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Re: [Cdk-user] MDLV2000Reader
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From: <a.s...@ch...> - 2007-05-23 11:54:33
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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 >>>>>>> Cdk...@li... >>>>>>> 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 >>>>>> sk...@ip... 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 >>>>>> Cdk...@li... >>>>>> 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 >>>>> Cdk...@li... >>>>> 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 >>> Cdk...@li... >>> 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 > Cdk...@li... > 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 >>>>>>> Cdk...@li... >>>>>>> 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 >>>>>> sk...@ip... 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 >>>>>> Cdk...@li... >>>>>> 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 >>>>> Cdk...@li... >>>>> 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 >>> Cdk...@li... >>> 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 > Cdk...@li... > 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/ |