mogli.py

#!/usr/bin/env python
# coding: utf-8
"""
Simple visualization of molecules.
"""

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals

from typing import List, Tuple, Optional

import argparse
import itertools

import numpy as np
import numpy.linalg as la
try:
    import pybel
except ImportError:
    pybel = None
import gr3
import glfw
from OpenGL.GL import glEnable, glDisable, glClear, glBindFramebuffer, glViewport,\
    GL_FRAMEBUFFER, GL_DEPTH_TEST, GL_DEPTH_BUFFER_BIT, GL_COLOR_BUFFER_BIT,\
    GL_MULTISAMPLE

# Atom color rgb tuples (used for rendering, may be changed by users)
ATOM_COLORS = np.array([(0, 0, 0),  # Avoid atomic number to index conversion
                        (255, 255, 255), (217, 255, 255), (204, 128, 255),
                        (194, 255, 0), (255, 181, 181), (144, 144, 144),
                        (48, 80, 248), (255, 13, 13), (144, 224, 80),
                        (179, 227, 245), (171, 92, 242), (138, 255, 0),
                        (191, 166, 166), (240, 200, 160), (255, 128, 0),
                        (255, 255, 48), (31, 240, 31), (128, 209, 227),
                        (143, 64, 212), (61, 225, 0), (230, 230, 230),
                        (191, 194, 199), (166, 166, 171), (138, 153, 199),
                        (156, 122, 199), (224, 102, 51), (240, 144, 160),
                        (80, 208, 80), (200, 128, 51), (125, 128, 176),
                        (194, 143, 143), (102, 143, 143), (189, 128, 227),
                        (225, 161, 0), (166, 41, 41), (92, 184, 209),
                        (112, 46, 176), (0, 255, 0), (148, 255, 255),
                        (148, 224, 224), (115, 194, 201), (84, 181, 181),
                        (59, 158, 158), (36, 143, 143), (10, 125, 140),
                        (0, 105, 133), (192, 192, 192), (255, 217, 143),
                        (166, 117, 115), (102, 128, 128), (158, 99, 181),
                        (212, 122, 0), (148, 0, 148), (66, 158, 176),
                        (87, 23, 143), (0, 201, 0), (112, 212, 255),
                        (255, 255, 199), (217, 225, 199), (199, 225, 199),
                        (163, 225, 199), (143, 225, 199), (97, 225, 199),
                        (69, 225, 199), (48, 225, 199), (31, 225, 199),
                        (0, 225, 156), (0, 230, 117), (0, 212, 82),
                        (0, 191, 56), (0, 171, 36), (77, 194, 255),
                        (77, 166, 255), (33, 148, 214), (38, 125, 171),
                        (38, 102, 150), (23, 84, 135), (208, 208, 224),
                        (255, 209, 35), (184, 184, 208), (166, 84, 77),
                        (87, 89, 97), (158, 79, 181), (171, 92, 0),
                        (117, 79, 69), (66, 130, 150), (66, 0, 102),
                        (0, 125, 0), (112, 171, 250), (0, 186, 255),
                        (0, 161, 255), (0, 143, 255), (0, 128, 255),
                        (0, 107, 255), (84, 92, 242), (120, 92, 227),
                        (138, 79, 227), (161, 54, 212), (179, 31, 212),
                        (179, 31, 186), (179, 13, 166), (189, 13, 135),
                        (199, 0, 102), (204, 0, 89), (209, 0, 79),
                        (217, 0, 69), (224, 0, 56), (230, 0, 46),
                        (235, 0, 38), (255, 0, 255), (255, 0, 255),
                        (255, 0, 255), (255, 0, 255), (255, 0, 255),
                        (255, 0, 255), (255, 0, 255), (255, 0, 255),
                        (255, 0, 255)], dtype=np.float32)/255.0

