Sorry - I did mean stuck. Maintaining stereo is tricky.
On 26 Dec 2016 8:34 p.m., "Noel O'Boyle" <baoille...@gmail.com> wrote:
> 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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