How To Install librdkit1 on Ubuntu

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

3 minutes • 458 words

Introduction

In this tutorial we learn how to install librdkit1 on Ubuntu.

What is `librdkit1`

librdkit1 is:

RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include:

Chemical reaction handling and transforms
Substructure searching with SMARTS
Canonical SMILES
Molecule-molecule alignment
Large number of molecular descriptors, including topological, compositional, EState, SlogP/SMR, VSA and Feature-map vectors
Fragmentation using RECAP rules
2D coordinate generation and depiction, including constrained depiction
3D coordinate generation using geometry embedding
UFF and MMFF94 forcefields
Chirality support, including calculation of (R/S) stereochemistry codes
2D pharmacophore searching
Fingerprinting, including Daylight-like, atom pairs, topological torsions, Morgan algorithm and MACCS keys
Calculation of shape similarity
Multi-molecule maximum common substructure
Machine-learning via clustering and information theory algorithms
Gasteiger-Marsili partial charge calculation

File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit binary format.

This package contains the shared libraries.

There are three methods to install librdkit1 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 librdkit1 Using apt-get

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

sudo apt-get update

After updating apt database, We can install librdkit1 using apt-get by running the following command:

sudo apt-get -y install librdkit1

Install librdkit1 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install librdkit1 using apt by running the following command:

sudo apt -y install librdkit1

Install librdkit1 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 librdkit1 using aptitude by running the following command:

sudo aptitude -y install librdkit1

How To Uninstall librdkit1 on Ubuntu

To uninstall only the librdkit1 package we can use the following command:

sudo apt-get remove librdkit1

Uninstall librdkit1 And Its Dependencies

To uninstall librdkit1 and its dependencies that are no longer needed by Ubuntu, we can use the command below:

sudo apt-get -y autoremove librdkit1

Remove librdkit1 Configurations and Data

To remove librdkit1 configuration and data from Ubuntu we can use the following command:

sudo apt-get -y purge librdkit1

Remove librdkit1 configuration, data, and all of its dependencies

We can use the following command to remove librdkit1 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge librdkit1

Dependencies

librdkit1 have the following dependencies:

References

librdkit1 website

Summary

In this tutorial we learn how to install librdkit1 package on Ubuntu using different package management tools: apt, apt-get and aptitude.