René's URL Explorer Experiment


Title: Getting Started with the RDKit in Python — The RDKit 2025.09.5 documentation

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rdkit-devel@lists.sourceforge.net

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Domain: www.rdkit.org

Links:

indexhttps://www.rdkit.org/docs/genindex.html
moduleshttps://www.rdkit.org/docs/py-modindex.html
nexthttps://www.rdkit.org/docs/RDKit_Book.html
previoushttps://www.rdkit.org/docs/Install.html
The RDKit 2025.09.5 documentationhttps://www.rdkit.org/docs/index.html
Getting Started with the RDKit in Pythonhttps://www.rdkit.org/docs/GettingStartedInPython.html
https://www.rdkit.org/docs/GettingStartedInPython.html#getting-started-with-the-rdkit-in-python
https://www.rdkit.org/docs/GettingStartedInPython.html#important-note
https://www.rdkit.org/docs/GettingStartedInPython.html#what-is-this
https://www.rdkit.org/docs/GettingStartedInPython.html#reading-drawing-and-writing-molecules
https://www.rdkit.org/docs/GettingStartedInPython.html#reading-single-molecules
rdkit.Chemhttps://www.rdkit.org/docs/source/rdkit.Chem.html#module-rdkit.Chem
rdkit.Chem.rdchem.Molhttps://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol
rdkit.Chem.rdchem.Molhttps://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol
rdkit.Chem.Draw.MolToImage()https://www.rdkit.org/docs/source/rdkit.Chem.Draw.html#rdkit.Chem.Draw.MolToImage
https://www.rdkit.org/docs/GettingStartedInPython.html#reading-sets-of-molecules
rdkit.Chem.rdmolfiles.SDMolSupplierhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SDMolSupplier
rdkit.Chem.rdmolfiles.SmilesMolSupplierhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SmilesMolSupplier
rdkit.Chem.rdmolfiles.ForwardSDMolSupplierhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.ForwardSDMolSupplier
https://www.rdkit.org/docs/GettingStartedInPython.html#writing-molecules
rdkit.Chemhttps://www.rdkit.org/docs/source/rdkit.Chem.html#module-rdkit.Chem
rdkit.Chem.AllChemhttps://www.rdkit.org/docs/source/rdkit.Chem.AllChem.html#module-rdkit.Chem.AllChem
Chem vs AllChemhttps://www.rdkit.org/docs/GettingStartedInPython.html#chem-vs-allchem
https://www.rdkit.org/docs/GettingStartedInPython.html#writing-sets-of-molecules
rdkit.Chem.rdmolfiles.SDWriterhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SDWriter
rdkit.Chem.rdmolfiles.SmilesWriterhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.SmilesWriter
rdkit.Chem.rdmolfiles.TDTWriterhttps://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.TDTWriter
https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-molecules
https://www.rdkit.org/docs/GettingStartedInPython.html#looping-over-atoms-and-bonds
https://www.rdkit.org/docs/GettingStartedInPython.html#ring-information
The SSSR Problemhttps://www.rdkit.org/docs/GettingStartedInPython.html#the-sssr-problem
rdkit.Chem.rdchem.RingInfohttps://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.RingInfo
https://www.rdkit.org/docs/GettingStartedInPython.html#modifying-molecules
rdkit.Chem.rdmolops.RemoveHs()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.RemoveHs
rdkit.Chem.rdmolops.Kekulize()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.Kekulize
rdkit.Chem.rdmolops.SanitizeMol()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.SanitizeMol
https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-2d-molecules-generating-depictions
rdkit.Chem.rdDepictor.Compute2DCoords()https://www.rdkit.org/docs/source/rdkit.Chem.rdDepictor.html#rdkit.Chem.rdDepictor.Compute2DCoords
https://www.rdkit.org/docs/_images/picture_1.png
