I'm attempting to install the OpenBabel Python bindings according to the
instructions on this page
(https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.htm
l). The problems occur when I try to execute OpenBabel instructions in the
Python console (command prompt readout is below):
C:\Users\umbci\Documents\Notebooks\complexity>obabel -V
Open Babel 3.1.1 -- May 16 2020 -- 11:57:55
C:\Users\umbci\Documents\Notebooks\complexity>obabel -Hsdf
sdf MDL MOL format
Reads and writes V2000 and V3000 versions
Open Babel supports an extension to the MOL file standard
that allows cis/trans and tetrahedral stereochemistry to be
stored in 0D MOL files. The tetrahedral stereochemistry is
stored as the atom parity, while the cis/trans stereochemistry
is stored using Up and Down bonds similar to how it is
represented in a SMILES string. Use the ``S`` option
when reading or writing if you want to avoid storing
or interpreting stereochemistry in 0D MOL files.
Read Options, e.g. -as
s determine chirality from atom parity flags
The default setting for 2D and 3D is to ignore atom parity and
work out the chirality based on the bond
stereochemistry (2D) or coordinates (3D).
For 0D the default is already to determine the chirality
from the atom parity.
S do not read stereochemistry from 0D MOL files
Open Babel supports reading and writing cis/trans
and tetrahedral stereochemistry to 0D MOL files.
This is an extension to the standard which you can
turn off using this option.
T read title only
P read title and properties only
When filtering an sdf file on title or properties
only, avoid lengthy chemical interpretation by
using the ``T`` or ``P`` option together with the
:ref:`copy format <Copy_raw_text>`.
Write Options, e.g. -x3
3 output V3000 not V2000 (used for >999 atoms/bonds)
a write atomclass if available
m write no properties
w use wedge and hash bonds from input (2D only)
v always specify the valence in the valence field
The default behavior is to only specify the valence if it
is not consistent with the MDL valence model.
So, for CH4 we don't specify it, but we do for CH3.
This option may be useful to preserve the correct number of
implicit hydrogens if a downstream tool does not correctly
implement the MDL valence model (but does honor the valence
field).
S do not store cis/trans stereochemistry in 0D MOL files
A output in Alias form, e.g. Ph, if present
E add an ASCII depiction of the molecule as a property
H use HYD extension (always on if mol contains zero-order bonds)
Specification at:
https://www.3dsbiovia.com/products/collaborative-science/biovia-draw/ctfile-
no-fee.html
C:\Users\umbci\Documents\Notebooks\complexity>dir "%BABEL_DATADIR%"\mr.txt
Volume in drive C is OS
Volume Serial Number is 3824-03F3
Directory of C:\Users\umbci\AppData\Roaming\OpenBabel-3.1.1\data
05/16/2020 05:43 AM 4,295 mr.txt
1 File(s) 4,295 bytes
0 Dir(s) 11,272,916,992 bytes free
C:\Users\umbci\Documents\Notebooks\complexity>py
Python 3.8.3rc1 (tags/v3.8.3rc1:802eb67, Apr 29 2020, 21:39:14) [MSC v.1924
64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from openbabel import pybel
>>> mol = pybel.readstring("smi", "CC(=O)Br")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"C:\Users\umbci\AppData\Roaming\Python\Python38\site-packages\openbabel\pybe
l.py", line 200, in readstring
raise ValueError("%s is not a recognised Open Babel format" % format)
ValueError: smi is not a recognised Open Babel format
Has anyone else encountered this problem when installing Python bindings for
Windows? How can I find and fix the error?
Thanks for your help,
-Chris M-B
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