Options parseOptions(int _argc, char * _argv[], Options defaults) {
/******************************************
* Pass the array of argument and the name of
* a configuration file to the ArgumentParser
* object. Then ask for the value of the argument
* and collect error and warnings.
*
* This function returns a Options structure
* defined at the head of this file
******************************************/
Options opt;
/******************************************
* Set the allowed and required options:
*
* Example of configuartion file:
*
******************************************/
vector<string> required;
vector<string> allowed;
opt.required.push_back("pdb");
opt.required.push_back("type");
opt.required.push_back("atomNames");
opt.required.push_back("value");
opt.allowed.push_back("outputPdb");
//opt.allowed.push_back("outputdir");
opt.allowed.push_back("configfile");
opt.allowed.push_back("version"); // --version
opt.allowed.push_back("v"); // -v is equivalent to --version
opt.allowed.push_back("help"); // --help
opt.allowed.push_back("h"); // -h is equivalent to --help
opt.equivalent.push_back(vector<string>());
opt.equivalent.back().push_back("v");
opt.equivalent.back().push_back("version");
opt.equivalent.push_back(vector<string>());
opt.equivalent.back().push_back("h");
opt.equivalent.back().push_back("help");
opt.defaultArgs.push_back("configfile");
//OptionParser OP(_argc, _argv);
OptionParser OP;
OP.setShortOptionEquivalent(opt.equivalent);
OP.readArgv(_argc, _argv);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.setRequired(opt.required);
OP.setAllowed(opt.allowed);
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0) {
usage();
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
opt.errorFlag = true;
opt.errorMessages += "Cannot read configuration file " + opt.configfile + "\n";
exit(1);
}
}
/*****************************************
* VERSION AND HELP
*
* --version or -v arguments print the version number
* --help prints the usage and help
*****************************************/
opt.version = OP.getBool("version");
//if (OP.fail()) {
// opt.version = OP.getBool("v");
//}
if (opt.version) {
version();
exit(0);
}
opt.help = OP.getBool("help");
// if (OP.fail()) {
// opt.help = OP.getBool("h");
// }
if (opt.help) {
help(defaults);
exit(0);
}
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
if (!OP.checkOptions()) {
opt.errorFlag = true;
opt.OPerrors = OP.getErrors();
return opt;
}
opt.errorFlag = false;
opt.warningFlag = false;
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
//opt.commandName = OP.getCommandName();
//if (!OP.checkOptions()) {
// opt.errorFlag = true;
// opt.disallowed = OP.getDisallowedOptions();
// opt.missing = OP.getMissingOptions();
// opt.ambiguous = OP.getAmbiguousOptions();
// return opt;
//}
opt.errorFlag = false;
opt.warningFlag = false;
opt.pdb = OP.getString("pdb");
if (OP.fail()) {
opt.errorMessages = "Option name of first pdb file \"pdb\" not specified";
opt.errorFlag = true;
}
opt.outputPdb = OP.getString("outputPdb");
if (OP.fail()) {
opt.warningMessages = "Option name of output edited pdb file \"outputPdb\" not specified";
opt.warningFlag = true;
string base = MslTools::pathTail(opt.pdb);
base = MslTools::pathRoot(base);
opt.outputPdb = base + (string)"-edited.pdb";
}
int index = 0;
while (true) {
DoF tmp;
tmp.type = OP.getString("type", index);
if (OP.fail()) {
break;
}
tmp.atomNames = OP.getStringVector("atomNames", index);
if (OP.fail()) {
break;
}
tmp.value = OP.getDouble("value", index);
if (OP.fail()) {
break;
}
opt.edits.push_back(tmp);
index++;
}
// return the Options structure
return opt;
}
Options parseOptions(int _argc, char * _argv[], Options defaults) {
/******************************************
* Pass the array of argument and the name of
* a configuration file to the ArgumentParser
* object. Then ask for the value of the argument
* and collect error and warnings.
