No problem,

So it’s still work in progress (before 1.6) and there are a couple of caveats and things to be aware of. Here’s some info that might not be obvious if you’re using the developer version. The current parser and generator will be more of a do it yourself SMILES with another utility class which will do it correct (i.e. ensure correct aromaticity etc).

Generator
 - The 6 seconds is still slow but that is likely due to the canonicalisation, strictly speaking isomeric SMILES is non-canonical (that would be absolute SMILES) and in future canonical generation won’t be on by default.
 - Aromaticity is no longer redone for SMILES generation. The generator outputs what ever you give it. If you’re using the SMILES for indexing structures they should be aromatised first (see below).
 - Tetrahedral and Double-Bond stereo chemistry are now round tripped between SMILES/InChI (working on MDL and interpreting depictions / 3D coordinates).
 - implicit hydrogen specification on the organic subset is now correct

Parser
 - molecules read from SMILES have their implicit hydrogen counts all set (depending on what else you use this means you might not need to atom type your structures)
 - SMILES are kekulised automatically on load - if a molecule could not be kekulised an exception is throw. The kekulisation is fast enough (< 10 s on 1 mil structures) that it’s a good sanity check. If you find a molecule throws an exceptions check with Daylight’s DEPICT service. If they accept it then it’s a bug - otherwise the generated SMILES is invalid (normally missing Hs on nitrogens). 

For the aromaticity, there is a new (faster) class. Need to go through and replaced the existing uses but here is a summary:

Aromaticity aromaticity = new Aromaticity(ElectronDontation.daylight(), // CDK model needs atom types, Daylight model need hydrogens
  Cycles.all());                // will timeout on fullerenes but I have a fix on the patch tracker

aromaticity.apply(molecule); // apply the aromaticity model to the container (removing any previous specification)

Cheers,
John

On 14 Nov 2013, at 18:49, Till Schäfer <till2.schaefer@tu-dortmund.de> wrote:

Hi,
the new isomeric SmilesGenerator (todays git) is incredible fast. For a small (110 mols) data set with huge molecules the smiles creation time went down from 110 seconds (scaffold hunters "optimized" 1.4.19 version) to 6 seconds!

in the following: the largest mol in the data set :-)

