---
name: "smi_isomorphism"
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_isomorphism"
---

# smi\_isomorphism(1)

detect isomorphism between SMILES

## NAME

smi\_isomorphism - detect isomorphism between SMILES

## DESCRIPTION

USAGE

-

  smi\_isomorphism \[\<args\>\] \[\<files\>\]

DESCRIPTION

-

  smi\_isomorphism reads in files with three tab-separated columns:

-

  \<ID\> \<SMILES\_1\> \<SMILES\_2\>

-

  The program then attempts to detect isomorphism between \<SMILES\_1\> and \<SMILES\_2\> on each line. If immediate isomorphism is not detected, step-by-step simplifications are performed in order to lead both SMILES to isomorphism.

OPTIONS

- **--remove-alkali-bonds**

  add alkali bond removal to the list of simplifications

- **--print-side-of-superfluous-moieties**

  identify which of the compared sides has superfluous molecular entities

- **--check-isomorphism**

  perform an extra isomorphism check on molecular entities detected as isomorphic by comparing their canonical representations

- **--help**

  print usage message and exit