int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
// Read PDB
System sys;
sys.readPdb(opt.pdb);
int centerResidueIndex = -1;
for (uint i = 0; i < sys.positionSize();i++){
if ((sys.getPosition(i).getResidueNumber() == opt.resnum) && (sys.getPosition(i).getChainId() == opt.chain)) {
centerResidueIndex = i;
break;
}
}
if (centerResidueIndex == -1){
cerr << "ERROR Couldn't find central residue"<<endl;
cerr << opt.pdb << endl;
cerr << opt.resnum << "\t" << opt.chain << endl;
exit(3);
}
cout << "Compute Frame.h"<<endl;
Frame f;
if (!f.computeFrameFromFunctionalGroup(sys.getPosition(centerResidueIndex).getCurrentIdentity())){
cerr << "Problem creating frame from central residue"<<endl;
cerr << opt.pdb << endl;
cerr << opt.resnum << "\t" << opt.chain << endl;
exit(324);
}
if (opt.printFrames){
cout << "Write out basic frame"<<endl;
ofstream fout;
fout.open("basicFrame.py");
fout << f.toString()<<endl;
fout.close();
}
// Align frame and atoms of sys to origin.
AtomPointerVector &av = sys.getAtomPointers();
f.transformToGlobalBasis(av);
Transforms t;
for (uint i = 0; i < sys.positionSize();i++){
if (i == centerResidueIndex) continue;
Residue &r = sys.getResidue(i);
CartesianPoint cp;
double angleBetweenFrames = MslTools::doubleMax;
if (r.getResidueName() == "ASP" &&
r.atomExists("CG") &&
r.atomExists("OD1") &&
r.atomExists("OD2")){
cp.setCoor( (r("CG").getX()+r("OD1").getX()+r("OD2").getX()) / 3,
(r("CG").getY()+r("OD1").getY()+r("OD2").getY()) / 3,
(r("CG").getZ()+r("OD1").getZ()+r("OD2").getZ()) / 3);
if (i != centerResidueIndex) {
f.transformFromGlobalBasis(r.getAtomPointers());
Frame floatingFrame;
floatingFrame.computeFrameFrom3Atoms(r("OD1"),r("CG"),r("OD2"));
if (opt.printFrames){
char name[80];
sprintf(name,"aspFrame%1s%03d.py",r.getChainId().c_str(),r.getResidueNumber());
ofstream fout;
fout.open(name);
fout << floatingFrame.toString()<<endl;
fout.close();
}
//cout << floatingFrame.toString()<<endl;
Matrix m = f.anglesBetweenFrame(floatingFrame);
angleBetweenFrames = m[2][2];// z vs z
f.transformToGlobalBasis(r.getAtomPointers());
}
}
if (r.getResidueName() == "ASN" &&
r.atomExists("CG") &&
r.atomExists("OD1") &&
r.atomExists("ND2")){
cp.setCoor( (r("CG").getX()+r("OD1").getX()+r("ND2").getX()) / 3,
(r("CG").getY()+r("OD1").getY()+r("ND2").getY()) / 3,
(r("CG").getZ()+r("OD1").getZ()+r("ND2").getZ()) / 3);
if (i != centerResidueIndex) {
f.transformFromGlobalBasis(r.getAtomPointers());
Frame floatingFrame;
floatingFrame.computeFrameFrom3Atoms(r("OD1"),r("CG"),r("ND2"));
if (opt.printFrames){
char name[80];
sprintf(name,"asnFrame%1s%03d.py",r.getChainId().c_str(),r.getResidueNumber());
ofstream fout;
fout.open(name);
fout << floatingFrame.toString()<<endl;
fout.close();
}
Matrix m = f.anglesBetweenFrame(floatingFrame);
angleBetweenFrames = m[2][2];// z vs z
f.transformToGlobalBasis(r.getAtomPointers());
}
}
if (r.getResidueName() == "GLU" &&
r.atomExists("CD") &&
r.atomExists("OE1") &&
r.atomExists("OE2")){
cp.setCoor( (r("CD").getX()+r("OE1").getX()+r("OE2").getX()) / 3,
(r("CD").getY()+r("OE1").getY()+r("OE2").getY()) / 3,
(r("CD").getZ()+r("OE1").getZ()+r("OE2").getZ()) / 3);
if (i != centerResidueIndex) {
f.transformFromGlobalBasis(r.getAtomPointers());
Frame floatingFrame;
floatingFrame.computeFrameFrom3Atoms(r("OE1"),r("CD"),r("OE2"));
