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.
- mol can be a Molecule object or something that can be easily converted to one, such as a systematic chemical name, an Entity, or an ExternalIdentifier.
- 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 <label1patt1,… > 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:
-
"AllAtom" display all hydrogens "Aromatic" aromatic bonds are shown as dashed lines or circles "HeavyAtom" hydrogen atoms are elided or combined with the connected heavy atom "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
Examples
open allclose allBasic Examples (2)
Scope (2)
Options (7)
AtomLabels (1)
AtomLabelStyle (1)
BondLabels (1)
BondLabelStyle (1)
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