Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml
Hi, On Fri, 2010-12-31 at 09:35 +, Peter Murray-Rust wrote: > This is a definition of a species (?element) with zero nuclear charge. > There are cases where it is a useful device to have a species without Ack, I haven't come across anything like that yet. Would there be different Xx's with different # of neutrons ? Anyway, then the purpose should be stated somewhere in the entry ? And the name changed to something more descriptive ? > The indexing from 0/1 is not relevant. It is up to any application how That was my point as well. > Computational chemistry makes considerable use of this concept and I > see no reason why this shouldn't be BO reference data. Given that > there is no body that oversees compchem (other than IUPAC by default) > the BO is as good an authority as any. We believe in Opennness and > standardization. Fully agreed. would it make sense to split elements.xml and place Xx into species.xml (or other suitable name) ? That would also be a good place for "Bq" or "Du" mentioned by Geoffrey. Otherwise when extracting data from elements.xml I'll have to check beforehand which are "real" elements that I can find e.g. in a mass spectrometry peak, and which are not. Otherwise, when calculating the elemental composition of m/z 46.042 I'll get C2H6OXx47 ... Yours, Steffen -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml
On Fri, Dec 31, 2010 at 1:57 AM, Neumann, Steffen < steffen.neum...@ipb-halle.de> wrote: > Hi, > > but is it bodr's job to take care of implementation details > about indexing ? What if someone is coding > in pascal (where arrays start from 1 ...) > The values are not indexes, they are atomicNumbers: 0 This is a definition of a species (?element) with zero nuclear charge. There are cases where it is a useful device to have a species without a nuclear charge. The only reason for not including it is that it probably an extension to IUPAC guidelines, but I wouldn't find that compelling. It By defining it we help to ensure consistency of nomenclature in an area where otherwise there would be random proliferation. The indexing from 0/1 is not relevant. It is up to any application how to index the data for the application's purpose. This could be be any field or by the serial number in the files (fragile) but that is not our concern. The atomic number happens to be a useful index, although some might index by atomic symbol to deal with the isotopes of hydrogen (I would not do this personally). > > To me elements.xml is reference data, > and I'd be quite surprised if my textbook PSE > also started to contain an Xx. Reference data > is not the place for dummies, let the individual program > take care of that. > > Computational chemistry makes considerable use of this concept and I see no reason why this shouldn't be BO reference data. Given that there is no body that oversees compchem (other than IUPAC by default) the BO is as good an authority as any. We believe in Opennness and standardization. If we find a better authority we can change to that. > Yours, > Steffen > > > From: Geoffrey Hutchison [geo...@pitt.edu] > Sent: 30 December 2010 23:34 > To: Neumann, Steffen > Cc: blueobelisk-discuss@lists.sourceforge.net > Subject: Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml > > > Is there any reason to have a dummy element ? > > What is the problem with having a dummy? It means all arrays will be > properly indexed from 0, for one. For another, many programs add "Bq" or > "Du" or "Xx" elements for ghost atoms, centroids, etc. > > -Geoff > > --- > Prof. Geoffrey Hutchison > Assistant Professor, Department of Chemistry > University of Pittsburgh > http://hutchison.chem.pitt.edu/ > Office: (412) 648-0492 > > > > -- > Learn how Oracle Real Application Clusters (RAC) One Node allows customers > to consolidate database storage, standardize their database environment, > and, > should the need arise, upgrade to a full multi-node Oracle RAC database > without downtime or disruption > http://p.sf.net/sfu/oracle-sfdevnl > ___ > Blueobelisk-discuss mailing list > Blueobelisk-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > -- Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml
On Fri, Dec 31, 2010 at 2:57 AM, Neumann, Steffen wrote: > but is it bodr's job to take care of implementation details > about indexing ? What if someone is coding > in pascal (where arrays start from 1 ...) Dummy atoms are at the level of atom types, and do not really belong in the elements file. Please file a bug report, and I'll try to make a new BODR release soon. Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml
Hi, but is it bodr's job to take care of implementation details about indexing ? What if someone is coding in pascal (where arrays start from 1 ...) To me elements.xml is reference data, and I'd be quite surprised if my textbook PSE also started to contain an Xx. Reference data is not the place for dummies, let the individual program take care of that. Yours, Steffen From: Geoffrey Hutchison [geo...@pitt.edu] Sent: 30 December 2010 23:34 To: Neumann, Steffen Cc: blueobelisk-discuss@lists.sourceforge.net Subject: Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml > Is there any reason to have a dummy element ? What is the problem with having a dummy? It means all arrays will be properly indexed from 0, for one. For another, many programs add "Bq" or "Du" or "Xx" elements for ghost atoms, centroids, etc. -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
Re: [BlueObelisk-discuss] Dummy element in bodr elements.xml
> Is there any reason to have a dummy element ? What is the problem with having a dummy? It means all arrays will be properly indexed from 0, for one. For another, many programs add "Bq" or "Du" or "Xx" elements for ghost atoms, centroids, etc. -Geoff --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
[BlueObelisk-discuss] Dummy element in bodr elements.xml
Hi, I just stumbled upon element "Xx" in http://bodr.svn.sourceforge.net/viewvc/bodr/trunk/bodr/elements/elements.xml?revision=57&view=markup#l29 Is there any reason to have a dummy element ? Could consider removing it ? It messes up using elements.xml without cleaning it ... Yours, Steffen -- IPB HalleAG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 -- Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl ___ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
