If you are still suck, let us know and I'll put an example together.
On 26 Dec 2016 8:33 p.m., "Noel O'Boyle" <baoille...@gmail.com> wrote:
> 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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