dwiddo / average-minimum-distance

    if remove_hydrogens:

        remove_sites.extend((i for i, num in enumerate(asym_types) if num == 1))

    if disorder != 'all_sites':

        for i, dis in enumerate(has_disorder):

            if i in remove_sites:

                continue

            if dis:

                if disorder == 'skip':

                    msg = f"{block.header} has disorder, pass " \

                            "disorder='ordered_sites' or 'all_sites' to " \

                            "remove/ignore disorder"

                    raise ParseError(msg)

                elif disorder == 'ordered_sites':

                    remove_sites.append(i)

    asym_unit = [xyz for i, xyz in enumerate(asym_unit) if i not in remove_sites]

        remove_sites.extend(i for i, num in enumerate(asym_types) if num == 1)

    # remove atoms with fractional occupancy or raise ParseError

    if disorder != 'all_sites':

        for i, dis in enumerate(has_disorder):

            if i in remove_sites:

                continue

            if dis:

                if disorder == 'skip':

                    msg = f"{block.name} has disorder, pass " \

                           "disorder='ordered_sites'or 'all_sites' to " \

                           "remove/ignore disorder"

                    raise ParseError(msg)

                elif disorder == 'ordered_sites':

                    remove_sites.append(i)

    asym_unit = [xyz for i, xyz in enumerate(asym_unit) if i not in remove_sites]