--- title: "MoleculePlot" language: "en" type: "Symbol" summary: "MoleculePlot[mol] creates a two-dimensional structure diagram of the molecule mol. MoleculePlot[mol, patt] creates a diagram of mol where all atoms and bonds matching the pattern patt are highlighted." keywords: - 2D molecule plot - chemical structure - chemistry - Lewis structure - molecular computation - molecular graphics - molecular visualization - molecule - structural depiction - structural diagram - structure diagram canonical_url: "https://reference.wolfram.com/language/ref/MoleculePlot.html" source: "Wolfram Language Documentation" related_guides: - title: "Physics & Chemistry: Data and Computation" link: "https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md" - title: "Molecular Structure & Computation" link: "https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md" --- [EXPERIMENTAL] # MoleculePlot MoleculePlot[mol] creates a two-dimensional structure diagram of the molecule mol. MoleculePlot[mol, patt] creates a diagram of mol where all atoms and bonds matching the pattern patt are highlighted. ## Details and Options * ``MoleculePlot`` returns a ``Graphics`` expression. * If the molecule does not have structure diagram coordinates, they will be generated automatically. * ``mol`` can be a ``Molecule`` object or something that can be easily converted to one, such as a systematic chemical name, a ``"Chemical"`` entity, a ``BioSequence`` or an ``ExternalIdentifier``. * ``MoleculePlot[MoleculePattern[…]]`` will return a depiction of the given molecule pattern. * Possible forms for ``patt`` include: | | | | ----------------------- | ------------------------------------- | | n | the index of a particular atom | | Atom[…] | a pattern for an atom | | Bond[…] | a pattern for a bond | | MoleculePattern[…] | a pattern for a molecule substructure | | {patt1, patt2, …} | a list of patterns | | <\|label1 -> patt1, …\|> | an Association of labels and patterns | * ``MoleculePlot`` has the same options as ``Graphics``, with the following additions and changes: [] | | | | | ---------------- | ----------- | ------------------------------------------------------------------------------------ | | AtomLabels | Automatic | labels and label placements for atoms | | AtomLabelStyle | Automatic | style to use for atom labels | | BondLabels | None | labels and label placements for bonds | | BondLabelStyle | Automatic | style to use for bond labels | | ColorRules | Automatic | a list of rules {elem1 -> col1, …} dictating which colors to use for atomic elements | | IncludeHydrogens | Automatic | whether to show hydrogen atoms | | PlotLegends | None | legends for highlights | | PlotTheme | \$PlotTheme | overall theme for the plot | * Supported plot themes include: | | | | | ------- | ------------ | -------------------------------------------------------------------- | | [image] | "AllAtom" | display all hydrogens | | [image] | "Aromatic" | aromatic bonds are shown as dashed lines or circles | | [image] | "HeavyAtom" | hydrogen atoms are elided or combined with the connected heavy atom | | [image] | "Monochrome" | all text and graphics are shown in black | * Typical settings for ``PlotLegends`` include: | | | | ---------------- | ---------------------------------- | | None | no legend | | Automatic | automatically determine legend | | {lbl1, lbl2, …} | use lbl1, lbl2, … as legend labels | | Placed[lspec, …] | specify placement for legend | ### List of all options | | | | | ---------------------- | --------------- | ------------------------------------------------------------------------------------ | | AlignmentPoint | Center | the default point in the graphic to align with | | AspectRatio | Automatic | ratio of height to width | | AtomLabels | Automatic | labels and label placements for atoms | | AtomLabelStyle | Automatic | style to use for atom labels | | Axes | False | whether to draw axes | | AxesLabel | None | axes labels | | AxesOrigin | Automatic | where axes should cross | | AxesStyle | {} | style specifications for the axes | | Background | None | background color for the plot | | BaselinePosition | Automatic | how to align with a surrounding text baseline | | BaseStyle | {} | base style specifications for the graphic | | BondLabels | None | labels and label placements for bonds | | BondLabelStyle | Automatic | style to use for bond labels | | ColorRules | Automatic | a list of rules {elem1 -> col1, …} dictating which colors to use for atomic elements | | ContentSelectable | Automatic | whether to allow contents to be selected | | CoordinatesToolOptions | Automatic | detailed behavior of the coordinates tool | | Epilog | {} | primitives rendered after the main plot | | FormatType | TraditionalForm | the default format type for text | | Frame | False | whether to put a frame around the plot | | FrameLabel | None | frame labels | | FrameStyle | {} | style specifications for the frame | | FrameTicks | Automatic | frame ticks | | FrameTicksStyle | {} | style specifications for frame ticks | | GridLines | None | grid lines to draw | | GridLinesStyle | {} | style specifications for grid lines | | ImageMargins | 0. | the margins to leave around the graphic | | ImagePadding | All | what extra padding to allow for labels etc. | | ImageSize | Automatic | the absolute size at which to render the graphic | | IncludeHydrogens | Automatic | whether to show hydrogen atoms | | LabelStyle | {} | style specifications for labels | | Method | Automatic | details of graphics methods to use | | PlotLabel | None | an overall label for the plot | | PlotLegends | None | legends for highlights | | PlotRange | All | range of values to include | | PlotRangeClipping | False | whether to clip at the plot range | | PlotRangePadding | Automatic | how much to pad the range of values | | PlotRegion | Automatic | the final display region to be filled | | PlotTheme | \$PlotTheme | overall theme for the plot | | PreserveImageOptions | Automatic | whether to preserve image options when displaying new versions of the same graphic | | Prolog | {} | primitives rendered before the main plot | | RotateLabel | True | whether to rotate y labels on the frame | | Ticks | Automatic | axes ticks | | TicksStyle | {} | style specifications for axes ticks | --- ## Examples (11) ### Basic Examples (2) Create a molecule and plot it: ```wl In[1]:= MoleculePlot[Molecule["NC(=O)C[C@H](C(=O)O)N"]] Out[1]= [image] ``` Highlight the first and third atoms: ```wl In[2]:= MoleculePlot[Molecule["NC(=O)C[C@H](C(=O)O)N"], {3, 8}] Out[2]= [image] ``` Highlight all oxygen atoms: ```wl In[3]:= MoleculePlot[Molecule["NC(=O)C[C@H](C(=O)O)N"], Atom["O"]] Out[3]= [image] ``` --- Highlight two different patterns: ```wl In[1]:= MoleculePlot["O=C(C1CCC1)S[C@@H]1CCC1(C)C", <|"carbonyl" -> Bond[{"C", "O"}, "Double"], "ring carbons" -> Atom["C", "RingAtomQ" -> True]|>] Out[1]= [image] ``` ### Scope (2) A pattern can match one or multiple positions in a molecule: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["N"], Atom["C"], Atom["O"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["O"], Atom["O"], Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["O"], Atom["O"], Atom["C"], Atom["C"], A ... er" -> 10, "Direction" -> "Clockwise", "FiducialAtom" -> 9, "Ligands" -> {11, 5, 34}], Association["StereoType" -> "Tetrahedral", "ChiralCenter" -> 16, "Direction" -> "Counterclockwise", "FiducialAtom" -> 15, "Ligands" -> {17, 20, 40}]}]; carbonylPattern = Bond[{"C", "O"}, "Double"]; ``` Highlight each carbonyl separately: ```wl In[2]:= MoleculePlot[m, carbonylPattern] Out[2]= [image] ``` Highlight each carbonyl as a single color: ```wl In[3]:= MoleculePlot[m, {carbonylPattern}] Out[3]= [image] ``` --- Highlight several patterns: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], A ... e"], Bond[{6, 22}, "Single"], Bond[{10, 23}, "Single"], Bond[{10, 24}, "Single"], Bond[{11, 25}, "Single"], Bond[{11, 26}, "Single"], Bond[{11, 27}, "Single"], Bond[{12, 28}, "Single"], Bond[{12, 29}, "Single"], Bond[{12, 30}, "Single"]}]; In[2]:= MoleculePlot[m, {1, Bond[{"C", "C"}, "Double"]}] Out[2]= [image] ``` ### Options (7) #### AtomLabels (1) Label all atoms by their index: ```wl In[1]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex"] Out[1]= [image] ``` Label only chlorine atoms by their index: ```wl In[2]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> {Atom["Cl"] -> "AtomIndex"}] Out[2]= [image] ``` Label non-hydrogen atoms by their hybridization: ```wl