[H]OC1([H])C([H])([H])C([H])(OC1([H])C([H])([H])OP(=O)(O[H])OC2([H])C([H])([H])C([H])(OC2([H])C([H])([H])OP(=O)(O[H])OC3([H])C([H])([H])C([H])(OC3([H])C([H])([H])OP(=O)(O[H])OC4([H])C([H])(O[H])C([H])(OC4([H])C([H])([H])OP(=O)(O[H])OC5([H])C([H])(O[H])C([H])(OC5([H])C([H])([H])OP(=O)(O[H])OC6([H])C([H])(O[H])C([H])(OC6([H])C([H])([H])OP(=O)(O[H])OC7([H])C([H])(O[H])C([H])(OC7([H])C([H])([H])OP(=O)(O[H])OC8([H])C([H])(O[H])C([H])(OC8([H])C([H])([H])OP(=O)(O[H])OC9([H])C([H])(O[H])C([H])(OC9([H])C([H])([H])OP(=O)(O[H])OC%10([H])C([H])(O[H])C([H])(OC%10([H])C([H])([H])OP(=O)(O[H])OC%11([H])C([H])(O[H])C([H])(OC%11([H])C([H])([H])OP(=O)(O[H])OC%12([H])C([H])(O[H])C([H])(OC%12([H])C([H])([H])OP(=O)(O[H])OC%13([H])C([H])(O[H])C([H])(OC%13([H])C([H])([H])OP(=O)(O[H])OC%14([H])C([H])(O[H])C([H])(OC%14([H])C([H])([H])OP(=O)(O[H])OC%15([H])C([H])(O[H])C([H])(OC%15([H])C([H])([H])OP(=O)(O[H])OC%16([H])C([H])(O[H])C([H])(OC%16([H])C([H])([H])OP(=O)(O[H])OC%17([H])C([H])(O[H])C([H])(OC%17([H])C([H])([H])OP(=O)(O[H])OC%18([H])C([H])(O[H])C([H])(OC%18([H])C([H])([H])OP(=O)(O[H])OC%19([H])C([H])(O[H])C([H])(OC%19([H])C([H])([H])OP(=O)(O[H])OC%20([H])C([H])(O[H])C([H])(OC%20([H])C([H])([H])OP(=O)(O[H])OC%21([H])C([H])(O[H])C([H])(OC%21([H])C([H])([H])OP(=O)(O[H])OC%22([H])C([H])(O[H])C([H])(OC%22([H])C([H])([H])OP(=O)(O[H])OC%23([H])C([H])(O[H])C([H])(OC%23([H])C([H])([H])OP(=O)(O[H])OC%24([H])C([H])(O[H])C([H])(OC%24([H])C([H])([H])OP(=O)(O[H])OC%25([H])C([H])(O[H])C([H])(OC%25([H])C([H])([H])OP(=O)(O[H])OC%26([H])C([H])([H])C([H])(OC%26([H])C([H])([H])OP(=O)(O[H])OC%27([H])C([H])([H])C([H])(OC%27([H])C([H])([H])OP(=O)(O[H])OC%28([H])C([H])([H])C([H])(OC%28([H])C([H])([H])OP(=O)(O[H])O[H])N%29C([H])=NC=%30C(=O)N([H])C(=NC%30%29)N([H])[H])N%31C([H])=NC=%32C(=O)N([H])C(=NC%32%31)N([H])[H])N%33C(=O)N=C(C([H])=C%33[H])N([H])[H])N%34C([H])=C([H])C(=O)N([H])C%34=O)N%35C([H])=NC=%36C(=O)N([H])C(=NC%36%35)N([H])[H])N%37C([H])=NC=%38C(=O)N([H])C(=NC%38%37)N([H])[H])N%39C([H])=NC=%40C(=O)N([H])C(=NC%40%39)N([H])[H])N%41C(=O)N=C(C([H])=C%41[H])N([H])[H])N%42C([H])=NC=%43C(=O)N([H])C(=NC%43%42)N([H])[H])N%44C(=O)N=C(C([H])=C%44[H])N([H])[H])N%45C([H])=NC%46=C(N=C([H])N=C%46%45)N([H])[H])N%47C(=O)N=C(C([H])=C%47[H])N([H])[H])N%48C([H])=C([H])C(=O)N([H])C%48=O)N%49C([H])=C([H])C(=O)N([H])C%49=O)N%50C(=O)N=C(C([H])=C%50[H])N([H])[H])N%51C([H])=NC=%52C(=O)N([H])C(=NC%52%51)N([H])[H])N%53C([H])=NC=%54C(=O)N([H])C(=NC%54%53)N([H])[H])N%55C([H])=C([H])C(=O)N([H])C%55=O)N%56C([H])=NC=%57C(=O)N([H])C(=NC%57%56)N([H])[H])N%58C(=O)N=C(C([H])=C%58[H])N([H])[H])N%59C([H])=NC=%60C(=O)N([H])C(=NC%60%59)N([H])[H])N%61C([H])=NC=%62C(=O)N([H])C(=NC%62%61)N([H])[H])N%63C([H])=C([H])C(=O)N([H])C%63=O)N%64C(=O)N=C(C([H])=C%64[H])N([H])[H])N%65C([H])=NC%66=C(N=C([H])N=C%66%65)N([H])[H])N%67C([H])=NC=%68C(=O)N([H])C(=NC%68%67)N([H])[H])N%69C(=O)N=C(C([H])=C%69[H])N([H])[H])N%70C(=O)N=C(C([H])=C%70[H])N([H])[H]


Thanks for the good work
Till Schäfer


--
Dipl.-Inf. Till Schäfer
Technische Universität Dortmund
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Raum 237
44227 Dortmund, Germany

e-mail: till.schaefer@cs.tu-dortmund.de
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