https://www.rdkit.org/docs/_images/picture_0.png
https://www.rdkit.org/docs/_images/picture_3.png
https://www.rdkit.org/docs/_images/picture_2.png
https://www.rdkit.org/docs/_images/picture_4.png
rdkit.Chem.rdDepictor.Compute2DCoordsMimicDistmat()https://www.rdkit.org/docs/source/rdkit.Chem.rdDepictor.html#rdkit.Chem.rdDepictor.Compute2DCoordsMimicDistmat
https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules
[1]https://www.rdkit.org/docs/GettingStartedInPython.html#blaney
[2]https://www.rdkit.org/docs/GettingStartedInPython.html#rappe
[18]https://www.rdkit.org/docs/GettingStartedInPython.html#riniker2
[12]https://www.rdkit.org/docs/GettingStartedInPython.html#mmff1
[13]https://www.rdkit.org/docs/GettingStartedInPython.html#mmff2
[14]https://www.rdkit.org/docs/GettingStartedInPython.html#mmff3
[15]https://www.rdkit.org/docs/GettingStartedInPython.html#mmff4
[16]https://www.rdkit.org/docs/GettingStartedInPython.html#mmffs
[18]https://www.rdkit.org/docs/GettingStartedInPython.html#riniker2
https://www.rdkit.org/docs/GettingStartedInPython.html#preserving-molecules
https://www.rdkit.org/docs/GettingStartedInPython.html#drawing-molecules
rdkit.Chem.Drawhttps://www.rdkit.org/docs/source/rdkit.Chem.Draw.html#module-rdkit.Chem.Draw
https://www.rdkit.org/docs/GettingStartedInPython.html#metadata-in-molecule-images
https://www.rdkit.org/docs/GettingStartedInPython.html#substructure-searching
https://www.rdkit.org/docs/GettingStartedInPython.html#stereochemistry-in-substructure-matches
https://www.rdkit.org/docs/GettingStartedInPython.html#atom-map-indices-in-smarts
Chemical Reactionshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
https://www.rdkit.org/docs/GettingStartedInPython.html#advanced-substructure-matching
https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-transformations
Chemical Reactionshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
https://www.rdkit.org/docs/GettingStartedInPython.html#substructure-based-transformations
rdkit.Chem.rdmolops.ReplaceCore()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.ReplaceCore
rdkit.Chem.rdmolops.GetMolFrags()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.GetMolFrags
https://www.rdkit.org/docs/GettingStartedInPython.html#murcko-decomposition
[7]https://www.rdkit.org/docs/GettingStartedInPython.html#bemis1
https://www.rdkit.org/docs/GettingStartedInPython.html#maximum-common-substructure
https://www.rdkit.org/docs/GettingStartedInPython.html#findmcs
https://www.rdkit.org/docs/GettingStartedInPython.html#rascalmces
https://www.rdkit.org/docs/GettingStartedInPython.html#clustering-with-rascal
https://match.pmf.kg.ac.rs/electronic_versions/Match48/match48_197-207.pdfhttps://match.pmf.kg.ac.rs/electronic_versions/Match48/match48_197-207.pdf
https://eprints.whiterose.ac.uk/77598/https://eprints.whiterose.ac.uk/77598/
https://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
https://www.rdkit.org/docs/GettingStartedInPython.html#rdkit-topological-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#atom-pairs-and-topological-torsions
[3]https://www.rdkit.org/docs/GettingStartedInPython.html#carhart
[4]https://www.rdkit.org/docs/GettingStartedInPython.html#nilakantan
https://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints-circular-fingerprints
[5]https://www.rdkit.org/docs/GettingStartedInPython.html#rogers
Feature Definitions Used in the Morgan Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#feature-definitions-used-in-the-morgan-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#maccs-keys
