I've fixed the problem. It took a bit more work than I expected. If
you use the latest code in github it should work for you. Remember to
recreate the bindings (-DPYTHON_BINDINGS=ON -DRUN_SWIG=ON).
The following code now works:
import pybel
ob = pybel.ob
r = ob.OBReaction()
m = ob.OBMol()
r.AddReactant(m)
- Noel
On 26 August 2013 01:59, Lee-Ping Wang <leep...@stanford.edu> wrote:
> Hi Noel,
>
> Thanks! I appreciate it. I will take a look tomorrow as well.
>
> - Lee-Ping
>
> On Aug 23, 2013, at 12:26 PM, Noel O'Boyle wrote:
>
>> Looks like a SWIG wrapping issue.
>>
>> If you are compiling the bindings yourself, adding:
>> %include <std_shared_ptr.i>
>> ...close to the start of the openbabel-python.i file might simply sort
>> out the problem. I'll take a look asap.
>>
>> - Noel
>>
>> On 20 August 2013 19:13, Lee-Ping Wang <leep...@stanford.edu> wrote:
>>> Hi there,
>>>
>>> I'm using OpenBabel in a Python script, and I created several OBMol
>>> objects that I would like to organize into an OBReaction object.
>>> However, I am getting the following TypeError:
>>>
>>> obm = ob.OBMol()
>>> obcsvg = ob.OBConversion()
>>> obcsvg.SetInAndOutFormats("xyz","svg")
>>> obcsvg.ReadFile(obm, sys.argv[1])
>>> obr = ob.OBReaction()
>>> obr.AddReactant(obm)
>>>
>>> Traceback (most recent call last):
>>> File "./xyzob.py", line 23, in <module>
>>> obr.AddReactant(obm)
>>> TypeError: in method 'OBReaction_AddReactant', argument 2 of type
>>> 'shared_ptr< OpenBabel::OBMol > const'
>>>
>>> It seems the AddReactant() method is expecting a shared_ptr, or
>>> something else that Python cannot provide. Am I doing something wrong,
>>> or should the wrapping be improved?
>>>
>>> Thanks,
>>>
>>> - Lee-Ping
>>>
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