    parser.add_argument('--low_memory', default=False, action='store_true',
        help='(flag) Use an more memory efficient (but slower) method for AMD comparisons.')

    # Remove some arguments before passing others to amd.compare
    kwargs = vars(parser.parse_args())
    path_or_refcodes = kwargs.pop('path_or_refcodes')
    outpath = kwargs.pop('outpath', None)
    if outpath is None:
        outpath = f"{kwargs['by']}_k={kwargs['k']}_dist_matrix"
    ext = kwargs.pop('format', 'csv')

    # Parameter is show_warnings, here it's a flag supress_warnings
    kwargs['show_warnings'] = not kwargs['supress_warnings']
    kwargs.pop('supress_warnings', None)

    crystals = path_or_refcodes[0]
    crystals_ = None
    if len(path_or_refcodes) == 2:
        crystals_ = path_or_refcodes[1]
    elif len(path_or_refcodes) > 2:
        msg = 'amd.compare accepts one or two collections of crystals for comparison.'
        raise ValueError(msg)

    df = compare(crystals, crystals_, **kwargs)

    if kwargs['verbose']:
        sys.stdout.write(df)

    if not outpath.endswith('.' + ext):
        outpath += '.' + ext

    try:
        output_func = getattr(df, 'to_' + ext)
        output_func(outpath)
    except AttributeError:
        sys.stdout.write(f'Unknown format {ext}, using csv.')
        df.to_csv(outpath + '.csv')