Find the Longest Path in a Molecule

Consider a tRNA connector:

In[1]:=

mol=Molecule["3'-deoxy-3'-[(L-methionyl-L-phenylalanyl)amino]adenosine 5'-(dihydrogen phosphate)"]

Out[1]=

Molecule

Formula:

C

24

H

33

N

8

O

8

PS

Atoms: 75 Bonds: 78

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The graph distance matrix contains the number of bonds between each pair of atoms:

In[2]:=

graphDistanceMatrix=GraphDistanceMatrix[MoleculeGraph[mol]];MatrixPlotgraphDistanceMatrix,

...

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Out[2]=

Find the atoms terminating the longest path:

In[3]:=

{atom1,atom2}=FirstPosition[graphDistanceMatrix,Max[graphDistanceMatrix]]

Out[3]=

{43,68}

Find the shortest path between these atoms:

In[4]:=

path=FindShortestPath[MoleculeGraph[mol],atom1,atom2]

Out[4]=

{43,1,2,3,4,5,7,9,10,18,20,21,22,24,25,34,28,29,30,68}

Highlight the path in 3D:

In[5]:=

MoleculePlot3D[mol,{BondList[mol,path]}]

Out[5]=

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