From: Stefan K. <st...@we...> - 2008-02-26 23:50:05
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Dear co-developers, the class GasteigerPEPEPartialCharges uses HueckelAromaticityDetector like this: if(HueckelAromaticityDetector.detectAromaticity(ac)) Am I correct to think that this means aromaticity detection is done each time? If so, I suggest: 1) To have a detectAromaticity flag and if this is set, to replace the above mentioned call with a loop checking if any aromaticity flag is in the atomcontainer on bonds or atoms AromaticityDetection is also done on AtomContainers from an acSet which is generated like this: IAtomContainerSet iSet = gR.getAllStructures(ac); Does this mean aromaticity is "propagated" to the new AtomContainers? If yes, I suggest 2) The same as in 1) for these AtomContainers. The PartialPiChargeDescriptor would also have the flag, which could lead to another boost in descriptor calculation time. Stefan |
From: Rajarshi G. <rg...@in...> - 2008-02-27 01:26:28
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This brings up the topic of caching - can we cache the fact that aromaticity has been detected or needs to be redetected? This would avoid the whole issue of passing around aromaticity flags. Anything that needs to use aromaticity would check the flag, and if not set, would redetect the aromaticity. I suppose the tricky part is how and when would this be propagated. As a first approximation any method that modifies atoms or bonds (addBond, addAtom) would set the flag to NOT_DETECTED and it would only be set to DETECTED by the CDKAromaticityDetector Also, I thought HueckelAromaticityDetector was deprecated? On Feb 26, 2008, at 6:49 PM, Stefan Kuhn wrote: > Dear co-developers, > the class GasteigerPEPEPartialCharges uses > HueckelAromaticityDetector like > this: > if(HueckelAromaticityDetector.detectAromaticity(ac)) > Am I correct to think that this means aromaticity detection is done > each time? > If so, I suggest: > 1) To have a detectAromaticity flag and if this is set, to replace > the above > mentioned call with a loop checking if any aromaticity flag is in the > atomcontainer on bonds or atoms > AromaticityDetection is also done on AtomContainers from an acSet > which is > generated like this: > IAtomContainerSet iSet = gR.getAllStructures(ac); > Does this mean aromaticity is "propagated" to the new AtomContainers? > If yes, I suggest > 2) The same as in 1) for these AtomContainers. > The PartialPiChargeDescriptor would also have the flag, which could > lead to > another boost in descriptor calculation time. > Stefan > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- AIBOHPHOBIA - the fear of palindromes. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkfEvDoACgkQZqGSLFHnnoRXQACfc3p/d1SAw5v3g/oZRqnnmFoW ZrwAn3rgr4G51ORLW35FCSsVJQY1IueZ =M536 -----END PGP SIGNATURE----- |
From: Rajarshi G. <rg...@in...> - 2008-02-29 18:35:00
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Feb 29, 2008, at 1:26 PM, Stefan Kuhn wrote: >> I suppose the tricky part is how and when would this be propagated. >> As a first approximation any method that modifies atoms or bonds >> (addBond, addAtom) would set the flag to NOT_DETECTED and it would >> only be set to DETECTED by the CDKAromaticityDetector > Problem: Also changes on atoms (e. g. charge) and perhaps bond > could make > aromaticity invalid. Since our atoms/bonds don't know about it's > molecule(s), > this sounds tricky. Correct - we'd have to set the flag to NOT_DETECTED in *all* classes and methods that change the state of some molecular feature - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- There's no problem so bad that you can't add some guilt to it to make it worse. -Calvin -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkfIUEkACgkQZqGSLFHnnoRIMACfYPhO5V3VAycKPiIHZbr/xC8P D00AoIVSYY+latXXzeU4H+3bp9EnU12z =Em5o -----END PGP SIGNATURE----- |
From: Miguel R. C. <m....@la...> - 2008-03-05 07:28:23
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> Hi Miguel, > do you know if the method getAllStructures in StructureResonanceGenerator > preserves aromaticity, i. e. if it is save to assume that if the input > structure has aromaticity detected also the results have? I saw you wrote the > class. The StructureResonanceGenerator with getStructures returns cloned atomContainers which are produced using reactions from an initial structure. The reactions don't remove the aromaticity flag if the clonation doesn't do it before. I suppose that for some reactions it should have to be removed the aromaticity flags but not for those reactions which only produce new resonance structures because they continue being aromatic. I will do a test to prove this concept. Sorry for waiting long time the answer. Cheers, Miquel On Wed, 2008-02-27 at 00:49 +0100, Stefan Kuhn wrote: > Dear co-developers, > the class GasteigerPEPEPartialCharges uses HueckelAromaticityDetector like > this: > if(HueckelAromaticityDetector.detectAromaticity(ac)) > Am I correct to think that this means aromaticity detection is done each time? Yes. It should not do it. Only one time. > If so, I suggest: > 1) To have a detectAromaticity flag and if this is set, to replace the above > mentioned call with a loop checking if any aromaticity flag is in the > atomcontainer on bonds or atoms > AromaticityDetection is also done on AtomContainers from an acSet which is > generated like this: > IAtomContainerSet iSet = gR.getAllStructures(ac); > Does this mean aromaticity is "propagated" to the new AtomContainers? > If yes, I suggest > 2) The same as in 1) for these AtomContainers. > The PartialPiChargeDescriptor would also have the flag, which could lead to > another boost in descriptor calculation time. > Stefan > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |