public static void main(String[] args) throws MinimizerException, LineSearchException {
init(args);
CommandList commands = new CommandList(commandsFileName);
Protein prot = new Protein(new AtomList(modelFileName), new ResidueExtendedAtoms(ADD_ATOMS));
for (int cc = 0; cc < prot.atoms().size(); cc++) prot.atoms().atomAt(cc).setChain(" ");
PutHydrogens.adjustHydrogens(commands, prot);
AtomList shiftedList = createShiftedThreading(commands, prot, delta);
try {
shiftedList.print(new MeshiWriter(outputFileName));
} catch (Exception e) {
System.out.print("\nThere was a problem writing the PDB:\n" + e + "\n\nContinuing...\n\n");
}
}
public static void main(String[] args) {
init(args);
Protein model = new ExtendedAtomsProtein(modelFileName, DO_NOT_ADD_ATOMS);
boolean[] goodRes = new boolean[model.residues().size() + 1];
for (int c = 0; c < goodRes.length; c++) goodRes[c] = false;
Protein compareTo = new ExtendedAtomsProtein(compareToFileName, DO_NOT_ADD_ATOMS);
String[] gaps = File2StringArray.f2a(gapsFileName);
for (int gapC = 0; gapC < gaps.length; gapC++) {
StringTokenizer st = new StringTokenizer(gaps[gapC]);
int gapFrom = (new Integer(st.nextToken())).intValue();
int gapTo = (new Integer(st.nextToken())).intValue();
for (int predC = 0; predC < NumPredToConsider; predC++) {
if ((new File(loopDirPath + "/Loop_" + gapFrom + "_" + gapTo + "/phase2/" + predC + ".pdb"))
.exists()) {
boolean[] goodInLoop = new boolean[gapTo + 1];
AtomList gapAtoms =
new AtomList(
loopDirPath + "/Loop_" + gapFrom + "_" + gapTo + "/phase2/" + predC + ".pdb");
// Finding consistent atoms between loop and the 'compareTo' protein
for (int resInLoop = gapFrom; resInLoop <= gapTo; resInLoop++) {
if (compareTo.atoms().findAtomInList("CA", resInLoop) == null) {
goodInLoop[resInLoop] = false;
} else {
goodInLoop[resInLoop] = false;
if (compareTo.atoms().findAtomInList("CB", resInLoop) != null) { // NOT a Glycin
if ((compareTo
.atoms()
.findAtomInList("CA", resInLoop)
.distanceFrom(gapAtoms.findAtomInList("CA", resInLoop))
< goodCutoff)
&& (compareTo
.atoms()
.findAtomInList("CB", resInLoop)
.distanceFrom(gapAtoms.findAtomInList("CB", resInLoop))
< goodCutoff)) {
goodInLoop[resInLoop] = true;
} else {
goodInLoop[resInLoop] = false;
}
} else {
if (compareTo
.atoms()
.findAtomInList("CA", resInLoop)
.distanceFrom(gapAtoms.findAtomInList("CA", resInLoop))
< goodCutoff) {
goodInLoop[resInLoop] = true;
} else {
goodInLoop[resInLoop] = false;
}
}
}
}
// Analyzing data - is there a consistent pattern between the loops and the 'compareTo'
// Protein.
for (int resInLoop = gapFrom + 4; resInLoop <= (gapTo - 4); resInLoop++) {
if (goodInLoop[resInLoop - 1] && goodInLoop[resInLoop] && goodInLoop[resInLoop + 1]) {
goodRes[resInLoop - 1] = true;
goodRes[resInLoop] = true;
goodRes[resInLoop + 1] = true;
System.out.println(
"The residues "
+ (resInLoop - 1)
+ " "
+ (resInLoop)
+ " "
+ (resInLoop + 1)
+ " were indicated by model "
+ predC
+ " from loop: "
+ gapFrom
+ "_"
+ gapTo);
}
}
}
}
}
AtomList finalList = new AtomList();
for (int c = 0; c < compareTo.atoms().size(); c++) {
if (goodRes[compareTo.atoms().atomAt(c).residueNumber()])
finalList.add(compareTo.atoms().atomAt(c));
}
try {
finalList.print(new MeshiWriter(modelFileName + ".common.pdb"));
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}