Beispiel #1
0
  /**
   * for whenever we need to only make sequence fragments
   *
   * @param pdb the entry to disassemble
   * @param l a list of protein fragments
   * @param fLength the desired length of protein fragments
   * @return the new list of fragments
   */
  public static LinkedList<char[]> disassemble(
      PDBEntry pdb, LinkedList<char[]> l, int fragmentLength) {
    char[] pdbChar = new char[pdb.length()];
    for (int i = 0; i < pdb.length(); i++) {
      pdbChar[i] = pdb.getAminoAcid(i).getName().getOneLetterCode().charAt(0);
    }

    for (int i = 0; i < pdb.length() - fragmentLength; i++) {
      char[] temp = new char[fragmentLength];
      for (int j = 0; j < fragmentLength; j++) {
        temp[j] = pdbChar[i + j];
      }
      l.add(temp);
    }
    return l;
  }
Beispiel #2
0
 /**
  * goes through a PDB Entry and reads protein fragments using the CA atoms
  *
  * @param pdb the entry to crunch
  * @param l a list of protein fragments
  * @param fLength the desired length of protein fragments
  * @return the new list of fragments
  */
 public static LinkedList<ProteinFragment> crunchBackboneN(
     PDBEntry pdb, String secStruct, LinkedList<ProteinFragment> l, int fLength) {
   try {
     String curSecStruct = "";
     for (int i = 0; i < pdb.length() - fLength; i++) {
       Atom[] temp = new Atom[fLength];
       for (int j = i; j < i + fLength; j++) {
         temp[j - i] = pdb.getAminoAcid(j).getAtomByType(AtomType.CA);
       }
       curSecStruct = secStruct.substring(i, i + fLength);
       ProteinFragment tempFrag =
           new ProteinFragment(pdb.getId() + "_" + i, curSecStruct, temp, fLength);
       l.add(tempFrag);
     }
     return l;
   } catch (Exception e) {
     System.out.println("Entry " + pdb.getId() + " probably has incomplete records.");
   }
   return null;
 }
Beispiel #3
0
 /**
  * alternative version that returns the sequence along with the other stuff.
  *
  * @param pdb the entry to crunch
  * @param l a list of protein fragments
  * @param fLength the desired length of protein fragments
  * @return the new list of fragments
  */
 public static List<ProteinFragment> crunchBackboneSeq(
     PDBEntry pdb, List<ProteinFragment> l, int fLength) {
   try {
     AminoAcid tempAA = new AminoAcid("ALA", 0);
     StringBuilder seq = new StringBuilder();
     for (int i = 0; i < pdb.length() - fLength; i++) {
       Atom[] temp = new Atom[fLength];
       seq.delete(0, fLength);
       for (int j = i; j < i + fLength; j++) {
         tempAA = pdb.getAminoAcid(j);
         seq.append(tempAA.getName().getOneLetterCode());
         temp[j - i] = tempAA.getAtomByType(AtomType.CA).clone();
       }
       ProteinFragment tempFrag =
           new ProteinFragment(pdb.getId() + "_" + i, seq.toString(), temp, fLength);
       l.add(tempFrag);
     }
     return l;
   } catch (Exception e) {
     System.out.println("Entry " + pdb.getId() + " probably has incomplete records.");
     e.printStackTrace();
   }
   return null;
 }