int main(int argc, char *argv[]){
// Option Parser
Options opt = setupOptions(argc,argv);
Transforms tr;
// Super-helical Radius Loop
for (double sr = opt.superHelicalRadius[0]; sr <= opt.superHelicalRadius[1]; sr += opt.superHelicalRadius[2]){
// Alpha-helical Phase Angle Loop
for (double aph = opt.alphaHelicalPhaseAngle[0]; aph < opt.alphaHelicalPhaseAngle[1];aph+=opt.alphaHelicalPhaseAngle[2]){
// Super-helical Pitch Angle loop added by David Slochower
for(double shpa = opt.superHelicalPitchAngle[0]; shpa < opt.superHelicalPitchAngle[1]; shpa+=opt.superHelicalPitchAngle[2]) {
double shPitch = (2*M_PI*sr)/tan(M_PI*shpa/180);
// Generate a coiled helix
CoiledCoils cc;
// Values used for previous work: cc.northCoiledCoils(sr, 1.5232, shPitch, 2.25, opt.numberOfResidues, 103.195, aph);
// March 31, 2010: Jason Donald
// Hard code values of h (rise/residue) = 1.51, r1 (alpha-helical radius), and theta (alpha helical frequency)
// based on median values observed by Gevorg Grigoryan
//cc.northCoiledCoils(sr, 1.51, shPitch, 2.26, opt.numberOfResidues, 102.8, aph);
AtomPointerVector coil = cc.getCoiledCoil(sr, 1.51, shPitch, 2.26, 102.8, aph, 0.0,opt.numberOfResidues);
// Apply symmetry operations to create a bundle
int C_axis = atoi(opt.symmetry.substr(1,(opt.symmetry.length()-1)).c_str());
if (opt.symmetry.substr(0,1) == "C"){
Symmetry sym;
sym.applyCN(coil,C_axis);
// Write out bundle
char filename[80];
sprintf(filename, "%s_%s_%03d_%05.2f_%05.2f_shp%05.2f.pdb", opt.name.c_str(),opt.symmetry.c_str(),opt.numberOfResidues, sr, aph, shpa);
cout << "Writing "<<filename<<endl;
PDBWriter pout;
pout.open(filename);
pout.write(sym.getAtomPointers());
pout.close();
}
else if (opt.symmetry.substr(0,1) == "D"){
// Z Rotate
for (double spa = opt.superHelicalPhaseAngle[0]; spa < opt.superHelicalPhaseAngle[1]; spa += opt.superHelicalPhaseAngle[2]){
coil.clearSavedCoor();
coil.saveCoor("preSPA");
Matrix zRot = CartesianGeometry::getZRotationMatrix(spa);
//coil.rotate(zRot);
tr.rotate(coil, zRot);
// Z Trans
for (double ztrans = opt.d2zTranslation[0];ztrans < opt.d2zTranslation[1]; ztrans += opt.d2zTranslation[2]){
coil.saveCoor("preZtrans");
CartesianPoint z(0,0,ztrans);
//coil.translate(z);
tr.translate(coil, z);
Symmetry sym;
sym.applyDN(coil,C_axis);
// Write out bundle
char filename[80];
sprintf(filename, "%s_%s_%03d_%05.2f_%05.2f_shp%05.2f_%05.2f_%05.2f.pdb", opt.name.c_str(),opt.symmetry.c_str(),opt.numberOfResidues,sr, aph, shpa, spa, ztrans);
cout << "Writing "<<filename<<endl;
PDBWriter pout;
pout.open(filename);
pout.write(sym.getAtomPointers());
pout.close();
coil.applySavedCoor("preZtrans");
} // Ztrans
coil.applySavedCoor("preSPA");
} // SHA
}
}
}
}
}
