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MoleculeModify

MoleculeModify[mol,"mod"]

给出对分子 mol 应用修改 "mod" 后得到的分子或分子列表.

MoleculeModify[mol,{"mod",specs}]

给出对分子 mol 应用带有额外指定 specs 的修改 "mod" 后得到的分子或分子列表.

MoleculeModify["mod"]

表示 MoleculeModify 的算符形式，可应用于分子.

更多信息和选项

对原子进行修改

修改分子的原子列表的操作：

	{"AddAtom",atom}	添加不相连的原子
	{"AddAtom",{atom₁,atom₂,…}}	添加一系列原子
	{"DeleteAtom",a}	删除索引为 a 的原子
	{"DeleteAtom",{a₁,a₂,…}}	删除列出的原子
	{"ReplaceAtom",aatom}	将索引为 a 的原子替换为 atom
	{"ReplaceAtom",{a₁atom₁,…}}	用 atom_i 替换原子 a_i

atom 应为以下形式：

	"sym"	原子符号为 "sym"（如 "C"、"Cl"）的原子
	Entity["Element",element]	给定元素的原子
	Entity["Isotope",isotope]	指定同位素的原子
	Atom["sym","prop"val,…]	具有指定属性的原子

"AddAtom" 将添加一个不相连的原子，与分子的其余部分之间没有键. 如果要添加一个新的原子和键，请使用 "AddBond".
"DeleteAtom" 将删除该原子的所有键.
当去除或替换一个原子时，可以调整显式氢原子的数量以保持合理的化合价. 断开的氢原子将会被删除. 如果想禁用此行为，请使用选项 ValenceErrorHandlingFalse.
按正常方式将隐式氢原子放入添加的原子中. 如果想禁用隐式氢原子，在新原子指定中使用 "HydrogenCount"None.
修改原子属性的操作有：

	{"SetFormalCharge",aval}	将索引为 a 的原子的形式电荷设为 val
	{"SetMassNumber",aval}	将索引为 a 的原子的质量数设为 val
	{"SetUnpairedElectronCount",aval}	为给定原子设置游离电子数

如果想改变多个原子的属性，可使用规则列表 {a₁val₁,a₂val₂,…}.

对键进行修改

修改分子的键列表的操作：

	{"AddBond",{a₁,a₂}}	在索引为 a₁ 和 a₂ 的原子间添加单键
	{"AddBond",Bond[{a₁,a₂},"type"]}	在给定原子间添加给定类型的键
	{"AddBond",Bond[{a₁,atom},type]}	索引为 a₁ 的原子和由 atom 表示的新原子之间的键
	{"DeleteBond",{a₁,a₂}}	移除给定索引的原子间的键
	{"SetBondType",{a₁,a₂}"type"}	设置索引为 a₁ 和 a₂ 的原子间的键的类型

普通修改

	"SetAromaticity"	将局部单键和双键转换为芳香键
	"Kekulize"	将芳香键转换为局部单键和双键
	{"RenumberAtoms",{a₁,a₂,…}}	对原子列表重新排序，使得索引为 a_i 的原子出现在原子列表中的位置 i
	{"SetMetaInformation",meta}	将分子的 MetaInformation 设为 meta，给定应为一个关联或键-值对
	"MakeHydrogensExplicit"	将隐式氢原子转换为显式氢原子
	"MakeHydrogensImplicit"	当从正常价态规则可以推断出氢原子的存在时，去除显式氢原子

对立体化学信息进行修改

关于分子的三维排列的信息（与三维几何结构无关）被保存在 StereochemistryElements 选项值中. 以下操作将改变立体元素：

	"AssignStereochemistryFromCoordinates"	根据 3D 坐标分配四面体和双键立体化学元素
	"RemoveStereochemistry"	删除任何已定义的立体化学信息

如果要修改原子或键的已定义的立体化学信息，请使用以下操作：
{"SetAtomChirality",aval} 设置原子的手性值为 "R" 或 "S"

{"SetBondStereo",{a₁,a₂}val} 将键的立体值设为 "E" 或 "Z"
修改原子或键的立体结构将影响按要求生成的 3D 坐标. 如果分子已经包含有 3D 坐标，在修改立体化学信息时会将其丢弃.

子结构的删除与替换

	{"DeleteSubstructure",patt}	删除分子中所有 patt 的出现位置
	{"ReplaceSubstructure",pattrepl}	将所有的 patt 替换为 repl
	{"ReplaceSubstructure",pattrepl,attchmts}	用 repl 替换 patt，只有指定的附着点
	{"ReplaceSubstructureList",pattrepl}	将所有的 patt 替换为 repl，并返回一个列表

此处，repl 应为 Molecule 对象或 SMILES 字符串，patt 可为以下形式：

	MoleculePattern[…]	有效的分子模式对象
	{a₁,a₂,…}	构成相连子结构的原子索引列表
	{{a₁,a₂,…},{b₁,b₂,…},…}	原子索引列表组成的列表，将每个原子索引列表替换为 repl

attchmts 应为规则列表 {p₁r₁,…}，从模式原子的索引到要替换的原子的索引. 如果没有提供附着点，则匹配模式和替换中的第一个和最后一个原子.

生成坐标

在二维或三维空间绘制分子时，分别从 AtomCoordinates 和 AtomDiagramCoordinates 选项值中获取坐标. 如果分子表达式中没有出现坐标，则自动生成坐标.
以下操作将预先自动计算坐标，并返回含有该坐标的 Molecule 对象：

	"ComputeAtomCoordinates"	自动计算分子的三维坐标
	{"ComputeAtomCoordinates",opts}	使用选项 opts 计算原子的坐标
	{"GenerateConformers",n}	用不同的种子计算三维坐标 n 次，返回一系列分子
	"ComputeAtomDiagramCoordinates"	计算二维坐标

"ComputeAtomCoordinates" 将使所有隐式氢变为显式氢以便嵌入分子.
"ComputeAtomCoordinates" 接受以下选项：

"Canonicalize"	True	是否规范化坐标
"EnergyMinimize"	True	是否在坐标上运行力场最小化
RandomSeeding	1234	怎样对随机性进行播种

默认情况下，"GenerateConformers" 将返回未被最小化的异象体.
"ComputeAtomDiagramCoordinates" 将使与碳相连的氢变为隐式氢，使与杂原子相连的氢变为显式氢，以便与 MoleculePlot 的默认输出匹配. 通过使用 {"ComputeAtomDiagramCoordinates",IncludeHydrogensTrue} 可包含所有原子.

