On Tuesday 29 May 2007 12:39, Andreas Schüller wrote: > I've filed the HydrogenAdder problem with carbocations as a bug report. And I made a test case for it. > So it doesn't get lost. > > -Andreas > > Andreas Schüller wrote: > > This doesn't work for C[N+], where 3 hydrogens should be added to the > > nitrogen. > > > > -Andreas > > > > Daniel Fontaine wrote: > >> Shouldn't the formula be the following since the polarity of the charge > >> is irrelevant, it only implies an unfilled valency? > >> > >> missingHydrogen = (int) (defaultAtom.getBondOrderSum() - bondOrderSum - > >> singleElectronSum - abs(atom.getFormalCharge())); > >> > >> this formula would work in both cases. > >> > >> On Wed, 2007-05-23 at 13:54 +0200, Andreas Schüller wrote: > >>> Hello, > >>> > >>> I would agree that the first molecule should have hydrogens added like this: > >>> > 1: 2 > >>> > 2: 0 > >>> > 3: 1 > >>> > 4: 2 > >>> > >>> A [C+] has three valence electrons to possibly form three single bonds. > >>> Molecular Operating Environment (MOE) 2006.08 adds hydrogens in > >>> compliance to the above scheme. > >>> > >>> Applying the modified formula > >>> > >>> > missingHydrogen = (int) (defaultAtom.getBondOrderSum() - > >>> > bondOrderSum - singleElectronSum - > >>> > atom.getFormalCharge()); > >>> > >>> to C3 of the first molecule suggests to add 4-2-0-(+1)=1 hydrogens, > >>> which seems correct. > >>> > >>> On the otherhand: > >>> > >>> Let's see for [O-] in e.g. C[O-]: > >>> 2-1-0-(-1)=2 (!!) > >>> This is definately wrong. Here, the original formula applies: > >>> 2-1-0+(-1)=0 > >>> > >>> For [N+] in C[N+]: > >>> 3-1-0+(+1)=3 > >>> Again, the original formula applies. > >>> > >>> I think that carbocations, [C+], are an exception, since they seek an > >>> electron sextet in their outer valence shell rather than an octet. They > >>> should probably be treated differently. > >>> If one assumed defaultAtom.getBondOrderSum() = 2 for a carbocation the > >>> original formula would apply: > >>> 2-2-0+(+1)=1 > >>> > >>> Best wishes, > >>> Andreas > >>> > >>> Daniel Fontaine wrote: > >>> > Stefan, > >>> > > >>> > As I said, I am not a chemist. However, I made the change you > >>> > suggested and recompiled CDK and all my test cases now run as > >>> > expected. I believe your suggestion of changing +charge to -charge > >>> > is correct. > >>> > > >>> > I appreciate all of your help. > >>> > Dan > >>> > > >>> > On Tue, 2007-05-22 at 17:17 +0200, Stefan Kuhn wrote: > >>> >> Looking at the situation I think indeed that atom 3 should have 1 > >>> > >>> hydrogen, > >>> > >>> >> since it is positivly charged. > >>> >> Could one of the chemists comment on this? > >>> >> If it is indeed 1, the code in SaturationChecker is wrong, which > >>> > >>> seems hard to > >>> > >>> >> believe. Right now the code is: > >>> >> missingHydrogen = (int) (defaultAtom.getBondOrderSum() - > >>> >> bondOrderSum - singleElectronSum + > >>> >> atom.getFormalCharge()); > >>> >> I think indeed it should be -charge, since, if the charge is > >>> > >>> negative, we need > >>> > >>> >> extra electrons. > >>> >> Again, the chemists please. > >>> >> > >>> >> On Tuesday 22 May 2007 16:32, Daniel Fontaine wrote: > >>> >>> I admit I am not much of a chemist, I am a programmer, but the > >>> >>> program that generated the fragment, Mass Frontier, has the first > >>> >>> molecule with 5 hydrogens rather than 7. I was told this is > >>> >>> correct due to the positive charge on the carbon? Does CDK not > >>> >>> handle this sort of thing? Or am I missing something? > >>> >>> > >>> >>> thanks for all of your help > >>> >>> Dan > >>> >>> > >>> >>> On Tue, 2007-05-22 at 15:48 +0200, Stefan Kuhn wrote: > >>> >>>> On Tuesday 22 May 2007 15:23, Daniel Fontaine wrote: > >>> >>>>> Thanks, but if this reader is working properly, why is the > >>> >>>>> hydrogen adder not taking charges into consideration? I am > >>> >>>>> getting two hydrogens too many added to that first fragment I > >>> >>>>> posted. > >>> >>>> > >>> >>>> Hm, I get for the first molecule the following implicit Hs after > >>> >>>> addImplicitHydrogensToSatisfyValency: > >>> >>>> 1: 2 > >>> >>>> 2: 0 > >>> >>>> 