Atom
Molecule
MoleculePattern
MoleculePlot
Bond

Chemistry
Visualization & Graphics

Highlight Patterns in Molecules

Define and visualize patterns for atoms, bonds and arbitrary substructures in a molecule

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Use

Atom

objects to define patterns representing individual atoms:

In[1]:=

atomPatterns={"O",Atom["FormalCharge"GreaterThan[0]],Atom["RingMemberQ"True]};

Create highlighting rules with a label for each pattern:

In[2]:=

labels={"oxygen atom","cation","ring atom"};highlightRules=AssociationThread[labels,atomPatterns]

Out[2]=

oxygen atomO,cationAtom[FormalChargeGreaterThan[0]],ring atomAtom[RingMemberQTrue]

Plot the molecule with highlighted patterns. The labels on the left-hand sides of the result automatically form a legend:

In[3]:=

MoleculePlot[Molecule["trinitrotoluene"],highlightRules]

Out[3]=

	oxygen atom
	cation
	ring atom

Patterns for bonds are defined using the

Bond

head:

In[4]:=

bondRules="N-N"Bond[{"N","N"}],"halogen bonds"Bond[{"Cl"|"F"|"Br"|"I",_}],"polar bond"Bond[{Atom["GasteigerPartialCharge"GreaterThan[0.2]],Atom["GasteigerPartialCharge"LessThan[-0.2]]}];

In[5]:=

MoleculePlot[Molecule["(4R)-4-benzoyl-5-fluoro-2-phenyl-4H-pyrazol-3-one"],bondRules]

Out[5]=

	N-N
	halogen bonds
	polar bond

Use

MoleculePattern

to represent complex patterns like a carboxylic ester, using a combination of atoms and bonds:

In[6]:=

carbonicEster=MoleculePattern[{"C","O",Atom["O","HeavyAtomCoordinationNumber"2],Atom["O","HeavyAtomCoordinationNumber"2]},{Bond[{1,2},"Double"],Bond[{1,3}],Bond[{1,4}]}];

Plot the molecule with the patterns. The pattern is highlighted without a caption when just the pattern is used:

In[7]:=

MoleculePlot3D

2-(tert-butoxycarbonyloxy)phenylboronic acid pinacol ester

CHEMICAL

,carbonicEster

Out[7]=

Related Symbols

Atom
Molecule
MoleculePattern
MoleculePlot
Bond

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Highlight Patterns in Molecules

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