对几何结构进行修改

如果要修改单个原子的坐标，可使用：
{"SetAtomPosition",a{x,y,z}} 设置指定原子的位置
如果要规范化原子的坐标而不改变内部的几何结果，请使用：
"CanonicalizeAtomCoordinates" 将分子的质心平移到原点，并使主轴与直角坐标轴对齐
要翻转特定原子周围的局部几何结构，请使用：
{"InvertAroundAtom",a} 翻转索引为的原子周围的几何结构

{"InvertAroundAtom",{a₁,a₂,…}} 翻转多个原子周围的几何结构
四面体原子通过交换两个最小的可移动配体实现构型翻转. 三角锥形原子通过移动最小的可移动配体实现翻转.可移动原子要么不在环中，要么位于同一环内. 被移动原子的坐标通过二重旋转进行变换，因此分子中所有其他的立体中心保持不变.
对于普通的几何转换，可使用：
{"TransformAtomCoordinates",tfun} 对坐标应用转换函数 tfun
此处，tfun 应为 TransformationFunction 对象，如 TranslationTransform、ReflectionTransform 等，或操作并返回 QuantityArray 对象的任意函数.
以下操作将修改内部坐标：

	{"SetBondLength", {a₁,a₂}val}	设置指定原子之间的键长
	{"SetBondAngle", {a₁,a₂,a₃}val}	设置指定原子之间的角度
	{"SetTorsionAngle",{a₁,a₂,a₃,a₄}val}	设置四个连续的由化学键联接的原子的扭转角

这些操作也支持长度列表或角度变化，如 {{a₁,a₂}val₁,…}.
此处，val 应为 Quantity 对象或数字. 如果是数字，则假定单位为 "Angstroms" 或 "AngularDegrees".
对于 "SetBondLength"，原子 a₁ 和 a₂ 必须成键，且它们之间的键不应成环. 与原子 a₂ 相连的所有原子都将被移除.
对于 "SetBondAngle"，原子 {a₁,a₂} 和 {a₂,a₃} 应成键，且这两个键都不应成环. 与原子 a₃ 相连的所有原子都将被移除.
对于 "SetTorsionAngle"，原子 {a₁,a₂}、{a₂,a₃} 和 {a₃,a₄} 应成键，且键 {a₂,a₃} 不应成环. 与原子 a₄ 相连的所有原子都将被移除.
如果要最小化相对于 MMFF 力场的坐标，请使用：

	"EnergyMinimizeAtomCoordinates"	最小化总力场能量
	{"EnergyMinimizeAtomCoordinates",ff}	用力场 ff（"UFF"、"MMFF94" 或 "MMFF94s" 之一最小化能量）
	{"EnergyMinimizeAtomCoordinates",constraints}	在给定的力场约束条件下将能量最小化

constraints 应为一系列键、角度或扭转角限制条件，可采用以下形式：

	{a₁,a₂}d	指定两个原子间的距离
	{a₁,a₂,a₃}θ	指定三个原子间的角度
	{a₁,a₂,a₃,a₄}θ	指定四个原子间的扭转角
	<\|…\|>	一个关联，其键为 "Atoms"、"Value" 和 "ForceConstant"

范例

打开所有单元关闭所有单元

基本范例 (4)

在丙烷中加入碳原子：

Wolfram Language code: MoleculeModify[Molecule["propane"], {"AddAtom", "C"}]

为新原子添加一个键：

Wolfram Language code: MoleculeModify[%, {"AddBond", Bond[{2, 12}]}]

Wolfram Language code: ToEntity[%]

添加一个键，将己烷转化为环己烷：

Wolfram Language code: m = Molecule["hexane"]

Wolfram Language code: MoleculeModify[m, {"AddBond", Bond[{1, 6}, "Single"]}]

删除一个键，将环己烷转化为己烷：

Wolfram Language code: m = Molecule["cyclohexane"]

Wolfram Language code: MoleculeModify[m, {"DeleteBond", Bond[{4, 3}, "Single"]}]

用甲基取代 TNT 中的所有硝基：

Wolfram Language code: nitro = MoleculePattern["[#7](~[#8])~[#8]"];

Wolfram Language code: MoleculeModify[Molecule["trinitrotoluene"], {"ReplaceSubstructure", nitro -> "C"}]

用 "ReplaceSubstructureList" 一次更换一个硝基：

Wolfram Language code: MoleculeModify[Molecule["trinitrotoluene"], {"ReplaceSubstructureList", nitro -> "C"}]

范围 (41)

"AddAtom" (1)

在分子中添加一个原子：

Wolfram Language code:

MoleculeModify[Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], 
  Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], 
  Atom["Cl"], Atom["Cl"]}, {Bond[{1, 2}, "Aromatic"], Bond ... romatic"], Bond[{10, 5}, "Aromatic"], 
  Bond[{3, 11}, "Single"], Bond[{4, 12}, "Single"], Bond[{6, 13}, "Single"], 
  Bond[{7, 14}, "Single"], Bond[{8, 15}, "Single"], Bond[{9, 16}, "Single"], 
  Bond[{17, 1}, "Single"], Bond[{18, 2}, "Single"]}], {"AddAtom", "Fe"}]

添加一组原子：

Wolfram Language code:

