How To Install indigo-utils on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 460 words

Introduction

In this tutorial we learn how to install indigo-utils on Ubuntu.

What is `indigo-utils`

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)

There are three methods to install indigo-utils on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install indigo-utils Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install indigo-utils using apt-get by running the following command:

sudo apt-get -y install indigo-utils

Install indigo-utils Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install indigo-utils using apt by running the following command:

sudo apt -y install indigo-utils

Install indigo-utils Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install indigo-utils using aptitude by running the following command:

sudo aptitude -y install indigo-utils

How To Uninstall indigo-utils on Ubuntu

To uninstall only the indigo-utils package we can use the following command:

sudo apt-get remove indigo-utils

Uninstall indigo-utils And Its Dependencies

To uninstall indigo-utils and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove indigo-utils

Remove indigo-utils Configurations and Data

To remove indigo-utils configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge indigo-utils

Remove indigo-utils configuration, data, and all of its dependencies

We can use the following command to remove indigo-utils configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge indigo-utils

Dependencies

indigo-utils have the following dependencies:

References

indigo-utils website

Summary

In this tutorial we learn how to install indigo-utils package on Ubuntu using different package management tools: apt, apt-get and aptitude.