How To Install rdkit on Fedora 34

rdkit is Chemical informatics and machine learning toolkit Chemical informatics and machine learning toolkit

Introduction

In this tutorial we learn how to install rdkit on Fedora 34.

What is `rdkit`

Chemical informatics and machine learning toolkit rdkit 2019.03.3 14.fc34 x86_64 3.0 M rdkit-2019.03.3-14.fc34.src.rpm fedora Chemical informatics and machine learning toolkit http BSD Chemical informatics and machine learning toolkit

We can use yum or dnf to install rdkit on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install rdkit.

Install rdkit on Fedora 34 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install rdkit using dnf by running the following command:

sudo dnf -y install rdkit

Install rdkit on Fedora 34 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

After updating yum database, We can install rdkit using yum by running the following command:

sudo yum -y install rdkit

How To Uninstall rdkit on Fedora 34

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

sudo dnf remove rdkit

rdkit Package Contents on Fedora 34

/usr/lib/.build-id
/usr/lib/.build-id/02
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/usr/lib/RDStreams/libRDKitRDStreams.so.1.2019.03.3
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/usr/lib/libRDKitCatalogs.so.1
/usr/lib/libRDKitCatalogs.so.1.2019.03.3
/usr/lib/libRDKitChemReactions.so.1
/usr/lib/libRDKitChemReactions.so.1.2019.03.3
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/usr/lib/libRDKitChemTransforms.so.1.2019.03.3
/usr/lib/libRDKitChemicalFeatures.so.1
/usr/lib/libRDKitChemicalFeatures.so.1.2019.03.3
/usr/lib/libRDKitDataStructs.so.1
/usr/lib/libRDKitDataStructs.so.1.2019.03.3
/usr/lib/libRDKitDepictor.so.1
/usr/lib/libRDKitDepictor.so.1.2019.03.3
/usr/lib/libRDKitDescriptors.so.1
/usr/lib/libRDKitDescriptors.so.1.2019.03.3
/usr/lib/libRDKitDistGeomHelpers.so.1
/usr/lib/libRDKitDistGeomHelpers.so.1.2019.03.3
/usr/lib/libRDKitDistGeometry.so.1
/usr/lib/libRDKitDistGeometry.so.1.2019.03.3
/usr/lib/libRDKitEigenSolvers.so.1
/usr/lib/libRDKitEigenSolvers.so.1.2019.03.3
/usr/lib/libRDKitFMCS.so.1
/usr/lib/libRDKitFMCS.so.1.2019.03.3
/usr/lib/libRDKitFileParsers.so.1
/usr/lib/libRDKitFileParsers.so.1.2019.03.3
/usr/lib/libRDKitFilterCatalog.so.1
/usr/lib/libRDKitFilterCatalog.so.1.2019.03.3
/usr/lib/libRDKitFingerprints.so.1
/usr/lib/libRDKitFingerprints.so.1.2019.03.3
/usr/lib/libRDKitForceField.so.1
/usr/lib/libRDKitForceField.so.1.2019.03.3
/usr/lib/libRDKitForceFieldHelpers.so.1
/usr/lib/libRDKitForceFieldHelpers.so.1.2019.03.3
/usr/lib/libRDKitFragCatalog.so.1
/usr/lib/libRDKitFragCatalog.so.1.2019.03.3
/usr/lib/libRDKitGraphMol.so.1
/usr/lib/libRDKitGraphMol.so.1.2019.03.3
/usr/lib/libRDKitInfoTheory.so.1
/usr/lib/libRDKitInfoTheory.so.1.2019.03.3
/usr/lib/libRDKitMMPA.so.1
/usr/lib/libRDKitMMPA.so.1.2019.03.3
/usr/lib/libRDKitMolAlign.so.1
/usr/lib/libRDKitMolAlign.so.1.2019.03.3
/usr/lib/libRDKitMolCatalog.so.1
/usr/lib/libRDKitMolCatalog.so.1.2019.03.3
/usr/lib/libRDKitMolChemicalFeatures.so.1