MoleculeModify[Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], 
  Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], 
  Atom["Cl"], Atom["Cl"]}, {Bond[{1, 2}, "Aromatic"], Bond ... romatic"], Bond[{10, 5}, "Aromatic"], 
  Bond[{3, 11}, "Single"], Bond[{4, 12}, "Single"], Bond[{6, 13}, "Single"], 
  Bond[{7, 14}, "Single"], Bond[{8, 15}, "Single"], Bond[{9, 16}, "Single"], 
  Bond[{17, 1}, "Single"], Bond[{18, 2}, "Single"]}], {"AddAtom", {"Na+", "Cl-"}}]

"AddBond" (1)

在分子中添加一组键：

Wolfram Language code: MoleculeModify[Molecule["cyclononane"], {"AddBond", {{2, 8}, {3, 6}}}]

"AssignStereochemistryFromCoordinates" (1)

用分子的 3D 坐标来推断立体化学结构. 首先用原子、键和坐标创建一个分子，但没有定义立体化学信息：

Wolfram Language code:

m = Molecule[IconizedObject[«atom list»], IconizedObject[«bond list»], AtomCoordinates -> QuantityArray[StructuredArray`StructuredData[{47, 3}, 
  {{{2.4265, -1.6857, -1.6031}, {3.9689, 0.2041, 0.0446}, {2.2747, 1.303, 2.1955}, 
    {-1.0178, -1.3778, 0.9927}, {-4.3652, -2.3641, 0.1309}, {-2.5758, -3.9668, 1.4015}, 
    {1.3208, -1.9591 ... 692, 0.7349, 1.5371}, {0.7256, 1.4585, -2.1836}, {-3.2418, 4.7619, -0.8261}, 
    {-1.913, 5.208, -1.8817}, {2.3128, -3.6443, -2.7289}, {4.2015, 1.6396, -1.6863}, 
    {1.5146, 3.3749, 1.7047}, {0.4457, 1.1452, 3.5146}}, "Angstroms", {{1}, {2}}}]]]

Wolfram Language code: m2 = MoleculeModify[m, "AssignStereochemistryFromCoordinates"]

Wolfram Language code: m2["StereochemistryElements"]//Dataset

"CanonicalizeAtomCoordinates" (1)

从 "XYZ" 文件导入一个结构，并规范化三维坐标：

Wolfram Language code: m = Import["ExampleData/caffeine.xyz"]

导入后，计算分子的质心和主轴：

Wolfram Language code: MoleculeValue[m, {"CenterOfMass", "PrincipalAxes"}]

"CanonicalizeAtomCoordinates" 将平移分子，将质心移动到原点，然后旋转以使主轴与直角坐标轴对齐：

Wolfram Language code:

m2 = MoleculeModify[m, "CanonicalizeAtomCoordinates"];
MoleculeValue[m2, {"CenterOfMass", "PrincipalAxes"}]

"ComputeAtomCoordinates" (2)

当使用诸如 SMILES 字符串或名称之类的标识符创建分子时，不会立即计算坐标：

Wolfram Language code:

m = Molecule["FCCN1CCC(CC1)COc1ccc(cc1)C#N"];
Options[m]

用 "ComputeAtomCoordinates" 计算坐标并将其保存在分子表达式中：

Wolfram Language code:

m2 = MoleculeModify[m, "ComputeAtomCoordinates"];
Options[m2]

使用 RandomSeeding 选项生成不同的分子构象：

Wolfram Language code:

{m1, m2, m3} = MoleculeModify[Molecule["4-[[1-(2-fluoroethyl)piperidin-4-yl]methoxy]benzonitrile"], {"ComputeAtomCoordinates", RandomSeeding -> #}]& /@ {1, 12, 23};

Wolfram Language code: MoleculePlot3D /@ {m1, m2, m3}

所得分子有不同的构象能：

Wolfram Language code: MoleculeValue[{m1, m2, m3}, "MMFFEnergy"]

"ComputeAtomDiagramCoordinates" (2)

当用 MoleculePlot 在二维空间可视化分子时，默认情况下，将与碳原子相连的氢原子隐藏起来. 默认情况下，在辛醇中只显示羟基氢：

Wolfram Language code: MoleculePlot[Molecule["2-octanol"]]

"ComputeAtomDiagramCoordinates" 将移除那些未显示的氢，将显示出来的变为显式氢：

Wolfram Language code: mol = MoleculeModify[Molecule["2-octanol"], "ComputeAtomDiagramCoordinates"]

现在将坐标存储在分子表达式中：

Wolfram Language code: Options[mol]

由于默认情况下仅显示一个氢，因此返回的分子只有一个显式氢：

Wolfram Language code: AtomList[mol, "H", "AtomIndex", IncludeHydrogens -> "ExplicitOnly"]

坐标与分子图中使用的坐标完全匹配：

Wolfram Language code:

coords = mol["AtomDiagramCoordinates", IncludeHydrogens -> "ExplicitOnly"];Show[Graphics[{Yellow, Disk[#, .2]& /@ coords}], MoleculePlot[mol]]

计算原子结构图中的坐标，绘制三个图，显示默认氢原子，所有氢原子或不显示氢原子：

Wolfram Language code:

highlightCoordinates[option_] := Module[{mol}, mol = MoleculeModify[Molecule["2-octanol"], {"ComputeAtomDiagramCoordinates", IncludeHydrogens -> option}];
	Show[
	Graphics[{Yellow, Disk[#, .2]& /@ mol["AtomDiagramCoordinates", IncludeHydrogens -> "ExplicitOnly"]}], MoleculePlot[mol, IncludeHydrogens -> option]]
	]

Wolfram Language code: GraphicsColumn[highlightCoordinates /@ {Automatic, True, False}]

"DeleteAtom" (2)

使用 "DeleteAtom" 将己醇转换为己烷：

Wolfram Language code: m = Molecule["2-hexanol"]

Wolfram Language code: AtomList[m, "O", "AtomIndex"]

Wolfram Language code: MoleculeModify[m, {"DeleteAtom", %}]

找出匹配的 Entity：

Wolfram Language code: ToEntity[%]

