How To Install python-rdkit on Debian 10

Learn how to install python-rdkit on Debian 10 with this tutorial. python-rdkit is Collection of cheminformatics and machine-learning software

Introduction

In this tutorial we learn how to install python-rdkit on Debian 10.

What is python-rdkit

python-rdkit 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.

There are three methods to install python-rdkit on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install python-rdkit Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install python-rdkit

Install python-rdkit Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install python-rdkit

Install python-rdkit 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

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

sudo aptitude -y install python-rdkit

How To Uninstall python-rdkit on Debian 10

To uninstall only the python-rdkit package we can use the following command:

sudo apt-get remove python-rdkit

Uninstall python-rdkit And Its Dependencies

To uninstall python-rdkit and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove python-rdkit

Remove python-rdkit Configurations and Data

To remove python-rdkit configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge python-rdkit

Remove python-rdkit configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge python-rdkit

Dependencies

python-rdkit have the following dependencies:

References

Summary

In this tutorial we learn how to install python-rdkit package on Debian 10 using different package management tools: apt, apt-get and aptitude.