3: 3 > >>> >>>> 4:2 > >>> >>>> For the second one: > >>> >>>> 1: 1 > >>> >>>> 2: 0 > >>> >>>> 3: 1 > >>> >>>> 4: 2 > >>> >>>> That looks ok, I would say, doesn't it? > >>> >>>> Stefan > >>> >>>> > >>> >>>>> thanks, > >>> >>>>> Dan > >>> >>>>> > >>> >>>>> On Tue, 2007-05-22 at 10:29 +0200, Stefan Kuhn wrote: > >>> >>>>>> Ok, the problem is you are using the wrong property. You should > >>> >>>>>> use getFormatCharge, which works and is supposed to give that > >>> >>>>>> sort of, well, > >>> >>>>>> formal charge. The getCharge is used by classes assigning > >>> >>>>>> partial charges and > >>> >>>>>> will always give 0 if you do not explicitly run one of them. > >>> >>>>>> Stefan > >>> >>>>>> > >>> >>>>>> On Monday 21 May 2007 20:28, Daniel Fontaine wrote: > >>> >>>>>>> Hello, I am new to CDK and the mailing list. > >>> >>>>>>> > >>> >>>>>>> I am reading in a list of compounds from an sdf file that > >>> >>>>>>> include charges. These charges don't appear on the atoms of > >>> >>>>>>> the > >>> >>>>>> > >>> >>>>>> corresponding > >>> >>>>>> > >>> >>>>>>> Molecules, however, when loading with MDLV2000Reader. All > >>> >>>>>>> atoms > >>> >>>>>> > >>> >>>>>> show a > >>> >>>>>> > >>> >>>>>>> charge of 0.0. > >>> >>>>>>> > >>> >>>>>>> This is a problem because I am trying to add implicit > >>> >>>>>>> hydrogens with HydrogenAdder. I frequently end up with too > >>> >>>>>>> many hydrogens and the > >>> >>>>>> > >>> >>>>>> wrong > >>> >>>>>> > >>> >>>>>>> mass. > >>> >>>>>>> > >>> >>>>>>> any help would be appreciated, > >>> >>>>>>> Dan > >>> > >>> --------------------------------------------------------------------- > >>> > >>> >>>>>> ---- > >>> >>>>>> > >>> >>>>>>> This SF.net email is sponsored by DB2 Express > >>> >>>>>>> Download DB2 Express C - the FREE version of DB2 express and > >>> >>>>>>> take control of your XML. No limits. Just data. Click to get > >>> >>>>>>> it now. http://sourceforge.net/powerbar/db2/ > >>> >>>>>>> _______________________________________________ > >>> >>>>>>> Cdk-user mailing list > >>> >>>>>>> [email protected] > >>> >>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>> >>>>>> > >>> >>>>>> -- > >>> >>>>>> Stefan Kuhn BSc MA > >>> >>>>>> IPB Halle > >>> >>>>>> AG Bioinformatik & Massenspektrometrie > >>> >>>>>> Weinberg 3 > >>> >>>>>> 06120 Halle > >>> >>>>>> http://www.ipb-halle.de http://msbi.bic-gh.de > >>> >>>>>> [EMAIL PROTECTED] Tel. +49 (0) 345 5582 1474 Fax.+49 (0) 345 > >>> >>>>>> 5582 1409 > >>> > >>> --------------------------------------------------------------------- > >>> > >>> >>>>>> ---- This SF.net email is sponsored by DB2 Express > >>> >>>>>> Download DB2 Express C - the FREE version of DB2 express and > >>> >>>>>> take control of your XML. No limits. Just data. Click to get it > >>> >>>>>> now. http://sourceforge.net/powerbar/db2/ > >>> >>>>>> _______________________________________________ > >>> >>>>>> Cdk-user mailing list > >>> >>>>>> [email protected] > >>> >>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>> > >>> ----------------------------------------------------------------------- > >>> > >>> >>>>> -- This SF.net email is sponsored by DB2 Express > >>> >>>>> Download DB2 Express C - the FREE version of DB2 express and > >>> >>>>> take control of your XML. No limits. Just data. Click to get it > >>> >>>>> now. http://sourceforge.net/powerbar/db2/ > >>> >>>>> _______________________________________________ > >>> >>>>> Cdk-user mailing list > >>> >>>>> [email protected] > >>> >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>> > >>> ----------------------------------------------------------------------- > >>>-- > >>> > >>> >>> This SF.net email is sponsored by DB2 Express > >>> >>> Download DB2 Express C - the FREE version of DB2 express and take > >>> >>> control of your XML. No limits. Just data. Click to get it now. > >>> >>> http://sourceforge.net/powerbar/db2/ > >>> >>> _______________________________________________ > >>> >>> Cdk-user mailing list > >>> >>> [email protected] > >>> >>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>> > > >>> > -------------------------------------------------------------------- > >>> >----- This