SMILES Tutorial: Branching

Branch specification

Branches are specified in SMILES by enclosing them in parentheses, which may be nested or stacked.

The syntax for branching is:

   branch : '(' <chain> ')'
          | '(' <chain> <branch> ')'
	  | '(' <branch> <chain> ')'
	  | '(' <chain> <branch> <chain> ')'
          ;

Advanced issues

The SMILES language specifies no predefined limit to how deep branching may be nested. Most implementations define such a limit, typically between 10 and 50. It's rarely a problem in practice, since the average connectivity of real molecular graphs is very low.

Examples

Table 5. Branch specification in SMILES.

Depiction	SMILES	Name	Remark
	CC(C)C(=O)O	isobutyric acid	If needed, bond symbols should appear inside branches.
	FC(F)F or C(F)(F)F	fluoroform	Branches may be stacked. One can start with any atom equally well.
	O=Cl(=O)(=O)[O-] or Cl(=O)(=O)(=O)[O-]	perchlorate anion	More branch stacking.
	CCCC(C(=O)O)CCC	4-heptanoic acid	Branches may be nested.