https://www.rdkit.org/docs/GettingStartedInPython.html#explaining-bits-from-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#rdkit-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#generating-images-of-fingerprint-bits
rdkit.Chem.Draw.DrawMorganBit()https://www.rdkit.org/docs/source/rdkit.Chem.Draw.html#rdkit.Chem.Draw.DrawMorganBit
rdkit.Chem.Draw.DrawRDKitBit()https://www.rdkit.org/docs/source/rdkit.Chem.Draw.html#rdkit.Chem.Draw.DrawRDKitBit
https://www.rdkit.org/docs/GettingStartedInPython.html#picking-diverse-molecules-using-fingerprints
rdkit.SimDivFiltershttps://www.rdkit.org/docs/source/rdkit.SimDivFilters.html#module-rdkit.SimDivFilters
[6]https://www.rdkit.org/docs/GettingStartedInPython.html#ashton
https://www.rdkit.org/docs/GettingStartedInPython.html#generating-similarity-maps-using-fingerprints
[17]https://www.rdkit.org/docs/GettingStartedInPython.html#riniker
rdkit.Chem.Draw.SimilarityMapshttps://www.rdkit.org/docs/source/rdkit.Chem.Draw.SimilarityMaps.html#module-rdkit.Chem.Draw.SimilarityMaps
https://www.rdkit.org/docs/GettingStartedInPython.html#descriptor-calculation
List of Available Descriptorshttps://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors
rdkit.Chem.Descriptorshttps://www.rdkit.org/docs/source/rdkit.Chem.Descriptors.html#module-rdkit.Chem.Descriptors
https://www.rdkit.org/docs/GettingStartedInPython.html#calculating-all-descriptors
rdkit.Chem.Descriptorshttps://www.rdkit.org/docs/source/rdkit.Chem.Descriptors.html#module-rdkit.Chem.Descriptors
https://www.rdkit.org/docs/GettingStartedInPython.html#calculating-partial-charges
https://www.rdkit.org/docs/GettingStartedInPython.html#visualization-of-descriptors
https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
[11]https://www.rdkit.org/docs/GettingStartedInPython.html#rxnsmarts
https://www.rdkit.org/docs/GettingStartedInPython.html#drawing-chemical-reactions
https://www.rdkit.org/docs/GettingStartedInPython.html#advanced-reaction-functionality
https://www.rdkit.org/docs/GettingStartedInPython.html#protecting-atoms
https://www.rdkit.org/docs/GettingStartedInPython.html#recap-implementation
[8]https://www.rdkit.org/docs/GettingStartedInPython.html#lewell
rdkit.Chem.Recaphttps://www.rdkit.org/docs/source/rdkit.Chem.Recap.html#module-rdkit.Chem.Recap
https://www.rdkit.org/docs/GettingStartedInPython.html#brics-implementation
[9]https://www.rdkit.org/docs/GettingStartedInPython.html#degen
https://www.rdkit.org/docs/GettingStartedInPython.html#other-fragmentation-approaches
https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features-and-pharmacophores
https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features
https://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints
The RDKit Bookhttps://www.rdkit.org/docs/RDKit_Book.html
rdkit.Chem.Pharm2D.Generatehttps://www.rdkit.org/docs/source/rdkit.Chem.Pharm2D.Generate.html#module-rdkit.Chem.Pharm2D.Generate
[10]https://www.rdkit.org/docs/GettingStartedInPython.html#gobbi
rdkit.Chem.Pharm2D.Gobbi_Pharm2Dhttps://www.rdkit.org/docs/source/rdkit.Chem.Pharm2D.Gobbi_Pharm2D.html#module-rdkit.Chem.Pharm2D.Gobbi_Pharm2D
https://www.rdkit.org/docs/GettingStartedInPython.html#molecular-fragments
rdkit.Chem.rdfragcatalog.FragCataloghttps://www.rdkit.org/docs/source/rdkit.Chem.rdfragcatalog.html#rdkit.Chem.rdfragcatalog.FragCatalog
rdkit.Chem.rdfragcatalog.FragCatParamshttps://www.rdkit.org/docs/source/rdkit.Chem.rdfragcatalog.html#rdkit.Chem.rdfragcatalog.FragCatParams
rdkit.Chem.rdfragcatalog.FragCatalog.GetEntryDownIds()https://www.rdkit.org/docs/source/rdkit.Chem.rdfragcatalog.html#rdkit.Chem.rdfragcatalog.FragCatalog.GetEntryDownIds