删除原子时，与其相连的所有氢也将被去除，用隐式氢填充重原子上未填充的化合价. 通过 ValenceErrorHandling->False 可禁用此行为，留下未配对的电子：

Wolfram Language code: MoleculeModify[Molecule@"CCCP[C@@H]1C[C@@H]1C", {"DeleteAtom", 4}, ValenceErrorHandling -> #]& /@ {True, False}

Wolfram Language code: MoleculePlot /@ %

"DeleteBond" (2)

删除非环状键以创建不相连的结构：

Wolfram Language code: m = Molecule["diphenylamine"]

Wolfram Language code: BondList[m, Bond[{"N", "C"}]]

Wolfram Language code: MoleculeModify[m, {"DeleteBond", First@%}]

Wolfram Language code: MoleculePlot@%

删除环键：

Wolfram Language code:

MoleculeModify[Molecule[{"C", "C", "C", "N", "C", "C", "C", "N", "O", "S", "O"}, 
 {Bond[{4, 5}, "Single"], Bond[{5, 3}, "Aromatic"], Bond[{3, 2}, "Aromatic"], 
  Bond[{2, 1}, "Aromatic"], Bond[{1, 7}, "Aromatic"], Bond[{7, 6}, "Aromatic"], 
  Bond[{1, 10}, "Single"], Bond[{10, 9}, "Double"], Bond[{10, 11}, "Double"], 
  Bond[{10, 8}, "Single"], Bond[{6, 5}, "Aromatic"]}, {}], {"DeleteBond", {7, 6}}]

"DeleteSubstructure" (1)

该分子含有两个胺基：

Wolfram Language code:

MoleculePlot[mol = Molecule[{"C", "C", "C", "N", "C", "C", "C", "N", "O", "S", "O"}, 
 {Bond[{4, 5}, "Single"], Bond[{5, 3}, "Aromatic"], Bond[{3, 2}, "Aromatic"], 
  Bond[{2, 1}, "Aromatic"], Bond[{1, 7}, "Aromatic"], Bond[{7, 6}, "Aromatic"], 
  Bond[{1, 10}, "Single"], Bond[{10, 9}, "Double"], Bond[{10, 11}, "Double"], 
  Bond[{10, 8}, "Single"], Bond[{6, 5}, "Aromatic"]}, {}]]

去除胺基：

Wolfram Language code: MoleculeModify[mol, {"DeleteSubstructure", MoleculePattern["[NH2]"]}]

可视化结果：

Wolfram Language code: MoleculePlot[%]

"EnergyMinimizeAtomCoordinates" (1)

从 "XYZ" 文件中导入结构并使用 MMFF 力场最小化能量：

Wolfram Language code: m = Import["ExampleData/caffeine.xyz"]

Wolfram Language code: m2 = MoleculeModify[m, "EnergyMinimizeAtomCoordinates"]

验证构象能变小了：

Wolfram Language code: MoleculeValue[{m, m2}, "MMFFEnergy"]

显示新的结构与旧的结构：

Wolfram Language code:

Show[
	MoleculePlot3D[m, ColorRules -> {_ -> Directive[Opacity[0.4], Gray]}], MoleculePlot3D[m2]
	]

"GenerateConformers" (1)

通常希望给出分子的一组构象，例如，对较大部分的能量分布进行采样. 为环己烷生成 100 个构象：

Wolfram Language code: mols = MoleculeModify[Molecule["cyclohexane"], {"GenerateConformers", 100}];

构象的能量分布很广：

Wolfram Language code: Histogram[MoleculeValue[mols, "MMFFEnergy"], PlotTheme -> "Detailed"]

在利用立场对构象进行最小化后，按能量分为两个组：

Wolfram Language code:

mols2 = MoleculeModify["EnergyMinimizeAtomCoordinates"] /@ mols;
Histogram[MoleculeValue[mols2, "MMFFEnergy"], PlotTheme -> "Detailed"]

这样的分组对应于所谓的 "chair" 和 "twist-boat" 构象，分别为势能曲面的全局和局部最小值. 从每一组中选取一个构象，在三维空间进行绘制：

Wolfram Language code:

twistBoat = SelectFirst[mols2, #["MMFFEnergy"] > Quantity[0, "KilocaloriesThermochemical"/"Moles"]&];
chair = SelectFirst[mols2, #["MMFFEnergy"] < Quantity[0, "KilocaloriesThermochemical"/"Moles"]&];

Wolfram Language code: GraphicsRow[MoleculePlot3D[#, ViewPoint -> Left, PlotTheme -> "Tubes"]& /@ {chair, twistBoat}, ImageSize -> 500]

"InvertAroundAtom" (3)

显示 R-仲丁醇：

Wolfram Language code:

mol = Molecule["R-sec-butanol"];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

翻转该分子：

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 3}];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

检查手性：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 3}]

也可对环中的原子进行翻转. 翻转顺式环己烷-1,3-二醇中的一个甲醇基原子：

Wolfram Language code:

mol = Molecule["cis-cyclohexan-1,3-diol"];
MoleculePlot3D[%, {2}, IconizedObject[«viewOptions»]]

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 2}];
MoleculePlot3D[%, {2}, IconizedObject[«viewOptions»]]

检查手性：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 2}]

另一个醇羟基的构型未发生变化：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 6}]

可同时翻转多个原子. 显示 (-)-薄荷醇：

Wolfram Language code:

minusMenthol = Molecule["O[C@H]1[C@H](C(C)C)CC[C@@H](C)C1"];
MoleculePlot3D[%, {{2, 9}}, IconizedObject[«viewOptions»]]

将原子 2（带有羟基）和原子 9（带有甲基）翻转，以生成 (+)-新异薄荷醇：

Wolfram Language code:

plusNeoisomenthol = MoleculeModify[minusMenthol, {"InvertAroundAtom", {2, 9}}];
MoleculePlot3D[%, {{2, 9}}, IconizedObject[«viewOptions»]]

