Options setupOptions(int theArgc, char * theArgv[]){
// Create the options
Options opt;
// Parse the options
OptionParser OP;
OP.readArgv(theArgc, theArgv);
OP.setRequired(opt.required);
OP.setAllowed(opt.optional);
// OP.setShortOptionEquivalent(opt.equivalent);
OP.setDefaultArguments(opt.defaultArgs); // the default argument is the --configfile option
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0){
cout << "Usage:" << endl;
cout << endl;
cout << "mutate CONF\n";
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
string errorMessages = "Cannot read configuration file " + opt.configfile + "\n";
cerr << "ERROR 1111 "<<errorMessages<<endl;
}
}
if (OP.getBool("help")){
cout << "# PDB "<<endl;
cout << "pdb foo.pdb"<<endl<<endl;
cout << "# Output pdb" <<endl;
cout << "outpdb /tmp/out"<<endl<<endl;
cout << "# Rotamer library"<<endl;
cout << "rotlib /library/rotlib/balanced/rotlib-balanced-200.txt"<<endl<<endl;
cout << "# Position"<<endl;
cout << "position B,2"<<endl;
cout << "# New residue"<<endl;
cout << "newRes PHE"<<endl<<endl;
cout << "# Number of rotamers"<<endl;
cout << "numRot 10"<<endl<<endl;
exit(1);
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 no pdb file"<<endl;
}
opt.rotlib = OP.getString("rotlib");
if (OP.fail()){
cerr << "ERROR 1111 no rotlib file"<<endl;
exit(1111);
}
opt.position = OP.getString("position");
if (OP.fail()){
cerr << "ERROR 1111 no position"<<endl;
exit(1111);
}
opt.newRes = OP.getString("newRes");
if (OP.fail()){
cerr << "ERROR 1111 no new residue (newRes)"<<endl;
exit(1111);
}
opt.outpdb = OP.getString("outpdb");
if (OP.fail()){
opt.outpdb = "/tmp/out";
cerr << "WARNING no outpdb file specifed will write to: "<<opt.outpdb<<endl;
}
opt.numRot = OP.getInt("numRot");
if (OP.fail()){
cerr << "numRot defaults to 10"<<endl;
opt.numRot = 10;
}
opt.debug = OP.getBool("debug");
if (OP.fail()){
opt.debug = false;
}
return opt;
}
Options setupOptions(int theArgc, char * theArgv[]){
Options opt;
OptionParser OP;
OP.setRequired(opt.required);
OP.setAllowed(opt.optional);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
OP.readArgv(theArgc, theArgv);
if (OP.countOptions() == 0){
cout << "Usage:" << endl;
cout << endl;
cout << "addSequenceConservation --pdb PDB --fasta FASTA_FILE --refCounts REF_COUNTS_FILE\n";
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
cerr << "ERROR couldn't read : "<<opt.configfile<<endl;
exit(1);
}
}
opt.fasta = OP.getString("fasta");
if (OP.fail()){
cerr << "ERROR 1111 fasta not specified.\n";
exit(1111);
}
opt.refSeqName = OP.getString("refSeqName");
if (OP.fail()){
cerr << "WARNING 1111 refSeqName not specified.\n";
opt.refSeqName = "";
}
opt.seq = OP.getString("seq");
if (OP.fail()){
opt.seq = "";
}
if (opt.seq == ""){
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 pdb not specified.\n";
exit(1111);
}
opt.refAACounts = OP.getString("refAACounts");
if (OP.fail()){
cerr << "ERROR 1111 refAACounts not specified.\n";
exit(1111);
}
opt.sel = OP.getString("sel");
if (OP.fail()){
cerr << "ERROR 1111 sel not specified.\n";
exit(1111);
}
opt.refSeqOffset = OP.getInt("refSeqOffset");
if (OP.fail()){
cerr << "WARNING 1111 refSeqOffset not specified.\n";
opt.refSeqOffset = 0;
}
opt.freq = OP.getBool("freq");
if (OP.fail()){