# Atom numbers mapped to their symbols
ATOM_NUMBERS = {"H": 1, "HE": 2, "LI": 3, "BE": 4, "B": 5, "C": 6, "N": 7,
                "O": 8, "F": 9, "NE": 10, "NA": 11, "MG": 12, "AL": 13,
                "SI": 14, "P": 15, "S": 16, "CL": 17, "AR": 18, "K": 19,
                "CA": 20, "SC": 21, "TI": 22, "V": 23, "CR": 24, "MN": 25,
                "FE": 26, "CO": 27, "NI": 28, "CU": 29, "ZN": 30, "GA": 31,
                "GE": 32, "AS": 33, "SE": 34, "BR": 35, "KR": 36, "RB": 37,
                "SR": 38, "Y": 39, "ZR": 40, "NB": 41, "MO": 42, "TC": 43,
                "RU": 44, "RH": 45, "PD": 46, "AG": 47, "CD": 48, "IN": 49,
                "SN": 50, "SB": 51, "TE": 52, "I": 53, "XE": 54, "CS": 55,
                "BA": 56, "LA": 57, "CE": 58, "PR": 59, "ND": 60, "PM": 61,
                "SM": 62, "EU": 63, "GD": 64, "TB": 65, "DY": 66, "HO": 67,
                "ER": 68, "TM": 69, "YB": 70, "LU": 71, "HF": 72, "TA": 73,
                "W": 74, "RE": 75, "OS": 76, "IR": 77, "PT": 78, "AU": 79,
                "HG": 80, "TL": 81, "PB": 82, "BI": 83, "PO": 84, "AT": 85,
                "RN": 86, "FR": 87, "RA": 88, "AC": 89, "TH": 90, "PA": 91,
                "U": 92, "NP": 93, "PU": 94, "AM": 95, "CM": 96, "BK": 97,
                "CF": 98, "ES": 99, "FM": 100, "MD": 101, "NO": 102,
                "LR": 103, "RF": 104, "DB": 105, "SG": 106, "BH": 107,
                "HS": 108, "MT": 109, "DS": 110, "RG": 111, "CN": 112,
                "UUB": 112, "UUT": 113, "UUQ": 114, "UUP": 115, "UUH": 116,
                "UUS": 117, "UUO": 118}

# Atom valence radii in Å (used for bond calculation)
ATOM_VALENCE_RADII = np.array([0,  # Avoid atomic number to index conversion
                               230, 930, 680, 350, 830, 680, 680, 680, 640,
                               1120, 970, 1100, 1350, 1200, 750, 1020, 990,
                               1570, 1330, 990, 1440, 1470, 1330, 1350, 1350,
                               1340, 1330, 1500, 1520, 1450, 1220, 1170, 1210,
                               1220, 1210, 1910, 1470, 1120, 1780, 1560, 1480,
                               1470, 1350, 1400, 1450, 1500, 1590, 1690, 1630,
                               1460, 1460, 1470, 1400, 1980, 1670, 1340, 1870,
                               1830, 1820, 1810, 1800, 1800, 1990, 1790, 1760,
                               1750, 1740, 1730, 1720, 1940, 1720, 1570, 1430,
                               1370, 1350, 1370, 1320, 1500, 1500, 1700, 1550,
                               1540, 1540, 1680, 1700, 2400, 2000, 1900, 1880,
                               1790, 1610, 1580, 1550, 1530, 1510, 1500, 1500,
                               1500, 1500, 1500, 1500, 1500, 1500, 1600, 1600,
                               1600, 1600, 1600, 1600, 1600, 1600, 1600, 1600,
                               1600, 1600, 1600, 1600, 1600, 1600],
                              dtype=np.float32)/1000.0
# Prevent unintentional changes
ATOM_VALENCE_RADII.flags.writeable = False

# Atom radii in Å (used for rendering, scaled down by factor 0.4, may be
# changed by users)
ATOM_RADII = np.array(ATOM_VALENCE_RADII, copy=True)*0.4

# Bond radius in Å (used for rendering, may be changed by users)
BOND_RADIUS = 0.1

# Shade of gray used to render bond (from 0 black to 1 white)
BOND_GRAY_SHADE = 0.3


def _create_rotation_matrix(angle, x, y, z):
    """ Creates a 3x3 rotation matrix. """
    if la.norm((x, y, z)) < 0.0001:
        return np.eye(3, dtype=np.float32)
    x, y, z = np.array((x, y, z))/la.norm((x, y, z))
    matrix = np.zeros((3, 3), dtype=np.float32)
    cos = np.cos(angle)
    sin = np.sin(angle)
    matrix[0, 0] = x*x*(1-cos)+cos
    matrix[1, 0] = x*y*(1-cos)+sin*z
    matrix[0, 1] = x*y*(1-cos)-sin*z
    matrix[2, 0] = x*z*(1-cos)-sin*y
    matrix[0, 2] = x*z*(1-cos)+sin*y
    matrix[1, 1] = y*y*(1-cos)+cos
    matrix[1, 2] = y*z*(1-cos)-sin*x
    matrix[2, 1] = y*z*(1-cos)+sin*x
    matrix[2, 2] = z*z*(1-cos)+cos
    return matrix

