Molecule
MoleculeGraph
FindFundamentalCycles
FindGraphPartition
FindGraphCommunities
MoleculePlot
MoleculePlot3D

Chemistry
Visualization & Graphics

Analyze Components and Connectivity of Molecule Graphs

Create the graph underpinning a molecule and visualize cycles, partitions and communities in the graph

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Create a molecular graph using the flavonoid myricetin:

In[1]:=

myricetin=Molecule["3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4-chromenone"]

Out[1]=

Molecule

Formula:

Atoms: 33 Bonds: 35



Use

MoleculeGraph

to get the underlying graph:

In[2]:=

graph=MoleculeGraph[myricetin]

Out[2]=

Find the cycle basis:

In[3]:=

FindFundamentalCycles[graph]

Out[3]=

{{2021,2123,2316,1617,1718,1820},{1623,232,23,35,515,1516},{1214,146,67,78,810,1012}}

Highlight the cycle in 3D:

In[4]:=

MoleculePlot3D[myricetin,%]

Out[4]=

Find a graph partition:

In[5]:=

FindGraphPartition[graph]

Out[5]=

{{1,2,3,5,15,16,17,18,19,20,21,22,23,30,31,32,33},{4,6,7,8,9,10,11,12,13,14,24,25,26,27,28,29}}

Show the molecule and highlight the partition:

In[6]:=

MoleculePlot[myricetin,%]

Out[6]=

Find graph communities:

In[7]:=

communities=FindGraphCommunities[MoleculeGraph[myricetin],Method"Spectral"]

Out[7]=

{{5,6,7,14,25,29},{20,21,22,32,33},{10,12,13,28},{15,16,17,30},{1,2,23},{3,4,24},{8,9,26},{18,19,31},{11,27}}

Show the molecule and highlight the communities. These communities differ from the chemical notions of ligands and functional groups:

In[8]:=

MoleculePlot[myricetin,Map[BondList[myricetin,#]&,communities]]

Out[8]=

Related Symbols

Molecule
MoleculeGraph
FindFundamentalCycles
FindGraphPartition
FindGraphCommunities
MoleculePlot
MoleculePlot3D

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Analyze Components and Connectivity of Molecule Graphs

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