RDKit Installation Options

Provides a quick introduction of RDKit installation options on Linux systems. None of them is easy.

There are several options to install RDKit on Linux systems. But none of them is easy.

1. Go to RDKit GitHub site at https://github.com/rdkit/rdkit.

2. Click "RPMs for RedHat Enterprise Linux, CentOS, and Fedora. Contributed by Gianluca Sforna" link in the binary installation section. I see the "rdkit" binary package Website at https://copr.fedorainfracloud.org/coprs/giallu/rdkit/.

3. Try the suggested installation command. I see the following error. The last build on fedorainfracloud.org was in 2017 and failed.

herong$ sudo dnf install python-rdkit

No match for argument: python-rdkit
Error: Unable to find a match: python-rdkit

4. Try to install it with Python 2 package installer. I got the error saying that the RDKit package available does not support for Python 2.7. Too bad. Nobody is updating RDKit package in pypi.org.

herong$ python2 --version
Python 2.7.16

herong$ python2 -m pip search rdkit
rdkit (2009.Q1-1)                   - RDKit Cheminformatics Library

herong$ python2 -m pip install rdkit
Collecting rdkit
Could not find a version that satisfies the requirement rdkit
   (from versions: )
No matching distribution found for rdkit

5. The last option is to go back to the RDKit GitHub site, click "Clone or Download" and build it from the downloaded source code. See the next tutorial for more information.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Molecule Mass and Weight

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

RDKit: Open-Source Cheminformatics Software

 What Is RDKit

RDKit Installation Options

 Build RDKit from Source Code on CentOS System

 Compile, Link and Run RDKit C++ API Examples

 Try RDKit Python API

 PyMol Installation

 PyMol GUI and CLI

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 HGNC (HUGO Gene Nomenclature Committee)

 Resources and Tools

 Molecule Related Terminologies


 Full Version in PDF/EPUB