I've filed the HydrogenAdder problem with carbocations as a bug report. 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 -- 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/ ------------------------------------------------------------------------- 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
