MoleculePlot3D

MoleculePlot3D[mol]
creates a three-dimensional model of the molecule mol.
MoleculePlot3D[mol,patt]
creates a model of mol where all atoms and bonds matching the pattern patt are highlighted.
Details and Options



- If the molecule does not have structure diagram coordinates, they will be generated automatically according to the molecule's AtomCoordinates option.
- mol can be a Molecule object or something that can be easily converted to one, such as a systematic chemical name, a "Chemical" entity or 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 - Patterns entered as Style[patt,spec]will be styled according to spec.
- MoleculePlot3D has the same options as Graphics3D, with the following additions and changes:
-
AtomLabels None 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 Boxed False whether to draw the bounding box ColorRules Automatic a list of rules IncludeHydrogens True whether to show hydrogen atoms PlotLegends None legends for highlights PlotTheme Automatic overall theme for the plot - Supported plot themes include:
-
"HeavyAtom" do not display hydrogens "BallAndStick" display atoms and bonds using Sphere and Cylinder primitives "Spacefilling" atoms are depicted with spheres with radius matching the van der Waals radius "Tubes" atoms omitted "Wireframe" bonds rendered as lines - 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 - When patt is entered as an Association, the labeli will be used in the PlotLegends.
Examples
open allclose allBasic Examples (3)
Scope (2)
Options (7)
AtomLabels (1)
AtomLabelStyle (1)
BondLabels (1)
BondLabelStyle (1)
Wolfram Research (2019), MoleculePlot3D, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot3D.html (updated 2021).
Text
Wolfram Research (2019), MoleculePlot3D, Wolfram Language function, https://reference.wolfram.com/language/ref/MoleculePlot3D.html (updated 2021).
CMS
Wolfram Language. 2019. "MoleculePlot3D." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/MoleculePlot3D.html.
APA
Wolfram Language. (2019). MoleculePlot3D. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/MoleculePlot3D.html