SMI_CANONICALISE

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]

--random-order

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

--help

print usage message and exit