Re: [Biojava-l] error using the proteomic package

[Roger Moraga]

I've put together this in 2 minutes, but it works,
check it out:

import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.proteomics.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.symbol.*;
import
org.biojava.bio.symbol.SymbolList.EmptySymbolList;
import org.biojava.bio.symbol.SimpleAtomicSymbol;
import org.biojava.bio.seq.ProteinTools.*;
import org.biojava.bio.seq.impl.*;


public class Seq {
  public static void main (String args[]) {

    try {
      Protease pp = new Protease("RK", true, "P");
      ProteinTools protT= new ProteinTools();

      SymbolList myProt=
protT.createProtein("MAADSIPLKREDTMEALIEWLIPKKEDDGHGKLE");
      SimpleSequence s = new SimpleSequence( myProt, 
                                             ":P",
                                             "Test
Protein",
                                             new
Annotation.EmptyAnnotation());
    
      Digest digest = new Digest();
    
      digest.setSequence(s);
      digest.setProtese(pp);
      digest.setMaxMissedCleavages(1);
      digest.addDigestFeatures();
    
      Iterator it = s.features();
    
      while (it.hasNext()) {
      
        SimpleFeature sf = (SimpleFeature) it.next();
        SymbolList ss = sf.getSymbols();

        // ^^ That looks needlessly messy, doesn't it.
      
        double mass = 0;
        SymbolPropertyTable st= 
         
ProteinTools.getSymbolPropertyTable("MONO_MASS");
        Alphabet as=ProteinTools.getAlphabet();
        MassCalc mc= new MassCalc(st.MONO_MASS, true);

        mass=mc.getMass(ss,st.MONO_MASS,true);
        System.out.println(ss.seqString() + " " +
mass);
      }
    }
    catch (Exception e){
      e.printStackTrace();
    }
  }
}



--- Robert Stones <[EMAIL PROTECTED]> wrote:
> I keep getting this error using the proteomic
> package when performing
> simulated digests on proteins and some peptides with
> masses are not
> being generated:
> 
> Has anybody got an example code for setting
> proteases and working out
> masses?  
> 
> org.biojava.bio.symbol.IllegalSymbolException: No
> mass Set for Symbol
> [GLU SER GLY PHE LEU PRO ALA VAL ASN SEC HIS MET THR
> TYR ARG ILE LYS GLN
> TRP CYS ASP]
> at
>
org.biojava.bio.proteomics.MassCalc.getVMasses(MassCalc.java:365)
> 
> my code
> 
>       try
>       {
>       seq = si.nextSequence();        
>       Annotation anno = seq.getAnnotation();
>                               
>       it = seq.features(); 
>       }//try 
>       catch (BioException bex)
>       {
>       System.out.println(bex);
>       }
>               
>       while ( it.hasNext() ) 
>       {
>       Feature f = (Feature) it.next();
> 
>               if (f.getType().equals("Peptide"))
>               {
>                       try
>                       {
>                       MassCalc  massCalc = new
> MassCalc(SymbolPropertyTable.MONO_MASS,
> true);
>                       double[] masses =
> massCalc.getVariableMasses(f.getSymbols());
>                       double mass = masses[0];
>                       }//try
>             
>                               
>                       catch(Exception is)
>                       {                               
>                       is.printStackTrace();
>                       }
>               }
>       }       
> 
> [EMAIL PROTECTED] wrote:


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