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MoleculeFeatureDistance[mol1,mol2]

gives a distance measure between mol1 and mol2.

Details and Options
Details and Options Details and Options
Examples  
Basic Examples  
Scope  
Neat Examples  
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MoleculeFeatureDistance

MoleculeFeatureDistance[mol1,mol2]

gives a distance measure between mol1 and mol2.

Details and Options

Examples

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Basic Examples  (1)

Find the distance between two molecules:

Wolfram Language code: MoleculeFeatureDistance[Molecule[{"C", "O", "C", "C", "C", "C", "C", "C", "P", "C", "C", "C", "C", "C", "C", "O", "C", "C", "C", "C", "C", "C", "C", "O", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Aromatic"], Bond[ ... }, "Aromatic"], Bond[{20, 21}, "Aromatic"], Bond[{21, 22}, "Aromatic"], Bond[{22, 23}, "Aromatic"], Bond[{21, 24}, "Single"], Bond[{24, 25}, "Single"], Bond[{8, 3}, "Aromatic"], Bond[{15, 10}, "Aromatic"], Bond[{23, 18}, "Aromatic"]}, {}], Molecule[{"C", "O", "C", "C", "C", "C", "C", "C", "C", "C", "N", "C", "O", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "O"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Aromati ... 24}, "Aromatic"], Bond[{24, 25}, "Aromatic"], Bond[{25, 26}, "Single"], Bond[{26, 27}, "Double"], Bond[{8, 3}, "Aromatic"], Bond[{13, 9}, "Aromatic"], Bond[{19, 14}, "Aromatic"], Bond[{25, 20}, "Aromatic"], Bond[{26, 18}, "Single"]}, {}]]

Find the distance between two less similar molecules:

Wolfram Language code: MoleculeFeatureDistance[Molecule[{"C", "O", "C", "C", "C", "C", "C", "C", "P", "C", "C", "C", "C", "C", "C", "O", "C", "C", "C", "C", "C", "C", "C", "O", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Aromatic"], Bond[ ... }, "Aromatic"], Bond[{20, 21}, "Aromatic"], Bond[{21, 22}, "Aromatic"], Bond[{22, 23}, "Aromatic"], Bond[{21, 24}, "Single"], Bond[{24, 25}, "Single"], Bond[{8, 3}, "Aromatic"], Bond[{15, 10}, "Aromatic"], Bond[{23, 18}, "Aromatic"]}, {}], Molecule[{"O", "C", "O", "C", "C", "C", "C", "O", "O", "F", "F"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Double"], Bond[{2, 4}, "Single"], Bond[{4, 5}, "Single"], Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{7, 8}, "Double"], Bond[{7, 9}, "Single"], Bond[{6, 10}, "Single"], Bond[{6, 11}, "Single"]}, {}]]

Scope  (2)

Find the molecule distance between two "Chemical" entities:

Wolfram Language code: MoleculeFeatureDistance[Entity["Chemical", "Caffeine"], Entity["Chemical", "Adenosine"]]

Find the five entities in a list that are most similar to a target:

Wolfram Language code: TakeSmallestBy[EntityList[EntityClass["Chemical", "Alkenes"]], MoleculeFeatureDistance[Molecule[{"C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{4, 5}, "Single"], Bond[{5, 6}, "Doubl ... ssociation["StereoType" -> "DoubleBond", "StereoBond" -> {13, 14}, "Ligands" -> {12, 15}, "Value" -> "Opposite"], Association["StereoType" -> "DoubleBond", "StereoBond" -> {20, 21}, "Ligands" -> {19, 22}, "Value" -> "Opposite"]}}], #]&, 5]

Neat Examples  (1)

Create a NearestFunction to find the entities most similar to any molecule:

Wolfram Language code: nf = Nearest[DeleteMissing[EntityValue[EntityList["Chemical"], "Molecule", "EntityAssociation"]], DistanceFunction -> MoleculeFeatureDistance]

Use the nearest function on an input molecule:

Wolfram Language code: nf[Molecule["2-(2-nitrophenyl)sulfanyl-5-phenylcyclohexane-1,3-dione"]]
Wolfram Language code: MoleculePlot[First[%]]

Find the five nearest molecules to a given molecule:

Wolfram Language code: nf[Molecule[{"C", "O", "C", "C", "C", "C", "N", "C", "C", "C", "C", "C", "O", "C", "C", "N", "C", "C", "O", "C", "C", "C", "C", "C", "C", "O", "C", "N"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Ar ... ingle"], Bond[{12, 3}, "Aromatic"], Bond[{25, 20}, "Aromatic"], Bond[{10, 5}, "Aromatic"]}, {StereochemistryElements -> {Association["StereoType" -> "DoubleBond", "StereoBond" -> {15, 16}, "Ligands" -> {7, 17}, "Value" -> "Opposite"]}}], 5]
Wolfram Language code: MoleculePlot /@ %
Wolfram Research (2025), MoleculeFeatureDistance, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html.

Text

Wolfram Research (2025), MoleculeFeatureDistance, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html.

CMS

Wolfram Language. 2025. "MoleculeFeatureDistance." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html.

APA

Wolfram Language. (2025). MoleculeFeatureDistance. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html

BibTeX

@misc{reference.wolfram_2026_moleculefeaturedistance, author="Wolfram Research", title="{MoleculeFeatureDistance}", year="2025", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html}", note=[Accessed: 13-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_moleculefeaturedistance, organization={Wolfram Research}, title={MoleculeFeatureDistance}, year={2025}, url={https://reference.wolfram.com/language/ref/MoleculeFeatureDistance.html}, note=[Accessed: 13-June-2026]}