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MoleculePattern
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MoleculePattern

[Experimental]

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

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

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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.

Examples

Basic Examples  (3)Summary of the most common use cases

Define a pattern for sulfur-oxygen bonds:

In[1]:=1
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-ge6nnj
Out[1]=1

Use MoleculeContainsQ to verify the molecule matches the pattern:

In[2]:=2
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-szu7z6
Out[2]=2

Use the pattern in MoleculePlot to visualize:

In[3]:=3
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-oxu06h
Out[3]=3

Find bonds between carbon and heavier atoms:

In[1]:=1
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-gt4dhf
In[2]:=2
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-drg3ky
In[3]:=3
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-3bfamu
Out[3]=3
In[4]:=4
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-3b8rrt
Out[4]=4
In[5]:=5
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-3x5myg
Out[5]=5
In[6]:=6
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-vlq6e5
Out[6]=6

Make a molecule pattern from part of a molecule:

In[1]:=1
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-6gs49y
In[2]:=2
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-9k66pb

Find this pattern in the parent molecule:

In[3]:=3
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-dch2au
Out[3]=3

Visualize the pattern with MoleculePlot:

In[4]:=4
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https://wolfram.com/xid/0cf1mg4w2yvo0pe-bcupwc
Out[4]=4
Wolfram Research (2019), MoleculePattern, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePattern.html.
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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.

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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.

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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

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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: 09-May-2025 ]}

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@misc{reference.wolfram_2025_moleculepattern, author="Wolfram Research", title="{MoleculePattern}", year="2019", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculePattern.html}", note=[Accessed: 09-May-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: 09-May-2025 ]}

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@online{reference.wolfram_2025_moleculepattern, organization={Wolfram Research}, title={MoleculePattern}, year={2019}, url={https://reference.wolfram.com/language/ref/MoleculePattern.html}, note=[Accessed: 09-May-2025 ]}