I have fixed the MassCalc problem. Here are the cvs comments. ************************************************************************ **** Fixed major bug which miscalculated the C-Terminal mass of peptides. Accidentally added two OH groups instead of two H groups if the peptide was an MH+ type.
Also changed the Constructor for MassCalc so that the user has to specify up fr ont whether or not it is a MH+ type of peptide. This may be a pain for some users but it I much safer. added one public method public double getTermMass() So the user can double check that term was calculated correctly. This will be m ore useful when I get C-Term and N-term mods in there. Added on private method. calcTermMass(String isotopicType, boolean MH_PLUS) This just consolidates the calculation t was performed in some other methods. This should help me to track down errors like this in the future. CVS: ---------------------------------------------------------------------- CVS: Enter Log. Lines beginning with `CVS:' are removed automatically CVS: CVS: Committing in . CVS: CVS: Modified Files: CVS: MassCalc.java CVS: ---------------------------------------------------------------------- ~ ~ ~ >-----Original Message----- >From: Jones, Mike >Sent: Friday, April 19, 2002 11:21 AM >To: Roger Moraga; [EMAIL PROTECTED] >Subject: RE: [Biojava-l] org.biojava.bio.proteomics > > >I will chech into this today. Thanks for the heads up. > >>-----Original Message----- >>From: Roger Moraga [mailto:[EMAIL PROTECTED]] >>Sent: Friday, April 19, 2002 7:49 AM >>To: [EMAIL PROTECTED] >>Subject: [Biojava-l] org.biojava.bio.proteomics >> >> >> Hello people, >> >> I've been using biojava for a few weeks now, and I've >>found a couple of problems with the proteomics tools. >> >> First, org.biojava.bio.proteomics.MassCalc gives me >>inaccurate masses for the peptides. I noticed that the >>masses given by the Expasy mass calculator were a bit >>smaller for the peptides. Looking at the code I think >>I found out why: The code adds two times the mass of >>the OH group, whereas it should be added only once for >>the C-terminal, since the N-terminal gains an H, NOT >>an OH. Additionally, if the boolean MH_PLUS is set to >>true, a third OH is added instead of an (H+). >> >> Second, I've found that if I create more than one >>protease, when trying to digest a sequence the last >>created protease will be used, regardless of which one >>was specified with digest.setProtese(). So, if I want >>to use more than one (like digest with CnBR, grab the >>fragments longer than X, digest them with trypsin), I >>have to define it just before the digest, so I have to >>store the parameters for that protease somewhere else. >>Or am I missing something? >> >> Cheers, >> >> Roger Moraga. >> >>__________________________________________________ >>Do You Yahoo!? >>Yahoo! Tax Center - online filing with TurboTax >>http://taxes.yahoo.com/ >>_______________________________________________ >>Biojava-l mailing list - [EMAIL PROTECTED] >>http://biojava.org/mailman/listinfo/biojava-l >> >_______________________________________________ >Biojava-l mailing list - [EMAIL PROTECTED] >http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