opt.freq = false;
}
opt.applyToAllChains = OP.getBool("applyToAllChains");
if (OP.fail()){
opt.applyToAllChains = false;
}
opt.regexForFasta = OP.getString("regexForFasta");
if (OP.fail()){
opt.regexForFasta = "";
}
opt.outPdb = OP.getString("outPdb");
if (OP.fail()){
opt.outPdb = MslTools::stringf("%s_seqcons.pdb",MslTools::getFileName(opt.pdb).c_str());
cerr << "WARNING --outPdb is set to : "<<opt.outPdb<<endl;
}
}
return opt;
}
Options setupOptions(int theArgc, char * theArgv[]){
// Create the options
Options opt;
// Parse the options
OptionParser OP;
OP.readArgv(theArgc, theArgv);
OP.setRequired(opt.required);
OP.setDefaultArguments(opt.defaultArgs); // the default argument is the --configfile option
if (OP.countOptions() == 0){
cout << "Usage: designCheck " << endl;
cout << endl;
cout << "\n";
cout << "pdb PDB\n";
cout << endl;
exit(0);
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 no pdb specified."<<endl;
exit(1111);
}
opt.prosite = OP.getString("prosite");
if (OP.fail()){
opt.prosite = SYSENV.getEnv("MSL_PROSITE");
if (opt.prosite == "UNDEF"){
cerr << "ERROR 1111 prosite undefined"<<endl;
exit(1111);
} else {
cerr << "WARNING prosite defaulted to: "<<opt.prosite<<endl;
}
}
opt.ref = OP.getString("ref");
opt.topfile = OP.getString("topfile");
if (OP.fail()){
opt.topfile = SYSENV.getEnv("MSL_CHARMM_TOP");
if (opt.topfile == "UNDEF"){
cerr << "ERROR 1111 topfile not defined\n";
exit(1111);
} else {
cerr << "WARNING topfile defaulted to: "<<opt.topfile<<endl;
}
}
opt.parfile = OP.getString("parfile");
if (OP.fail()){
opt.parfile = SYSENV.getEnv("MSL_CHARMM_PAR");
if (opt.parfile == "UNDEF"){
cerr << "ERROR 1111 parfile not defined\n";
exit(1111);
}else {
cerr << "WARNING parfile defaulted to: "<<opt.parfile<<endl;
}
}
opt.hbondfile = OP.getString("hbondfile");
if (OP.fail()){
opt.hbondfile = SYSENV.getEnv("MSL_HBOND_PAR");
if (opt.hbondfile == "UNDEF"){
cerr << "WARNING 1111 hbondfile not defined - not building hydrogen bond interactions\n";
opt.hbondfile = "";
}else {
cerr << "WARNING hbondfile defaulted to: "<<opt.hbondfile<<endl;
}
}
opt.baselinefile = OP.getString("baselinefile");
if (OP.fail()){
opt.baselinefile = "";
cerr << "WARNING no baselinefile specified " <<endl;
}
opt.dielectric = OP.getDouble("dielectric");
if (OP.fail()){
opt.dielectric = 80;
}
opt.distanceDependentElectrostatics = OP.getBool("distanceDependentElectrostatics");
if (OP.fail()){
opt.distanceDependentElectrostatics = false;
}
opt.vdwScale = OP.getDouble("vdwScale");
if (OP.fail()){
opt.vdwScale = 1.0;
}
opt.cuton = OP.getDouble("cuton");
if (OP.fail()){
opt.cuton = 9.0;
}
opt.cutoff = OP.getDouble("cutoff");
if (OP.fail()){
opt.cutoff = 15.0;
}
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("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("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;
}
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 << "multiSearchDM --inputPDB PDB --pdbList LIST --searchCriteria SEARCH_STRING --windowSize NUM [ --numberOfIterations NUM --allowIntraChainCompare --likenessTolernace TOL --alignPdbs --debug ]\n";
cout << endl<<"\tsearchCriteria can be:\n";
cout << "\tstandard - sum of the diff. for every item between two MatrixWindows.\n";
