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MoleculePattern[{atom1,atom2,… }, { bond1,bond2,… }]

represents a molecule pattern with atoms atomi and bonds bondi for use in substructure searching.

MoleculePattern["smarts"]

represents a molecule pattern from the input SMARTS pattern.

Details and Options
Details and Options Details and Options
Examples  
Basic Examples  
Options  
AtomDiagramCoordinates  
StereochemistryElements  
Properties & Relations  
See Also
Related Guides
History
Cite this Page

MoleculePattern

MoleculePattern[{atom1,atom2,… }, { bond1,bond2,… }]

represents a molecule pattern with atoms atomi and bonds bondi for use in substructure searching.

MoleculePattern["smarts"]

represents a molecule pattern from the input SMARTS pattern.

Details and Options

  • The atoms and bonds in a MoleculePattern are not checked for proper valence, and no implicit hydrogens are added.
  • Possible forms for the atom patterns include:
  • "sym"an atom with atomic symbol "sym"
    Atom["sym",prop->val]an atom with properties described by rules
    patt1|patt2|…an atom matching any of the patti
  • A bond is entered as Bond[{id1,id2},"type"]. If the bond type is omitted, it will match any type.
  • Possible options include:
  • AtomDiagramCoordinates Automatictwo-dimensional coordinates
    StereochemistryElements Nonea list specifying a stereochemical arrangement

Examples

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Basic Examples  (3)

Define a pattern for sulfur-oxygen bonds:

Use MoleculeContainsQ to verify the molecule matches the pattern:

Use the pattern in MoleculePlot to visualize:

Find bonds between carbon and heavier atoms:

Make a molecule pattern from part of a molecule:

Find this pattern in the parent molecule:

Visualize the pattern with MoleculePlot:

Options  (2)

AtomDiagramCoordinates  (1)

By default, diagram coordinates will be automatically generated:

StereochemistryElements  (1)

Create a molecule pattern with defined stereo:

Select the enantiomer that matches the pattern:

Properties & Relations  (1)

An invalid molecule pattern can be detected with MoleculePatternQ:

Fixing the string creates a valid pattern:

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

Text

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

CMS

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

APA

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

BibTeX

@misc{reference.wolfram_2025_moleculepattern, author="Wolfram Research", title="{MoleculePattern}", year="2019", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculePattern.html}", note=[Accessed: 18-August-2025]}

BibLaTeX

@online{reference.wolfram_2025_moleculepattern, organization={Wolfram Research}, title={MoleculePattern}, year={2019}, url={https://reference.wolfram.com/language/ref/MoleculePattern.html}, note=[Accessed: 18-August-2025]}