检查手性：

Wolfram Language code: MoleculeValue[minusMenthol, {"AtomChirality", {2, 3, 9}}]

Wolfram Language code: MoleculeValue[plusNeoisomenthol, {"AtomChirality", {2, 3, 9}}]

"Kekulize" (1)

默认情况下，芳香族分子具有离域 "Aromatic" 键类型：

Wolfram Language code: m1 = Molecule["benzene"]

Wolfram Language code: BondList[m1, Bond[{"C", "C"}]]

Wolfram Language code: MoleculeModify[m1, "Kekulize"]

Wolfram Language code: BondList[%, Bond[{"C", "C"}]]

"MakeHydrogensImplicit" (1)

去除分子中的所有氢原子：

Wolfram Language code: mol = Molecule["cholesterol"]

Wolfram Language code: mol["ElementCounts", IncludeHydrogens -> "ExplicitOnly"]

Wolfram Language code: mol2 = MoleculeModify[mol, "MakeHydrogensImplicit"]

Wolfram Language code: mol2["ElementCounts", IncludeHydrogens -> "ExplicitOnly"]

"RemoveStereochemistry" (1)

删除分子中明确的立体信息，使手性未定义：

Wolfram Language code: mol = Molecule["L-threonine"]

Wolfram Language code: AtomList[mol, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

Wolfram Language code: mol2 = MoleculeModify[mol, "RemoveStereochemistry"]

Wolfram Language code: AtomList[mol2, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

"RenumberAtoms" (1)

改变分子中原子的顺序：

Wolfram Language code: m = Molecule["l-alanine"]

Wolfram Language code: m2 = MoleculeModify[m, {"RenumberAtoms", {13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1}}]

Wolfram Language code: AtomList /@ {m, m2}

Wolfram Language code: MoleculeMatchQ[m, m2]

"ReplaceAtom" (1)

用不同的原子类型替换分子中的特定原子；例如，将乙酸转化为硫代乙酸：

Wolfram Language code: mol = Molecule["acetic acid"]

Wolfram Language code: MoleculeModify[mol, {"ReplaceAtom", 3 -> "S"}]

"ReplaceSubstructure" (1)

用碳酰基取代雌二醇的脂肪族 D 环中的羟基以形成雌酮：

Wolfram Language code: estradiol = Molecule["C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CC[C@@H]2O)O"]

Wolfram Language code: estrone = MoleculeModify[estradiol, {"ReplaceSubstructure", MoleculePattern["CO"] -> "C=O"}]

Wolfram Language code: MoleculePlot /@ {estradiol, estrone}

"ReplaceSubstructureList" (1)

制备甘油的每种甲基醚：

Wolfram Language code: mol = Molecule["glycerol"]

Wolfram Language code: MoleculePlot /@ MoleculeModify[mol, {"ReplaceSubstructureList", MoleculePattern["CO"] -> "COC"}]

"SetAromaticity" (1)

将定域单键或双键转换为芳香键：

Wolfram Language code:

m = Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], Atom["H"], 
  Atom["H"], Atom["H"], Atom["H"], Atom["H"]}, {Bond[{1, 2}, "Double"], Bond[{2, 3}, "Single"], 
  Bond[{3, 4}, "Double"], Bond[{4, 5}, "Single"], Bond[{5, 6}, "Double"], Bond[{6, 1}, "Single"], 
  Bond[{1, 7}, "Single"], Bond[{2, 8}, "Single"], Bond[{3, 9}, "Single"], Bond[{4, 10}, "Single"], 
  Bond[{5, 11}, "Single"], Bond[{6, 12}, "Single"]}, IncludeAromaticBonds -> False];

Wolfram Language code: BondList[m, Bond[{"C", "C"}]]

Wolfram Language code: m2 = MoleculeModify[m, "SetAromaticity"]

Wolfram Language code: BondList[m2, Bond[{"C", "C"}]]

"SetAtomChirality" (1)

将 D-葡萄糖转化为 D-甘露糖：

Wolfram Language code: glucose = Molecule["D-glucose"]

Wolfram Language code: AtomList[glucose, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

Wolfram Language code: mannose = MoleculeModify[glucose, {"SetAtomChirality", 3 -> "S"}]

Wolfram Language code: AtomList[mannose, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

Wolfram Language code: MoleculePlot3D[#, Style[3, Blue], ImageSize -> Small]& /@ {glucose, mannose}//Row

"SetAtomPosition" (1)

导入一个分子，设置单个原子的坐标：

Wolfram Language code:

m = Import["ExampleData/caffeine.xyz"];
m2 = MoleculeModify[m, {"SetAtomPosition", 2 -> {Quantity[1, "Angstroms"], Quantity[2, "Angstroms"], Quantity[3, "Angstroms"]}}]

Wolfram Language code: Normal@MoleculeValue[m2, {"AtomCoordinates", 2}]

"SetBondAngle" (3)

设置三个原子间的角度：

Wolfram Language code: m = Molecule["acetone"]

Wolfram Language code: MoleculeModify[m, {"SetBondAngle", {1, 2, 4} -> Quantity[120, "AngularDegrees"]}]

Wolfram Language code: %[{"BondAngle", {1, 2, 4}}]

设置多个键角：

Wolfram Language code:

MoleculeModify[m, {"SetBondAngle", {{1, 2, 4} -> Quantity[(3*Pi)/4, "Radians"], {1, 2, 3}  -> Quantity[106., "AngularDegrees"]}}]

Wolfram Language code: %[{"BondAngle", {{1, 2, 4}, {1, 2, 3}}}]

不能设置不成键的原子间的角度：

Wolfram Language code:

MoleculeModify[Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["C"], Atom["O"], Atom["C"], 
  Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], 
  Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], A ... "], Bond[{13, 34}, "Single"], Bond[{13, 35}, "Single"], 
  Bond[{13, 36}, "Single"], Bond[{14, 37}, "Single"], Bond[{14, 38}, "Single"], 
  Bond[{14, 39}, "Single"], Bond[{15, 40}, "Single"], Bond[{15, 41}, "Single"], 
  Bond[{15, 42}, "Single"]}], {"SetBondAngle", {9, 6, 7} -> Quantity[103, "AngularDegrees"]}]

