Generating Sequence From Pdb File Using Biojava

import java.util.Map;
import org.biojava.bio.structure.*;
import org.biojava.bio.structure.io.PDBFileReader;
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava.bio.structure.io.StructureSequenceMatcher;
public class sequence {
   PDBFileReader pdbreader = new PDBFileReader();
   StructureSequenceMatcher sqm = new StructureSequenceMatcher();
   Structure structure = null;
   Map<Integer,Group> map= null;
    public sequence()throws Exception
    {
      structure = pdbreader.getStructure("2K25.pdb");
      System.out.println(sqm.getProteinSequenceForStructure(structure, map));

    }

    public static void main(String args[])throws Exception
    {

        new sequence();
    }
}

Error:

Exception in thread "main" java.lang.NoSuchMethodError:       org.biojava.bio.structure.io.SeqRes2AtomAligner.getFullAtomSequence(Ljava/util/List;Ljava/util/Map;)Ljava/lang/String;
at org.biojava.bio.structure.io.StructureSequenceMatcher.getProteinSequenceForStructure(StructureSequenceMatcher.java:64)
at sequence.<init>(sequence.java:15)
at sequence.main(sequence.java:22)
Java Result: 1
BUILD SUCCESSFUL (total time: 0 seconds)

Hi! I am a newbie to biojava. I was trying my hand at retrieving the protein sequence from the pdb file using structure object. In one of my earlier post, it was suggested to me that all that would be required for this process is, the structure object and an empty map. I tried as instructed, but to no avail. Please help!

sequence pdb biojava

• 4,845 views • link

updated 13.4 years ago by andreas.prlic

• written 13.5 years ago by potassiumiodide0990

how did you run the main method ? how was "java" invoked ? (or show us the build.xml if any)

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written 13.5 years ago by Pierre Lindenbaum

it is just an exception your code looks fine to me.

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written 13.5 years ago by Medhat

so how do i exactly get the code working?

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written 13.5 years ago by potassiumiodide0990

IMHO, It's a CLASSPATH or a version problem....

• 0 views • link

written 13.5 years ago by Pierre Lindenbaum

1 answer

I would do it like this:



import org.biojava.bio.structure.Chain;
import org.biojava.bio.structure.Structure;
import org.biojava3.structure.StructureIO;

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

        try {

            Structure s = StructureIO.getStructure("4hhb");

            for ( Chain c : s.getChains()) {

                // only the observed residues
                System.out.println(c.getAtomSequence());

                // print biological sequence
                System.out.println(c.getSeqResSequence());
            }

        } catch (Exception e) {

            e.printStackTrace();
        }        
    }
}

• 0 views • link

written 13.4 years ago by andreas.prlic