smi_canonicalise - canonicalise SMILES
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]
- --random-order
- instead of canonical, output SMILES in random order (useful for
testing)
- --help
- print usage message and exit