/**
* @param pdb
* @param type
* @return voronoi data reuced and decomposited by given pdbmodel no grid will be used
*/
public VoronoiData prepareSimple(PDBEntry pdb, VoroPrepType type) {
VoronoiData data;
data = new VoronoiData(pdb.getId());
data.reducePDB(type, pdb);
voro.decomposite(data);
return data;
}
/**
* voronoi data container for multiple sequence scoring on model will be initialized
*
* @param model
* @return voronoi data reuced and decomposited by given pdbmodel grid will be used and generated
*/
@Override
public void prepareSequenceScoring(Object model) {
PDBEntry entry = (PDBEntry) model;
data = new VoronoiData(entry.getId());
data.reducePDB(entry);
data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
voro.decomposite(data);
data.detectOuterGrid(minContact);
}
/**
* normal preparation of data in solvent
*
* @param pdb
* @param gridExtend
* @param gridDensity
* @param gridClash
* @param minContact
* @return voronoi data reuced and decomposited by given pdbmodel grid will be used and generated
*/
public VoronoiData prepareWithGrid(
PDBEntry pdb, double gridExtend, double gridDensity, double gridClash, double minContact) {
VoronoiData data;
data = new VoronoiData(pdb.getId());
data.reducePDB(pdb);
data.fillGridWithoutClashes(gridExtend, gridDensity, gridClash);
voro.decomposite(data);
data.detectOuterGrid(minContact);
return data;
}
/**
* 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;
}
