Hello Loris,
This problem is due to the PairData object getting destroyed by
Python, while the C++ OBMol still wants to keep it. The solution is to
use CloneData instead of SetData. In other words, *never* use SetData
from Python or any other scripting language. I will update the Python
documentation to make this clear.
You might find it useful to look at the code of pybel.py to see how I
do things there.
Noel
On 16/09/2008, Loris Moretti <lor...@ch...> wrote:
> Hi all,
>
> I am quite new to OpenBabel I am trying to develop a script in Python with
> OpenBabel. The script reads a multiple sdf file, takes a molecule per time and
> calculates some properties. It adds the property value and attribute to the
> OBMol object with OBPairData and then, it writes out the molecules into a
> multiple sdf file with the new field.
>
> a very simple form of the script:
>
> #########################################################
> #!/usr/bin/python
>
> import openbabel
>
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("sdf", "sdf")
>
> mol = openbabel.OBMol()
>
> iteratorMol = obConversion.ReadFile(mol, "molecules.sdf")
>
> while iteratorMol:
>
> newData = openbabel.OBPairData()
> newData.SetAttribute("NEWDATA")
> newData.SetValue("blabla")
> mol.SetData(newData)
>
> print obConversion.WriteString(mol)
>
> iteratorMol = obConversion.Read(mol)
> #########################################################
>
> The script works for the first molecule of the input file but fails for the
> others with a "segmentation fault" error.
> I tested it line by line and I saw there is a problem to reuse the OBPairData
> object.
>
> It might be a trivial error of mine but I cannot see it!
> It might be an error of the system I use!
>
> Can anyone help, please.
>
> Thanks in advance,
> loris...
>
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