Basic Examples 
(3)
 

Interactively select the imidazole ring inside of ATP:
In[1]:=
mol=Molecule["adenosine triphosphate"]
Out[1]=
Molecule
Formula:
C
10
H
16
N
5
O
13
P
3
Atoms: 47 Bonds: 49

In[2]:=
atoms=
[◼]
SelectAtoms3D
[mol];
Return the atoms:
In[3]:=
atoms
Out[3]=
{6,10,9,8,7}
Verify using
FindMoleculeSubstructure
:
In[4]:=
Values@FindMoleculeSubstructure[mol,MoleculePattern["c1c[n]cn1"]]
Out[4]=
{{6,7,8,9,10}}