Hi all, I think I'm missing something simple in how I am trying to convert a FASTA file to SMILES:
% obabel -V Open Babel 3.0.0 -- Mar 31 2020 -- 14:14:15 % printf ">test\nA\n" > test.fasta % obabel test.fasta -O test.smi 1 molecule converted % cat test.smi [H].[O].[P].[O].[O].[O].[C].[C].[O].[C].[O].[C].[C].[N].[C].[N].[C].[C].[N].[N].[C].[N].[C].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[O].[P].[O].[O].[O].[C].[C].[O].[C].[O].[C].[C].[N].[C].[O].[N].[C].[O].[C].[C].[C].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H] test % That means Open Babel interprets the sequence as double-stranded DNA (not protein), though it doesn't create any bonds. % obabel -L fasta One of the formats fasta -- FASTA format A file format used to exchange information between genetic sequence databases Read Options e.g. -as 1 Output single-stranded DNA t <turns> Use the specified number of base pairs per turn (e.g., 10) s Output single bonds only b Disable bonding entirely Write Options e.g. -xn n Omit title and comments Specification at: http://www.ebi.ac.uk/help/formats_frame.html I tried to change the settings manually, and while I was able to switch to single-stranded DNA, I couldn't get the bonding to work: % obabel test.fasta -O test.smi -a1b 1 molecule converted % cat test.smi [H].[O].[P].[O].[O].[O].[C].[C].[O].[C].[O].[C].[C].[N].[C].[N].[C].[C].[N].[N].[C].[N].[C].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H] test % obabel test.fasta -O test.smi -as 1 molecule converted % cat test.smi [H].[O].[P].[O].[O].[O].[C].[C].[O].[C].[O].[C].[C].[N].[C].[N].[C].[C].[N].[N].[C].[N].[C].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[O].[P].[O].[O].[O].[C].[C].[O].[C].[O].[C].[C].[N].[C].[O].[N].[C].[O].[C].[C].[C].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H].[H] test A cursory look at the code doesn't reveal anything obviously wrong. Perhaps it's me? Andrew da...@dalkescientific.com _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