SF.net email is sponsored by DB2 Express > >>> > Download DB2 Express C - the FREE version of DB2 express and take > >>> > control of your XML. No limits. Just data. Click to get it now. > >>> > http://sourceforge.net/powerbar/db2/ > >>> > _______________________________________________ > >>> > Cdk-user mailing list > >>> > [email protected] > >>> > https://lists.sourceforge.net/lists/listinfo/cdk-user > >>> > >>> -- > >>> Andreas Schüller > >>> PhD student in the research group of Prof. Dr. Gisbert Schneider > >>> > >>> Johann Wolfgang Goethe University > >>> Beilstein-endowed Chair for Chemoinformatics > >>> Building B - 3rd floor > >>> Siesmayerstr. 70 > >>> 60323 Frankfurt am Main > >>> Germany > >>> > >>> Tel.: +49 69 798 24879 > >>> Fax: +49 69 798 24880 > >>> http://www.modlab.de/ > >>> > >>> Daniel Fontaine wrote: > >>>> Stefan, > >>>> > >>>> As I said, I am not a chemist. However, I made the change you > >>>> suggested and recompiled CDK and all my test cases now run as > >>>> expected. I believe your suggestion of changing +charge to -charge is > >>>> correct. > >>>> > >>>> I appreciate all of your help. > >>>> Dan > >>>> > >>>> On Tue, 2007-05-22 at 17:17 +0200, Stefan Kuhn wrote: > >>>>> Looking at the situation I think indeed that atom 3 should have 1 > >>>>> hydrogen, since it is positivly charged. > >>>>> Could one of the chemists comment on this? > >>>>> If it is indeed 1, the code in SaturationChecker is wrong, which > >>>>> seems hard to believe. Right now the code is: > >>>>> missingHydrogen = (int) (defaultAtom.getBondOrderSum() - > >>>>> bondOrderSum - singleElectronSum + > >>>>> atom.getFormalCharge()); > >>>>> I think indeed it should be -charge, since, if the charge is > >>>>> negative, we need extra electrons. > >>>>> Again, the chemists please. > >>>>> > >>>>> On Tuesday 22 May 2007 16:32, Daniel Fontaine wrote: > >>>>>> I admit I am not much of a chemist, I am a programmer, but the > >>>>>> program that generated the fragment, Mass Frontier, has the first > >>>>>> molecule with 5 hydrogens rather than 7. I was told this is correct > >>>>>> due to the positive charge on the carbon? Does CDK not handle this > >>>>>> sort of thing? Or am I missing something? > >>>>>> > >>>>>> thanks for all of your help > >>>>>> Dan > >>>>>> > >>>>>> On Tue, 2007-05-22 at 15:48 +0200, Stefan Kuhn wrote: > >>>>>>> On Tuesday 22 May 2007 15:23, Daniel Fontaine wrote: > >>>>>>>> Thanks, but if this reader is working properly, why is the > >>>>>>>> hydrogen adder not taking charges into consideration? I am > >>>>>>>> getting two hydrogens too many added to that first fragment I > >>>>>>>> posted. > >>>>>>> > >>>>>>> Hm, I get for the first molecule the following implicit Hs after > >>>>>>> addImplicitHydrogensToSatisfyValency: > >>>>>>> 1: 2 > >>>>>>> 2: 0 > >>>>>>> 3: 3 > >>>>>>> 4:2 > >>>>>>> For the second one: > >>>>>>> 1: 1 > >>>>>>> 2: 0 > >>>>>>> 3: 1 > >>>>>>> 4: 2 > >>>>>>> That looks ok, I would say, doesn't it? > >>>>>>> Stefan > >>>>>>> > >>>>>>>> thanks, > >>>>>>>> Dan > >>>>>>>> > >>>>>>>> On Tue, 2007-05-22 at 10:29 +0200, Stefan Kuhn wrote: > >>>>>>>>> Ok, the problem is you are using the wrong property. You should > >>>>>>>>> use getFormatCharge, which works and is supposed to give that > >>>>>>>>> sort of, well, > >>>>>>>>> formal charge. The getCharge is used by classes assigning partial > >>>>>>>>> charges and > >>>>>>>>> will always give 0 if you do not explicitly run one of them. > >>>>>>>>> Stefan > >>>>>>>>> > >>>>>>>>> On Monday 21 May 2007 20:28, Daniel Fontaine wrote: > >>>>>>>>>> Hello, I am new to CDK and the mailing list. > >>>>>>>>>> > >>>>>>>>>> I am reading in a list of compounds from an sdf file that > >>>>>>>>>> include charges. These charges don't appear on the atoms of the > >>>>>>>>> > >>>>>>>>> corresponding > >>>>>>>>> > >>>>>>>>>> Molecules, however, when loading with MDLV2000Reader. All atoms > >>>>>>>>> > >>>>>>>>> show a > >>>>>>>>> > >>>>>>>>>> charge of 0.0. > >>>>>>>>>> > >>>>>>>>>> This is a problem because I am trying to add implicit hydrogens > >>>>>>>>>> with HydrogenAdder. I frequently end up with too many hydrogens > >>>>>>>>>> and