I think I've been misunderstanding the square brackets. I need to RTFM, I think, after which I'll post here again if still confused.
Noel On 14/04/2008, Noel O'Boyle <[email protected]> wrote: > I've been trying to get my head around what's happening when I read > and write isomeric smiles. As a user, I hope that the same molecule > will also have the same isomeric SMILES. However, look at the > following examples using cinfony which read a SMILES string and write > an isomeric SMILES string... > > I'm trying to specify the chirality of the carbon in > chlorobromomethane, but RDKit is not picking up on the chirality: > > >>> rdk.readstring("smi", "[C](Cl)Br").write("iso") > 'ClCBr' > (No chirality, as expected) > > >>> rdk.readstring("smi", "[C@@H](Cl)Br").write("iso") > 'Cl[CH]Br' > >>> rdk.readstring("smi", "[...@](Cl)Br").write("iso") > 'ClCBr' > >>> rdk.readstring("smi", "c...@]br").write("iso") > 'ClCBr' > >>> rdk.readstring("smi", "Cl[C@@H]Br").write("iso") > 'Cl[CH]Br' > (Expected chirality, but didn't get it) > > Let's try 1-chloro,1-bromoethane: > > >>> rdk.readstring("smi", "Cl[C@@](Br)C").write("iso") > 'CC(Cl)Br' > (Expected chirality, but didn't get it) > >>> rdk.readstring("smi", "Cl[C@@H](Br)C").write("iso") > 'C[C@@H](Cl)Br' > (Expected chirality, and got it) > > Is the problem with me or with RDKit? > > On a related note, I have found that RDKit, when reading SDF files, > turns all of the hydrogens into implicit hydrogens. However, when > reading SMILES strings, it retains any explicit hydrogens specified in > C@@H expressions. This doesn't seem to be consistent and requires the > user to remove hydrogens if he/she wants to create a canonical smiles > string. > > Apologies in advance if my understanding of SMILES is shaky. > > Regards, > > Noel >