/usr/lib/libRDKitMolChemicalFeatures.so.1.2019.03.3
/usr/lib/libRDKitMolDraw2D.so.1
/usr/lib/libRDKitMolDraw2D.so.1.2019.03.3
/usr/lib/libRDKitMolHash.so.1
/usr/lib/libRDKitMolHash.so.1.2019.03.3
/usr/lib/libRDKitMolStandardize.so.1
/usr/lib/libRDKitMolStandardize.so.1.2019.03.3
/usr/lib/libRDKitMolTransforms.so.1
/usr/lib/libRDKitMolTransforms.so.1.2019.03.3
/usr/lib/libRDKitOptimizer.so.1
/usr/lib/libRDKitOptimizer.so.1.2019.03.3
/usr/lib/libRDKitPartialCharges.so.1
/usr/lib/libRDKitPartialCharges.so.1.2019.03.3
/usr/lib/libRDKitRDBoost.so.1
/usr/lib/libRDKitRDBoost.so.1.2019.03.3
/usr/lib/libRDKitRDGeneral.so.1
/usr/lib/libRDKitRDGeneral.so.1.2019.03.3
/usr/lib/libRDKitRDGeometryLib.so.1
/usr/lib/libRDKitRDGeometryLib.so.1.2019.03.3
/usr/lib/libRDKitRDInchiLib.so.1
/usr/lib/libRDKitRDInchiLib.so.1.2019.03.3
/usr/lib/libRDKitRGroupDecomposition.so.1
/usr/lib/libRDKitRGroupDecomposition.so.1.2019.03.3
/usr/lib/libRDKitReducedGraphs.so.1
/usr/lib/libRDKitReducedGraphs.so.1.2019.03.3
/usr/lib/libRDKitSLNParse.so.1
/usr/lib/libRDKitSLNParse.so.1.2019.03.3
/usr/lib/libRDKitShapeHelpers.so.1
/usr/lib/libRDKitShapeHelpers.so.1.2019.03.3
/usr/lib/libRDKitSimDivPickers.so.1
/usr/lib/libRDKitSimDivPickers.so.1.2019.03.3
/usr/lib/libRDKitSmilesParse.so.1
/usr/lib/libRDKitSmilesParse.so.1.2019.03.3
/usr/lib/libRDKitStructChecker.so.1
/usr/lib/libRDKitStructChecker.so.1.2019.03.3
/usr/lib/libRDKitSubgraphs.so.1
/usr/lib/libRDKitSubgraphs.so.1.2019.03.3
/usr/lib/libRDKitSubstructLibrary.so.1
/usr/lib/libRDKitSubstructLibrary.so.1.2019.03.3
/usr/lib/libRDKitSubstructMatch.so.1
/usr/lib/libRDKitSubstructMatch.so.1.2019.03.3
/usr/lib/libRDKitTrajectory.so.1
/usr/lib/libRDKitTrajectory.so.1.2019.03.3
/usr/lib/libRDKithc.so.1
/usr/lib/libRDKithc.so.1.2019.03.3
/usr/share/doc/rdkit
/usr/share/doc/rdkit/ReleaseNotes.md
/usr/share/licenses/rdkit
/usr/share/licenses/rdkit/license.txt
/usr/lib/.build-id
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/usr/lib64/RDStreams/libRDKitRDStreams.so.1
/usr/lib64/RDStreams/libRDKitRDStreams.so.1.2019.03.3
/usr/lib64/libRDKitAlignment.so.1
/usr/lib64/libRDKitAlignment.so.1.2019.03.3
/usr/lib64/libRDKitCatalogs.so.1
/usr/lib64/libRDKitCatalogs.so.1.2019.03.3
/usr/lib64/libRDKitChemReactions.so.1
/usr/lib64/libRDKitChemReactions.so.1.2019.03.3
/usr/lib64/libRDKitChemTransforms.so.1
/usr/lib64/libRDKitChemTransforms.so.1.2019.03.3
/usr/lib64/libRDKitChemicalFeatures.so.1
/usr/lib64/libRDKitChemicalFeatures.so.1.2019.03.3
/usr/lib64/libRDKitDataStructs.so.1
/usr/lib64/libRDKitDataStructs.so.1.2019.03.3
/usr/lib64/libRDKitDepictor.so.1
/usr/lib64/libRDKitDepictor.so.1.2019.03.3
/usr/lib64/libRDKitDescriptors.so.1
/usr/lib64/libRDKitDescriptors.so.1.2019.03.3
/usr/lib64/libRDKitDistGeomHelpers.so.1
/usr/lib64/libRDKitDistGeomHelpers.so.1.2019.03.3
/usr/lib64/libRDKitDistGeometry.so.1
/usr/lib64/libRDKitDistGeometry.so.1.2019.03.3
/usr/lib64/libRDKitEigenSolvers.so.1
/usr/lib64/libRDKitEigenSolvers.so.1.2019.03.3
/usr/lib64/libRDKitFMCS.so.1
/usr/lib64/libRDKitFMCS.so.1.2019.03.3