*
* This function returns a Options structure
* defined at the head of this file
******************************************/
Options opt;
/******************************************
* Set the allowed and required options:
*
* Example of configuartion file:
*
******************************************/
vector<string> required;
vector<string> allowed;
opt.required.push_back("sequence");
opt.required.push_back("startPos");
opt.required.push_back("startRegPos");
opt.required.push_back("r0_start");
opt.required.push_back("r0_end");
opt.required.push_back("r0_step");
opt.required.push_back("r1_start");
opt.required.push_back("r1_end");
opt.required.push_back("r1_step");
opt.required.push_back("w1_start");
opt.required.push_back("w1_end");
opt.required.push_back("w1_step");
opt.required.push_back("phi1_start");
opt.required.push_back("phi1_end");
opt.required.push_back("phi1_step");
opt.required.push_back("rpr_start");
opt.required.push_back("rpr_end");
opt.required.push_back("rpr_step");
opt.required.push_back("pitch_start");
opt.required.push_back("pitch_end");
opt.required.push_back("pitch_step");
opt.required.push_back("nRes");
opt.required.push_back("symmetry");
opt.required.push_back("N");
//opt.required.push_back("testNo");
opt.allowed.push_back("setState");
opt.allowed.push_back("rotamerStates");
opt.allowed.push_back("rotamerSamplingSize");
opt.allowed.push_back("seed");
opt.required.push_back("rotamerLibrary"); //filename of rotamer library file
opt.allowed.push_back("outputdir");
opt.allowed.push_back("outputfile"); //filename of output file
opt.allowed.push_back("version"); // --version
opt.allowed.push_back("v"); // -v is equivalent to --version
opt.allowed.push_back("help"); // --help
opt.allowed.push_back("h"); // -h is equivalent to --help
opt.allowed.push_back("configfile");
opt.allowed.push_back("runDEE");
opt.allowed.push_back("runEnum");
opt.allowed.push_back("runSCMF");
opt.allowed.push_back("runMCO");
opt.equivalent.push_back(vector<string>());
opt.equivalent.back().push_back("v");
opt.equivalent.back().push_back("version");
opt.equivalent.push_back(vector<string>());
opt.equivalent.back().push_back("h");
opt.equivalent.back().push_back("help");
opt.defaultArgs.push_back("configfile");
//OptionParser OP(_argc, _argv);
OptionParser OP;
OP.setShortOptionEquivalent(opt.equivalent);
OP.readArgv(_argc, _argv);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.setRequired(opt.required);
OP.setAllowed(opt.allowed);
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0) {
usage();
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
opt.errorFlag = true;
opt.errorMessages += "Cannot read configuration file " + opt.configfile + "\n";
exit(1);
}
}
/*****************************************
* VERSION AND HELP
*
* --version or -v arguments print the version number
* --help prints the usage and help
*****************************************/
opt.version = OP.getBool("version");
//if (OP.fail()) {
// opt.version = OP.getBool("v");
//}
if (opt.version) {
version();
exit(0);
}
opt.help = OP.getBool("help");
// if (OP.fail()) {
// opt.help = OP.getBool("h");
// }
if (opt.help) {
help(defaults);
exit(0);
}
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
if (!OP.checkOptions()) {
opt.errorFlag = true;
opt.OPerrors = OP.getErrors();
return opt;
}
opt.errorFlag = false;
opt.warningFlag = false;
/*****************************************
* OUTPUT DIR AND FILES
*****************************************/
opt.outputdir = OP.getString("outputdir");
if (OP.fail() || opt.outputdir == "") {
opt.outputdir = defaults.outputdir;
}
opt.outputfile = OP.getString("outputfile");
if (OP.fail()) {
opt.outputfile = defaults.outputfile;
}
if (opt.outputfile != "" && opt.outputfile != "STDOUT") {
opt.coutRedirected = true;
opt.cout_fs = new ofstream();
opt.cerr_fs = new ofstream();
} else {
opt.coutRedirected = false;
opt.cout_fs = NULL;
opt.cerr_fs = NULL;
}
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
//opt.commandName = OP.getCommandName();
//if (!OP.checkOptions()) {
// opt.errorFlag = true;
// opt.disallowed = OP.getDisallowedOptions();
// opt.missing = OP.getMissingOptions();
// opt.ambiguous = OP.getAmbiguousOptions();
// return opt;
//}
opt.errorFlag = false;
opt.warningFlag = false;
opt.sequence= OP.getString("sequence");
if (OP.fail()) {
opt.errorMessages = "sequence not specified";
opt.errorFlag = true;
}
opt.startPos = OP.getStringVector("startPos");
if (OP.fail()) {
opt.errorMessages = "startPos not specified";
opt.errorFlag = true;
}
opt.startRegPos = OP.getString("startRegPos");
if (OP.fail()) {
