distance_matrix.py 文件源码

def get_distance_matrix(pdb_path):
    parser = PDBParser()
    structure = parser.get_structure('structure', pdb_path).get_list()[0]
    residue_positions = get_residue_positions(structure)
    pdb_dist_mat = scipy.spatial.distance.squareform(scipy.spatial.distance.pdist(residue_positions, 'euclidean'))
    pdb_dist_mat[numpy.isnan(pdb_dist_mat)] = float('inf')
    return pdb_dist_mat