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FindMoleculeSubstructure

FindMoleculeSubstructure[mol,patt]

求 mol 中原子索引和 mol 中出现的所有 patt 之间的映射.

FindMoleculeSubstructure[mol,patt,All]

找出 mol 中出现的所有 patt，并返回所有的映射.

FindMoleculeSubstructure[mol,patt,n]

给出最多 n 个映射.

范例

打开所有单元关闭所有单元

基本范例 (2)

找到分子中的苯环：

Wolfram Language code:

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"]]

找出所有酒精官能团：

Wolfram Language code:

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]

范围 (4)

用原子符号字符串作为模式：

Wolfram Language code: FindMoleculeSubstructure[Molecule[{"O", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}, {}], "O"]

Wolfram Language code: FindMoleculeSubstructure[Molecule[{"O", "H", "H"}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}, {}], "H", All]

在原子符号中指明电荷或质量数：

Wolfram Language code:

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"]}];

Wolfram Language code: FindMoleculeSubstructure[m, Atom["O", "FormalCharge" -> -1]]

Wolfram Language code: FindMoleculeSubstructure[m, Atom["C", "MassNumber" -> 14]]

用 Atom 指定更广义的模式. 找出所有带电原子：

Wolfram Language code: m = Molecule[Entity["Chemical", "Methyl4Nitrobutyrate"]];

Wolfram Language code: FindMoleculeSubstructure[m, Atom["FormalCharge" -> Except[0]], All]

找出带正电的原子：

Wolfram Language code: FindMoleculeSubstructure[m, Atom["FormalCharge" -> GreaterThan[0]], All]

找出带负电的原子：

Wolfram Language code: FindMoleculeSubstructure[m, Atom["FormalCharge" -> LessEqualThan[-1]], All]

用 Bond 定义双键模式：

Wolfram Language code: m = Molecule["2-[[(1E,4E)-1,5-bis(5-nitrofuran-2-yl)penta-1,4-dien-3-ylidene]amino]guanidine"]

Wolfram Language code: FindMoleculeSubstructure[m, Bond[_, "Double"], All]

只找出含氮原子的双键：

Wolfram Language code: FindMoleculeSubstructure[m, Bond[{"N", _}, "Double"], All]

找出含有带电原子的双键：

Wolfram Language code: FindMoleculeSubstructure[m, Bond[{Atom["FormalCharge" -> Except[0]], _}, "Double"], All]

选项 (3)

IgnoreStereochemistry (1)

默认情况下，立体异构体不匹配：

Wolfram Language code:

FindMoleculeSubstructure[Molecule["l-alanine"], 
	MoleculePattern["C[C@@H](N)C(=O)O"]]

使用 IgnoreStereochemistryTrue 以获得正匹配：

Wolfram Language code:

FindMoleculeSubstructure[Molecule["l-alanine"], 
	MoleculePattern["C[C@@H](N)C(=O)O"], IgnoreStereochemistry -> True]

IncludeHydrogens (1)

默认情况下，除非模式包含明确的氢原子，否则将使用分子的隐氢图进行子结构匹配：

Wolfram Language code:

FindMoleculeSubstructure[Molecule[{"C", "C", "C", "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], 
  Bond[{2, 4}, "Single"]}, {}], Bond[{"C", "H"}, "Single"], All]

对于更复杂的模式，某些与氢原子的匹配会被忽略. 在下面的示例中，模式为碳原子与氢原子或氯原子结合，但只能找到 C-Cl 键：

Wolfram Language code:

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]

使用选项 IncludeHydrogensTrue 以确保氢原子在模式匹配中被视为显式：

Wolfram Language code:

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]

Overlaps (1)

默认情况下，会对子结构匹配进行剪枝，以移除与同一组原子的多个匹配：

Wolfram Language code: FindMoleculeSubstructure[Molecule["hexane"], MoleculePattern["CCCCC"], All]

使用选项 OverlapsTrue 来查找模式和分子之间所有可能的匹配：

Wolfram Language code: FindMoleculeSubstructure[Molecule["hexane"], MoleculePattern["CCCCC"], All, Overlaps -> True]

应用 (1)

编写一个可定位蛋白质 N-末端的氮和羰基碳的函数：

Wolfram Language code:

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]]]
	]

将函数应用于肽：

Wolfram Language code:

peptide = BioSequence["Peptide", "VGSA"];
nterminus[peptide]

高亮二维图中的原子：

Wolfram Language code: MoleculePlot[peptide, %]

Top

IgnoreStereochemistry	False	是否忽略立体化学
IncludeHydrogens	Automatic	是否包含氢原子
Overlaps	False	是否包含重叠的匹配

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FindMoleculeSubstructure

更多信息和选项

范例

基本范例 (2)

范围 (4)

选项 (3)

IgnoreStereochemistry (1)

IncludeHydrogens (1)

Overlaps (1)

应用 (1)

文本

CMS

APA

BibTeX

BibLaTeX

FindMoleculeSubstructure

更多信息和选项

范例

基本范例 (2)

范围 (4)

选项 (3)

IgnoreStereochemistry (1)

IncludeHydrogens (1)

Overlaps (1)

应用 (1)

参见

相关指南

历史

文本

CMS

APA

BibTeX

BibLaTeX