Hi!
I stumbled upon some odd behavior when starting PyMol in an interactive
IPython Session.
PyMol can be launched from interactive IPython like this:
In [1]: import pymol
In [2]: from pymol import cmd
In [3]: pymol.finish_launching()
In [4]: cmd.fetch("1xyz")So far, everything is normal. However, when I want to
get the
coordinates of the structure the following happens: In [5]:
cmd.get_coords("1xyz") Out[5]: array([[ 41., 25., 36.], [ 40., 25.,
35.], [ 39., 24., 35.], ..., [ 11., 26., 67.], [ 4., 32., 95.], [ 22.,
45., 49.]], dtype=float32) Even though the datatype is float32
apparently the decimals got lost somehow. The coordinates of the first
atom should be: 41.511 25.152 36.876 Repeating the above in a normal
interactive Python Session everything works just fine:
>>> import pymol >>> from pymol import cmd >>> pymol.finish_launching() >>>
cmd.fetch("1xyz") >>> cmd.get_coords("1xyz") array([[ 41.51100159,
25.15200043, 36.87599945], [ 40.9070015 , 25.55500031, 35.56299973], [
39.68399811, 24.70700073, 35.10599899], ..., [ 11.88700008, 26.97699928,
67.03900146], [ 4.45699978, 32.77299881, 95.16600037], [ 22.64100075,
45.7840004 , 49.03900146]], dtype=float32) As I use IPython only for
debugging of PyMol scripts/plugins this is not a very big problem. Still
I'm interested in what causes this strange behavior. Is it a problem/bug
in IPython or in PyMol? Maybe someone has more insights here and can
give clarity! Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
Thanks! regards Leonhard
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