the > >>>>>>>>> > >>>>>>>>> wrong > >>>>>>>>> > >>>>>>>>>> mass. > >>>>>>>>>> > >>>>>>>>>> any help would be appreciated, > >>>>>>>>>> Dan > >>>>>>>>> > >>>>>>>>> ----------------------------------------------------------------- > >>>>>>>>>---- ---- > >>>>>>>>> > >>>>>>>>>> This SF.net email is sponsored by DB2 Express > >>>>>>>>>> Download DB2 Express C - the FREE version of DB2 express and > >>>>>>>>>> take control of your XML. No limits. Just data. Click to get it > >>>>>>>>>> now. http://sourceforge.net/powerbar/db2/ > >>>>>>>>>> _______________________________________________ > >>>>>>>>>> Cdk-user mailing list > >>>>>>>>>> [email protected] > >>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> Stefan Kuhn BSc MA > >>>>>>>>> IPB Halle > >>>>>>>>> AG Bioinformatik & Massenspektrometrie > >>>>>>>>> Weinberg 3 > >>>>>>>>> 06120 Halle > >>>>>>>>> http://www.ipb-halle.de http://msbi.bic-gh.de > >>>>>>>>> [EMAIL PROTECTED] Tel. +49 (0) 345 5582 1474 Fax.+49 (0) 345 > >>>>>>>>> 5582 1409 > >>>>>>>>> > >>>>>>>>> ----------------------------------------------------------------- > >>>>>>>>>---- ---- This SF.net email is sponsored by DB2 Express > >>>>>>>>> Download DB2 Express C - the FREE version of DB2 express and take > >>>>>>>>> control of your XML. No limits. Just data. Click to get it now. > >>>>>>>>> http://sourceforge.net/powerbar/db2/ > >>>>>>>>> _______________________________________________ > >>>>>>>>> Cdk-user mailing list > >>>>>>>>> [email protected] > >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>>>>>>> > >>>>>>>> ------------------------------------------------------------------ > >>>>>>>>----- -- This SF.net email is sponsored by DB2 Express > >>>>>>>> Download DB2 Express C - the FREE version of DB2 express and take > >>>>>>>> control of your XML. No limits. Just data. Click to get it now. > >>>>>>>> http://sourceforge.net/powerbar/db2/ > >>>>>>>> _______________________________________________ > >>>>>>>> Cdk-user mailing list > >>>>>>>> [email protected] > >>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>>>>> > >>>>>> -------------------------------------------------------------------- > >>>>>>----- This SF.net email is sponsored by DB2 Express > >>>>>> Download DB2 Express C - the FREE version of DB2 express and take > >>>>>> control of your XML. No limits. Just data. Click to get it now. > >>>>>> http://sourceforge.net/powerbar/db2/ > >>>>>> _______________________________________________ > >>>>>> Cdk-user mailing list > >>>>>> [email protected] > >>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >>>> > >>>> ---------------------------------------------------------------------- > >>>>--- This SF.net email is sponsored by DB2 Express > >>>> Download DB2 Express C - the FREE version of DB2 express and take > >>>> control of your XML. No limits. Just data. Click to get it now. > >>>> http://sourceforge.net/powerbar/db2/ > >>>> _______________________________________________ > >>>> Cdk-user mailing list > >>>> [email protected] > >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user > >> > >> ------------------------------------------------------------------------ > >>- This SF.net email is sponsored by DB2 Express > >> Download DB2 Express C - the FREE version of DB2 express and take > >> control of your XML. No limits. Just data. Click to get it now. > >> http://sourceforge.net/powerbar/db2/ > >> _______________________________________________ > >> Cdk-user mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/cdk-user > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by DB2 Express > > Download DB2 Express C - the FREE version of DB2 express and take > > control of your XML. No limits. Just data. Click to get it now. > > http://sourceforge.net/powerbar/db2/ > > _______________________________________________ > > Cdk-user mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/cdk-user
-- Stefan Kuhn BSc MA IPB Halle AG Bioinformatik & Massenspektrometrie Weinberg 3 06120 Halle http://www.ipb-halle.de http://msbi.bic-gh.de [EMAIL PROTECTED] +49 (0) 345 5582 1474 Fax.+49 (0) 345 5582 1409 ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
