Example Commands

The following section shows several common command-line executions of tautomers. Each example is followed by an explanation of what the program will do.

Consider the following input file, guanine.smi, that contains just the following line: c1[nH]c2c(=O)[nH]c(nc2n1)N

prompt> tautomers guanine.smi output.smi

Which should write the following 15 structures to the file output.smi.

c1[nH]c2c(=O)[nH]c(nc2n1)N untitled1_1
c1[nH]c2c(n1)c(=O)[nH]c(n2)N untitled1_2

Please note that if tautomers fails to find tautomers for a molecule, it will output the molecule to a fail file. This occurs if the algorithm times out. e.g. benzene would not be in the fail file but a very large peptide might be. Name of the fail file is either ‘tautomers.fail’ or ‘prefix.fail’ if prefix is specified by -prefix flag.