[Avalontoolkit-discuss] SMILES valence model

[Noel O'B. <bao...@gm...>]

Hi there,

My previous emails have gone unanswered, but here is one last try...

The Avalon toolkit doesn't fully adhere to the SMILES valence model when
reading SMILES. Specifically, the spec describes that halides should only
be rounded up with implicit hydrogens to a valence of 1 when reading SMILES.

However, Avalon added a hydrogen to the chlorine in Cl(C)C and in
Cl(C)(C)(C)C. It also does this for the equivalent SMILES with bromine and
iodine. These six disagreements, if resolved, would allow the toolkit to
read SMILES exactly like Daylight.

I also note in passing that Avalon rejects, in error, the SMILES "[C@
@]1(Cl)(F)I.Br1".

Regards,
- Noel