Options setupOptions(int theArgc, char * theArgv[]){
Options opt;
OptionParser OP;
OP.readArgv(theArgc, theArgv);
OP.setRequired(opt.required);
OP.setAllowed(opt.optional);
if (OP.countOptions() == 0){
cout << "Usage:" << endl;
cout << endl;
cout << "generateCoiledBundles --symmetry SYM --superHelicalRadius LOW HIGH STEP --alphaHelicalPhaseAngle LOW HIGH STEP --superHelicalPitchAngle LOW HIGH STEP --numberOfResidues NUM [ --d2zTranslation LOW HIGH STEP --superHelicalPhaseAngle LOW HIGH STEP --name OUTFILE]\n";
cout << "Recommended parameters:" << endl;
cout << "--symmetry: C2, C3, D2, D3, etc." << endl;
cout << "--superHelicalRadius: radius from center in Angstroms" << endl;
cout << "--alphaHelicalPhaseAngle: phase angle of the helices (0-360 degrees)" << endl;
cout << "--superHelicalPitchAngle: often 5-20 degrees, but depends on the coil (average around 12)" << endl;
cout << "--d2zTranslation: z offset between D_N symmetric coils, usually small" << endl;
cout << "--superHelicalPhaseAngle: angle in degrees. Value of 90/N for D_N typically works well, but larger and smaller values are possible" << endl;
exit(0);
}
opt.symmetry = OP.getString("symmetry");
if (OP.fail()){
cerr << "ERROR 1111 symmetry not specified.\n";
exit(1111);
}
opt.superHelicalRadius = OP.getDoubleVector("superHelicalRadius");
if (OP.fail()){
cerr << "ERROR 1111 superHelicalRadius not specified.\n";
exit(1111);
}
opt.alphaHelicalPhaseAngle = OP.getDoubleVector("alphaHelicalPhaseAngle");
if (OP.fail()){
cerr << "ERROR 1111 alphaHelicalPhaseAngle not specified.\n";
exit(1111);
}
opt.superHelicalPitchAngle = OP.getDoubleVector("superHelicalPitchAngle");
if (OP.fail()){
cerr << "ERROR 1111 superHelicalPitchAngle not specified.\n";
exit(1111);
}
opt.numberOfResidues = OP.getInt("numberOfResidues");
if (OP.fail()){
cerr << "ERROR 1111 numberOfResidues not specified.\n";
exit(1111);
}
opt.d2zTranslation = OP.getDoubleVector("d2zTranslation");
opt.superHelicalPhaseAngle = OP.getDoubleVector("superHelicalPhaseAngle");
if (opt.d2zTranslation.size() == 0) { vector<double> tmp; tmp.push_back(0.0); tmp.push_back(1.0); tmp.push_back(100.0); opt.d2zTranslation = tmp; cerr << "Warning, d2zTranslation not defined (required for D2, D3)" << endl; }
if (opt.superHelicalPhaseAngle.size() == 0) {
int _N = atoi(opt.symmetry.substr(1,(opt.symmetry.length()-1)).c_str());
double recommendedValue = 90./double(_N);
vector<double> tmp; tmp.push_back(recommendedValue); tmp.push_back((recommendedValue + 1.)); tmp.push_back(100.0); opt.superHelicalPhaseAngle = tmp; cerr << "Warning, superHelicalPhaseAngle not defined (required for D2, D3)" << endl;
}
opt.name = OP.getString("name");
if (OP.fail()){
opt.name = "CoiledBundle";
}
return opt;
}