不能设置环中的键角：

Wolfram Language code: MoleculeModify[Molecule["benzene"], {"SetBondAngle", {1, 2, 3} -> Quantity[115, "AngularDegrees"]}]

"SetBondLength" (1)

设置两个成键原子间的距离：

Wolfram Language code: mol = Molecule["chloroform"]

Wolfram Language code: mol[{"BondLength", {2, 5}}]

Wolfram Language code: MoleculeModify[mol, {"SetBondLength", {2, 5} -> Quantity[1.3, "Angstroms"]}]

Wolfram Language code: %[{"BondLength", {2, 5}}]

Wolfram Language code: MoleculeModify[mol, {"SetBondLength", {1, 3} -> Quantity[1.3, "Angstroms"]}]

"SetBondStereo" (1)

将天然 E-肉桂醛转化为 Z-形式：

Wolfram Language code: cinnE = Molecule["c1ccc(cc1)/C=C/C=O"]

Wolfram Language code: cinnZ = MoleculeModify[cinnE, {"SetBondStereo", {7, 8} -> "Z"}]//MoleculeModify["ComputeAtomCoordinates"]

Wolfram Language code: MoleculePlot3D[#, ImageSize -> Small]& /@ {cinnE, cinnZ}//Row

"SetBondType" (1)

改变烷烃中的键类型：

Wolfram Language code: MoleculeModify[Molecule["octane"], {"SetBondType", {3, 4} -> "Double"}]

反应生成的产物是烯烃：

Wolfram Language code: MoleculeName[%]

"SetFormalCharge" (1)

制作苯丙氨酸的兼性离子：

Wolfram Language code: m = MoleculeModify[Molecule["phenylalanine"], {"SetFormalCharge", {12 -> -1, 1 -> +1}}]

Wolfram Language code: MoleculePlot[m]

Wolfram Language code: AtomList[m, Atom["FormalCharge" -> Except[0]], {"AtomIndex", "AtomicSymbol"}]

"SetMassNumber" (1)

通过将质量数设置为 13，用 ¹³C 标记甲羟戊酸内酯的 C-2：

Wolfram Language code: mvl = Molecule["(4R)-4-hydroxy-4-methyloxan-2-one"]

Wolfram Language code: MoleculeModify[mvl, {"SetMassNumber", 9 -> 13}]

用 AtomList 找到标记的碳：

Wolfram Language code: AtomList[%, Atom["MassNumber" -> 13], "AtomIndex"]

通过将质量数设置为 2，用氘标记甲羟戊酸内酯的 5-pro-S 氢：

Wolfram Language code: labeledH = MoleculeModify[mvl, {"SetMassNumber", 19 -> 2}]

Wolfram Language code: MoleculePlot3D[labeledH, Atom["MassNumber" -> 2]]

"SetMetaInformation" (1)

通常，实验室对样品和笔记本使用复合编号系统，化学家在撰写内部报告、研究论文和专利时会使用这些标识号. 可使用分子的元信息来存储此类数据.

为分子添加元数据：

Wolfram Language code:

mol = MoleculeModify[Molecule[{Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["O"], 
  Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], 
  Atom["Cl"], Atom["C"], Atom["O"], Atom["C"], Atom["C"],  ... r" -> 6, 
    "Direction" -> "Counterclockwise", "FiducialAtom" -> 5, "Ligands" -> {7, 14, 2}], 
   Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 14, "Direction" -> "Clockwise", 
    "FiducialAtom" -> 13, "Ligands" -> {15, 6, 31}]}], {"SetMetaInformation", <|"C-number" -> "123456-789"|>}]

Wolfram Language code: mol["MetaInformation"]

将实验数据保存到该属性中：

Wolfram Language code:

mol = MoleculeModify[mol, {"SetMetaInformation", <|"SpecificRotation" -> {Quantity[364, "AngularDegrees"], "@ 20°C, sat. CHCl3"}|>}]

Wolfram Language code: mol["MetaInformation"]

用空关联删除元数据：

Wolfram Language code: MoleculeModify[mol, {"SetMetaInformation", <||>}]

Wolfram Language code: %["MetaInformation"]

"SetTorsionAngle" (1)

将分子的几何结构设置为所需的构象，例如内部氢键：

Wolfram Language code: mol = Molecule["OCCC=O", IncludeHydrogens -> True];

Wolfram Language code: mol2 = MoleculeModify[mol, {"SetTorsionAngle", {{6, 1, 2, 3} -> 60, {1, 2, 3, 4} -> -60, {2, 3, 4, 5} -> 60}}];

Wolfram Language code: MoleculeValue[{mol, mol2}, {"TorsionAngle", {{6, 1, 2, 3}, {1, 2, 3, 4}, {2, 3, 4, 5}}}]

Wolfram Language code: MoleculePlot3D /@ {mol, mol2}

"SetUnpairedElectronCount" (1)

通过修改水分子产生羟基自由基：

Wolfram Language code:

MoleculeModify[Molecule[{Atom["O"], Atom["H"], Atom["H"]}, {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"]}], {"SetUnpairedElectronCount", 1 -> 1}]

Wolfram Language code: AtomList@%

"TransformAtomCoordinates" (2)

通过在空间中转换坐标创建分子的副本：

Wolfram Language code: m1 = Molecule["(2S)-3-hydroxy-2-[[(2S)-pyrrolidine-2-carbonyl]amino]propanoic acid"];

Wolfram Language code:

m2 = MoleculeModify[m1, {"TransformAtomCoordinates", TranslationTransform[{Quantity[10, "Angstroms"], Quantity[10, "Angstroms"], Quantity[10, "Angstroms"]}]}]

Wolfram Language code: Show[MoleculePlot3D[#]& /@ {m1, m2}]

