Good afternoon!
Using RDKit C++ version 2023-03-1, I am trying to generate the
stereochemistry of this molecule using the smiles format:
string molecule = "C[C@H]1CC[C@@H](C)NC1";
RDKit::ROMol* mol = RDKit::SmilesToMol(molecule);
vector
Thanks Paolo - I should have found this before posting!
Cheers
James
On 9 May 2021, at 15:05, Paolo Tosco wrote:
Hi James,
IIRC that's a known open issue with the way spirocyclic pseudochiral centers
are handled:
https://github.com/rdkit/rdkit/issues/3490
Cheers,
p.
On Sun, May 9, 2021
Hi James,
IIRC that's a known open issue with the way spirocyclic pseudochiral
centers are handled:
https://github.com/rdkit/rdkit/issues/3490
Cheers,
p.
On Sun, May 9, 2021 at 10:15 AM James Davidson
wrote:
> Dear All,
>
>
>
> I am having some issues with tetrahedral stereochemistry
Dear All,
I am having some issues with tetrahedral stereochemistry perception in RDKit
(2020.09.4) for a certain class of molecule.
Here's an example (rendered using cdk-depict):
[cid:image002.png@01D744AE.E7C7ACA0]
R/S labels.
-greg
>
>
> Lukas
>
>
>
> *From: *Greg Landrum
> *Date: *Wednesday, 30 October 2019 at 04:28
> *To: *Lukas Pravda
> *Cc: *RDKIT mailing list
> *Subject: *Re: [Rdkit-discuss] Stereochemistry in rdkit
>
>
>
> Hi Lukas,
>
>
>
> The stereoc
: [Rdkit-discuss] Stereochemistry in rdkit
Hi Lukas,
The stereochemistry tags that the RDKit uses in determining bond wedging (or
for SMILES, generating 3D coordinates, etc.) are the ChiralTags on the atoms:
CHI_TETRAHEDRAL_CW and CHI_TETRAHEDRAL_CCW. The current RDKit stereo
representation
Hi everyone,
I tried to virtually deprotect molecules using
the AllChem.ReplaceSubstructs() function. Stereochemistry of adjacent atoms
gets inverted in ChiralTag but not in _CIPCode. This gives me the wrong
output SMILES:
from rdkit import Chem
from rdkit.Chem import AllChem
from
To close the loop on this: the bug fix is now merged onto master. The ring
stereochemistry code now handles spiro centers.
Here's the little demo of that:
In [2]: print(Chem.CanonSmiles('O[C@H]1CC[C@]11CC[C@@](Cl)(Br)CC1'))
O[C@H]1CC[C@]12CC[C@@](Cl)(Br)CC2
Unlike previously (see the bug report)
SetIsotope(0)
>
> sdf.write(mol)
>
>
>
>
>
> GIST is updated to include this: https://gist.github.com/jepdavidson/
> fdfbf6366a17f4829de3d4de22f3b442
>
>
>
> Kind regards
>
>
>
> James
>
>
>
>
>
> *From:* Greg Landrum [mailto:greg
2017 03:45
To: James Davidson
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral
centres(?)
Hi James,
This is definitely a bug. The problem seems to be connected to the way what the
RDKit calls "ring stereochemistry" i
Hi James,
This is definitely a bug. The problem seems to be connected to the way what
the RDKit calls "ring stereochemistry" is handled when there are spiro
linkages.
Here's the github issue: https://github.com/rdkit/rdkit/issues/1294
I'll take a look.
Best,
-greg
On Tue, Feb 7, 2017 at
Dear All,
I have hit what I think is a problem with stereochemistry perception/handling
for certain types of pseudochiral and/or spirocyclic systems.
Basically I am observing that some types of input tetrahedral stereochemical
information gets lost when an RDKit molecule is generated.
But I
Sure !
I was only looking for a way of doing the things with bonds that
would be similar to the one with the atoms.
All the best,
Jean-Marc
Le 19/12/2016 à 11:55, Paul Emsley a écrit :
> On 19/12/2016 10:42, Jean-Marc Nuzillard wrote:
>> Thank you all!
>>
>> One more point:
>>
>> How do I get
On 19/12/2016 10:42, Jean-Marc Nuzillard wrote:
> Thank you all!
>
> One more point:
>
> How do I get the bond indexes for which the E/Z configuration has been set?
