--- title: "FindMoleculeSubstructure" language: "en" type: "Symbol" summary: "FindMoleculeSubstructure[mol, patt] finds a mapping between the atom indices in mol and an occurrence of patt in mol. FindMoleculeSubstructure[mol, patt, All] finds all occurrences of patt in mol and returns all mappings. FindMoleculeSubstructure[mol, patt, n] finds at most n mappings." keywords: - functional group - molecule substructure - cheminformatics canonical_url: "https://reference.wolfram.com/language/ref/FindMoleculeSubstructure.html" source: "Wolfram Language Documentation" related_guides: - title: "Molecular Structure & Computation" link: "https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md" - title: "Physics & Chemistry: Data and Computation" link: "https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md" related_functions: - title: "Molecule" link: "https://reference.wolfram.com/language/ref/Molecule.en.md" - title: "MoleculeContainsQ" link: "https://reference.wolfram.com/language/ref/MoleculeContainsQ.en.md" - title: "MoleculePattern" link: "https://reference.wolfram.com/language/ref/MoleculePattern.en.md" - title: "MoleculeMatchQ" link: "https://reference.wolfram.com/language/ref/MoleculeMatchQ.en.md" - title: "MoleculeSubstructureCount" link: "https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.en.md" - title: "MoleculeFreeQ" link: "https://reference.wolfram.com/language/ref/MoleculeFreeQ.en.md" - title: "MoleculePlot" link: "https://reference.wolfram.com/language/ref/MoleculePlot.en.md" - title: "AtomList" link: "https://reference.wolfram.com/language/ref/AtomList.en.md" - title: "BondList" link: "https://reference.wolfram.com/language/ref/BondList.en.md" --- [EXPERIMENTAL] # FindMoleculeSubstructure FindMoleculeSubstructure[mol, patt] finds a mapping between the atom indices in mol and an occurrence of patt in mol. FindMoleculeSubstructure[mol, patt, All] finds all occurrences of patt in mol and returns all mappings. FindMoleculeSubstructure[mol, patt, n] finds at most n mappings. ## Details and Options * ``FindMoleculeSubstructure`` returns a list of associations ``Association[p1 -> m1, p2 -> m2, …]`` where ``pi`` and ``mi`` are atom indices in ``patt`` and ``mol``, respectively. * By default, substructure matches are pruned to remove multiple matches to the same set of atoms. Use the option ``Overlaps -> True`` to disable this behavior. * ``FindMoleculeSubstructure`` takes the following options: | | | | | ---------------------- | --------- | --------------------------------------- | | IgnoreStereochemistry | False | whether to ignore stereochemistry | | IncludeHydrogens | Automatic | whether to include hydrogen atoms | | Overlaps | False | whether to include matches that overlap | --- ## Examples (10) ### Basic Examples (2) Find phenyl rings in a molecule: ```wl In[1]:= FindMoleculeSubstructure[Molecule[{"C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{4, 5}, "Aromatic"], Bond[{5, 6}, "Aromatic ... }, "Aromatic"], Bond[{16, 17}, "Aromatic"], Bond[{17, 18}, "Aromatic"], Bond[{18, 19}, "Aromatic"], Bond[{19, 20}, "Aromatic"], Bond[{14, 21}, "Single"], Bond[{21, 22}, "Single"], Bond[{9, 4}, "Aromatic"], Bond[{20, 15}, "Aromatic"]}, {}], MoleculePattern["c1ccccc1"]] Out[1]= {<|1 -> 4, 2 -> 5, 3 -> 6, 4 -> 7, 5 -> 8, 6 -> 9|>} ``` --- Find all alcohol functional groups: ```wl In[1]:= FindMoleculeSubstructure[Molecule[{"C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "C", "O", "C", "C", "C", "C", "C", "C", "C", "O", "C", "C", "C", "O", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H ... "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 