opt.errorMessages = "startRegPos not specified";
opt.errorFlag = true;
}
opt.r0_start = OP.getDouble("r0_start");
if (OP.fail()) {
opt.errorMessages = "r0 not specified";
opt.errorFlag = true;
}
opt.r0_end = OP.getDouble("r0_end");
if (OP.fail()) {
opt.errorMessages = "r0 not specified";
opt.errorFlag = true;
}
opt.r0_step = OP.getDouble("r0_step");
if (OP.fail()) {
opt.errorMessages = "r0 not specified";
opt.errorFlag = true;
}
opt.r1_start = OP.getDouble("r1_start");
if (OP.fail()) {
opt.errorMessages = "r1 not specified";
opt.errorFlag = true;
}
opt.r1_end = OP.getDouble("r1_end");
if (OP.fail()) {
opt.errorMessages = "r1 not specified";
opt.errorFlag = true;
}
opt.r1_step = OP.getDouble("r1_step");
if (OP.fail()) {
opt.errorMessages = "r1 not specified";
opt.errorFlag = true;
}
opt.w1_start = OP.getDouble("w1_start");
if (OP.fail()) {
opt.errorMessages = "w1 not specified";
opt.errorFlag = true;
}
opt.w1_end = OP.getDouble("w1_end");
if (OP.fail()) {
opt.errorMessages = "w1 not specified";
opt.errorFlag = true;
}
opt.w1_step = OP.getDouble("w1_step");
if (OP.fail()) {
opt.errorMessages = "w1 not specified";
opt.errorFlag = true;
}
opt.phi1_start = OP.getDouble("phi1_start");
if (OP.fail()) {
opt.errorMessages = "phi1 not specified";
opt.errorFlag = true;
}
opt.phi1_end = OP.getDouble("phi1_end");
if (OP.fail()) {
opt.errorMessages = "phi1 not specified";
opt.errorFlag = true;
}
opt.phi1_step = OP.getDouble("phi1_step");
if (OP.fail()) {
opt.errorMessages = "phi1 not specified";
opt.errorFlag = true;
}
opt.rpr_start = OP.getDouble("rpr_start");
if (OP.fail()) {
opt.errorMessages = "rpr not specified";
opt.errorFlag = true;
}
opt.rpr_end = OP.getDouble("rpr_end");
if (OP.fail()) {
opt.errorMessages = "rpr not specified";
opt.errorFlag = true;
}
opt.rpr_step = OP.getDouble("rpr_step");
if (OP.fail()) {
opt.errorMessages = "rpr not specified";
opt.errorFlag = true;
}
opt.pitch_start = OP.getDouble("pitch_start");
if (OP.fail()) {
opt.errorMessages = "pitch not specified";
opt.errorFlag = true;
}
opt.pitch_end = OP.getDouble("pitch_end");
if (OP.fail()) {
opt.errorMessages = "pitch not specified";
opt.errorFlag = true;
}
opt.pitch_step = OP.getDouble("pitch_step");
if (OP.fail()) {
opt.errorMessages = "pitch not specified";
opt.errorFlag = true;
}
opt.nRes = OP.getInt("nRes");
if (OP.fail()) {
opt.errorMessages = "number of residues not specified";
opt.errorFlag = true;
}
opt.symmetry = OP.getString("symmetry");
if (OP.fail()) {
opt.errorMessages = "symmetry not specified";
opt.errorFlag = true;
}
opt.N = OP.getInt("N");
if (OP.fail()) {
opt.errorMessages = "N not specified";
opt.errorFlag = true;
}
opt.rotamerLibrary = OP.getString("rotamerLibrary");
if (OP.fail()) {
opt.errorMessages = "rotamerLibrary not specified";
opt.errorFlag = true;
}
opt.outputfile = OP.getString("outputfile");
if (OP.fail()) {
opt.errorMessages = "outputfile not specified";
opt.errorFlag = true;
}
/*
opt.testNo = OP.getInt("testNo");
if (OP.fail()) {
opt.errorMessages = "testNo not specified";
opt.errorFlag = true;
}
*/
opt.rotamerSamplingSize = OP.getString("rotamerSamplingSize");
opt.seed = OP.getInt("seed");
opt.runDEE = OP.getBool("runDEE");
opt.runEnum = OP.getBool("runEnum");
opt.runSCMF = OP.getBool("runSCMF");
opt.runMCO = OP.getBool("runMCO");
opt.setState = OP.getBool("setState");
opt.rotamerStates = OP.getUnsignedIntVector("rotamerStates");
opt.rerunConf = "########################################################\n";
opt.rerunConf += "# This configuration file was automatically generated,\n";
opt.rerunConf += "# it will rerun this job with the same options. Run as:\n";
opt.rerunConf += "#\n";
opt.rerunConf += "# Run as:\n";
opt.rerunConf += "#\n";
opt.rerunConf += "# % " + programName + " --configfile " + opt.rerunConfFile + "\n";
opt.rerunConf += "#\n";
opt.rerunConf += "# Job started on " + (string)ctime(&start_time);
opt.rerunConf += "# on host " + opt.host + ", path " + opt.pwd + "\n";
if (opt.seed == 0) {
opt.rerunConf += "# seed " + MslTools::intToString(opt.seed) + " (time based)\n";
} else {
opt.rerunConf += "# seed " + MslTools::intToString(opt.seed) + "\n";
}
opt.rerunConf += "########################################################\n";
opt.rerunConf += "\n";
opt.rerunConf += OP.getConfFile();
// return the Options structure
return opt;
}
Options parseOptions(int _argc, char * _argv[], Options defaults) {
/******************************************
* Pass the array of argument and the name of
* a configuration file to the ArgumentParser
* object. Then ask for the value of the argument
* and collect error and warnings.
