import argparse
import sys
import numpy as np
from scipy.spatial.ckdtree import cKDTree

HH_BOND_LENGTH = 0.74


def get_coordinates(filename: str) -> np.ndarray:
    coordinates = []
    with open(filename) as f:
        for line in f:
            if line.startswith('ATOM'):
                coordinates.append([line[30:38], line[38:46], line[46:54]])

    return np.array(coordinates)


def get_minimum_distance(coordinates: np.ndarray) -> float:
    distances, _ = cKDTree(coordinates).query(coordinates, k=2)
    return np.min(distances[:, 1])


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('file', type=str, help='PDB file to process')
    args = parser.parse_args()

    try:
        coordinates = get_coordinates(args.file)
    except IOError:
        print(f'{args.file} cannot be opened')
        sys.exit(1)

    min_distance = get_minimum_distance(coordinates)
    print(f'{args.file}: {min_distance:5.3f}: ', end='')
    if min_distance > HH_BOND_LENGTH:
        print('Valid')
    else:
        print('Invalid')


if __name__ == '__main__':
    main()