if (opt.printFrames){
char name[80];
sprintf(name,"gluFrame%1s%03d.py",r.getChainId().c_str(),r.getResidueNumber());
ofstream fout;
fout.open(name);
fout << floatingFrame.toString()<<endl;
fout.close();
}
Matrix m = f.anglesBetweenFrame(floatingFrame);
angleBetweenFrames = m[2][2];// z vs z
f.transformToGlobalBasis(r.getAtomPointers());
}
}
if (r.getResidueName() == "GLN" &&
r.atomExists("CD") &&
r.atomExists("OE1") &&
r.atomExists("NE2")){
cp.setCoor( (r("CD").getX()+r("OE1").getX()+r("NE2").getX()) / 3,
(r("CD").getY()+r("OE1").getY()+r("NE2").getY()) / 3,
(r("CD").getZ()+r("OE1").getZ()+r("NE2").getZ()) / 3);
if (i != centerResidueIndex) {
f.transformFromGlobalBasis(r.getAtomPointers());
Frame floatingFrame;
floatingFrame.computeFrameFrom3Atoms(r("OE1"),r("CD"),r("NE2"));
if (opt.printFrames){
char name[80];
sprintf(name,"glnFrame%1s%03d.py",r.getChainId().c_str(),r.getResidueNumber());
ofstream fout;
fout.open(name);
fout << floatingFrame.toString()<<endl;
fout.close();
}
Matrix m = f.anglesBetweenFrame(floatingFrame);
angleBetweenFrames = m[2][2];// z vs z
f.transformToGlobalBasis(r.getAtomPointers());
}
}
SphericalPoint spRes = t.transform(cp);
if (angleBetweenFrames == MslTools::doubleMax){
angleBetweenFrames = 0;
} else {
if (angleBetweenFrames > 90){
angleBetweenFrames = 180 - angleBetweenFrames;
}
}
fprintf(stdout, "RES %10s %1s %04d %3s %8.3f %8.3f %8.3f %8.3f\n",MslTools::getFileName(opt.pdb).c_str(),r.getChainId().c_str(),r.getResidueNumber(),r.getResidueName().c_str(),spRes.getRadius(), spRes.getSigma(),spRes.getTheta(),angleBetweenFrames*M_PI/180);
AtomPointerVector &ats = r.getAtomPointers();
for (uint j = 0; j < ats.size();j++){
SphericalPoint sp = t.transform(ats(j).getCoor());
//fprintf(stdout, "ATM %10s %1s %04d %3s %4s %8.3f %8.3f %8.3f\n",MslTools::getFileName(opt.pdb).c_str(),ats(j).getChainId().c_str(),ats(j).getResidueNumber(),r.getResidueName().c_str(),ats(j).getName().c_str(),sp.getRadius(), sp.getSigma(),sp.getTheta());
Residue ¢ = sys.getPosition(centerResidueIndex).getCurrentIdentity();
if (cent.getResidueName() == "LYS"){
double lysDihedral = 0;
double lysAngle = 0;
lysDihedral = cent("CD").getCoor().dihedral(cent("CE").getCoor(),cent("NZ").getCoor(),ats(j).getCoor());
lysAngle = cent("CE").getCoor().angle(cent("NZ").getCoor(),ats(j).getCoor());
fprintf(stdout, "ATM %10s %04d %1s %04d %3s %4s %8.3f %8.3f %8.3f %8.3f %8.3f\n",MslTools::getFileName(opt.pdb).c_str(),opt.resnum,ats(j).getChainId().c_str(),ats(j).getResidueNumber(),r.getResidueName().c_str(),ats(j).getName().c_str(),sp.getRadius(), sp.getSigma(),sp.getTheta(),lysAngle,lysDihedral);
}
else {
// JEDONALD WAY..
fprintf(stdout, "ATM %10s %04d %1s %04d %3s %4s %8.3f %8.3f %8.3f %8.3f\n",MslTools::getFileName(opt.pdb).c_str(),opt.resnum,ats(j).getChainId().c_str(),ats(j).getResidueNumber(),r.getResidueName().c_str(),ats(j).getName().c_str(),sp.getRadius(), sp.getSigma(),sp.getTheta(), angleBetweenFrames*M_PI/180);
}
}
}
cout << "Done."<<endl;
}
Point::Point(const SphericalPoint & sp) :
x(sp.getRadius() * (sin(sp.getTheta().getValue()) * cos(sp.getPhi().getValue()))), y(
sp.getRadius() * (sin(sp.getTheta().getValue()) * sin(sp.getPhi().getValue()))), z(
sp.getRadius() * cos(sp.getTheta().getValue())) {
}