> I seems there are no "magic" properties for bonds and no HasProp() function
> for bonds.
Iterate through the bond list and use
Thank you all!
One more point:
How do I get the bond indexes for which the E/Z configuration has been set?
I seems there are no "magic" properties for bonds and no HasProp()
function for bonds.
All the best,
Jean-Marc
Le 19/12/2016 à 04:40, Greg Landrum a écrit :
One more piece that
One more piece that might help: the allHsExplicit to MolToSmiles() is there
to make sure that implicit Hs (Hs not actually in the graph) show up in the
output SMILES inside square brackets:
In [12]: m = Chem.MolFromSmiles('CC(O)(Cl)')
In [13]: Chem.MolToSmiles(m,allHsExplicit=True)
Out[13]:
On Mon, Dec 19, 2016 at 1:00 AM, Paolo Tosco wrote:
>
> It looks like allHsExplicit=True prevents SMILES chirality specifications
> from being output:
>
In [8]: m = Chem.MolFromSmiles('C[C@H](F)(Cl)')
In [9]: Chem.MolToSmiles(m,isomericSmiles=True,allHsExplicit=True)
Dear Jean-Marc,
as lactic2.sdf is a 3D structure which does not carry any
stereochemistry information in the SDF file, you will need to perceive
stereochemistry from the 3D structure with
Chem.AssignAtomChiralTagsFromStructure(mol)
before calling Chem.AssignStereochemistry().
It looks like
Hi again,
When I run:
#
from rdkit import Chem
molfilename = "lactic2.sdf"
mol = Chem.SDMolSupplier(molfilename, removeHs = False)[0]
Chem.AssignStereochemistry(mol, cleanIt=False, force=False,
flagPossibleStereoCenters=True)
chiralAtoms = [a for a in mol.GetAtoms() if
Rob,
You're actually correct in the first instance, that SMILES is correct and
you can define the stereochemistry like that. Although the molecule may not
be constitutionally chiral, those atoms are and are (pseudo)asymetric. In
Cahn-Ingold-Prelog notation they get a lower case r or s.
Try
Thank you very much Peter & Peter.
The result makes perfect sense now. As I suspected, I did miss something
obvious - the mirror plane.
Best regards,
Rob
On Fri, May 27, 2016 at 3:14 PM, Peter Gedeck
wrote:
> Hello Rob
>
> The compound is not chiral. There is a
Hello Rob
The compound is not chiral. There is a mirror plane that contains the
5-ring and the C-NH3 bond. There is a cis / trans stereoisomers here like
in 1,4-dichloro-cyclohexane. That cannot be defined using the @symbols.
However I cannot tell you how to do this for cases like this in SMILES.
Hi all,
I know there's been a lot of discussion about stereochemistry in RDKit, and
I don't really want to open the can of worms particularly, but I would
appreciate gaining a little more understanding to help explain an
observation I've had (and it could be I've missed something really obvious).
On Mon, Mar 14, 2016 at 6:39 AM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
>
> You might want also to consider nitrones
> https://en.wikipedia.org/wiki/Nitrone
> that are sometimes written (CAS does it!) with
> a nitrogen atom surrounded by a C=C and a C=O double bond.
>
Dear all,
for sure, having a double bond surrounded by four single bonds makes
the assignment of the E/Z configuration simpler.
You might want also to consider nitrones
https://en.wikipedia.org/wiki/Nitrone
that are sometimes written (CAS does it!) with
a nitrogen atom surrounded by a C=C and a
Dear all,
for sure, having a double bond surrounded by four single bonds makes
the assignment of the E/Z configuration simpler.
My might want also to consider nitrones
https://en.wikipedia.org/wiki/Nitrone
that are sometimes written (CAS does it!) with
a nitrogen atom surrounded by a C=C and a
Im agree with you but if you consider triphenylphosphorane such as
ethoxycarbonylmethylene triphenylphosphorane you will have different
equilibrium between the cis and trans form function of the organic solvent. If
you increase the polarity of the solvent, the equilibrium shifts in the
Le 11/03/2016 10:38, Giuseppe Marco Randazzo a écrit :
An example can be the case of this isomerism is given by
triphenylphosphorane (Witting reagents).
Wittig reagents with their three identical phenyl groups on the
phosphorus atom
do not present any intriguing configuration problem around
I think these are all different. The substructure in question here is
R1O/P(=O)=C/R2
I think I managed to convince myself that stereochemistry here is
reasonable by rewriting the structure as:
R1O/[P+]([O-])=C/R2
but I would still certainly like some real examples.
