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: getSphericalCoordinates conf" << endl;
cout << endl;
cout << "\n";
cout << "pdb PDB\n";
cout << endl;
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;
}
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 no pdb specified."<<endl;
exit(1111);
}
opt.resnum = OP.getInt("resnum");
if (OP.fail()){
cerr << "ERRROR 1111 no resnum\n";
exit(1111);
}
opt.chain = OP.getString("chain");
if (OP.fail()){
cerr << "ERRROR 1111 no chain\n";
exit(1111);
}
opt.negativeRes = OP.getBool("neg");
if (OP.fail()){
opt.negativeRes = false;
}
if (opt.negativeRes) {
opt.resnum = -1*opt.resnum;
}
opt.printFrames = OP.getBool("printFrames");
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 << "pdb PDB"<<endl;
exit(0);
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 no pdb file"<<endl;
}
opt.tol = OP.getDouble("tol");
if (OP.fail()){
opt.tol = 1.88;
cerr << "WARNING tol set to default: "<<opt.tol<<endl;
}
opt.interfaceOnly = OP.getBool("interfaceOnly");
if (OP.fail()){
opt.interfaceOnly = false;
}
opt.atomPair = OP.getString("atomPair");
if (OP.fail()){
opt.atomPair = "";
}
opt.elementPair = OP.getString("elementPair");
if (OP.fail()){
opt.elementPair = "";
}
opt.printAll = OP.getBool("printAll");
if (OP.fail()){
opt.printAll = false;
}
return opt;
}
int main(int argc, char *argv[]){
vector<string> required;
required.push_back("flatfile");
vector<string> optional;
optional.push_back("reread");
optional.push_back("outfile");
OptionParser OP;
OP.readArgv(argc,argv);
OP.setRequired(required);
OP.setAllowed(optional);
string flatfile = OP.getString("flatfile");
if (OP.fail()){
cout << "Usage: ./testMolecularInterfaceDatabase --flatfile FLAT.mid [ --outfile mid.ckpt --reread --archive text ]\n";
exit(0);
}
string outfile = OP.getString("outfile");
if (OP.fail()){
outfile = "mid.ckpt";
}
string archive = OP.getString("archive");
if (OP.fail()){
archive = "text";
}
// Create from flat file
MIDReader mread;
mread.open(flatfile);
mread.read(archive);
MoleculeInterfaceDatabase &mid = mread.getMoleculeInterfaceDatabase();
cout << "MID size: "<<mid.size()<<endl;
// Write out to binary
mid.setArchiveType(archive);
mid.save_checkpoint(outfile);
// Re-read if option set..
bool reread = OP.getBool("reread");
if (!OP.fail() && reread){
cout << "Re-reading binary MolecularInterfaceDatabase.\n";
Timer t;
double start = t.getWallTime();
MoleculeInterfaceDatabase mid2;
mid2.setArchiveType(archive);
mid2.load_checkpoint(outfile);
cout << "MID2 size: "<<mid2.size()<<" read in "<<(t.getWallTime() - start)<<" seconds."<<endl;
}
}
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 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 << "querySeqCons--fasta FASTA_FILE --seq 'NAME,STARTPOS,ENDPOS' \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.refAACounts = OP.getString("refAACounts");
if (OP.fail()){
opt.refAACounts = "";
}
opt.logodds = OP.getBool("logodds");
if (OP.fail()){
opt.logodds = false;
}
opt.seq = OP.getString("seq");
if (OP.fail()){
opt.seq = "";
}
if (opt.seq == ""){
opt.refSeqName = OP.getString("refSeqName");
if (OP.fail()){
cerr << "WARNING 1111 refSeqName not specified.\n";
opt.refSeqName = "";
}
opt.pdb = OP.getString("pdb");
if (OP.fail()){
cerr << "ERROR 1111 pdb 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.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;
}
string type = OP.getString("type");
if (OP.fail()){
cerr << "WARNING type set to default: freq"<<endl;
opt.valueType = Options::freq;
} else {
map<string,int>::iterator it = opt.valueMap.find(type);
if (it == opt.valueMap.end()){
cerr << "ERROR 1111 type '"<<type<<"' not found."<<endl;
exit(1111);
} else {
opt.valueType = opt.valueMap[type];
}
}
}
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 << "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[]){
// 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 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 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;
}