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] Problem with kekulization of molecule

Another thing to be aware of is that if there are multiple valid kekulizations that differ only in implicit hydrogen layout, RDKit will refuse to pick one. e.g. imidazole: "c1cncn1" will give you a "Can't kekulize mol" error, whereas "c1c[nH]cn1" and "c1cnc[nH]1" are sanitized without a problem.

Re: [Rdkit-discuss] Question about Run Reaction

Hi Taka, Yes, you need to sanitize every product molecule, after each step. Best wishes, Michal On 7 February 2016 at 01:58, Taka Seri wrote: > Hi Michal, > > Thank you for your quick and kind response. > I tried to sanitize mol according to your advice. > And my code worked

Re: [Rdkit-discuss] Problem with kekulization of molecule

Expanding a very small amount on Paolo's answer: The general rule of thumb is that you should be able to draw a valid conjugated Kekule structure for the molecule where the ring has 4N+2 electrons. That works for C1=[S+]SC=N1, which produces the output SMILES c1nc[s+]s1. -greg On Mon, Feb 8,

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

Dear Andrew, You can find an chemical example there:

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] rdkit 2015.09.2 in Anaconda still version 2015.03.1

hi, I am facing the same problem (in windows 7) Installed rdkit in miniconda by following command conda install -c https://conda.anaconda.org/rdkit rdkit by conda list command it is showing *rdkit 2015.09.2 np110py27_0rdkit* but with ​​ from rdkit import

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