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MoleculeSubstructureCount[mol,patt]

gives a count of the number of times patt appears as a substructure in mol.

MoleculeSubstructureCount[patt]

represents an operator form of MoleculeSubstructureCount that can be applied to a molecule.

Details and Options
Details and Options Details and Options
Examples  
Basic Examples  
Scope  
Options  
IgnoreStereochemistry  
IncludeHydrogens  
Overlaps  
Applications  
See Also
Related Guides
History
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MoleculeSubstructureCount

MoleculeSubstructureCount[mol,patt]

gives a count of the number of times patt appears as a substructure in mol.

MoleculeSubstructureCount[patt]

represents an operator form of MoleculeSubstructureCount that can be applied to a molecule.

Details and Options

Examples

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Basic Examples  (3)

Count all carboxylic acid groups that are in a molecule:

Wolfram Language code: MoleculeSubstructureCount[Molecule[{"O", "C", "O", "C", "C", "C", "C", "O", "O", "N", "N", "H", "H", "H", "H"}, {Bond[{1, 2}, "Double"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"], Bond[{4, 5}, "Aromatic"], Bond[{5, 6}, "Aromatic"], Bond[{6, 7}, "Single"], Bond[{7, 8}, "Double"], Bond[{7, 9}, "Single"], Bond[{6, 10}, "Aromatic"], Bond[{10, 11}, "Aromatic"], Bond[{11, 4}, "Aromatic"], Bond[{3, 12}, "Single"], Bond[{5, 13}, "Single"], Bond[{9, 14}, "Single"], Bond[{10, 15}, "Single"]}, {}], MoleculePattern["C(=O)[OH]"]]

Visualize the acidic groups:

Wolfram Language code: MoleculePlot[Molecule[{"O", "C", "O", "C", "C", "C", "C", "O", "O", "N", "N", "H", "H", "H", "H"}, {Bond[{1, 2}, "Double"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"], Bond[{4, 5}, "Aromatic"], Bond[{5, 6}, "Aromatic"], Bond[{6, 7}, "Single"], Bond[{7, 8}, "Double"], Bond[{7, 9}, "Single"], Bond[{6, 10}, "Aromatic"], Bond[{10, 11}, "Aromatic"], Bond[{11, 4}, "Aromatic"], Bond[{3, 12}, "Single"], Bond[{5, 13}, "Single"], Bond[{9, 14}, "Single"], Bond[{10, 15}, "Single"]}, {}], MoleculePattern["C(=O)[OH]"]]

Count carbonyls adjacent to nitrogen atoms:

Wolfram Language code: MoleculeSubstructureCount[Molecule[{"C", "N", "C", "O", "C", "C", "N", "C", "N", "C", "N", "C", "C", "O", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Aromatic"], Bond[{3, 4}, "Double"], Bond[{3, 5}, "Aromatic"], Bond[{5, 6 ... ], Bond[{1, 16}, "Single"], Bond[{1, 17}, "Single"], Bond[{8, 18}, "Single"], Bond[{10, 19}, "Single"], Bond[{10, 20}, "Single"], Bond[{10, 21}, "Single"], Bond[{12, 22}, "Single"], Bond[{12, 23}, "Single"], Bond[{12, 24}, "Single"]}, {}], MoleculePattern[{"N", "C", "O"}, {Bond[{1, 2}, "Single" | "Aromatic"], Bond[{2, 3}, "Double"]}]]

Use the operator form:

Wolfram Language code: MoleculeSubstructureCount[MoleculePattern["CNC"]] /@ {Molecule[{"C", "C", "C", "C", "C", "C", "N", "C", "C", "O", Atom["C", "HydrogenCount" -> 1], Atom["C", "HydrogenCount" -> 1], Atom["N", "FormalCharge" -> 1, "UnpairedElectronCount" -> 1], "C", Atom["C", "HydrogenCount" -> 1], Atom["O", "Forma ... , Association["StereoType" -> "DoubleBond", "StereoBond" -> {8, 9}, "Value" -> "Opposite", "Ligands" -> {7, 10}], Association["StereoType" -> "DoubleBond", "StereoBond" -> {46, 47}, "Value" -> "Together", "Ligands" -> {51, 48}]}}], Molecule[{"O", Atom["C", "HydrogenCount" -> 1], Atom["C", "HydrogenCount" -> 1], "O", "P", "O", "O", "O", Atom["C", "HydrogenCount" -> 1], "O", Atom["C", "HydrogenCount" -> 1], "N", "C", "N", Atom["C", "HydrogenCount" -> 1], Atom["C", "Hydrog ... n" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 18, "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 25, "Direction" -> "Counterclockwise"]}}], Molecule[{"O", "C", "N", "C", "C", "Cl", "C", "C", "C", "C", "Cl", "N", "C", "N", "C", "C", "N", "C", Atom["C", "HydrogenCount" -> 1], "C", "O", "N", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "F", "C", "C", "C", "C", "C", "C", "F ... , Bond[{10, 4}, "Aromatic"], Bond[{19, 14}, "Single"], Bond[{33, 28}, "Aromatic"], Bond[{40, 35}, "Aromatic"]}, {StereochemistryElements -> {Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 19, "Direction" -> "Clockwise"]}}]}

