Oops - you're right. OBAlign wasn't exposed in the Python bindings in
OB 2.3.0. I see that I added support on Nov 4 so you'll have to try
the development version and regenerate the bindings (-DRUN_SWIG=ON).

- Noel

On 12 March 2011 16:07, JP <jeanpaul.ebe...@inhibox.com> wrote:
> Noel,
> What version of OB does this script run against?
> I am having problems with pybel.ob.OBAlign():
>>
>> Traceback (most recent call last):
>>   File "./calculate_spread.py", line 55, in <module>
>>     main()
>>   File "./calculate_spread.py", line 52, in main
>>     spread_values = calculate_spread(molecules_file)
>>   File "./calculate_spread.py", line 24, in calculate_spread
>>     align = pybel.ob.OBAlign()
>> AttributeError: 'module' object has no attribute 'OBAlign'
>
> Thanks
> JP
> On 7 March 2011 13:48, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> Hi JP,
>>
>> Please find attached a Python script that calculates the RMSD for a
>> set of conformers versus a set of crystal structures. RMSD is symmetry
>> corrected and based on heavy atoms. The order of the heavy atoms is
>> assumed to be the same for the conformers as for the reference
>> structure.
>>
>> - Noel
>>
>> On 7 March 2011 13:08, JP <jeanpaul.ebe...@inhibox.com> wrote:
>> >
>> > Any ideas where I can find an example/documentation on how to calculate
>> > RMSD
>> > values
>> > for two molecules which are chemically the same (but have different
>> > conformers) - using pybel ?
>> > Many Thanks
>> >
>> >
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>
>
>
> --
>
> Jean-Paul Ebejer
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