Get coords

get_coords is an API only function that returns the coordinates of a selection as a numpy array.

New in PyMOL 1.7.4

The order of coordinates is that of the internal atom ordering, like in iterate, and unlike in iterate_state. The function considers the object state and TTT matrices, like in get_model.

PyMOL API

cmd.get_coords(str selection='all', int state=1)

Returns: ndarray, shape (N, 3), where N is the number of atoms if state > 0, or (natoms * nstates) if state=0.

Arguments

• selection = str: atom selection {default: all}
• state = int: state index or all states if state=0 {default: 1}

See Also

• set_coords
• get_coordset
• Get Coordinates I

For state > 0, the function is equivalent to:

numpy.array(cmd.get_model(selection, state).get_coord_list())