用 ReflectionTransform 创建分子的对映异构体：

Wolfram Language code: m = Molecule["(2S)-3-phenyl-2-[(2-phenylacetyl)amino]propanoic acid"]

Wolfram Language code: AtomList[m, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

Wolfram Language code: m2 = MoleculeModify[m, {"TransformAtomCoordinates", ReflectionTransform[{0, 0, 1}, {0, 0, 4}]}]

Wolfram Language code: AtomList[m2, Atom["AtomChirality" -> Except[None]], {"AtomIndex", "AtomChirality"}]

Wolfram Language code: Show[MoleculePlot3D /@ {m, m2}, ViewPoint -> Front]

推广和延伸 (4)

"InvertAtom" (4)

可对胺类化合物进行翻转：

Wolfram Language code:

mol = Molecule[{"C", "N", "C", "C", "C", Atom["C", "HydrogenCount" -> 1], "Cl", "C"}, 
 {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{2, 5}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{6, 8}, "Single"]}, 
 {StereochemistryElements -> {Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 6, 
     "Direction" -> "Counterclockwise"]}}];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 2}];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

检查面外角：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"OutOfPlaneAngle", {1, 2, 3, 5}}]

检查含氯碳原子的手性是否未发生变化：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 6}]

螺旋中心也可被翻转：

Wolfram Language code:

mol = Molecule[{"C", Atom["C", "HydrogenCount" -> 1], "O", "C", "C", "C", "C", 
  Atom["C", "HydrogenCount" -> 1], "Cl", "C", "C"}, {Bond[{1, 2}, "Single"], 
  Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"], Bond[{4, 5}, "Single"], Bond[{5, 6}, "Single"] ...      "Direction" -> "Clockwise"], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 2, 
     "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", 
     "ChiralCenter" -> 8, "Direction" -> "Counterclockwise"]}}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 1}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

检查螺原子的手性：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 1}]

检查其他元素的手性是否未发生变化：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", {2, 8}}]

可翻转具有足够大环的环融合原子：

Wolfram Language code:

mol = Molecule[{"C", "C", "C", "C", "C", "C", Atom["C", "HydrogenCount" -> 1], "C", "C", "C", "C"}, 
 {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{4, 5}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond ... gle"]}, {StereochemistryElements -> 
   {Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 1, 
     "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", 
     "ChiralCenter" -> 7, "Direction" -> "Clockwise"]}}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 1}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

检查手性：

Wolfram Language code: MoleculeValue[{mol, invMol}, {"AtomChirality", 1}]

可翻转具有足够大环的桥头原子：

Wolfram Language code:

mol = Molecule[{"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}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{7, 8}, "Single"], Bond[{5, 9}, "Single"], 
  Bond[{9, 10}, "Single"], Bond[{10, 11}, "Single"], Bond[{8, 1}, "Single"], 
  Bond[{11, 1}, "Single"]}, {}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

Wolfram Language code:

invMol = MoleculeModify[mol, {"InvertAroundAtom", 1}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

应用 (1)

"InvertAroundAtom" (1)

翻转 α-D-葡萄糖的异头碳：

Wolfram Language code:

alphaDglucose = Molecule["alpha-D-glucose"];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

Wolfram Language code:

betaDglucose = MoleculeModify[alphaDglucose, {"InvertAroundAtom", 5}];
MoleculePlot3D[%, IconizedObject[«viewOptions»]]

确认只有原子 5 的立体构型发生了变化：

Wolfram Language code:

(AssociationThread[Range[#["AtomCount"]], MoleculeValue[#, "AtomChirality"]]//DeleteCases[None])& /@ {alphaDglucose, betaDglucose}

可能存在的问题 (4)

"InvertAroundAtom" (4)

具有小环的环融合原子不会被翻转：

Wolfram Language code:

mol = Molecule[{"C", "C", "C", "C", "C", Atom["C", "HydrogenCount" -> 1], "C", "C", "C"}, 
 {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{4, 5}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{7, 8}, " ... ingle"]}, 
 {StereochemistryElements -> {Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 1, 
     "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", 
     "ChiralCenter" -> 6, "Direction" -> "Clockwise"]}}];
MoleculePlot3D[%, {1}]

Wolfram Language code: MoleculeModify[mol, {"InvertAroundAtom", 1}]

Wolfram Language code:

MoleculeModify[Molecule[{"C", "C", "C", "C", "C", Atom["C", "HydrogenCount" -> 1], "C", "C", "C"}, 
 {Bond[{1, 2}, "Single"], Bond[{1, 3}, "Single"], Bond[{3, 4}, "Single"], Bond[{4, 5}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{7, 8}, " ... ingle"]}, 
 {StereochemistryElements -> {Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 1, 
     "Direction" -> "Counterclockwise"], Association["StereoType" -> "Tetrahedral", 
     "ChiralCenter" -> 6, "Direction" -> "Clockwise"]}}], {"InvertAroundAtom", 1}]

具有小环的桥头原子不会被翻转：

Wolfram Language code:

mol = Molecule[{"C", "C", "O", "C", "C", "C", "C"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], 
  Bond[{3, 4}, "Single"], Bond[{4, 5}, "Single"], Bond[{4, 6}, "Single"], Bond[{6, 7}, "Single"], 
  Bond[{5, 1}, "Single"], Bond[{7, 1}, "Single"]}, {}];
MoleculePlot3D[%, {1}, IconizedObject[«viewOptions»]]

Wolfram Language code: MoleculeModify[mol, {"InvertAroundAtom", 1}]

三环及更大环系中的桥头原子不会被翻转：

Wolfram Language code:

mol = Molecule[{"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}, "Single"], 
  Bond[{5, 6}, "Single"], Bond[{6, 7}, "Single"], Bond[{7, 8}, "Single"], Bond[{5, 9}, "Single"], 
  Bond[{9, 10}, "Single"], Bond[{10, 11}, "Single"], Bond[{5, 1}, "Single"], 
  Bond[{8, 1}, "Single"], Bond[{11, 1}, "Single"]}, {}];
MoleculePlot3D[%, {1}, PlotTheme -> "Tubes", IncludeHydrogens -> None, IconizedObject[«viewOptions»]]