16, "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 19, "Direction" -> "Clockwise"]}}], MoleculePattern[{"C", "O", "H"}, {Bond[{1, 2}], Bond[{2, 3}]}], All] Out[1]= {<|1 -> 11, 2 -> 12, 3 -> 35|>, <|1 -> 19, 2 -> 20, 3 -> 43|>, <|1 -> 23, 2 -> 24, 3 -> 50|>} ``` ### Scope (4) Use an atomic symbol string as a pattern: ```wl In[1]:= FindMoleculeSubstructure[Molecule[{"O", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}, {}], "O"] Out[1]= {<|1 -> 1|>} In[2]:= FindMoleculeSubstructure[Molecule[{"O", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}, {}], "H", All] Out[2]= {<|1 -> 2|>, <|1 -> 3|>} ``` --- Indicate charge or mass number in the atomic symbol: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["C", "MassNumber" -> 14], Atom["O"], Atom["O", "FormalCharge" -> -1], Atom["H"], Atom["H"], Atom["H"]}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Double"], Bond[{2, 4}, "Single"], Bond[{1, 5}, "Single"], Bond[{1, 6}, "Single"], Bond[{1, 7}, "Single"]}]; In[2]:= FindMoleculeSubstructure[m, Atom["O", "FormalCharge" -> -1]] Out[2]= {<|1 -> 4|>} In[3]:= FindMoleculeSubstructure[m, Atom["C", "MassNumber" -> 14]] Out[3]= {<|1 -> 2|>} ``` --- Use ``Atom`` to make a more general pattern. Find all charged atoms: ```wl In[1]:= m = Molecule[Entity["Chemical", "Methyl4Nitrobutyrate"]]; In[2]:= FindMoleculeSubstructure[m, Atom["FormalCharge" -> Except[0]], All] Out[2]= {<|1 -> 3|>, <|1 -> 5|>} ``` Find positively charged atoms: ```wl In[3]:= FindMoleculeSubstructure[m, Atom["FormalCharge" -> GreaterThan[0]], All] Out[3]= {<|1 -> 5|>} ``` Find negatively charged atoms: ```wl In[4]:= FindMoleculeSubstructure[m, Atom["FormalCharge" -> LessEqualThan[-1]], All] Out[4]= {<|1 -> 3|>} ``` --- Use ``Bond`` to define a pattern for any double bond: ```wl In[1]:= m = Molecule["2-[[(1E,4E)-1,5-bis(5-nitrofuran-2-yl)penta-1,4-dien-3-ylidene]amino]guanidine"] Out[1]= Molecule[{"N", "C", "N", "N", "N", "C", "C", "C", "C", "C", "C", "C", Atom["N", "FormalCharge" -> 1], "O", Atom["O", "FormalCharge" -> -1], "O", "C", "C", "C", "C", "C", "C", Atom["N", "FormalCharge" -> 1], "O", Atom["O", "FormalCharge" -> -1 ... -> {Association["StereoType" -> "DoubleBond", "StereoBond" -> {7, 8}, "Ligands" -> {6, 9}, "Value" -> "Opposite"], Association["StereoType" -> "DoubleBond", "StereoBond" -> {17, 18}, "Ligands" -> {6, 19}, "Value" -> "Opposite"]}}] In[2]:= FindMoleculeSubstructure[m, Bond[_, "Double"], All] Out[2]= {<|1 -> 2, 2 -> 4|>, <|1 -> 5, 2 -> 6|>, <|1 -> 7, 2 -> 8|>, <|1 -> 13, 2 -> 14|>, <|1 -> 17, 2 -> 18|>, <|1 -> 23, 2 -> 24|>} ``` Find only double bonds with a nitrogen atom: ```wl In[3]:= FindMoleculeSubstructure[m, Bond[{"N", _}, "Double"], All] Out[3]= {<|1 -> 4, 2 -> 2|>, <|1 -> 5, 2 -> 6|>, <|1 -> 13, 2 -> 14|>, <|1 -> 23, 2 -> 24|>} ``` Find double bonds with a charged atom: ```wl In[4]:= FindMoleculeSubstructure[m, Bond[{Atom["FormalCharge" -> Except[0]], _}, "Double"], All] Out[4]= {<|1 -> 13, 2 -> 14|>, <|1 -> 23, 2 -> 24|>} ``` ### Options (3) #### IgnoreStereochemistry (1) By default, stereoisomers do not match: ```wl In[1]:= FindMoleculeSubstructure[Molecule["l-alanine"], MoleculePattern["C[C@@H](N)C(=O)O"]] Out[1]= {} ``` Use ``IgnoreStereochemistry -> True`` to get a positive match: ```wl In[2]:= FindMoleculeSubstructure[Molecule["l-alanine"], MoleculePattern["C[C@@H](N)C(=O)O"], IgnoreStereochemistry -> True] Out[2]= {<|1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, 5 -> 5, 6 -> 6|>} ``` #### IncludeHydrogens (1) By default, substructure matching is performed using a molecule's hydrogen-suppressed graph, unless the pattern contains explicit hydrogen atoms: ```wl