Wolfram Language Paclet Repository

Community-contributed installable additions to the Wolfram Language

WolframChemistry/ChemistryFunctions

(1.0.0) current version: 1.4.1 »

Wolfram Language functions for Chemistry

Contributed by: Jason Biggs, Wolfram Research

This package provides a wide range of capabilities for chemists, biochemists, and anyone else who works with molecular structures. The functions defined here expand upon the existing chemistry functions built into the Wolfram Language. With functions for substructure matching, molecule joining, and visualization, as well as dynamic controls and predicate functions, this package can help you explore and analyze molecules in new and powerful ways. Whether you're looking to identify rings, test for stereochemistry, or arrange molecule plots in a grid, the functions in this package can help you get the job done efficiently and accurately.

Installation Instructions

To install this paclet in your Wolfram Language environment, evaluate this code:
PacletInstall["WolframChemistry/ChemistryFunctions"]

Paclet Guide

Examples

Basic Examples (6) 

Find the empirical formula for a compound that is 64.3% carbon, 7.2% hydrogen, and 28.5% oxygen:

In[1]:=
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Out[1]=

Create a plot showing the electrons in the radioactive element californium:

In[2]:=
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Out[2]=

Join two benzene molecules to make biphenyl:

In[3]:=
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Out[3]=

Join 15 benzene molecules together in a ring and plot it in 3D:

In[4]:=
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Out[4]=

Remove waters of hydration from a molecule downloaded from an external database:

In[5]:=
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Out[5]=

Create a grid of molecule diagrams:

In[6]:=
SeedRandom[13]; InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 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Out[4]=

Find the scaffold for a molecule and highlight it in a 2D plot:

In[7]:=
MoleculePlot[ m = Molecule[ "3-[3-hydroxy-2-oxo-2,3-dihydro-1H-indol-3-yl]-L-alanine"], InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 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Out[7]=

Scope

In[8]:=
InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 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Out[8]=

Publisher

WolframChemistry

Compatibility

Wolfram Language Version 13.1

Version History

  • 1.4.1 – 21 August 2024
  • 1.3.0 – 06 August 2024
  • 1.2.0 – 05 February 2024
  • 1.1.0 – 05 December 2023
  • 1.0.2 – 26 June 2023
  • 1.0.1 – 26 June 2023
  • 1.0.0 – 23 June 2023

License Information

MIT License

Paclet Source

See Also