In[3]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> {Atom[Except["H"]] -> MoleculeProperty["OrbitalHybridization"]}] Out[3]= [image] ``` #### AtomLabelStyle (1) Set all labels to have the same style: ```wl In[1]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex", AtomLabelStyle -> Directive[FontSize -> 12, Blue]] Out[1]= [image] ``` Set the label style depending on atom type: ```wl In[2]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], AtomLabels -> "AtomIndex", AtomLabelStyle -> {Atom["C"] -> Directive[12, Blue], Atom["O"] -> Directive[8, Purple, Bold], _ -> Italic}] Out[2]= [image] ``` #### BondLabels (1) Label all bonds by their index: ```wl In[1]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex"] Out[1]= [image] ``` Label only bonds to chlorine atoms by their bond type: ```wl In[2]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> {Bond[{"Cl", _}] -> MoleculeProperty["BondType"]}] Out[2]= [image] ``` #### BondLabelStyle (1) Give all bond labels the same style: ```wl In[1]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex", BondLabelStyle -> Directive[FontSize -> 22, Red]] Out[1]= [image] ``` Label bonds differently based on their atoms: ```wl In[2]:= MoleculePlot[Molecule["2,3-dichloro-4-nitro-1H-pyrrole"], BondLabels -> "BondIndex", BondLabelStyle -> {Bond[{"N", _}] -> Directive[FontSize -> 22, Red], Bond[{"Cl", _}] -> Directive[FontSize -> 22, Blue]}] Out[2]= [image] ``` #### ColorRules (1) Specify different colors for atomic elements: ```wl In[1]:= MoleculePlot["Nc1nccc(n1)c1c(C)onc1c1ccccc1", ColorRules -> {"C" -> RGBColor[0.79, 0.34, 0.5], "N" -> RGBColor[0.5, 0.51, 0.81], _ -> Black}] Out[1]= [image] ``` #### PlotLegends (1) Use placeholders for plot legends: ```wl In[1]:= m = Molecule[{Atom["C"], Atom["N"], Atom["C"], Atom["C"], Atom["C"], Atom["N"], Atom["C"], Atom["O"], Atom["C"], Atom["C"], Atom["C"], Atom["C"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], Atom["H"], A ... e"], Bond[{6, 22}, "Single"], Bond[{10, 23}, "Single"], Bond[{10, 24}, "Single"], Bond[{11, 25}, "Single"], Bond[{11, 26}, "Single"], Bond[{11, 27}, "Single"], Bond[{12, 28}, "Single"], Bond[{12, 29}, "Single"], Bond[{12, 30}, "Single"]}]; In[2]:= MoleculePlot[m, {1, Bond[{"C", "C"}, "Double"]}, PlotLegends -> Automatic] Out[2]= [image] ``` Use the expressions to label the highlights: ```wl In[3]:= MoleculePlot[m, {1, Bond[{"C", "C"}, "Double"]}, PlotLegends -> Placed["Expressions", Below]] Out[3]= [image] ``` #### PlotTheme (1) By default, aromatic bonds are shown in their delocalized Kekule form. Use the ``"Aromatic"`` plot theme to show which bonds are aromatic. Phenyl rings are shown with a circle to indicate the delocalized bonding electrons. Aromatic heterocycles use dashed lines for aromatic bonds: ```wl In[1]:= MoleculePlot["Nc1nccc(n1)c1c(C)onc1c1ccccc1", PlotTheme -> "Aromatic"] Out[1]= [image] ``` Combine different plot themes: ```wl In[2]:= MoleculePlot["Nc1nccc(n1)c1c(C)onc1c1ccccc1", PlotTheme -> {"Aromatic", "AllAtom", "Monochrome"}] Out[2]= [image] ``` ## See Also * [`MoleculePlot3D`](https://reference.wolfram.com/language/ref/MoleculePlot3D.en.md) * [`Molecule`](https://reference.wolfram.com/language/ref/Molecule.en.md) * [`MoleculeRecognize`](https://reference.wolfram.com/language/ref/MoleculeRecognize.en.md) * [`AtomLabels`](https://reference.wolfram.com/language/ref/AtomLabels.en.md) * [`AtomLabelStyle`](https://reference.wolfram.com/language/ref/AtomLabelStyle.en.md) * [`BondLabels`](https://reference.wolfram.com/language/ref/BondLabels.en.md) * [`BondLabelStyle`](https://reference.wolfram.com/language/ref/BondLabelStyle.en.md) * [`Chemical`](https://reference.wolfram.com/language/ref/entity/Chemical.en.md) * [`Protein`](https://reference.wolfram.com/language/ref/entity/Protein.en.md) ## Related Guides * [Physics & Chemistry: Data and Computation](https://reference.wolfram.com/language/guide/PhysicsAndChemistryDataAndComputation.en.md) * [Molecular Structure & Computation](https://reference.wolfram.com/language/guide/MolecularStructureAndComputation.en.md) ## History * [Introduced in 2019 (12.0)](https://reference.wolfram.com/language/guide/SummaryOfNewFeaturesIn120.en.md) \| [Updated in 2021 (13.0)](https://reference.wolfram.com/language/guide/SummaryOfNewFeaturesIn130.en.md)