cout << "\tdiagnol - sum of the diff. for the diagnol (top left-bottom right) between two MatrixWindows.\n";
cout << "\tdoubleDiagnol - sum of the diff. for both diagnols between two MatrixWindows.\n";
cout << "\tminDistance - sum of the diff. between the minimal distance for each row,col of the given MatrixWindows.\n";
cout << "\tminDistanceRow - sum of the diff. between the minimal distance for each row of the given MatrixWindows.\n";
exit(0);
}
opt.inputPDB = OP.getString("inputPDB");
if (OP.fail()){
cerr << "ERROR 1111 inputPDB not specified.\n";
exit(1111);
}
opt.pdbList = OP.getString("pdbList");
if (OP.fail()){
cerr << "ERROR 1111 pdbList not specified.\n";
exit(1111);
}
opt.searchCriteria = OP.getString("searchCriteria");
if (OP.fail()){
cerr <<"ERROR 1111 searchCriteria not specified."<<endl;
exit(1111);
}
opt.windowSize = OP.getInt("windowSize");
if (OP.fail()){
cerr << "ERROR 1111 windowSize not specified."<<endl;
exit(1111);
}
opt.numberOfIterations = OP.getInt("numberOfIterations");
if (OP.fail()){
opt.numberOfIterations = 1;
}
opt.intraChainCompare = OP.getBool("allowIntraChainCompare");
if (OP.fail()){
opt.intraChainCompare = false;
}
opt.likenessTolerance = OP.getDouble("likenessTolerance");
if (OP.fail()){
opt.likenessTolerance = MslTools::doubleMax;
}
opt.alignPdbs = OP.getBool("alignPdbs");
if (OP.fail()){
opt.alignPdbs = false;
}
opt.rmsdTol = OP.getDouble("rmsdTol");
if (OP.fail()) {
opt.rmsdTol = 2.0;
}
opt.debug = OP.getBool("debug");
if (OP.fail()){
opt.debug = false;
}
return opt;
}
Options setupOptions(int theArgc, char * theArgv[]){
Options opt;
OptionParser OP;
OP.setRequired(opt.required);
OP.setAllowed(opt.optional);
OP.setDefaultArguments(opt.defaultArgs); // a pdb file value can be given as a default argument without the --pdbfile option
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
OP.readArgv(theArgc, theArgv);
if (OP.countOptions() == 0){
cout << "Usage:" << endl;
cout << endl;
cout << "resurfaceSaltBridges --pdb PDB\n";
cout << "\nprogram options: "<<endl;
for (uint i = 0; i < opt.required.size();i++){
cout <<"R --"<<opt.required[i]<<" "<<endl;
}
cout <<endl;
for (uint i = 0; i < opt.optional.size();i++){
cout <<"O --"<<opt.optional[i]<<" "<<endl;
}
cout << endl;
exit(0);
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 pdb not specified.\n";
exit(1111);
}
opt.sb_prop_table = OP.getString("sb_prop_table");
if (OP.fail()){
opt.sb_prop_table = SYSENV.getEnv("MSL_SB_PROP_TABLE");
cout << "SB_PROP_TABLE: "<<opt.sb_prop_table<<endl;
if (opt.sb_prop_table == "UNDEF"){
std::cerr << "ERROR 1111 no sb_prop_table specified."<<std::endl;
exit(1111);
} else {
if (MslTools::fileExists(opt.sb_prop_table)){
cerr << "WARNING sb_prop_table defaulted to: "<<opt.sb_prop_table<<endl;
} else {
std::cerr << "ERROR 1111 no sb_prop_table specified and couldn't find default one: "<<opt.sb_prop_table<<std::endl;
exit(1111);
}
}
}
opt.topfile = OP.getString("topfile");
if (OP.fail()){
opt.topfile = SYSENV.getEnv("MSL_CHARMM_TOP");
cerr << "WARNING: charmmtopfile not specified, using " << opt.topfile << "\n";
}
if (!MslTools::fileExists(opt.topfile)){
cerr << "ERROR 1111 CHARMM TOPFILE DOESN'T EXIST: "<<opt.topfile<<endl;
exit(1111);
}
opt.parfile = OP.getString("parfile");
if (OP.fail()){