_mouse_dragging = False
_previous_mouse_position = None
_camera = None


def _mouse_move_callback(window, x, y):
    """ Mouse move event handler for GLFW. """
    global _previous_mouse_position, _camera
    if _mouse_dragging and _camera is not None:
        width, height = glfw.get_window_size(window)
        dx = (x-_previous_mouse_position[0])/width
        dy = (y-_previous_mouse_position[1])/height
        rotation_intensity = la.norm((dx, dy)) * 2
        eye, center, up = _camera
        camera_distance = la.norm(center-eye)
        forward = (center-eye)/camera_distance
        right = np.cross(forward, up)
        rotation_axis = (up*dx+right*dy)
        rotation_matrix = _create_rotation_matrix(-rotation_intensity,
                                                  rotation_axis[0],
                                                  rotation_axis[1],
                                                  rotation_axis[2])
        forward = np.dot(rotation_matrix, forward)
        up = np.dot(rotation_matrix, up)
        eye = center-forward*camera_distance
        _camera = eye, center, up
        _previous_mouse_position = (x, y)


def _mouse_click_callback(window, button, status, modifiers):
    """ Mouse click event handler for GLFW. """
    global _mouse_dragging, _previous_mouse_position
    if button == glfw.MOUSE_BUTTON_LEFT:
        if status == glfw.RELEASE:
            _mouse_dragging = False
            _previous_mouse_position = None
        elif status == glfw.PRESS:
            _mouse_dragging = True
            _previous_mouse_position = glfw.get_cursor_pos(window)


class Molecule(object):
    """
    A class for storing information about a Molecule. The atomic bonds need to
    be explicitly calculated using the calculate_bonds function.
    """
    def __init__(self, atomic_numbers, positions):
        self.atomic_numbers = atomic_numbers
        self.positions = positions
        self.bonds = None
        self._atomic_radii = None
        self._atom_colors = None
    
    @property
    def atom_count(self) -> int:
        return len(self.atomic_numbers)
    
    @property
    def atom_colors(self) -> Optional[List[Tuple[float]]]:
        return self._atom_colors

    @atom_colors.setter
    def atom_colors(self, colors: Optional[List[Tuple[float]]]) -> None:
        if colors is None:
            self._atom_colors = None
        else:
            if len(colors) != len(self.atomic_numbers):
                raise RuntimeError("The number of colors must match the number of atoms in the Molecule")
            
            for color in colors:

                if len(color) != 3:
                    raise RuntimeError(f"The value {color} is not a valid color tuple")
                
                for channel in color:
                    if channel < 0 or channel > 1:
                        raise RuntimeError("The value of each color channel must be between 0 and 1")
            
            self._atom_colors = colors

    @property
    def atomic_radii(self):
        if self._atomic_radii is None:
            self._atomic_radii = ATOM_RADII[self.atomic_numbers]
        return self._atomic_radii

    def calculate_bonds(self, method='radii', param=None):
        """
        This function calculates which pair of atoms forms an atomic bond.
        Pairs of indices are returned, indicating that the two associated atoms
        form a bond.

        The method used for this is specified with the parameter 'method'.
        Currently two methods are supported:
         - using the valence radii of the atoms (optionally multiplied by
             param)
         - using a constant delta as maximum distance between to bonded atoms
        """
        method = method.lower()
        if method not in ('radii', 'constant_delta'):
            raise ValueError("method should be either 'radii' or 'constant "
                             "delta', not '%s'" % method)

        if self.bonds is not None:
            # Bonds were calculated for this molecule already.
            # Reuse those, if the method and optional parameter are like those
            # provided to this function.
            if self.bonds.method == method:
                if self.bonds.param == param:
                    return
                elif param is None:
                    # Allow reuse when default param is used.
                    if method == 'radii' and self.bonds.param == 1.0:
                        return

        if method == 'radii':
            radii = ATOM_VALENCE_RADII[self.atomic_numbers]
            if param is None:
                param = 1.0

        if method == 'constant_delta':
            if param is None:
                raise ValueError("method 'constant_delta' requires param to "
                                 "specify the maximum distance between two "
                                 "atoms to cause a bond between them.")

