Thanks Noel, it works like a charm!
On Wed, Dec 28, 2016 at 8:13 AM, Noel O'Boyle 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 us
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 work
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(ato
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):
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 wrote:
> Sorry - I did mean stuck. Maintaining stereo is tricky.
>
> On 26 Dec 2016 8:34 p.m., "No
Sorry - I did mean stuck. Maintaining stereo is tricky.
On 26 Dec 2016 8:34 p.m., "Noel O'Boyle" 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" wrote:
>
>> Configs are immutable. You need to create a new config, and the
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" 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"
> wrote:
>
>> Thank
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"
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.
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 wrote:
> Look at the
> 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.
As Noel indicated, OBStereoFacade (and related classes) are used to track
stereochemistry. The "Up/Down
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"
wrote:
> Hello all,
>
> I am trying to break a molecule into two fragme
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