opt.parfile = SYSENV.getEnv("MSL_CHARMM_PAR");
cerr <<"WARNING charmmparfile not specified, using " << opt.parfile << "\n";
}
if (!MslTools::fileExists(opt.parfile)){
cerr << "ERROR 1111 CHARMM parFILE DOESN'T EXIST: "<<opt.parfile<<endl;
exit(1111);
}
opt.rotlib = OP.getString("rotlib");
if (OP.fail()){
opt.rotlib = SYSENV.getEnv("MSL_ROTLIB");
cerr << "WARNING rotlib not specified, using " << opt.rotlib << "\n";
}
if (!MslTools::fileExists(opt.rotlib)){
cerr << "ERROR 1111 rotamer library DOESN'T EXIST: "<<opt.rotlib<<endl;
exit(1111);
}
opt.numStructuralModels = OP.getInt("numStructuralModels");
if (OP.fail()){
opt.numStructuralModels = 10;
}
opt.numSequenceModels = OP.getInt("numSequenceModels");
if (OP.fail()){
opt.numSequenceModels = 30;
}
opt.numMCcycles = OP.getInt("numMCcycles");
if (OP.fail()){
opt.numMCcycles = 100;
}
opt.startMCtemp = OP.getDouble("startMCtemp");
if (OP.fail()){
opt.startMCtemp = 100.0;
}
opt.endMCtemp = OP.getDouble("endMCtemp");
if (OP.fail()){
opt.endMCtemp = 1.0;
}
opt.scoreOnly = OP.getBool("scoreOnly");
opt.selectPositions = OP.getString("selectPositions");
if (OP.fail()){
opt.selectPositions = "";
}
opt.percentSasa = OP.getDouble("percentSasa");
if (OP.fail()){
opt.percentSasa = 0.4;
}
MSLOUT.stream() << "Options:\n"<<OP<<endl;
return opt;
}
Options setupOptions(int theArgc, char * theArgv[]){
// Create the options
Options opt;
// Parse the options
OptionParser OP;
OP.readArgv(theArgc, theArgv);
OP.setRequired(opt.required);
OP.setAllowed(opt.optional);
// OP.setShortOptionEquivalent(opt.equivalent);
OP.setDefaultArguments(opt.defaultArgs); // the default argument is the --configfile option
OP.autoExtendOptions(); // if you give option "solvat" it will be autocompleted to "solvationfile"
if (OP.countOptions() == 0){
cout << "Usage:" << endl;
cout << endl;
cout << "fillInSideChains CONF\n";
exit(0);
}
opt.configfile = OP.getString("configfile");
if (opt.configfile != "") {
OP.readFile(opt.configfile);
if (OP.fail()) {
string errorMessages = "Cannot read configuration file " + opt.configfile + "\n";
cerr << "ERROR 1111 "<<errorMessages<<endl;
}
}
if (OP.getBool("help")){
cout << "# PDB "<<endl;
cout << "pdb foo.pdb"<<endl<<endl;
cout << "# Output pdb" <<endl;
cout << "outpdb /tmp/out.pdb"<<endl<<endl;
cout << "# Rotamer library"<<endl;
cout << "rotlib /library/rotlib/balanced/rotlib-balanced-200.txt"<<endl<<endl;
cout << "# CHARMM Topology"<<endl;
cout << "topfile /library/charmmTopPar/top_all27_prot_lipid.inp"<<endl<<endl;
cout << "# CHARMM Parameter"<<endl;
cout << "parfile /library/charmmTopPar/par_all27_prot_lipid.inp"<<endl<<endl;
exit(1);
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 no pdb file"<<endl;
}
opt.rotlib = OP.getString("rotlib");
if (OP.fail()){
cerr << "ERROR 1111 no rotlib file"<<endl;
}
opt.topfile = OP.getString("topfile");
if (OP.fail()){
cerr << "ERROR 1111 no topfile file"<<endl;
}
opt.parfile = OP.getString("parfile");
if (OP.fail()){
cerr << "ERROR 1111 no parfile file"<<endl;
}
opt.outpdb = OP.getString("outpdb");
if (OP.fail()){
opt.outpdb = "/tmp/out.pdb";
cerr << "WARNING no outpdb file specifed will write to: "<<opt.outpdb<<endl;
}
opt.debug = OP.getBool("debug");
if (OP.fail()){
opt.debug = false;
}
return opt;
}