Question

I am trying to use the SMILES format for encoding molecules from handwritten logbooks. The molecules often contain abbreviations, such as "Ph" for a Phenyl group. Is there a way to have these abbreviated structures in SMILES?

Answer 1

Yes, it is possible to include abbreviated structures in SMILES format by using bracket notation.

Step-by-step explanation:

Yes, it is possible to include abbreviated structures in SMILES format. SMILES (Simplified Molecular Input Line Entry System) is a string-like notation for representing molecular structures.

It allows for the representation of complex structures using simple character strings. To represent an abbreviation like 'Ph' for a Phenyl group in SMILES, you can use the bracket notation.

For example, the SMILES representation for benzene can be written as 'c1ccccc1' or using the bracket notation as 'c1ccccc1' or even 'C6H5'.

By using the bracket notation, you can include various abbreviations in SMILES to represent different groups or substituents.