        index_pair_list = []
        for index, position in enumerate(self.positions):
            distance_vectors = self.positions[index+1:] - position
            distances_squared = np.sum(np.power(distance_vectors, 2), axis=1)
            if method == 'radii':
                deltas = np.square((radii[index+1:]+radii[index])*param)
            elif method == 'constant_delta':
                deltas = param**2
            nonzero_indices = np.nonzero(distances_squared <= deltas)
            num_bonds = len(nonzero_indices[0])
            if num_bonds > 0:
                index_pairs = np.hstack((np.ones(num_bonds, dtype=np.uint32)
                                         .reshape(num_bonds, 1)*index,
                                         index+1+nonzero_indices[0]
                                         .reshape(num_bonds, 1)))
                index_pair_list.append(index_pairs)
        if index_pair_list:
            index_pairs = np.vstack(index_pair_list)
        else:
            index_pairs = np.zeros((0, 2))
        self.bonds = Bonds(method, param, index_pairs)


class Bonds(object):
    """
    A simple class for storing information about atomic bonds in a molecule.
    """
    def __init__(self, method, param, index_pairs):
        self.method = method
        self.param = param
        self.index_pairs = index_pairs

    def __len__(self):
        return len(self.index_pairs)


class UnknownFileFormatException(Exception):
    """
    This exception will be raised when read() is called with file name that
    cannot be mapped to a known file format.
    """
    pass


def read(file_name, file_format=None):
    """
    Reads molecules from a file. If available, pybel will be used to read the
    file, otherwise only xyz files can be read.
    If the file_format is unknown, a UnknownFileFormatException will be raised.
    """
    if pybel:
        if file_format is None:
            file_extension = file_name.split('.')[-1]
            if file_extension in pybel.informats.keys():
                file_format = file_extension
            else:
                message = ("The file format {format} is  not supported by "
                           "pybel. If the file extension does not match the "
                           "actual format, please use the file_format "
                           "parameter.".format(format=file_extension))
                raise UnknownFileFormatException(message)
        elif file_format not in pybel.informats.keys():
            message = ("The file format {format} is not supported by pybel, so"
                       "mogli cannot understand it yet. Sorry!"
                       .format(format=file_format))
            raise UnknownFileFormatException(message)
        try:
            # Try reading the file with the 'b' option set. This speeds up
            # file reading dramatically for some formats (e.g. pdb).
            # If this fails for some reasons, use pybel.readfile().
            molecules = []
            conv = pybel.ob.OBConversion()
            conv.SetOptions("b".encode('ascii'), conv.INOPTIONS)
            success = conv.SetInFormat(file_format.encode('ascii'))
            if success:
                mol = pybel.ob.OBMol()
                has_molecule = conv.ReadFile(mol, file_name.encode('ascii'))
                while has_molecule:
                    num_atoms = mol.NumAtoms()
                    atomic_numbers = np.zeros(num_atoms, dtype=np.uint8)
                    positions = np.zeros((num_atoms, 3), dtype=np.float32)
                    for i, atom in enumerate(pybel.ob.OBMolAtomIter(mol)):
                        atomic_numbers[i] = atom.GetAtomicNum()
                        positions[i] = (atom.GetX(), atom.GetY(), atom.GetZ())
                    molecules.append(Molecule(atomic_numbers, positions))
                    has_molecule = conv.Read(mol)
        except:
            molecule_file = pybel.readfile(file_format.encode('ascii'),
                                           file_name.encode('ascii'))
            molecules = []
            for molecule in molecule_file:
                atoms = molecule.atoms
                atomic_numbers_iterator = (atom.atomicnum for atom in atoms)
                atomic_numbers = np.fromiter(atomic_numbers_iterator,
                                             dtype=np.uint8, count=len(atoms))
                positions_iterator = itertools.chain.from_iterable(atom.coords
                                                                   for atom
                                                                   in atoms)
                positions = np.fromiter(positions_iterator,
                                        dtype=np.float32, count=len(atoms)*3)
                positions.shape = (len(atoms), 3)
                molecules.append(Molecule(atomic_numbers, positions))
        return molecules
    else:
        if (file_format == 'xyz' or
                (file_format is None and file_name.endswith('.xyz'))):
            with open(file_name, 'r') as input_file:
                file_content = input_file.readlines()
            molecules = []
            while file_content:
                num_atoms = int(file_content[0])
                atom_strings = file_content[2:2+num_atoms]
                file_content = file_content[2+num_atoms:]
                atomic_numbers = [ATOM_NUMBERS[atom_string.split()[0].upper()]
                                  for atom_string
                                  in atom_strings]
                positions = np.array([(float(atom_string.split()[1]),
                                       float(atom_string.split()[2]),
                                       float(atom_string.split()[3]))
                                      for atom_string
                                      in atom_strings])
                molecules.append(Molecule(atomic_numbers, positions))
            return molecules
        else:
            message = ("Failed to import pybel. Currently mogli only supports "
                       "xyz files if pybel is not installed.")
            raise UnknownFileFormatException(message)


