public static AtomList createShiftedThreading(CommandList commands, Protein prot, int delta) {
AtomList newList = new AtomList();
Protein newProt;
DistanceMatrix dm;
DunbrackLib lib = new DunbrackLib(commands, 1.0, 90);
// Copying the coordiantes to the new atoms.
for (int resNum =
Math.max(
prot.residues().firstNonDummyResidueNumber(),
prot.residues().firstNonDummyResidueNumber() - delta);
resNum
<= Math.min(
((Residue) prot.residues().last()).number,
((Residue) prot.residues().last()).number - delta);
resNum++) {
Atom atom = prot.atoms().findAtomInList("N", resNum + delta);
if (atom != null) {
Atom newAtom =
new Atom(
atom.x(),
atom.y(),
atom.z(),
"N",
prot.residue(resNum).nameThreeLetters(),
resNum,
-1);
newList.add(newAtom);
}
atom = prot.atoms().findAtomInList("CA", resNum + delta);
if (atom != null) {
Atom newAtom =
new Atom(
atom.x(),
atom.y(),
atom.z(),
"CA",
prot.residue(resNum).nameThreeLetters(),
resNum,
-1);
newList.add(newAtom);
}
atom = prot.atoms().findAtomInList("C", resNum + delta);
if (atom != null) {
Atom newAtom =
new Atom(
atom.x(),
atom.y(),
atom.z(),
"C",
prot.residue(resNum).nameThreeLetters(),
resNum,
-1);
newList.add(newAtom);
}
atom = prot.atoms().findAtomInList("O", resNum + delta);
if (atom != null) {
Atom newAtom =
new Atom(
atom.x(),
atom.y(),
atom.z(),
"O",
prot.residue(resNum).nameThreeLetters(),
resNum,
-1);
newList.add(newAtom);
}
atom = prot.atoms().findAtomInList("H", resNum + delta);
if (atom != null) {
Atom newAtom =
new Atom(
atom.x(),
atom.y(),
atom.z(),
"H",
prot.residue(resNum).nameThreeLetters(),
resNum,
-1);
newList.add(newAtom);
}
}
// Filling the atoms
newProt = new Protein(newList, new ResidueExtendedAtoms(ADD_ATOMS));
// adjusting hydrogens and SCMODing
dm = new DistanceMatrix(newProt.atoms(), 5.5, 2.0, 4);
double[][] pp = RotamericTools.putIntoRot1(newProt, dm, lib);
PutHydrogens.adjustHydrogens(commands, prot);
newProt.defrost();
try {
newProt.atoms().print(new MeshiWriter(outputFileName + ".rot1.pdb"));
} catch (Exception e) {
System.out.print("\nThere was a problem writing the PDB:\n" + e + "\n\nContinuing...\n\n");
}
SCMOD.scmod(commands, lib, newProt, 2, 0.0, pp);
// Final minimzation
EnergyCreator[] energyCreators = {
new BondCreator(1.0),
new AngleCreator(1.0),
new PlaneCreator(10.0),
new OutOfPlaneCreator(1.0),
new LennardJonesCreator(0.4),
new SimpleHydrogenBond_Dahiyat_HighAccuracy_Creator(3.0),
new RamachandranSidechainEnergyCreator(1.0)
};
newProt.atoms().freeze(new AtomList.BackboneFilter());
dm = new DistanceMatrix(newProt.atoms(), 5.5, 2.0, 4);
TotalEnergy energy = new TotalEnergy(newProt, dm, energyCreators, commands);
Minimizer minimizer = new LBFGS(energy, 0.001, 50000, 1000);
try {
System.out.println(minimizer.minimize());
} catch (Exception e) {
throw new RuntimeException("ERROR in minimization");
}
// printing a LJ values histogram - Start
// --------------------------------------
double firstBin = -1.0;
double lastBin = 4.0;
double binSpacing = 0.05;
int[] bins = new int[(int) Math.ceil((lastBin - firstBin) / binSpacing)];
for (int c = 0; c < bins.length; c++) bins[c] = 0;
energy.resetAtomEnergies();
LennardJones lj = (LennardJones) energy.getEnergyTerm(new LennardJones());
lj.evaluateAtoms();
double Elj = 0.0;
int ind = 0;
for (int at = 0; at < newProt.atoms().size(); at++) {
Elj = newProt.atoms().atomAt(at).energy();
ind = (int) Math.round((Elj - firstBin) / binSpacing);
if (ind < 0) ind = 0;
if (ind >= bins.length) ind = bins.length - 1;
bins[ind]++;
}
Elj = firstBin;
for (int c = 0; c < bins.length; c++) {
System.out.println("000 " + Elj + " " + bins[c]);
Elj += binSpacing;
}
// --------------------------------------
// printing the LJ values histogram - END
return newProt.atoms();
}
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();
}
}