[Biojava-l] org.biojava.bio.proteomics

[Jones, Mike]

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; biojava-l@biojava.org
>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:bioram1976@yahoo.com] 
>>Sent: Friday, April 19, 2002 7:49 AM
>>To: biojava-l@biojava.org
>>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  -  Biojava-l@biojava.org
>>http://biojava.org/mailman/listinfo/biojava-l
>>
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l@biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>