Examples of org.biojava.bio.structure.Group

org.biojava.bio.structure.Group

      return atom.getName();
    }


    public String getGroup3() {


      Group parent = atom.getParent();
      if (parent != null) {


        return parent.getPDBName();
      }
      return null;
    }

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      }
      return null;
    }


    public int getSequenceNumber() {
      Group g = atom.getParent();
      if (g != null) {


        try {
          return Integer.parseInt(g.getPDBCode());
        } catch (NumberFormatException e) {
          // e.printStackTrace();
        }
      }

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      } else
        return (char) 0;
    }


    public char getInsertionCode() {
      Group g = atom.getParent();
      if (g != null) {
        String pdbresnum = g.getPDBCode();
        try {
          Integer.parseInt(pdbresnum);
        } catch (NumberFormatException ex) {


          String insertionCode = pdbresnum.substring(pdbresnum

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      }
      return (char) 0;
    }


    public boolean getIsHetero() {
      Group parent = atom.getParent();
      if (parent != null) {
        if (parent.getType().equals(HetatomImpl.type)) {
          // System.out.println(atom + " is hetero");
          return true;
        }
      }

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   * @return
   */
  private int getSeqPosFromPdb(String pdbresnum, Chain currentChain) {
    List<Group> groups = currentChain.getAtomGroups();
    try {
      Group g = currentChain.getGroupByPDB(pdbresnum);
      return groups.indexOf(g);


    } catch (StructureException e) {
      return -1;
    }

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    Atom a = new AtomImpl();
    a.setName("CA");
    a.setFullName(" CA ");
    a.setCoords(new double[] { 47.866, 28.415, 2.952 });


    Group g = new AminoAcidImpl();
    g.setPDBCode("9");
    try {
      g.setPDBName("GLY");
    } catch (PDBParseException e) {
      e.printStackTrace();
    }
    g.addAtom(a);


    Chain c = new ChainImpl();
    c.addGroup(g);


    Structure s = new StructureImpl();

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  private String getSelectStr(int chainNumber, int start, int end) {
    Chain chain = structure.getChain(chainNumber) ;
        if ( chain == null) return "" ;
        String chainid = chain.getName() ;
        
        Group gs = getGroupNext( chain,(start-1), true);
        //Group gs = chain.getGroup(start-1);  
        Group ge = getGroupNext( chain,(end-1), false);
        
        String startpdb = gs.getPDBCode() ;
        String endpdb = ge.getPDBCode() ;
        String cmd =  "select "+startpdb+"-"+endpdb;
        
        if ( ! chainid.equals(" ")) 
            cmd += ":" +chainid + "/1";
        else

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   */
  private Group getGroupNext(Chain chain, int startpos, boolean increment) {
          if ( chain == null) return null ;
          
          while ( (startpos >= 0 ) && (startpos < chain.getAtomLength())){
              Group g = chain.getAtomGroup(startpos);  
        //System.out.println("checking " + startpos + " " + g );
              if (g.has3D()){
                  return g ;
              }
              if ( increment) {
                  startpos += 1;
              } else {

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Related Classes of org.biojava.bio.structure.Group

jSimMacs.jmol.JSimJmolAdapter$ProjectedAtomIterator

jSimMacs.jmol.JSimJmolTranslator

jSimMacs.jmol.StructurePanel

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