obabel -Hinchi lists the options. Read option 'n' will do it. obabel -:"InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3 Noel" -iinchi -osmi -an CCO Noel
More importantly, do not convert InChIs to SMILES without understanding the caveats. InChI is not a storage format for chemical structures. Regards, Noel On Fri, 7 Jul 2023 at 02:26, Francois Berenger <mli...@ligand.eu> wrote: > Dear Sivani, > > Maybe, put all the identifiers in a new file using shell commands: > > $ obabel input.inchi -O output.smi > $ cut -f2 input.inchi > input.names > > If the obabel conversion doesn't remove any line, it should be safe > to use the following unix command: > > $ paste output.smi input.names > named_output.smi > > Regards, > F. > > On 29/06/2023 23:23, Sivani Baskaran via OpenBabel-discuss wrote: > > Hello, > > > > I am trying to generate a SMILES notation from standardized InChIs. I > > have a long list of chemicals and would like to retain an identifier > > in the output file like you do when parsing other conversions. > > > > I've tried a few different ways of doing this based on the > > documentation, but the identifier is never included in the output > > file. > > > > System/Version: Windows 11, CL Open Babel 3.1.1 > > > > Goal: Convert an InChI file with InChI followed by the name or a > > number of a chemical to a .smi file with the SMILES and the identifier > > (name/integer) for a set of chemicals. > > > > Failed attempts: > > * obabel "./substances.inchi" -O "./substances.SMI" > > * obabel "./substances.inchi" -O "./substances.SMI" -n > > * obabel -i inchi "./substances.inchi" -o smi -O "./substances.SMI" > > * obabel -i inchi "./substances.inchi" -o smi -O "./substances.SMI" -n > > * obabel -i inchi "./substances.inchi" -n -o smi -O "./substances.SMI" > > > > Contents of "substances.inchi" (also attached) > > InChI=1S/C6H4ClNO2/c7-5-1-3-6(4-2-5)8(9)10/h1-4H name > > InChI=1S/C6H6N2O2/c7-5-1-3-6(4-2-5)8(9)10/h1-4H,7H2 another, name > > InChI=1S/C6H5NO3/c8-6-3-1-5(2-4-6)7(9)10/h1-4,8H 3 > > InChI=1S/C6H5ClO2S/c7-5-1-3-6(4-2-5)10(8)9/h1-4H,(H,8,9) name-2 > > > > What I want the output to look like: > > c1cc(ccc1Cl)N(=O)=O name > > c1cc(ccc1N)N(=O)=O another, name > > c1cc(ccc1N(=O)=O)O 3 > > c1cc(ccc1Cl)S(=O)O name-2 > > > > How can I ensure the output will also have the identifier without > > resorting to having an individual InChI file for each chemical? Please > > note, all my identifiers are integers, but for testing purposes I > > included text string examples. > > > > Thanks, > > Sivani > > The confidentiality or integrity of this message can not be guaranteed > > following transmission on the Internet. The addressee should be aware > > of this before using the contents of this message. > > > > _______________________________________________ > > OpenBabel-discuss mailing list > > OpenBabel-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