Scope  (2)

Create a molecule from an ExternalIdentifier and find how many carbon-oxygen bonds it has:

Wolfram Language code: MoleculeSubstructureCount[ Molecule[ExternalIdentifier["WikidataID", "Q27269295", <|"Label" -> "detorubicin", "Description" -> "chemical compound"|>]], Bond[{"C", "O"}] ]

Find the three molecules with the most halogen atoms:

Wolfram Language code: TakeLargestBy[Molecule /@ IconizedObject[«list of 20 SMILES strings»], MoleculeSubstructureCount[Atom["Cl" | "F" | "Br" | "I"]], 3]

Options  (3)

IgnoreStereochemistry  (1)

By default, stereoisomers do not match:

Wolfram Language code: MoleculeSubstructureCount[Molecule["l-alanine"], MoleculePattern["C[C@@H](N)C(=O)O"]]

Use IgnoreStereochemistryTrue to get a positive match:

Wolfram Language code: MoleculeSubstructureCount[Molecule["l-alanine"], MoleculePattern["C[C@@H](N)C(=O)O"], IgnoreStereochemistry -> True]

IncludeHydrogens  (1)

By default, substructure matching is performed using a molecule's hydrogen-suppressed graph, unless the pattern contains explicit hydrogen atoms:

Wolfram Language code: MoleculeSubstructureCount[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", "H"}, "Single"]]

Some matches to hydrogen will be missed for more involved patterns. In the following example, the pattern is for a carbon atom bonded to either a hydrogen or chlorine atom, but only finds the C-Cl bond:

Wolfram Language code: MoleculeSubstructureCount[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", Atom["AtomicNumber" -> (1 | 17)]}, "Single"]]

Use the option IncludeHydrogensTrue to make sure hydrogens are treated as explicit for the purposes of pattern matching:

Wolfram Language code: MoleculeSubstructureCount[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", Atom["AtomicNumber" -> (1 | 17)]}, "Single"], IncludeHydrogens -> All]

Overlaps  (1)

By default, six carbon‐carbon bonds are found in benzene:

Wolfram Language code: MoleculeSubstructureCount[Molecule["benzene"], Bond[{"C", "C"}, _]]

By default, substructure matches are pruned to remove multiple matches to the same set of atoms. Use the option OverlapsTrue to count each match separately:

Wolfram Language code: MoleculeSubstructureCount[Molecule["benzene"], Bond[{"C", "C"}, _], Overlaps -> True]

Applications  (1)

A list of amino acids:

Wolfram Language code: aalist = EntityList[EntityClass["Chemical", "AminoAcids"]]

Create a pattern for the carboxyl group:

Wolfram Language code: carboxylPattern = MoleculePattern["C(=O)[OH]"]

Select all amino acids that contain two carboxyl groups:

Wolfram Language code: Select[aalist, MoleculeSubstructureCount[#, carboxylPattern] === 2&]

Show the selected molecules with the carboxyl groups highlighted:

Wolfram Language code: MoleculePlot[#, carboxylPattern]& /@ %
Wolfram Research (2021), MoleculeSubstructureCount, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html.

Text

Wolfram Research (2021), MoleculeSubstructureCount, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html.

CMS

Wolfram Language. 2021. "MoleculeSubstructureCount." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html.

APA

Wolfram Language. (2021). MoleculeSubstructureCount. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html

BibTeX

@misc{reference.wolfram_2026_moleculesubstructurecount, author="Wolfram Research", title="{MoleculeSubstructureCount}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html}", note=[Accessed: 13-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_moleculesubstructurecount, organization={Wolfram Research}, title={MoleculeSubstructureCount}, year={2021}, url={https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.html}, note=[Accessed: 13-June-2026]}