NAME

       smi_canonicalise - canonicalise SMILES

DESCRIPTION

       USAGE

              smi_canonicalise [<args>] [<files>]

       DESCRIPTION

              smi_canonicalise  reads in files with SMILES descriptors and outputs them according to stable atom
              ordering established by Graph::Nauty.  Moieties, if more than one, are  ordered  in  lexicographic
              order.

       OPTIONS

       --infer-hydrogens
              infer hydrogen atom counts according to valency rules [default]

       --no-infer-hydrogens
              do not infer hydrogen atom counts

       --aromatise
              aromatise Kekule structures (experimental)

       --no-aromatise
              do not attempt to aromatise [default]

       --kekulise
              kekulise simple aromatic structures (experimental)

       --no-kekulise
              do not attempt to kekulise [default]

       --canonicalise-haloanions
              canonicalise the representation of haloanions [default]

       --no-canonicalise-haloanions
              retain input representation of haloanions

       --canonicalise-nitro-groups
              canonicalise  the  representation  of  nitro  groups  by  converting  them  from *-[N+]([O-])=O to
              *-N(=O)=O

       --no-canonicalise-nitro-groups
              retain input representation of nitro groups [default]

       --ignore-class
              ignore SMILES atom class in canonicalisation (useful for testing)

       --random-order
              instead of canonical, output SMILES in random order (useful for testing)

       --help print usage message and exit

smi_canonicalise 0.3.0+svn878+branch+system+deps   March 2025                                SMI_CANONICALISE(1)