Wolfram Function Repository
Instant-use add-on functions for the Wolfram Language
Function Repository Resource:
Search the PubChem database for similar compounds
ResourceFunction["PubChemSimilaritySearch"][mol] returns a list of "PubChemCompoundID" identifiers for compounds similar to the molecule or chemical entity mol. | |
ResourceFunction["PubChemSimilaritySearch"][mol,"Molecule"] returns a list of Molecule objects constructed from the external identifiers similar to mol. |
"Similarity2DSearch" | Tanimoto similarity of topological fingerprints |
"Similarity3DSearch" | Tanimoto similarity of 3D shape fingerprints |
"Original" | exact match to input |
"Parent" | parent compound |
"SameStereo" | same stereo |
"SameIsotopes" | same isotopes |
"SameConnectivity" | same connectivity |
"SameFormula" | same molecular formula |
"SameTautomer" | same tautomer |
"SameParent" | same parent |
"SameParentStereo" | same parent stereo |
"SameParentIsotopes" | same parent isotopes |
"SameParentConnectivity" | same parent connectivity |
"SameParentTautomer" | same parent tautomer |
Find the compound ID for a similar molecules:
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Perform the same search, but return the results as Molecule objects:
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Visualize the results using MoleculePlot:
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Search PubChem for tautomers:
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Get a list of molecules with the same connectivity as adenosine:
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Visualize the molecules using MoleculePlot:
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Get a list of IDs for compounds with the same parent:
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Get a list of isomers by using the "SameFormula" search type:
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PubChemSimilaritySearch can be used with Entity or Molecule objects:
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PubChemSimilaritySearch will automatically thread over lists:
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By adjusting the Tanimoto threshold, the number of similar compounds returned can be controlled:
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Use ListLogPlot to visualize the relationship between threshold and the size of the similarity space:
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This work is licensed under a Creative Commons Attribution 4.0 International License