How To Install python-rdkit on Ubuntu 18.04
Introduction
In this tutorial we learn how to install python-rdkit
on Ubuntu 18.04.
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 alogrithm 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 Ubuntu 18.04. 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 Ubuntu. 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 Ubuntu 18.04
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 Ubuntu 18.04, 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 Ubuntu 18.04 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
References
Summary
In this tutorial we learn how to install python-rdkit
package on Ubuntu 18.04 using different package management tools: apt
, apt-get
and aptitude
.