def show(molecule, width=500, height=500,
         show_bonds=True, bonds_method='radii', bonds_param=None,
         camera=None, title='mogli'):
    """
    Interactively show the given molecule with OpenGL. By default, bonds are
    drawn, if this is undesired the show_bonds parameter can be set to False.
    For information on the bond calculation, see Molecule.calculate_bonds.
    If you pass a tuple of camera position, center of view and an up vector to
    the camera parameter, the camera will be set accordingly. Otherwise the
    molecule will be viewed in the direction of the z axis, with the y axis
    pointing upward.
    """
    global _camera
    molecule.positions -= np.mean(molecule.positions, axis=0)
    max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
    if show_bonds:
        molecule.calculate_bonds(bonds_method, bonds_param)

    # If GR3 was initialized earlier, it would use a different context, so
    # it will be terminated first.
    gr3.terminate()

    # Initialize GLFW and create an OpenGL context
    glfw.init()
    glfw.window_hint(glfw.SAMPLES, 16)
    window = glfw.create_window(width, height, title, None, None)
    glfw.make_context_current(window)
    glEnable(GL_MULTISAMPLE)

    # Set up the camera (it will be changed during mouse rotation)
    if camera is None:
        camera_distance = -max_atom_distance*2.5
        camera = ((0, 0, camera_distance),
                  (0, 0, 0),
                  (0, 1, 0))
    camera = np.array(camera)
    _camera = camera

    # Create the GR3 scene
    gr3.setbackgroundcolor(255, 255, 255, 0)
    _create_gr3_scene(molecule, show_bonds)

    # Configure GLFW
    glfw.set_cursor_pos_callback(window, _mouse_move_callback)
    glfw.set_mouse_button_callback(window, _mouse_click_callback)
    glfw.swap_interval(1)
    # Start the GLFW main loop
    while not glfw.window_should_close(window):
        glfw.poll_events()
        width, height = glfw.get_window_size(window)
        glViewport(0, 0, width, height)
        _set_gr3_camera()
        glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
        gr3.drawimage(0, width, 0, height,
                      width, height, gr3.GR3_Drawable.GR3_DRAWABLE_OPENGL)
        glfw.swap_buffers(window)
    glfw.terminate()
    gr3.terminate()


def draw(molecule,
         xmin=0, xmax=1, ymin=0, ymax=1, width=500, height=500,
         show_bonds=True, bonds_method='radii', bonds_param=None,
         camera=None):
    """
    Draw the given molecule with the GR framework. By default, bonds are drawn,
    if this is undesired the show_bonds parameter can be set to False.
    For information on the bond calculation, see Molecule.calculate_bonds.
    If you pass a tuple of camera position, center of view and an up vector to
    the camera parameter, the camera will be set accordingly. Otherwise the
    molecule will be viewed in the direction of the z axis, with the y axis
    pointing upward.
    """
    global _camera
    molecule.positions -= np.mean(molecule.positions, axis=0)
    max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
    if show_bonds:
        molecule.calculate_bonds(bonds_method, bonds_param)

    if camera is None:
        camera_distance = -max_atom_distance*2.5
        camera = ((0, 0, camera_distance),
                  (0, 0, 0),
                  (0, 1, 0))
    camera = np.array(camera)
    _camera = camera

