Hi, thanks for the detailed explanations. I have a few further qustions: Am Freitag, 15. November 2013, 09:58:06 schrieb John May: > 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). Currently, i just tested the things out and it is not used in any release versions. However, i am looking into integrating the speed boost. Is there any plan when the 1.6 stable will be released? Does it make sense to use a 1.5.x version or are the interfaces to unstable at the moment? > > 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. We need canonical SMILES. Do i understand correctly, that the current git versions isomeric SMILES are canonical? Will a 1.6 canonical string match a 1.4 canonical string? We use the SMILES to match molecules.
> - 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). Good to know! Applying the aromaticity does not seem to add a measurable amount of computation time to the SMILES generation. Greetings Till > - 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.schae...@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.schae...@cs.tu-dortmund.de phone: +49(231)755-7706 fax: +49(231)755-7740 web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
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