-greg
On Fri, Mar 11, 2016
I do not have the feeling that the handling of a C=P bond should be
different of the one of a C=C bond.
Jean-Marc
Le 11/03/2016 10:12, Greg Landrum a écrit :
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard
> wrote:
On Fri, Mar 11, 2016 at 10:05 AM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
>
> Le 11/03/2016 05:11, Greg Landrum a écrit :
>
>
> Here's a question for the chemists in the group: do we need to be
> concerned about representing the stereochemistry of the P=C bond in
> substructures
Dear all,
Le 11/03/2016 05:11, Greg Landrum a écrit :
Dear all,
Here's a question for the chemists in the group: do we need to be
concerned about representing the stereochemistry of the P=C bond in
substructures like O=P(/O)=C/C under normal circumstances?
It has a meaning to write that
ahhh :-) now i understand. Ok it’s an other point of question so…
if the oxygen bonded to the Phosphor of the group C=P is in Cis or Trans. Yes,
describe this feature make sense.
The bond C=P is blocked, so the oxygen is not free to be rotated along the bond
C=P.
Finally, i think is
Hi Marco,
Sorry I wasn't clear in the original question. I was asking about the
cis/trans stereochemistry of the C=P bond. I agree that it's not generally
useful to think of bonds as being chiral.[1]
-greg
[1] There's an argument to be made here about the best way to represent
atropisomers, but
Dear Greg,
as i know from organic/inorganic and physical chemistry courses a
stereochemistry like that is unreal and i think it’s a bug of the pubchem
depiction generator.
Atoms can be chiral.
Bonds are not chiral.
Why bonds are not chiral? The answer is given by the molecular orbital
Dear all,
Here's a question for the chemists in the group: do we need to be concerned
about representing the stereochemistry of the P=C bond in substructures
like O=P(/O)=C/C under normal circumstances?
Here's a pubchem compound example that has the double bond crossed
(possibly leading one to
Interesting discussion, never decided myself whether it was worth handling
two implied neighbors:
C[S@H](=O)
Probably v. low barrier to inversion for this example but thought I'd share.
John
--
Site24x7 APM Insight:
On Feb 10, 2016, at 6:09 AM, Greg Landrum wrote:
> I agree that this is a bug.
Glad to hear. I was wondering how I would get my code to handle that case
otherwise.
On Feb 10, 2016, at 4:19 PM, David Cosgrove wrote:
> As chiralities go, this one has turned out to be quite valuable!
You can
Not sure that the anything[S@H](=O) molecules exist...
Jean-Marc
Le 11/02/2016 11:04, John M a écrit :
Interesting discussion, never decided myself whether it was worth
handling two implied neighbors:
C[S@H](=O)
Probably v. low barrier to inversion for this example but thought I'd
Hi Andrew,
As chiralities go, this one has turned out to be quite valuable!
https://en.wikipedia.org/wiki/Esomeprazole
Dave
On Mon, Feb 8, 2016 at 3:05 PM, Andrew Dalke
wrote:
> Hi!
>
> Could someone explain to this non-chemist what the chirality means in
> the
I agree that this is a bug.
Here's a simpler reproducible:
In [11]: Chem.CanonSmiles("C[S@](Cl)=O")
Out[11]: 'C[S@@](=O)Cl'
In [12]: Chem.CanonSmiles("C[S@]2=O.Cl2")
Out[12]: 'C[S@](=O)Cl'
Note that it seems to have something to do with the special handling of the
S=O, because this looks fine:
The other thing to remember is that at room temperature and pressure, small
sulphoxides will be able to interconvert forms from R to S rapidly. It's only
when the groups on the sulphur get big enoough (or interconnected, like in a 3
or 4 member ring) that they actually can be resolved and
On Feb 8, 2016, at 7:03 PM, Paolo Tosco wrote:
> ... there is a "ghost" atom involved in determining the sulfur chirality,
> which is the sulfur lone pair. Even if this is not in the Daylight specs, the
> lone-pair is usually treated as an implicit hydrogen, and therefore
> considered as the
Dear Andrew,
that functional group is a sulfoxide, and it is indeed chiral because
has a lone pair on the sulfur, which is pyramidal; there is a short
description here:
https://en.wikipedia.org/wiki/Sulfoxide
So it is the same (R,S) chirality you would have on a tetrahedral
carbon. The carbon
Thanks Paolo and Hannes for pointing me to sulfoxide. I am enlightened!
