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