rdkit.Chem.rdfragcatalog.FragCataloghttps://www.rdkit.org/docs/source/rdkit.Chem.rdfragcatalog.html#rdkit.Chem.rdfragcatalog.FragCatalog
rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRankerhttps://www.rdkit.org/docs/source/rdkit.ML.InfoTheory.rdInfoTheory.html#rdkit.ML.InfoTheory.rdInfoTheory.InfoBitRanker
https://www.rdkit.org/docs/GettingStartedInPython.html#r-group-decomposition
rdkit.Chem.rdRGroupDecomposition.RGroupDecompose()https://www.rdkit.org/docs/source/rdkit.Chem.rdRGroupDecomposition.html#rdkit.Chem.rdRGroupDecomposition.RGroupDecompose
https://www.rdkit.org/docs/GettingStartedInPython.html#searching-synthon-spaces
Enaminehttps://enamine.net
ChemSpacehttps://chem-space.com
https://www.rdkit.org/docs/GettingStartedInPython.html#how-it-works
Liphardt and Sanderhttps://doi.org/10.1021/acs.jcim.3c00290
https://www.rdkit.org/docs/GettingStartedInPython.html#database-preparation
https://www.rdkit.org/docs/GettingStartedInPython.html#memory-usage
https://www.rdkit.org/docs/GettingStartedInPython.html#id20
https://www.rdkit.org/docs/GettingStartedInPython.html#similarity-searching
https://www.rdkit.org/docs/GettingStartedInPython.html#limiting-hits
https://www.rdkit.org/docs/GettingStartedInPython.html#incremental-search
https://www.rdkit.org/docs/GettingStartedInPython.html#non-chemical-functionality
https://www.rdkit.org/docs/GettingStartedInPython.html#bit-vectors
https://www.rdkit.org/docs/GettingStartedInPython.html#discrete-value-vectors
https://www.rdkit.org/docs/GettingStartedInPython.html#d-grids
https://www.rdkit.org/docs/GettingStartedInPython.html#points
https://www.rdkit.org/docs/GettingStartedInPython.html#getting-help
https://www.rdkit.org/docs/GettingStartedInPython.html#advanced-topics-warnings
https://www.rdkit.org/docs/GettingStartedInPython.html#editing-molecules
rdkit.Chem.rdchem.RWMolhttps://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.RWMol
https://www.rdkit.org/docs/GettingStartedInPython.html#miscellaneous-tips-and-hints
https://www.rdkit.org/docs/GettingStartedInPython.html#chem-vs-allchem
rdkit.Chemhttps://www.rdkit.org/docs/source/rdkit.Chem.html#module-rdkit.Chem
rdkit.Chem.AllChemhttps://www.rdkit.org/docs/source/rdkit.Chem.AllChem.html#module-rdkit.Chem.AllChem
https://www.rdkit.org/docs/GettingStartedInPython.html#the-sssr-problem
rdkit.Chem.rdmolops.GetSSSR()https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.GetSSSR
https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors
http://www.chemcomp.com/journal/vsadesc.htmhttp://www.chemcomp.com/journal/vsadesc.htm
http://www.chemcomp.com/journal/vsadesc.htmhttp://www.chemcomp.com/journal/vsadesc.htm
http://www.chemcomp.com/journal/vsadesc.htmhttp://www.chemcomp.com/journal/vsadesc.htm
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-3d-descriptors
https://doi.org/10.1002/9780470125861.ch5https://doi.org/10.1002/9780470125861.ch5
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9780470125861.ch5https://doi.org/10.1002/9780470125861.ch5
https://doi.org/10.1063/1.464689https://doi.org/10.1063/1.464689
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/9783527618279.ch37https://doi.org/10.1002/9783527618279.ch37
https://doi.org/10.1002/jcc.540160303https://doi.org/10.1002/jcc.540160303
https://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#feature-definitions-used-in-the-morgan-fingerprints
https://www.rdkit.org/docs/GettingStartedInPython.html#filtering-molecular-datasets
https://www.rdkit.org/docs/GettingStartedInPython.html#lipinski-rule-of-5
[19]https://www.rdkit.org/docs/GettingStartedInPython.html#lipinski
https://www.rdkit.org/docs/GettingStartedInPython.html#filtering-unwanted-substructures