I assume this is something that every chemist knows, but it's not mentioned in
the Daylight SMILES documentation (or the OpenSMILES documentation), so I had
no clue. I wonder how many more cases there are like that.
Any
On Mon, 8 Feb 2016 16:05:46 +0100
Andrew Dalke wrote:
> Hi!
>
> Could someone explain to this non-chemist what the chirality means
> in the following?
>
> CN[S@@](=O)C1=CC=CC=C1
>
> It comes from PubChem id 12194260 at
>
Hi!
Could someone explain to this non-chemist what the chirality means in the
following?
CN[S@@](=O)C1=CC=CC=C1
It comes from PubChem id 12194260 at
https://pubchem.ncbi.nlm.nih.gov/compound/12194260 .
Isn't this a symmetric structure, which can't have an orientation at that
point? Even
De : Andrew Dalke <da...@dalkescientific.com>
Envoyé : lundi 8 février 2016 16:05
À : rdkit-discuss@lists.sourceforge.net Discuss
Objet : [Rdkit-discuss] stereochemistry of S with degree 3
Hi!
Could someone explain to this non-chemist what the chirality
Sorry for the noise, this is the same message as before, just with less
typos and repetitions. I couldn't help re-sending it after reading what
I had written!
Dear Andrew,
the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns
'CN[S@@](=O)c1c1'
and
Dear Andrew,
the reason why Chem.CanonSmiles("CN[S@@](=O)C1=CC=CC=C1") returns
'CN[S@@](=O)c1c1'
and Chem.CanonSmiles("CN1.[S@@]1(=O)C1=CC=CC=C1") returns
'CN[S@](=O)c1c1'
is that there is a "ghost" atom involved in determining the sulfur
chirality, which is a lone pair, which is the
On Wed, Nov 18, 2015 at 1:13 PM, Dante wrote:
> Hi all,
>
> I have run across some errors when attempting to use RunReactants on
> molecules with specified stereochemistry, as show in the below two example
> cases:
>
> I notice that the same molecules will run without
Hi all,
I have run across some errors when attempting to use RunReactants on
molecules with specified stereochemistry, as show in the below two example
cases:
I notice that the same molecules will run without errors using this
reaction specification if stereochemistry is turned off.
case 1:
>>>
Hi James,
I know that my opinion might sound extreme but I had this discussion
many times (mostly regarding tautomerism which is, however, similar in
some way). The problem is, you can look at a chemical structure in
many different ways - two scenarios are:
1. What can I perceive from a chemical
Hehe, that is why I keep my computers always really cold when I run RDKit ...
-
| Markus Sitzmann
| markus.sitzm...@gmail.com
On 20.08.2015, at 04:33, Peter Shenkin shen...@gmail.com wrote:
Maybe when you have a toolkit as blazingly fast as RDKit it
This isn't a simple one, so it may take a bit to get to an answer that's
comprehensible.
There are two things going on here in the RDKit:
1) Ring stereochemistry
2) stereochemistry about nitrogen centers
Let's start with the second, because it's easier: RDKit does not generally
believe in
I agree with remove - the chance that you destroy actual information
by this is low - or in other words, the chance that steroinformation
on three-coordinate N is spurious I would expect as high.
Markus
On Thu, Aug 20, 2015 at 4:30 PM, Greg Landrum greg.land...@gmail.com wrote:
This isn't a
Dear RDKit community,
I'm trying to use RDKit to read in Corina generated stereoisomers (from a
Mol file), assign chiral tags and stereochemistry to the structure and
output the canonical smiles string for each isomer of a given molecule (in
Python), when I do this, half the canonical smiles
Maybe when you have a toolkit as blazingly fast as RDKit it captures the
chirality of N center before it has time to interconvert
-P.
On Wed, Aug 19, 2015 at 10:17 PM, John M john.wilkinson...@gmail.com
wrote:
More odd is the carbon stereocentre with two methyls...
Generally trivalent
Hi Rob,
The results below are quite strange. As John has already pointed out: there
really shouldn't be chirality present on either the N+ or the C that has
two methyls attached.
I tried to reproduce the problem by running corina myself using the same
command-line options you provided (from
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