Re: [OpenBabel-scripting] OBPairData problem

[Noel O'B. <bao...@gm...>]

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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