*
* This function returns a Options structure
* defined at the head of this file
******************************************/
Options opt;
/******************************************
* Set the allowed and required options:
*
* Example of configuartion file:
*
******************************************/
vector<string> required;
vector<string> allowed;
opt.required.push_back("pdbFile");
opt.required.push_back("helicalAxisPdbFile");
opt.required.push_back("output");
opt.required.push_back("xShiftStart");
opt.required.push_back("xShiftEnd");
opt.required.push_back("xShiftSteps");
opt.required.push_back("zShiftAStart");
opt.required.push_back("zShiftAEnd");
opt.required.push_back("zShiftASteps");
opt.required.push_back("zShiftBStart");
opt.required.push_back("zShiftBEnd");
opt.required.push_back("zShiftBSteps");
opt.required.push_back("axialRotAStart");
opt.required.push_back("axialRotAEnd");
opt.required.push_back("axialRotASteps");
opt.required.push_back("axialRotBStart");
opt.required.push_back("axialRotBEnd");
opt.required.push_back("axialRotBSteps");
opt.required.push_back("crossingAngleStart");
opt.required.push_back("crossingAngleEnd");
opt.required.push_back("crossingAngleSteps");
//opt.required.push_back("rotCount");
opt.required.push_back("topFile");
opt.required.push_back("parFile");
opt.required.push_back("solvFile");
opt.required.push_back("hBondFile");
//opt.equivalent.push_back(vector<string>());
//opt.equivalent.back().push_back("v");
//opt.equivalent.back().push_back("version");
//opt.equivalent.push_back(vector<string>());
//opt.equivalent.back().push_back("h");
//opt.equivalent.back().push_back("help");
//opt.defaultArgs.push_back("configfile");
//OptionParser OP(_argc, _argv);
OptionParser OP;
OP.setShortOptionEquivalent(opt.equivalent);
OP.readArgv(_argc, _argv);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.setRequired(opt.required);
OP.setAllowed(opt.allowed);
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0) {
usage();
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
opt.errorFlag = true;
opt.errorMessages += "Cannot read configuration file " + opt.configfile + "\n";
exit(1);
}
}
/*****************************************
* VERSION AND HELP
*
* --version or -v arguments print the version number
* --help prints the usage and help
*****************************************/
opt.version = OP.getBool("version");
//if (OP.fail()) {
// opt.version = OP.getBool("v");
//}
if (opt.version) {
version();
exit(0);
}
opt.help = OP.getBool("help");
// if (OP.fail()) {
// opt.help = OP.getBool("h");
// }
if (opt.help) {
help(defaults);
exit(0);
}
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
if (!OP.checkOptions()) {
opt.errorFlag = true;
opt.OPerrors = OP.getErrors();
return opt;
}
opt.errorFlag = false;
opt.warningFlag = false;
/*****************************************
* OUTPUT DIR AND FILES
*****************************************/
/*****************************************
* CHECK THE GIVEN OPTIONS
*****************************************/
opt.errorFlag = false;
opt.warningFlag = false;
opt.pdbFile = OP.getString("pdbFile");
if (OP.fail()) {
opt.errorMessages = "pdb file not specified";
opt.errorFlag = true;
}
opt.helicalAxisPdbFile = OP.getString("helicalAxisPdbFile");
if (OP.fail()) {
