WolframChemistry/ IsomerGeneration

Generate Isomers from Chemical Formulas

Contributed by: Jason Biggs, Wolfram Research

Starting from a chemical formula, generate all possible molecular structures with correct valence. Quickly create millions of isomers or more and read them in as "SMILES" strings or Molecule objects using a stream-like interface. Customize the structure generation by filtering out predefined substructure patterns, e.g. triple bonds in small rings or molecules with bridging double bonds, or define new valence rules for atoms outside the common organic set. This package uses the external application surge, based on the canonical generation path method.

Installation Instructions

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


To load the code after installation, evaluate this code:
Needs["WolframChemistry`IsomerGeneration`"]

Details

The functions defined in the IsomerGeneration paclet rely on the open-source application Surge to generate chemical structures. See "Surge: A Fast Open-Source Chemical Graph Generator" for implementation details.
Options are provided to pre-filter certain substructures. Specify the number of bonds, only create isomers with 2 or fewer 5-membered rings, require the underlying Graph to be PlanarGraphQ, exclude molecules with triple bonds, etc.
Elements supported include carbon, boron, nitrogen, phosphorus, oxygen, sulfur, hydrogen, chlorine, fluorine, bromine, and iodine at their lowest valences. Other elements can be included by providing their valence.
Ions (charged molecules) and zwitterions (neutral molecules with positive and negative parts) are not supported.
Stereoisomers are not generated.
For many chemical formulas it is possible to generate billions of isomers, with memory footprints of many gigabytes. The isomers are stored as text files filled with "SMILES" strings, located easily in your $WolframDocumentsDirectory.

Paclet Guide

Examples

Basic Examples (2) 

List and plot all the isomers of dichlorobutane:

In[1]:=
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Out[1]=
In[2]:=
MoleculePlot /@ %
Out[2]=

Count the number of isomers of C10H16O without listing them:

In[3]:=
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Out[3]=

Substitute fluorine for two of they hydrogens and count the isomers:

In[4]:=
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  "C10H14OF2"] // AbsoluteTiming
Out[4]=

Generate all the isomers for C10H16OF2 asynchronously:

In[5]:=
res = 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[5]=

Check the status of the isomer generation:

In[6]:=
ProcessStatus[res]
Out[6]=

Find information about the isomers:

In[7]:=
Information[res]
Out[7]=

Read the first SMILES string from the result:

In[8]:=
Read[res]
Out[8]=

Read the next entry as a Molecule:

In[9]:=
Read[res, Molecule]
Out[9]=

Search through all 3.5 million isomers, lazily selecting only the first 100 that have both fluorine atoms on the same carbon atom:

In[10]:=
Select[res, MoleculeContainsQ[MoleculePattern["[F][C][F]"]], 100] // Short
Out[10]=
In[11]:=
MoleculePlot /@ RandomSample[%, 5]
Out[11]=

Scope (4) 

This is just a drop in the bucket compared to the seventy-five million possible isomers:

In[12]:=
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 Entity["Chemical", "2Ethyl4,2,2,3Trimethyl3Cyclopenten1Yl2Buten1Ol"]]
Out[12]=

Filtering out unphysical substructures and you still have fifty-six million isomers:

In[13]:=
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 Entity["Chemical", "2Ethyl4,2,2,3Trimethyl3Cyclopenten1Yl2Buten1Ol"],
  "ForbiddenSubstructures" -> All]
Out[13]=

Note however there is a limitation with respect to stereochemistry. The cis- and trans- isomers of this simple alkene are not returned by ListIsomers:

In[14]:=
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 Molecule["1-bromo-2-chloroethene"], Molecule]
Out[14]=

When searching PubChem with FindIsomers, you will find both stereoisomers but will also find many hypervalent species:

In[15]:=
FindIsomers[Molecule["1-bromo-2-chloroethene"]]
Out[15]=

Publisher

WolframChemistry

Disclosures

Compatibility

Wolfram Language Version 12.3

Version History

  • 1.0.3 – 22 November 2023
  • 1.0.2 – 15 October 2022
  • 1.0.1 – 12 October 2022
  • 1.0.0 – 07 October 2022
  • 0.0.9 – 01 October 2022

License Information

MIT License

Paclet Source

Source Metadata

See Also