WolframChemistry/ ChemistryFunctions

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. These functions expand upon the existing chemistry functions built into the Wolfram Language. With functions for substructure matching, joining molecules, and visualization, as well as dynamic controls and predicate functions, this package can help you explore and analyze molecules in new and powerful ways.

Installation Instructions

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

To load the code after installation, evaluate this code:
Needs["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]:=

${m = Molecule[ ExternalIdentifier["PubChemCompoundID", "6093252"]], 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.`, 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Out[5]=

Create a grid of molecule diagrams:

In[6]:=

Out[4]=

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

In[7]:=

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Out[7]=

Scope

In[8]:=

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