[20]https://www.rdkit.org/docs/GettingStartedInPython.html#pains
[21]https://www.rdkit.org/docs/GettingStartedInPython.html#brenk
[22]https://www.rdkit.org/docs/GettingStartedInPython.html#jadhav
[23]https://www.rdkit.org/docs/GettingStartedInPython.html#doveston
1https://www.rdkit.org/docs/GettingStartedInPython.html#id1
2https://www.rdkit.org/docs/GettingStartedInPython.html#id2
3https://www.rdkit.org/docs/GettingStartedInPython.html#id11
4https://www.rdkit.org/docs/GettingStartedInPython.html#id12
5https://www.rdkit.org/docs/GettingStartedInPython.html#id13
6https://www.rdkit.org/docs/GettingStartedInPython.html#id14
7https://www.rdkit.org/docs/GettingStartedInPython.html#id10
8https://www.rdkit.org/docs/GettingStartedInPython.html#id17
9https://www.rdkit.org/docs/GettingStartedInPython.html#id18
10https://www.rdkit.org/docs/GettingStartedInPython.html#id19
11https://www.rdkit.org/docs/GettingStartedInPython.html#id16
The RDKit Bookhttps://www.rdkit.org/docs/RDKit_Book.html
12https://www.rdkit.org/docs/GettingStartedInPython.html#id4
13https://www.rdkit.org/docs/GettingStartedInPython.html#id5
14https://www.rdkit.org/docs/GettingStartedInPython.html#id6
15https://www.rdkit.org/docs/GettingStartedInPython.html#id7
16https://www.rdkit.org/docs/GettingStartedInPython.html#id8
17https://www.rdkit.org/docs/GettingStartedInPython.html#id15
1https://www.rdkit.org/docs/GettingStartedInPython.html#id3
2https://www.rdkit.org/docs/GettingStartedInPython.html#id9
19https://www.rdkit.org/docs/GettingStartedInPython.html#id21
20https://www.rdkit.org/docs/GettingStartedInPython.html#id22
21https://www.rdkit.org/docs/GettingStartedInPython.html#id23
22https://www.rdkit.org/docs/GettingStartedInPython.html#id24
23https://www.rdkit.org/docs/GettingStartedInPython.html#id25
https://www.rdkit.org/docs/GettingStartedInPython.html#license
http://creativecommons.org/licenses/by-sa/4.0/http://creativecommons.org/licenses/by-sa/4.0/
https://www.rdkit.org/docs/index.html
Table of Contentshttps://www.rdkit.org/docs/index.html
Getting Started with the RDKit in Pythonhttps://www.rdkit.org/docs/GettingStartedInPython.html
Important notehttps://www.rdkit.org/docs/GettingStartedInPython.html#important-note
What is this?https://www.rdkit.org/docs/GettingStartedInPython.html#what-is-this
Reading, Drawing, and Writing Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#reading-drawing-and-writing-molecules
Reading single moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#reading-single-molecules
Reading sets of moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#reading-sets-of-molecules
Writing moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#writing-molecules
Writing sets of moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#writing-sets-of-molecules
Working with Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#working-with-molecules
Looping over Atoms and Bondshttps://www.rdkit.org/docs/GettingStartedInPython.html#looping-over-atoms-and-bonds
Ring Informationhttps://www.rdkit.org/docs/GettingStartedInPython.html#ring-information
Modifying moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#modifying-molecules
Working with 2D molecules: Generating Depictionshttps://www.rdkit.org/docs/GettingStartedInPython.html#working-with-2d-molecules-generating-depictions
Working with 3D Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules
Preserving Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#preserving-molecules
Drawing Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#drawing-molecules