    # Create the GR3 scene
    gr3.setbackgroundcolor(255, 255, 255, 0)
    _set_gr3_camera()
    _create_gr3_scene(molecule, show_bonds)
    glEnable(GL_DEPTH_TEST)
    gr3.setquality(gr3.GR3_Quality.GR3_QUALITY_OPENGL_2X_SSAA)
    gr3.drawimage(xmin, xmax, ymin, ymax,
                  width, height, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
    glBindFramebuffer(GL_FRAMEBUFFER, 0)
    glDisable(GL_DEPTH_TEST)


def export(molecule, file_name, width=500, height=500,
           show_bonds=True, bonds_method='radii', bonds_param=None,
           camera=None):
    """
    Draw the given molecule into a given file. The file type is determined by
    the file extension, e.g. '.png' or '.html'. By default, bonds are drawn,
    if this is undesired the show_bonds parameter can be set to False.
    For information on the bond calculation, see Molecule.calculate_bonds.
    If you pass a tuple of camera position, center of view and an up vector to
    the camera parameter, the camera will be set accordingly. Otherwise the
    molecule will be viewed in the direction of the z axis, with the y axis
    pointing upward.
    """
    global _camera
    molecule.positions -= np.mean(molecule.positions, axis=0)
    max_atom_distance = np.max(la.norm(molecule.positions, axis=1))
    if show_bonds:
        molecule.calculate_bonds(bonds_method, bonds_param)

    if camera is None:
        if _camera is None:
            camera_distance = -max_atom_distance*2.5
            camera = ((0, 0, camera_distance),
                      (0, 0, 0),
                      (0, 1, 0))
        else:
            camera = _camera
    camera = np.array(camera)
    _camera = camera

    # Create the GR3 scene
    gr3.setbackgroundcolor(255, 255, 255, 0)
    _set_gr3_camera()
    _create_gr3_scene(molecule, show_bonds)
    glEnable(GL_DEPTH_TEST)
    gr3.export(file_name, width, height)
    glBindFramebuffer(GL_FRAMEBUFFER, 0)
    glDisable(GL_DEPTH_TEST)


def _set_gr3_camera():
    """ Set the GR3 camera, using the global _camera variable. """
    eye, center, up = _camera
    gr3.cameralookat(eye[0], eye[1], eye[2],
                     center[0], center[1], center[2],
                     up[0], up[1], up[2])


def _create_gr3_scene(molecule: Molecule, show_bonds=True):
    """
    Create the GR3 scene from the provided molecule and - if show_bonds is
    True (default) - the atomic bonds in the molecule.
    """
    gr3.clear()
    num_atoms = len(molecule.atomic_numbers)
    colors = molecule.atom_colors if molecule.atom_colors else ATOM_COLORS[molecule.atomic_numbers]

    gr3.drawspheremesh(num_atoms,
                       molecule.positions,
                       colors,
                       molecule.atomic_radii)
    
    if show_bonds and len(molecule.bonds.index_pairs) > 0:
        index_pairs = molecule.bonds.index_pairs
        num_bonds = len(molecule.bonds)
        bond_positions = molecule.positions[index_pairs[:, 0]]
        bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
        bond_lengths = la.norm(bond_directions, axis=1)
        bond_directions /= bond_lengths.reshape(num_bonds, 1)
        bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
        bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*BOND_GRAY_SHADE
        gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
                             bond_colors, bond_radii, bond_lengths)


def main():
    """
    Command line interface
    """
    parser = argparse.ArgumentParser()

    show_bonds_group = parser.add_mutually_exclusive_group()
    show_bonds_group.add_argument('--show_bonds',
                                  action='store_true', default=True,
                                  help='show atomic bonds (default)')
    show_bonds_group.add_argument('--hide_bonds',
                                  action='store_false', dest='show_bonds',
                                  help='do not show atomic bonds')
    parser.add_argument('-m', '--bond_method',
                        default='radii', choices=['radii', 'constant_delta'])
    parser.add_argument('-p', '--bond_param', default=1.0, type=float)
    parser.add_argument('-i', '--molecule', default=0, type=int,
                        help='the molecule index for files with multiple'
                             ' molecules')
    parser.add_argument('-f', '--format', type=str)
    parser.add_argument('file_name')
    args, unknown = parser.parse_known_args()
    if unknown:
        print('The following arguments were ignored:')
        print(' '.join(unknown))
    molecules = read(args.file_name, args.format)
    show(molecules[args.molecule],
         show_bonds=args.show_bonds,
         bonds_method=args.bond_method,
         bonds_param=args.bond_param)


if __name__ == '__main__':
    main()