> I tried this with mdl mol files and here the result is as expected (all files > identical), > so this might occur with xyz files only, but since no warning is issued when > combining > xyz files and the --canonical flag this is rather dangerous..
I'm not sure where you would give such a warning. The problem is that the canonicalization algorithm requires the bond graph. In an xyz file, that has to be perceived. I haven't analyzed your case in particular, but I suspect that the perception is somewhat different between the various files (e.g., if you output canonical SMILES instead). -Geoff
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