---
name: "smi_canonicalise"
section: "1"
platform: "linux"
package: "smiles-scripts"
version: "0.3.0+svn878+branch+system+deps-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/smi_canonicalise"
---

# smi\_canonicalise(1)

canonicalise SMILES

## 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