Metadata in Molecule Imageshttps://www.rdkit.org/docs/GettingStartedInPython.html#metadata-in-molecule-images
Substructure Searchinghttps://www.rdkit.org/docs/GettingStartedInPython.html#substructure-searching
Stereochemistry in substructure matcheshttps://www.rdkit.org/docs/GettingStartedInPython.html#stereochemistry-in-substructure-matches
Atom Map Indices in SMARTShttps://www.rdkit.org/docs/GettingStartedInPython.html#atom-map-indices-in-smarts
Advanced substructure matchinghttps://www.rdkit.org/docs/GettingStartedInPython.html#advanced-substructure-matching
Chemical Transformationshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-transformations
Substructure-based transformationshttps://www.rdkit.org/docs/GettingStartedInPython.html#substructure-based-transformations
Murcko Decompositionhttps://www.rdkit.org/docs/GettingStartedInPython.html#murcko-decomposition
Maximum Common Substructurehttps://www.rdkit.org/docs/GettingStartedInPython.html#maximum-common-substructure
FindMCShttps://www.rdkit.org/docs/GettingStartedInPython.html#findmcs
RascalMCEShttps://www.rdkit.org/docs/GettingStartedInPython.html#rascalmces
Clustering with Rascalhttps://www.rdkit.org/docs/GettingStartedInPython.html#clustering-with-rascal
Fingerprinting and Molecular Similarityhttps://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
RDKit (Topological) Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#rdkit-topological-fingerprints
Atom Pairs and Topological Torsionshttps://www.rdkit.org/docs/GettingStartedInPython.html#atom-pairs-and-topological-torsions
Morgan Fingerprints (Circular Fingerprints)https://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints-circular-fingerprints
MACCS Keyshttps://www.rdkit.org/docs/GettingStartedInPython.html#maccs-keys
Explaining bits from fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#explaining-bits-from-fingerprints
Morgan Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#morgan-fingerprints
RDKit Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#rdkit-fingerprints
Generating images of fingerprint bitshttps://www.rdkit.org/docs/GettingStartedInPython.html#generating-images-of-fingerprint-bits
Picking Diverse Molecules Using Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#picking-diverse-molecules-using-fingerprints
Generating Similarity Maps Using Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#generating-similarity-maps-using-fingerprints
Descriptor Calculationhttps://www.rdkit.org/docs/GettingStartedInPython.html#descriptor-calculation
Calculating All Descriptorshttps://www.rdkit.org/docs/GettingStartedInPython.html#calculating-all-descriptors
Calculating Partial Chargeshttps://www.rdkit.org/docs/GettingStartedInPython.html#calculating-partial-charges
Visualization of Descriptorshttps://www.rdkit.org/docs/GettingStartedInPython.html#visualization-of-descriptors
Chemical Reactionshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
Drawing Chemical Reactionshttps://www.rdkit.org/docs/GettingStartedInPython.html#drawing-chemical-reactions
Advanced Reaction Functionalityhttps://www.rdkit.org/docs/GettingStartedInPython.html#advanced-reaction-functionality
Protecting Atomshttps://www.rdkit.org/docs/GettingStartedInPython.html#protecting-atoms
Recap Implementationhttps://www.rdkit.org/docs/GettingStartedInPython.html#recap-implementation
BRICS Implementationhttps://www.rdkit.org/docs/GettingStartedInPython.html#brics-implementation
Other fragmentation approacheshttps://www.rdkit.org/docs/GettingStartedInPython.html#other-fragmentation-approaches
Chemical Features and Pharmacophoreshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features-and-pharmacophores
