smi_canonicalise1

Overview

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