Thanks Noel, I figured it out thanks to your hint. Is there a function that
allows to change the refs? It seems that in python Config.ref returns a
tuple. I am trying to change the old ref_id to a new one.
Thanks for your help.
On Sun, Nov 20, 2016 at 5:38 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Look at the docs for OBStereoFacade and related classes. Stereo is stored
> in a Config object with refs to the four IDs of the atoms connected to the
> atoms of the double bond.
>
> On 19 Nov 2016 11:35 p.m., "Sam Tonddast-Navaei" <s.tondd...@gmail.com>
> wrote:
>
>> Hello all,
>>
>> I am trying to break a molecule into two fragments using Pybel yet
>> keeping the cis/trans stereochemisty information at the cleavage point when
>> I substitute it by a dummy atom. Currently I am trying to copy the bond
>> property (IsUp or IsDown) and assign it to the new bonds (bonds assign tot
>> he dummy atoms). However I figured out that both functions are returning
>> False values.
>>
>> I did a loop over all bonds and printed the following:
>>
>> for temp_bond in openbabel.OBMolBondIter(mol2.OBMol):
>>>
>>> print temp_bond.GetIdx(), temp_bond.GetBO(),
>>> temp_bond.IsDown(), temp_bond.IsUp(), temp_bond.IsCisOrTrans()
>>
>>
>> SMILES: OCCCC#CC#C/C=C/C(=O)OC
>>> 0 1 False False False
>>> 1 1 False False False
>>> 2 1 False False False
>>> 3 1 False False False
>>> 4 3 False False False
>>> 5 1 False False False
>>> 6 3 False False False
>>> 7 1 False False False
>>> 8 2 False False False
>>> 9 1 False False False
>>> 10 2 False False False
>>> 11 1 False False False
>>> 12 1 False False False
>>
>>
>> Can someone help me what I am missing here and whether there is a smarter
>> way of doing this?
>>
>> Thanks for your time,
>> Sam
>>
>> ------------------------------------------------------------
>> ------------------
>>
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>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>>
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