Daniel Lowe

Just to give a brief update, this isn't as straight forward to support as I anticipated due to how thio sugars are handled: https://iupac.qmul.ac.uk/2carb/14n15.html#15 Would you expect `5a-Thio-β-D-glucopyranose` to be...

OPSIN's initialisation message can also be silenced using: Logger.getLogger("uk.ac.cam.ch.wwmm.opsin").setLevel(Level.ERROR); before OPSIN is instantiated. Unless you've set the log level below INFO it should not be outputting any messages other than...

> O-(1-Methyl-2-methoxycarbonylvinyl) 4-Bromophenylthionophosphonic monochloride is another example where I get confused, I thought the O- should indicate that there is a P-ester, but I get a trivalent Cl CC(=CC(=O)OC)[ClH]P(O)(=O)C1=CC=C(C=C1)Br I...

`; ` is implemented in a really weird way (it's fudged as a space). I think it should be simple enough to support semicolon more like how space/hyphen are allowed...

> No rush, I fudge it in the reaction extractor anyways :-). Just thought a useful addition/relaxation. Yeah I think it's definitely a good idea. My initial idea of treating...

OPSIN definitely does support your second example: https://opsin.ch.cam.ac.uk/#sodium%20(35S)-methanesulfonate As OPSIN doesn't output Mol files, how is OPSIN's output being converted to Mol? I think this may also be the answer...

>Would it be difficult to reverse OPSIN? Yes, my understanding is that the reverse would require almost entirely different code. The only synergies I can immediately think of is that...

Sorry for the delay in following up on this. Which tool are you using to read the CML? OpenBabel and CDK give the R enantiomer. I did observe that MarvinJS...

This is unfortunately a "limitation in OPSIN's implementation of the sequence rules". The symmetry of the molecule means that the stereocentre at position 4 is dependant on the configuration of...

This can be done via the API as follows: ``` NameToStructure nts = NameToStructure.getInstance(); NameToStructureConfig n2sconfig = NameToStructureConfig.getDefaultConfigInstance(); n2sconfig.setWarnRatherThanFailOnUninterpretableStereochemistry(true); OpsinResult o = nts.parseChemicalName("(1S,2R,4s)-1,2,4-TRIMETHYLCYCLOPENTANE", n2sconfig); System.out.println(o.getMessage()); System.out.println(o.getSmiles()); ``` From the command-line...