Sep
28
SMILES to become an Open Standard
Craig James wants to make SMILES an open standard, and this has been received with much enthusiasm. SMILES (Simplified molecular input line entry specification) is a de facto standard in chemoinformatics, but the specification is not overly clear, which Craig wants to address. The draft is CC-licensed and will be discussed on the new Blue Obelisk blueobelisk-smiles mailing list.
Illustrative is my confusion about the sp2 hybridized atoms, which use lower case element symbols in SMILES. Very often this is seen as indicating aromaticity. I have written up the arguments supporting both views in the CDK wiki. I held the position that lower case elements indicated sp2 hybridization, and the CDK SMILES parser was converted accordingly some years ago.
Illustrative is my confusion about the sp2 hybridized atoms, which use lower case element symbols in SMILES. Very often this is seen as indicating aromaticity. I have written up the arguments supporting both views in the CDK wiki. I held the position that lower case elements indicated sp2 hybridization, and the CDK SMILES parser was converted accordingly some years ago.
