Daniel Lowe

Tangentially given an input like `rel-(1R,2S,5R)-2-Isopropyl-5-methylcyclohexanol` if OPSIN is asked for extended SMILES (`-o extendedsmi` on the command-line) this relative stereochemistry is indicated in the extended SMILES `C(C)(C)[C@H]1[C@@H](C[C@@H](CC1)C)O |$_AV:1;;;2;1;6;5;4;3;1;O$,o1:3,4,6|` via...

The verbose output does also handle cis/trans e.g. `trans` I think the full list of types are: `EorZ`, `RorS`, `cisOrTrans`, `alphaOrBeta`, `relativeCisTrans`, `opticalRotation`, `endoExoSynAnti`, `axial`, `RAC`, `REL`, `dlStereochemistry`, `carbohydrateConfigurationalPrefix`. (and...

The error it's giving is due to it being unable to assign each stereochemistry description to a distinct stereocenter. Assuming the structure is intended to be: ``` C(C)C=1C(=CC=C2C=C(C=C(C12)C1=C(C=C2C(=NC(=NC2=C1F)OC[C@]12CCCN2C[C@@H](C1)F)N1C[C@H]2C[C@H]([C@@H](C1)C2)O)F)O)F ``` There...

>Do you know when OPSIN will support axial chirality Probably not for awhile as it's relatively rarely besides with BINAP compounds >if there’s any software that support this kind of...

@dkatzel-ncats My colleague ran into this issue. I've added pull request #23 which I believe resolves this issue. The issue was reproducible on the latest version from GitHub, when producing...

OPSIN does have a similar mechanism to this for handling structures like `imidazoline` which would out of the box support triple bonds. What it doesn't expect is the second locant...

`(E)-1-Cyclohexyl-4,4,4-trifluorobut-2-en-1-yl-2-cyano-2-diazoacetate` should presumably be `(E)-1-Cyclohexyl-4,4,4-trifluorobut-2-en-1-yl 2-cyano-2-diazoacetate`. OPSIN does try and infer when a hyphen was intended to be a space, but isn't perfect at doing so. For `(±)-(1R,5R,3R)-N-Benzyl-1-cyano-2-(hydroxymethyl)-3-(trifluoromethyl)cyclopropane-1-carboxamide` and `(±)-(1R,5R,3R)-N-Benzyl-1-cyano-2-(hydroxymethyl)-3-(pentafluoro-λ6-sulfanyl)cyclo-propane-1-carboxamide`...

The IUPAC recommendation is to put the stereochemistry first. As it was somewhat common in the literature for names like `octa-3E,5E-diene` to be given support was added, but the implementation...

OPSIN's implementation of the CIP rules is to the best of my knowledge robust. The depiction producted by OPSIN and CDKdepict are equivalent

As far as I'm aware the carbene takes precedence: https://iupac.qmul.ac.uk/BlueBook/P4.html According to that list radicals are the most preferred of all functional groups, while nitriles are rank 14. So I...