Hahaha, I actually do suck and still stuck :)
An example script is always helpful and I would really appreciate it if you
get a chance to
thanks again
On Mon, Dec 26, 2016 at 3:38 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> 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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