opt.errorMessages = "helicalAxisPdbFile file not specified";
opt.errorFlag = true;
}
opt.output = OP.getString("output");
if (OP.fail()) {
opt.errorMessages = "output not specified";
opt.errorFlag = true;
}
opt.xShiftStart = OP.getDouble("xShiftStart");
if (OP.fail()) {
opt.errorMessages = "xShiftStart not specified";
opt.errorFlag = true;
}
opt.xShiftEnd = OP.getDouble("xShiftEnd");
if (OP.fail()) {
opt.errorMessages = "xShiftEnd not specified";
opt.errorFlag = true;
}
opt.xShiftSteps = OP.getDouble("xShiftSteps");
if (OP.fail()) {
opt.errorMessages = "xShiftSteps not specified";
opt.errorFlag = true;
}
opt.zShiftAStart = OP.getDouble("zShiftAStart");
if (OP.fail()) {
opt.errorMessages = "zShiftAStart not specified";
opt.errorFlag = true;
}
opt.zShiftAEnd = OP.getDouble("zShiftAEnd");
if (OP.fail()) {
opt.errorMessages = "zShiftAEnd not specified";
opt.errorFlag = true;
}
opt.zShiftASteps = OP.getDouble("zShiftASteps");
if (OP.fail()) {
opt.errorMessages = "zShiftASteps not specified";
opt.errorFlag = true;
}
opt.zShiftBStart = OP.getDouble("zShiftBStart");
if (OP.fail()) {
opt.errorMessages = "zShiftBStart not specified";
opt.errorFlag = true;
}
opt.zShiftBEnd = OP.getDouble("zShiftBEnd");
if (OP.fail()) {
opt.errorMessages = "zShiftBEnd not specified";
opt.errorFlag = true;
}
opt.zShiftBSteps = OP.getDouble("zShiftBSteps");
if (OP.fail()) {
opt.errorMessages = "zShiftBSteps not specified";
opt.errorFlag = true;
}
opt.axialRotAStart = OP.getDouble("axialRotAStart");
if (OP.fail()) {
opt.errorMessages = "axialRotAStart not specified";
opt.errorFlag = true;
}
opt.axialRotAEnd = OP.getDouble("axialRotAEnd");
if (OP.fail()) {
opt.errorMessages = "axialRotAEnd not specified";
opt.errorFlag = true;
}
opt.axialRotASteps = OP.getDouble("axialRotASteps");
if (OP.fail()) {
opt.errorMessages = "axialRotASteps not specified";
opt.errorFlag = true;
}
opt.axialRotBStart = OP.getDouble("axialRotBStart");
if (OP.fail()) {
opt.errorMessages = "axialRotBStart not specified";
opt.errorFlag = true;
}
opt.axialRotBEnd = OP.getDouble("axialRotBEnd");
if (OP.fail()) {
opt.errorMessages = "axialRotBEnd not specified";
opt.errorFlag = true;
}
opt.axialRotBSteps = OP.getDouble("axialRotBSteps");
if (OP.fail()) {
opt.errorMessages = "axialRotBSteps not specified";
opt.errorFlag = true;
}
opt.crossingAngleStart = OP.getDouble("crossingAngleStart");
if (OP.fail()) {
opt.errorMessages = "crossingAngleStart not specified";
opt.errorFlag = true;
}
opt.crossingAngleEnd = OP.getDouble("crossingAngleEnd");
if (OP.fail()) {
opt.errorMessages = "crossingAngleEnd not specified";
opt.errorFlag = true;
}
opt.crossingAngleSteps = OP.getDouble("crossingAngleSteps");
if (OP.fail()) {
opt.errorMessages = "crossingAngleSteps not specified";
opt.errorFlag = true;
}
opt.topFile = OP.getString("topFile");
if (OP.fail()) {
opt.errorMessages = "topFile not specified";
opt.errorFlag = true;
}
opt.parFile = OP.getString("parFile");
if (OP.fail()) {
opt.errorMessages = "parFile not specified";
opt.errorFlag = true;
}
opt.solvFile = OP.getString("solvFile");
if (OP.fail()) {
opt.errorMessages = "solvFile not specified";
opt.errorFlag = true;
}
opt.hBondFile = OP.getString("hBondFile");
if (OP.fail()) {
opt.errorMessages = "hBondFile not specified";
opt.errorFlag = true;
}
// return the Options structure
return opt;
}