Chemical Featureshttps://www.rdkit.org/docs/GettingStartedInPython.html#chemical-features
2D Pharmacophore Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#d-pharmacophore-fingerprints
Molecular Fragmentshttps://www.rdkit.org/docs/GettingStartedInPython.html#molecular-fragments
R-Group Decompositionhttps://www.rdkit.org/docs/GettingStartedInPython.html#r-group-decomposition
Searching Synthon Spaceshttps://www.rdkit.org/docs/GettingStartedInPython.html#searching-synthon-spaces
How It Workshttps://www.rdkit.org/docs/GettingStartedInPython.html#how-it-works
Database Preparationhttps://www.rdkit.org/docs/GettingStartedInPython.html#database-preparation
Memory Usagehttps://www.rdkit.org/docs/GettingStartedInPython.html#memory-usage
Substructure Searchinghttps://www.rdkit.org/docs/GettingStartedInPython.html#id20
Similarity Searchinghttps://www.rdkit.org/docs/GettingStartedInPython.html#similarity-searching
Limiting Hitshttps://www.rdkit.org/docs/GettingStartedInPython.html#limiting-hits
Incremental Searchhttps://www.rdkit.org/docs/GettingStartedInPython.html#incremental-search
Non-Chemical Functionalityhttps://www.rdkit.org/docs/GettingStartedInPython.html#non-chemical-functionality
Bit vectorshttps://www.rdkit.org/docs/GettingStartedInPython.html#bit-vectors
Discrete value vectorshttps://www.rdkit.org/docs/GettingStartedInPython.html#discrete-value-vectors
3D gridshttps://www.rdkit.org/docs/GettingStartedInPython.html#d-grids
Pointshttps://www.rdkit.org/docs/GettingStartedInPython.html#points
Getting Helphttps://www.rdkit.org/docs/GettingStartedInPython.html#getting-help
Advanced Topics/Warningshttps://www.rdkit.org/docs/GettingStartedInPython.html#advanced-topics-warnings
Editing Moleculeshttps://www.rdkit.org/docs/GettingStartedInPython.html#editing-molecules
Miscellaneous Tips and Hintshttps://www.rdkit.org/docs/GettingStartedInPython.html#miscellaneous-tips-and-hints
Chem vs AllChemhttps://www.rdkit.org/docs/GettingStartedInPython.html#chem-vs-allchem
The SSSR Problemhttps://www.rdkit.org/docs/GettingStartedInPython.html#the-sssr-problem
List of Available Descriptorshttps://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-descriptors
List of Available 3D Descriptorshttps://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-3d-descriptors
List of Available Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#list-of-available-fingerprints
Feature Definitions Used in the Morgan Fingerprintshttps://www.rdkit.org/docs/GettingStartedInPython.html#feature-definitions-used-in-the-morgan-fingerprints
Filtering Molecular Datasetshttps://www.rdkit.org/docs/GettingStartedInPython.html#filtering-molecular-datasets
Lipinski Rule of 5https://www.rdkit.org/docs/GettingStartedInPython.html#lipinski-rule-of-5
Filtering Unwanted Substructureshttps://www.rdkit.org/docs/GettingStartedInPython.html#filtering-unwanted-substructures
Licensehttps://www.rdkit.org/docs/GettingStartedInPython.html#license
Installationhttps://www.rdkit.org/docs/Install.html
The RDKit Bookhttps://www.rdkit.org/docs/RDKit_Book.html
Show Sourcehttps://www.rdkit.org/docs/_sources/GettingStartedInPython.rst.txt
indexhttps://www.rdkit.org/docs/genindex.html
moduleshttps://www.rdkit.org/docs/py-modindex.html
nexthttps://www.rdkit.org/docs/RDKit_Book.html
previoushttps://www.rdkit.org/docs/Install.html
The RDKit 2025.09.5 documentationhttps://www.rdkit.org/docs/index.html
Getting Started with the RDKit in Pythonhttps://www.rdkit.org/docs/GettingStartedInPython.html
Sphinxhttps://www.sphinx-doc.org/

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