How can I highlight a single atom in MoleculePlot?

MoleculePlot[mol1, First @ AtomList[mol1,"O","AtomIndex"]]

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MoleculePlot[mol1, Last @ AtomList[mol1,"O","AtomIndex"]]

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Actually, there is no need to specify a MoleculePattern for what you want to do. If you read the documentation carefully you merely want to specify an Integer atom index (or a list of Integer atom indices) as the second argument to MoleculePlot, not a pattern. Here's an example:

mol1 = Molecule[
   "O=C(N(CC(NCC(F)(F)F)=O)CN1C2=CC=CC=C2)C31CCN(C(C4=CC(C=NN5)=C5C=\
C4)=O)CC3"];
MoleculePlot[mol1, 1]

highlighting the atom index 1 in the MoleculePlot

MoleculePlot[mol1, {1, 3, 5}]

list of atom indices, highlights multiple atoms

Tags:

Chemistry

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