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

Examples

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Basic Examples  (2)

Create a molecule and plot it:

Highlight the first and third atoms:

Highlight all oxygen atoms:

Highlight two different patterns:

Scope  (2)

A pattern can match one or multiple positions in a molecule:

Highlight each carbonyl separately:

Highlight each carbonyl as a single color:

Highlight several patterns:

Options  (7)

AtomLabels  (1)

Label all atoms by their index:

Label only chlorine atoms by their index:

Label non-hydrogen atoms by their hybridization:

AtomLabelStyle  (1)

Set all labels to have the same style:

Set the label style depending on atom type:

BondLabels  (1)

Label all bonds by their index:

Label only bonds to chlorine atoms by their bond type:

BondLabelStyle  (1)

Give all bond labels the same style:

Label bonds differently based on their atoms:

ColorRules  (1)

Specify different colors for atomic elements:

PlotLegends  (1)

Use placeholders for plot legends:

Use the expressions to label the highlights:

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:

Combine different plot themes:

Wolfram Research (2019), MoleculePlot, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot.html (updated 2021).

Text

Wolfram Research (2019), MoleculePlot, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot.html (updated 2021).

CMS

Wolfram Language. 2019. "MoleculePlot." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/MoleculePlot.html.

APA

Wolfram Language. (2019). MoleculePlot. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculePlot.html

BibTeX

@misc{reference.wolfram_2025_moleculeplot, author="Wolfram Research", title="{MoleculePlot}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/MoleculePlot.html}", note=[Accessed: 20-April-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_moleculeplot, organization={Wolfram Research}, title={MoleculePlot}, year={2021}, url={https://reference.wolfram.com/language/ref/MoleculePlot.html}, note=[Accessed: 20-April-2025 ]}