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
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