R groups (alkyl)

Issue #39 resolved
Jiri Novotny
created an issue


having this IUPAC: alkyl(dimethyl)[2-(hydroxyimino)-2-(pyridin-2-yl)ethyl]ammonium

I get this error: alkyl(dimethyl)[2-(hydroxyimino)-2-(pyridin-2-yl)ethyl]ammonium was uninterpretable due to the following section of the name: alkyl The following was not understandable in the context it was used: alk

Is it possible to also support these alkyl (R) groups? They are normally noted with * in SMILES.



Comments (5)

  1. Daniel Lowe repo owner

    Hi Jiri,

    Unfortunately due to a conflict of interest with my day job, I am unable to add support for generic structures to the official version of OPSIN.

    If you feel adventurous it is very easy to add basic support for them to OPSIN. e.g. Using the latest code in the repository, add the following to simpleSubstituents.xml

    <token value="-*" homology="Alkyl">alkyl</token>

    (the homology attribute helps indicate the meaning of the *, and prevents OPSIN confusing it with an attachment point [one of OPSIN's output options represents attachment points as *s])

    OPSIN's SMILES output for that structure is then:


    Using OPSIN's extended SMILES output [ OpsinResult#getExtendedSmiles() ] this produces:

    *[N+](CC(C1=NC=CC=C1)=NO)(C)C |$Alkyl_p$|

    Some tools like MarvinSketch and the CDK toolkit will assign the * atom the pseudoatom value of "Alkyl" if given the extended SMILES.

  2. Jiri Novotny reporter

    Nice! I will try that. OPSIN command-line interface also supports extended SMILES?

    Just one question, what are the commands to build OPSIN jar with dependencies? I have tried Maven, but without success (dependencies were not included). Thanks.

  3. Daniel Lowe repo owner

    I've just pushed a commit that adds extended SMILES to the command-line interface. e.g. -oextendedsmi At the moment, besides generics, only structure-based polymers and substituents (when used in combination with the wildcardRadicals option) have different extended SMILES output as compared to the standard SMILES output.

    Regarding building, in the root directory of OPSIN run the following command:

    mvn package assembly:assembly

    This will build a file called opsin-3.0-SNAPSHOT-jar-with-dependencies.jar in the target directory. I should probably add a section on building from source to the documentation. (the next version will actually be either 2.3.0 or 2.2.1, but having the next version always be 3.0-SNAPSHOT makes it easier to always depend on the latest version)

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