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MoleculeContainsQ[molecule,patt]

returns True if patt is a substructure of molecule, and False otherwise.

MoleculeContainsQ[patt]

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

Details and Options
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Examples  
Basic Examples  
Applications  
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MoleculeContainsQ

MoleculeContainsQ[molecule,patt]

returns True if patt is a substructure of molecule, and False otherwise.

MoleculeContainsQ[patt]

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

Details and Options

  • patt should be one of the following forms:
  • MoleculePattern[…]a valid molecule pattern
    Atom[…]a pattern for a single atom
    Bond[{a1,a2}]a bond between atoms with specified patterns

Examples

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Basic Examples  (4)

Test for the presence of oxygen atoms:

Wolfram Language code: MoleculeContainsQ[Molecule["water"], Atom["O"]]

Check for sulfur atoms:

Wolfram Language code: MoleculeContainsQ[Molecule["water"], Atom["S"]]

Select molecules with a carboxylic acid group:

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

Test for the presence of carbon-sulfur bonds in a molecule:

Wolfram Language code: m = Molecule["O=C(C1CCC1)S[C@@H]1CCC1(C)C"];MoleculeContainsQ[m, Bond[{"C", "S"}, "Single"]]

The bond order can be specified or not:

Wolfram Language code: MoleculeContainsQ[m, Bond[{"C", "S"}, _]]
Wolfram Language code: MoleculeContainsQ[m, Bond[{"C", "S"}, "Double"]]

Test if a molecule has rings:

Wolfram Language code: MoleculeContainsQ[Molecule[{"Cl", "C", "C", "C", "Cl", "C", "C", "C", "O", "C", "C", "C", "C", "C", "C", "Cl", "Cl", "H", "H", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Aromatic"], Bond[{3, 4}, "Aromatic"], Bond[{4, 5}, "Single"], Bond[{4, 6}, "Aromati ... ond[{15, 16}, "Single"], Bond[{13, 17}, "Single"], Bond[{8, 2}, "Aromatic"], Bond[{15, 10}, "Aromatic"], Bond[{11, 6}, "Aromatic"], Bond[{3, 18}, "Single"], Bond[{8, 19}, "Single"], Bond[{12, 20}, "Single"], Bond[{14, 21}, "Single"]}, {}], Atom["RingAtomQ" -> True]]

Applications  (1)

A list of nucleosides:

Wolfram Language code: nlist = EntityList[EntityClass["Chemical", "Nucleosides"]]

Create a pattern for the purine ring system:

Wolfram Language code: purinePattern = MoleculePattern[{"N", "C", "N", "C", "C", "C", "N", "C", "N"}, {Bond[{1, 2}], Bond[{2, 3}], Bond[{3, 4}], Bond[{4, 5}], Bond[{5, 6}], Bond[{6, 1}], Bond[{6, 7}], Bond[{7, 8}], Bond[{8, 9}], Bond[{9, 5}]}]

Select all nucleosides that contain purine:

Wolfram Language code: Select[nlist, MoleculeContainsQ[purinePattern]]

Show the selected molecules with the purine ring highlighted:

Wolfram Language code: MoleculePlot[#, purinePattern]& /@ %
Wolfram Research (2019), MoleculeContainsQ, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeContainsQ.html.

Text

Wolfram Research (2019), MoleculeContainsQ, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculeContainsQ.html.

CMS

Wolfram Language. 2019. "MoleculeContainsQ." Wolfram Language & System Documentation Center. Wolfram Research. https://reference.wolfram.com/language/ref/MoleculeContainsQ.html.

APA

Wolfram Language. (2019). MoleculeContainsQ. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculeContainsQ.html

BibTeX

@misc{reference.wolfram_2026_moleculecontainsq, author="Wolfram Research", title="{MoleculeContainsQ}", year="2019", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculeContainsQ.html}", note=[Accessed: 13-June-2026]}

BibLaTeX

@online{reference.wolfram_2026_moleculecontainsq, organization={Wolfram Research}, title={MoleculeContainsQ}, year={2019}, url={https://reference.wolfram.com/language/ref/MoleculeContainsQ.html}, note=[Accessed: 13-June-2026]}