Thanks Noel, it works like a charm!
On Wed, Dec 28, 2016 at 8:13 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> You have an off-by-one due to a misunderstanding of where the stereo
> is stored. For cis-trans stereo, the stereobond is the double bond,
> not the up/down single bonds. On top of this, the stereo code uses
> atom Ids and not atom indices (I can't remember the rationale for
> this). Anyhoo, here is a working piece of code that does what you
> want:
>
> import pybel
> import openbabel as ob
>
> mol = pybel.readstring('smi','OC\C=C\Cl')
> m = mol.OBMol
>
> # Add a chlorine atom to the molecule
> a = m.NewAtom()
> a.SetAtomicNum(9)
>
> # Get the stereo bond - note! this is the double bond
> stereobond = m.GetBond(2) # This is the third bond (when read from the
> SMILES above)
> assert stereobond.GetBO() == 2
>
> facade = ob.OBStereoFacade(mol.OBMol)
> stereo = facade.GetCisTransStereo(stereobond.GetId()) # Note use of
> GetId() not GetIdx()
> config = stereo.GetConfig()
> print config.refs
>
> mol.OBMol.DeleteBond(m.GetBond(1)) # breaking the second bond
> mol.OBMol.AddBond(3, a.GetIdx(), 1)
>
> # Note that the refs uses atom Ids (4294967294 is used to mark an
> implicit stereo ref)
> config.refs = (a.GetId(), 4294967294, 4, 4294967294)
> stereo.SetConfig(config)
>
> print mol.write('smi') # OC.C(=C\Cl)/F
>
>
> On 27 December 2016 at 03:30, Sam Tonddast-Navaei <s.tondd...@gmail.com>
> wrote:
> > Dear colleagues,
> >
> > I just realized that if I add "addh()" before printing the SMILES I
> would
> > get the correct transferred SMILES.
> >
> > - Any clue why that makes it work?
> > - I also realized that in case of cis/trans stereo chemistry only one of
> the
> > carbons returns "True" when calling HasCisTransStereo(atom_index). Could
> > anyone elaborate why is this the case?
> >
> > Thanks,
> > Sam
> >
> > On Mon, Dec 26, 2016 at 5:08 PM, Sam Tonddast-Navaei <
> s.tondd...@gmail.com>
> > wrote:
> >>
> >> 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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>
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