[Cdk-devel] SmilesParser

[<Mar...@ep...>]

>I will update the SmilesParser class later today, but wanted to ask
about the
>parseSmilesWithAromaticityFixer() and parseSmiles2() methods. I could
not
>directly find where those are called...

I made new version which only has parseSmiles() method.

>Additionally, could you have a look at the JUnit test
>cdk.test.smiles.DeduceBondSystemToolTest?

My parser seems to work ok for this test molecule.

>BTW, the method DeduceBondSystemTool.findRingsToCheck(IMolecule m,
IRingSet
>rs) does not seem to use the IMolecule m at all...

You are correct- this has been fixed.


>I'm looking at the code once more... is the idea that only
>parseSmilesWithAromaticityFixer() reads SMILES properly, or should the
>original parseSmiles() be fixed??
>Todd, can you explain to me what the functions of the three
parseSmiles*()
>methods are, and how the relate, and which one should be used by end
users?

In latest version there is only 1 public parseSmiles method.  The
parseString method parses the smiles string but doesnt do any molecule
modifications (like saturate, aromaticity detection, etc.).

The new parseSmiles method tries to parse the smiles like was originally
implemented but if the resultant molecule doesnt meet the requirements
in the DeduceBondSystemToolTest.isOK method (e.g. the rings with lower
case symbols should be aromatic) it runs the aromaticity fixer on the
original version of the molecule from the parseString method.