Configs are immutable. You need to create a new config, and then use
setconfig or something like this.
On 26 Dec 2016 8:09 p.m., "Sam Tonddast-Navaei" <s.tondd...@gmail.com>
wrote:
> 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
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>>
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> OpenBabel-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>>
>
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