chemdiff command not found

In this troubleshooting guide we learn how to fix chemdiff command not found error message

Introduction

When you run more command in linux terminal / console, you get the following error message

chemdiff: command not found

or when using sudo you get the following error message

sudo: chemdiff: command not found

In Ubuntu chemdiff is provided by indigo-utils package.

indigo-utils is:

Indigo is a C++ based organic chemistry and cheminformatics software environment. Features Include:

Molecule and reaction rendering including SVG support
Automatic layout for SMILES-represented molecules and reactions
Canonical (isomeric) SMILES computation
Exact matching, substructure matching, SMARTS matching
Matching of tautomers and resonance structures
Molecule fingerprinting, molecule similarity computation
Fast enumeration of SSSR rings, subtrees, and edge sugraphs
Molecular weight, molecular formula computation
R-Group deconvolution and scaffold detection
Computation of the exact maximum common substructure for an arbitrary amount of input structures
Combinatorial chemistry * Plugin support in the API

File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and SMARTS.

This package contains the following utilities:

indigo-depict: Molecule and reaction rendering utility
indigo-cano: Canonical SMILES generator
indigo-deco: R-Group deconvolution utility
chemdiff: Visual comparison of two SDF or SMILES files (needs the JAVA libraries)

To fix this problem, we can install more using the command below.

sudo apt-get -y install indigo-utils

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install indigo-utils.

sudo apt -y install indigo-utils

Or if you have aptitude installed you can use the following command.

sudo aptitude install indigo-utils

In this tutorial we learn how to fix chemdiff command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.