Wolfram Language code: MoleculeModify[mol, {"InvertAroundAtom", 1}]

Wolfram Language code:

mol = Molecule[{"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}, "Single"], 
  Bond[{2, 6}, "Single"], Bond[{6, 7}, "Single"], Bo ... e"], 
  Bond[{1, 13}, "Single"], Bond[{13, 14}, "Single"], Bond[{14, 15}, "Single"], 
  Bond[{15, 16}, "Single"], Bond[{16, 17}, "Single"], Bond[{9, 1}, "Single"], 
  Bond[{17, 1}, "Single"], Bond[{13, 5}, "Single"], Bond[{17, 12}, "Single"]}, {}];
MoleculePlot3D[%, {1}, PlotTheme -> "Tubes", IncludeHydrogens -> None]

Wolfram Language code: MoleculeModify[mol, {"InvertAroundAtom", 1}]

不能翻转五配位原子：

Wolfram Language code:

mol = Molecule[{"P", "C", "C", "C", "C", "O", "C", "C", "F", "F", "F", "C", "C", "N", "C", "C", "C", "C", 
  "Cl"}, {Bond[{1, 2}, "Single"], Bond[{2, 3}, "Single"], Bond[{2, 4}, "Single"], 
  Bond[{2, 5}, "Single"], Bond[{1, 6}, "Single"], Bond[{6, 7}, " ... "], 
  Bond[{7, 12}, "Single"], Bond[{12, 13}, "Single"], Bond[{1, 14}, "Single"], 
  Bond[{14, 15}, "Single"], Bond[{15, 16}, "Single"], Bond[{14, 17}, "Single"], 
  Bond[{17, 18}, "Single"], Bond[{1, 19}, "Single"], Bond[{13, 1}, "Single"]}, {}];
MoleculePlot3D[%, PlotTheme -> "Tubes", IncludeHydrogens -> None, IconizedObject[«viewOptions»]]

Wolfram Language code: MoleculeModify[mol, {"InvertAroundAtom", 1}]

巧妙范例 (1)

对 MMFF 力场应用距离约束条件以找到满足两个原子之间给定距离的构象. 首先，创建基础分子：

Wolfram Language code:

m = Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], 
  Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], 
  Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["O"], A ... r" -> 33, 
    "Direction" -> "Clockwise", "FiducialAtom" -> 32, "Ligands" -> {34, 35, 107}], 
   Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 38, "Direction" -> "Clockwise", 
    "FiducialAtom" -> 37, "Ligands" -> {39, 40, 117}]}];

找到标准构型中距离最远的两个原子：

Wolfram Language code: dmat = m["DistanceMatrix"]

Wolfram Language code: {a1, a2} = FirstPosition[Normal[dmat], Max[dmat]]

默认构象中两个原子的间距为 32 埃 (ångström)：

Wolfram Language code: dmat[[a1, a2]]

Wolfram Language code: MoleculePlot3D[m, {Style[a1, Blue], Style[a2, Red]}]

用 "EnergyMinimizeAtomCoordinates" 找到这些原子间的距离满足特定条件的新构象：

Wolfram Language code:

mod = MoleculeModify[m, {"EnergyMinimizeAtomCoordinates", {a1, a2} -> #}]& /@ {Quantity[5, "Angstroms"], Quantity[10, "Angstroms"], Quantity[20, "Angstroms"], Quantity[40, "Angstroms"]}

验证返回的几何结构是否符合要求，并获取力场能量：

Wolfram Language code: MoleculeValue[mod, {{"InteratomicDistance", {a1, a2}}, "MMFFEnergy"}]

Wolfram Language code: MoleculePlot3D /@ mod

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	{"SetAtomChirality",aval}	设置原子的手性值为 "R" 或 "S"
	{"SetBondStereo",{a₁,a₂}val}	将键的立体值设为 "E" 或 "Z"

	{"InvertAroundAtom",a}	翻转索引为的原子周围的几何结构
	{"InvertAroundAtom",{a₁,a₂,…}}	翻转多个原子周围的几何结构

MoleculeModify

更多信息和选项

对原子进行修改

对键进行修改

普通修改

对立体化学信息进行修改

子结构的删除与替换

生成坐标

对几何结构进行修改

范例

基本范例 (4)

范围 (41)

"AddAtom" (1)

"AddBond" (1)

"AssignStereochemistryFromCoordinates" (1)

"CanonicalizeAtomCoordinates" (1)

"ComputeAtomCoordinates" (2)

"ComputeAtomDiagramCoordinates" (2)

"DeleteAtom" (2)

"DeleteBond" (2)

"DeleteSubstructure" (1)

"EnergyMinimizeAtomCoordinates" (1)

"GenerateConformers" (1)

"InvertAroundAtom" (3)

"Kekulize" (1)

"MakeHydrogensImplicit" (1)

"RemoveStereochemistry" (1)

"RenumberAtoms" (1)

"ReplaceAtom" (1)

"ReplaceSubstructure" (1)

"ReplaceSubstructureList" (1)

"SetAromaticity" (1)

"SetAtomChirality" (1)

"SetAtomPosition" (1)

"SetBondAngle" (3)

"SetBondLength" (1)

"SetBondStereo" (1)

"SetBondType" (1)

"SetFormalCharge" (1)

"SetMassNumber" (1)

"SetMetaInformation" (1)

"SetTorsionAngle" (1)

"SetUnpairedElectronCount" (1)

"TransformAtomCoordinates" (2)

推广和延伸 (4)

"InvertAtom" (4)

应用 (1)

"InvertAroundAtom" (1)

可能存在的问题 (4)

"InvertAroundAtom" (4)

巧妙范例 (1)

参见

相关指南

历史

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