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 } } } } }