In[1]:= FindMoleculeSubstructure[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", "H"}, "Single"], All] Out[1]= {<|1 -> 1, 2 -> 5|>, <|1 -> 1, 2 -> 6|>, <|1 -> 1, 2 -> 7|>, <|1 -> 2, 2 -> 8|>, <|1 -> 3, 2 -> 9|>, <|1 -> 3, 2 -> 10|>, <|1 -> 3, 2 -> 11|>} ``` 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: ```wl In[2]:= FindMoleculeSubstructure[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", Atom["AtomicNumber" -> (1 | 17)]}, "Single"], All] Out[2]= {<|1 -> 2, 2 -> 4|>} ``` Use the option ``IncludeHydrogens -> True`` to make sure hydrogens are treated as explicit for the purposes of pattern matching: ```wl In[3]:= FindMoleculeSubstructure[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"]}, {}], Bond[{"C", Atom["AtomicNumber" -> (1 | 17)]}, "Single"], All, IncludeHydrogens -> True] Out[3]= {<|1 -> 1, 2 -> 5|>, <|1 -> 1, 2 -> 6|>, <|1 -> 1, 2 -> 7|>, <|1 -> 2, 2 -> 4|>, <|1 -> 2, 2 -> 8|>, <|1 -> 3, 2 -> 9|>, <|1 -> 3, 2 -> 10|>, <|1 -> 3, 2 -> 11|>} ``` #### Overlaps (1) By default, substructure matches are pruned to remove multiple matches to the same set of atoms: ```wl In[1]:= FindMoleculeSubstructure[Molecule["hexane"], MoleculePattern["CCCCC"], All] Out[1]= {<|1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, 5 -> 5|>, <|1 -> 2, 2 -> 3, 3 -> 4, 4 -> 5, 5 -> 6|>} ``` Use the option ``Overlaps -> True`` to find all possible matchings between the pattern and molecule: ```wl In[2]:= FindMoleculeSubstructure[Molecule["hexane"], MoleculePattern["CCCCC"], All, Overlaps -> True] Out[2]= {<|1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, 5 -> 5|>, <|1 -> 2, 2 -> 3, 3 -> 4, 4 -> 5, 5 -> 6|>, <|1 -> 5, 2 -> 4, 3 -> 3, 4 -> 2, 5 -> 1|>, <|1 -> 6, 2 -> 5, 3 -> 4, 4 -> 3, 5 -> 2|>} ``` ### Applications (1) Write a function to locate the nitrogen and carbonyl carbon at the N-terminus of a protein: ```wl In[1]:= nterminus[mol_] := Module[ {patt, atomsOfInterest = {1, 3}}, patt = MoleculePattern[{Atom["N", "HydrogenCount" -> 2], Atom["C", "OrbitalHybridization" -> "SP3"], Atom["C"], Atom["O"], Atom["O" | "N"]}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Double"], Bond[{3, 5}, "Single"]}]; DeleteMissing[AssociationThread[{"amine", "carbonyl"}, Lookup[First[FindMoleculeSubstructure[mol, patt], {}], atomsOfInterest]]] ] ``` Apply the function to a peptide: ```wl In[2]:= peptide = BioSequence["Peptide", "VGSA"]; nterminus[peptide] Out[2]= <|"amine" -> 1, "carbonyl" -> 3|> ``` Highlight the atoms in a 2D plot: ```wl In[3]:= MoleculePlot[peptide, %] Out[3]= [image] ``` ## See Also * [`Molecule`](https://reference.wolfram.com/language/ref/Molecule.en.md) * [`MoleculeContainsQ`](https://reference.wolfram.com/language/ref/MoleculeContainsQ.en.md) * [`MoleculePattern`](https://reference.wolfram.com/language/ref/MoleculePattern.en.md) * [`MoleculeMatchQ`](https://reference.wolfram.com/language/ref/MoleculeMatchQ.en.md) * [`MoleculeSubstructureCount`](https://reference.wolfram.com/language/ref/MoleculeSubstructureCount.en.md) * [`MoleculeFreeQ`](https://reference.wolfram.com/language/ref/MoleculeFreeQ.en.md) * [`MoleculePlot`](https://reference.wolfram.com/language/ref/MoleculePlot.en.md) * [`AtomList`](https://reference.wolfram.com/language/ref/AtomList.en.md) * [`BondList`](https://reference.wolfram.com/language/ref/BondList.en.md) ## Related Guides * [Molecular Structure & Computation](https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md) * [Physics & Chemistry: Data and Computation](https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md) ## History * [Introduced in 2019 (12.0)](https://reference.wolfram.com/language/guide/SummaryOfNewFeaturesIn120.en.md)