Thank you all again for the great responses! :)
There seems to be a consensus between Andrew and Pavel that the solution is
with SetBondDir(). I've tried Pavel's functions get_unspec_double_bonds()
and set_double_bond_stereo() in python 2 (couldn't figure out how to get
RDkit set up in python 3, b
I just want to share my script, which I use for enumeration of
stereoisomers. Enumeration of double bonds was added quite recently and
thus I didn't test it extensively.
I put it on github: https://github.com/DrrDom/rdk
It seems to work well on quite complex queries like
CC1CCC(CC1)C1CC=C(C\C(=
So I may need a little guidance on this one from someone with a little more
historical knowledge of RDKit.
I found the findPotentialStereoBonds function inside Chirality.cpp that
appears to do what we want, detect double bonds with unspecified E/Z stereo
chemistry. That's at least what the comment
This has me quite curious now, how do we detect unspecified bond stereo
chemistry in RDKit?
m = Chem.MolFromSmiles("FC=CF")
assert m.HasProp("_StereochemDone")
for bond in m.GetBonds():
print(bond.GetBondDir(), bond.GetStereo())
Yields:
(rdkit.Chem.rdchem.BondDir.NONE, rdkit.Chem.rdchem.Bond
On Dec 9, 2016, at 9:50 PM, Brian Kelley wrote:
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles("F/C=C/F")
> >>> for bond in m.GetBonds():
> ...print bond.GetStereo()
> ...
> STEREONONE
> STEREOE
> STEREONONE
>
> However, setting bond stereo doesn't appear to be exposed.
I thought
bond.GetStereo
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles("F/C=C/F")
>>> for bond in m.GetBonds():
...print bond.GetStereo()
...
STEREONONE
STEREOE
STEREONONE
However, setting bond stereo doesn't appear to be exposed.
I suppose you could permute the smiles strings \ => / bu
Thank you all for your responses. I got R/S combos to work (awesome!), but
now I am working on E/Z. I am considering a similar approach (0 would be
interpreted as E, 1 as Z).
However to do this I would need two functions which I couldn't find
1.) Find double bonds that could be E/Z.
2.) Set the do
On Thu, 8 Dec 2016 23:21:24 -0800
James Johnson wrote:
> Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br
>
> Below is the code for making the smi to mol file. Can someone give me some
> guidance to generate all sterochem possibilities?
There are two ways to address this problem:
1
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