Hi Noel,
I made this script:
#!/usr/bin/python
> import pybel
> import openbabel as ob
>
> mol = pybel.readstring('smi','OC\C=C\Cl')
> print 'OC\C=C\Cl'
> facade = ob.OBStereoFacade(mol.OBMol)
> a = mol.OBMol.NewAtom()
> a.SetAtomicNum(9)
>
> bonds = []
> for bond in ob.OBMolBondIter(mol.OBMol):
> bonds.append(bond)
> a0_index = bonds[1].GetBeginAtomIdx() # C connected to O
> b0_index = bonds[1].GetEndAtomIdx() # first C in double-bond
> b0_stereo = facade.GetCisTransStereo(b0_index-1)
> b0_config = b0_stereo.GetConfig()
> print b0_config.refs
> mol.OBMol.DeleteBond(bonds[1]) # breaking the second bond
> mol.OBMol.AddBond(b0_index, a.GetIdx(),0)
> b0_config.refs = (5, 4294967294, 4, 4294967294)
> b0_stereo.SetConfig(b0_config)
> print b0_config.refs
> print mol.write('smi')
Trying to cut the second bond in the SMILES, and then replacing the ref
index of C to F in the Config using SetConfig. However at the end the final
SMILES does not have stereo in it
output:
OC\C=C\Cl
> (1L, 4294967294L, 4L, 4294967294L)
> (5L, 4294967294L, 4L, 4294967294L)
> OC.C(=CCl)F
Could you please let me know if I am missing something and how I can update
the SMILES?
On Mon, Dec 26, 2016 at 3:41 PM, Sam Tonddast-Navaei <s.tondd...@gmail.com>
wrote:
> 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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