/**
* 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;
}
/**
* 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;
}
/**
* 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;
}