Hi there,
Regarding 1, yes, but have you instead considered using a Python dictionary
or list to store the information? If I were you, I would avoid crossing
over to C++ to store this information.
Regarding 2, see
https://openbabel.org/docs/dev/UseTheLibrary/PythonDoc.html#accessing-obpairdata-obunitcell-and-other-obgenericdata.
Essentially, toPairData() does the cast.
Regarding 3, the number of lone pairs can be deduced from the atomic number
and the valence so we don't need to track the number of lone pairs.
Regards,
- Noel
On 25 January 2018 at 01:43, Xianghai Sheng <xsh...@ucmerced.edu> wrote:
> Dear developers,
>
> I was wondering what is the proper way to use OBPairData in python. For
> example, I want to store an OBPairData with attribute 'nLonePair' in an
> OBAtom. I managed to do this with the following code but don't know if it
> is the best way.
>
> d = ob.OBPairData()
> d.SetAttribute('nLonePair')
> nLonePair = 2
> d.SetValue(str(nLonePair))
> atom.CloneData(d)
>
> I wanted to use atom.SetData() as I found in the document
> <http://openbabel.org/dev-api/classOpenBabel_1_1OBGenericData.shtml#ac9527475c246fadbbab63a35376fd5fe>but
> an error shows up saying OBAtom does not have attribute SetData. So I used
> CloneData instead, which seems to do the job.
>
> Now I want to retrieve the value of the OBPairData. In C++ I would do
> things like
> pairData = (OBPairData*)atom.GetData('nLonePair')
> nLonePair = pairData.GetValue()
> However, when in python I do
> pairData = openbabel.OBPairData(atom.GetData('nLonePair')),
> an error shows up saying __init__() takes exactly 1 argument (2 given). I
> checked the swig file openbabel.py and OBPairData.__init__() does take
> 'self' as the only argument. The problem is that atom.GetData() returns a
> OBGenericData type which, without converting to an OBPairData type, doesn't
> allow a GetValue() method afaik.
>
> To sum up,
> 1. Is my way of storing an OBPairData in an atom correct?
> 2. How do I retrieve the value of an OBPairData in python?
> 3. Just by the way, is there anything in openbabel/pybel that keeps track
> of the number of lone pairs in an atom?
>
> Thank you in advance,
> Xianghai
>
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