/usr/lib64/libRDKitFileParsers.so.1
/usr/lib64/libRDKitFileParsers.so.1.2019.03.3
/usr/lib64/libRDKitFilterCatalog.so.1
/usr/lib64/libRDKitFilterCatalog.so.1.2019.03.3
/usr/lib64/libRDKitFingerprints.so.1
/usr/lib64/libRDKitFingerprints.so.1.2019.03.3
/usr/lib64/libRDKitForceField.so.1
/usr/lib64/libRDKitForceField.so.1.2019.03.3
/usr/lib64/libRDKitForceFieldHelpers.so.1
/usr/lib64/libRDKitForceFieldHelpers.so.1.2019.03.3
/usr/lib64/libRDKitFragCatalog.so.1
/usr/lib64/libRDKitFragCatalog.so.1.2019.03.3
/usr/lib64/libRDKitGraphMol.so.1
/usr/lib64/libRDKitGraphMol.so.1.2019.03.3
/usr/lib64/libRDKitInfoTheory.so.1
/usr/lib64/libRDKitInfoTheory.so.1.2019.03.3
/usr/lib64/libRDKitMMPA.so.1
/usr/lib64/libRDKitMMPA.so.1.2019.03.3
/usr/lib64/libRDKitMolAlign.so.1
/usr/lib64/libRDKitMolAlign.so.1.2019.03.3
/usr/lib64/libRDKitMolCatalog.so.1
/usr/lib64/libRDKitMolCatalog.so.1.2019.03.3
/usr/lib64/libRDKitMolChemicalFeatures.so.1
/usr/lib64/libRDKitMolChemicalFeatures.so.1.2019.03.3
/usr/lib64/libRDKitMolDraw2D.so.1
/usr/lib64/libRDKitMolDraw2D.so.1.2019.03.3
/usr/lib64/libRDKitMolHash.so.1
/usr/lib64/libRDKitMolHash.so.1.2019.03.3
/usr/lib64/libRDKitMolStandardize.so.1
/usr/lib64/libRDKitMolStandardize.so.1.2019.03.3
/usr/lib64/libRDKitMolTransforms.so.1
/usr/lib64/libRDKitMolTransforms.so.1.2019.03.3
/usr/lib64/libRDKitOptimizer.so.1
/usr/lib64/libRDKitOptimizer.so.1.2019.03.3
/usr/lib64/libRDKitPartialCharges.so.1
/usr/lib64/libRDKitPartialCharges.so.1.2019.03.3
/usr/lib64/libRDKitRDBoost.so.1
/usr/lib64/libRDKitRDBoost.so.1.2019.03.3
/usr/lib64/libRDKitRDGeneral.so.1
/usr/lib64/libRDKitRDGeneral.so.1.2019.03.3
/usr/lib64/libRDKitRDGeometryLib.so.1
/usr/lib64/libRDKitRDGeometryLib.so.1.2019.03.3
/usr/lib64/libRDKitRDInchiLib.so.1
/usr/lib64/libRDKitRDInchiLib.so.1.2019.03.3
/usr/lib64/libRDKitRGroupDecomposition.so.1
/usr/lib64/libRDKitRGroupDecomposition.so.1.2019.03.3
/usr/lib64/libRDKitReducedGraphs.so.1
/usr/lib64/libRDKitReducedGraphs.so.1.2019.03.3
/usr/lib64/libRDKitSLNParse.so.1
/usr/lib64/libRDKitSLNParse.so.1.2019.03.3
/usr/lib64/libRDKitShapeHelpers.so.1
/usr/lib64/libRDKitShapeHelpers.so.1.2019.03.3
/usr/lib64/libRDKitSimDivPickers.so.1
/usr/lib64/libRDKitSimDivPickers.so.1.2019.03.3
/usr/lib64/libRDKitSmilesParse.so.1
/usr/lib64/libRDKitSmilesParse.so.1.2019.03.3
/usr/lib64/libRDKitStructChecker.so.1
/usr/lib64/libRDKitStructChecker.so.1.2019.03.3
/usr/lib64/libRDKitSubgraphs.so.1
/usr/lib64/libRDKitSubgraphs.so.1.2019.03.3
/usr/lib64/libRDKitSubstructLibrary.so.1
/usr/lib64/libRDKitSubstructLibrary.so.1.2019.03.3
/usr/lib64/libRDKitSubstructMatch.so.1
/usr/lib64/libRDKitSubstructMatch.so.1.2019.03.3
/usr/lib64/libRDKitTrajectory.so.1
/usr/lib64/libRDKitTrajectory.so.1.2019.03.3
/usr/lib64/libRDKithc.so.1
/usr/lib64/libRDKithc.so.1.2019.03.3
/usr/share/doc/rdkit
/usr/share/doc/rdkit/ReleaseNotes.md
/usr/share/licenses/rdkit
/usr/share/licenses/rdkit/license.txt

References

[rdkit website](http://www.rdkit.org/ http://www.rdkit.org/)

Summary

In this tutorial we learn how to install rdkit on Fedora 34 using yum and dnf.