[Rdkit-discuss] Stereochemistry

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

Re: [Rdkit-discuss] Stereochemistry problem with spiro centre

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

Re: [Rdkit-discuss] Stereochemistry problem with spiro centre

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

[Rdkit-discuss] Stereochemistry problem with spiro centre

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]

Re: [Rdkit-discuss] Stereochemistry in rdkit

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

Re: [Rdkit-discuss] Stereochemistry in rdkit

: [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

[Rdkit-discuss] Stereochemistry inversion upon replacement

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

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

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)

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

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

Re: [Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

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

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" 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

[Rdkit-discuss] Stereochemistry issue for spirocycles/pseudochiral centres(?)

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

Re: [Rdkit-discuss] Stereochemistry

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

Re: [Rdkit-discuss] Stereochemistry

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

Re: [Rdkit-discuss] Stereochemistry

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

Re: [Rdkit-discuss] Stereochemistry

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]:

Re: [Rdkit-discuss] Stereochemistry

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)

Re: [Rdkit-discuss] Stereochemistry

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

[Rdkit-discuss] Stereochemistry

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

Re: [Rdkit-discuss] Stereochemistry Perception

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

Re: [Rdkit-discuss] Stereochemistry Perception

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

Re: [Rdkit-discuss] Stereochemistry Perception

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.

[Rdkit-discuss] Stereochemistry Perception

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).

Re: [Rdkit-discuss] Stereochemistry question

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. >

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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:

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] Stereochemistry question

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

[Rdkit-discuss] Stereochemistry question

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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:

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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:

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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 >

[Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] stereochemistry of S with degree 3

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

Re: [Rdkit-discuss] Stereochemistry breaks ReactionRunner.cpp

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

[Rdkit-discuss] Stereochemistry breaks ReactionRunner.cpp

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: >>>

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

[Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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

Re: [Rdkit-discuss] Stereochemistry - Differences between RDKit Indigo

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