Find the maximum common substructure for three molecules:

Highlight the structure in place:

Find the maximum common substructure between two short linear molecules:

By relaxing the match parameters to not look at atomic number, the size of the structure is increased:

Find the maximum common substructure among a group of medium-sized molecules:

Display the common substructure highlighted in place:

By default, atoms must have the same atomic number to match; oxygen does not match carbon:

Remove this restriction to get a larger substructure:

Formal charges are not considered by default when comparing atoms, so the zwitterionic and normal forms of glycine match:

Include "FormalCharge" as well as atom and bond types to make the pattern more restrictive:

Include "Valence" to control whether trivalent and pentavalent phosphorus match:

By default, atoms in rings will match atoms in straight chains:

Use "RingAtomQ" so that only ring atoms are matched:

Both of these molecules contain two cyclopentane rings connected by a single bond:

When "RingBondQ" is used, the connecting bond no longer matches because it is part of a larger ring in the second molecule:

Include atom chirality to restrict the matching between two enantiomers:

By default, partial rings can be included in the common substructure:

Use the "CompleteRings" parameter to ensure only full rings are matched:

Find the common substructure among a series of synthetic opioid analgesics:

Illustrate the "morphine rule" of medicinal chemistry by highlighting the substructure on morphine:

Define a function to compute the similarity between two molecules based on the number of bonds in the MCS:

Phenol and benzene have 6 out of 7 heavy atoms in common:

Choose the most similar molecules from a random set: