Why are there different SMARTS patterns for the members of a single MCS group?

Depending on the choice of MCS atom types, the resulting SMARTS patterns are often similar to but seldom identical to SMARTS atom types. This is especially so when hydrogens are added (-addh option to canvasMCS) or rings marked as cyclic or acyclic (-addring). This mismatch results in members of a given MCS group having different SMARTS patterns.

To illustrate the issue, suppose O and N are considered as the same atom type when searching for the common substructure. Suppose we have two molecules with an identical sequence in the middle (denoted by dots here):

N.......O
O.......N

These both contribute to the same common substructure. However, when we try to create a single SMARTS, pattern, we can only do something like the following:

[N,O]......[N,O]

This pattern will match the following structures as well:

N.......N
O.......O

Sometimes, this is not what is wanted: the single pattern is too general. If what is needed is

N.......O or O.......N

this cannot be represented readily in SMARTS notation.

Keywords: Canvas, maximum common substructure

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