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 patt1patt2… 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)
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:
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