/* * File: CheckEnvAndGetMode.cpp * Author: flong * * Created on January 10, 2013, 5:12 PM */ #include "CheckEnvAndGetMode.h" namespace LIBMOL { CheckEnvAndGetMode::CheckEnvAndGetMode():workMode(0) { // Currently CCP4 suite is the only requited thing char * pClibdMon = std::getenv("CLIBD_MON"); if (pClibdMon !=NULL) { if (envVars.find("CLIBD_MON") !=envVars.end()) { envVars["CLIBD_MON"].clear(); } envVars["CLIBD_MON"].append(pClibdMon); } else { std::cerr << "You need to setup CCP4 suite first " << std::endl; exit(1); } } CheckEnvAndGetMode::CheckEnvAndGetMode(int numArg, char** ArgVars) :workMode(0) { // Currently CCP4 suite is the only requited thing char * pClibdMon = std::getenv("CLIBD_MON"); if (pClibdMon !=NULL) { if (envVars.find("CLIBD_MON") !=envVars.end()) { envVars["CLIBD_MON"].clear(); } envVars["CLIBD_MON"].append(pClibdMon) ; } else { std::cerr << "You need to setup CCP4 suite first " << std::endl; exit(1); } /* char * pLibMon = std::getenv("LIBMOL_ROOT"); if (pLibMon !=NULL) { if (envVars.find("LIBMOL_ROOT") !=envVars.end()) { envVars["LIBMOL_ROOT"].clear(); } envVars["LIBMOL_ROOT"].append(pLibMon); } else { std::cerr << "You need to setup env variable $LIBMOL_ROOT first " << std::endl; exit(1); } */ // do not need the following declarations, put here in case...... //extern char *optarg; // extern int optind, opterr, optopt; // opterr = 0; if (numArg < 5) { // temporarily interface std::cerr << "Command line syntax: " << std::endl << "libmol -c CIFFILE -r monomer_name -o outputRestraintFile " << std::endl; exit(1); } int c, index; while ((c = getopt (numArg, ArgVars, "a:b:c:d:i:j:k:l:m:n:o:p:q:r:s:t:u:v:w:x:y:z:A:C:D:H:L:M:N:O:P:Q:R:S:T:U:W:X:Y:Z:1:2:3:4:")) != -1) { switch (c) { case 'a': IOEntries["CodBondAngleFileName"] = optarg; break; case 'b': IOEntries["inCifNameB"] = optarg; break; case 'c': IOEntries["inCifName"] = optarg; //std::cout << "Input cif file is : " << IOEntries["inCifName"] // << std::endl; break; case 'd': IOEntries["CodBondFileName"] = optarg; break; case 'i': IOEntries["inSmiName"] = optarg; // std::cout << "The input files are in " // << IOEntries["inFileDir"] << std::endl; break; case 'j': IOEntries["inFileDir"] = optarg; // std::cout << "The input files are in " // << IOEntries["inFileDir"] << std::endl; break; case 'k': IOEntries["inMol2Name"] = optarg; //std::cout << "The input Mol2 files are in " // << IOEntries["inMol2Name"] << std::endl; break; case 'l': IOEntries["enableNeu"] = optarg; // std::cout << "The input files are in " // << IOEntries["inFileDir"] << std::endl; break; case 'm': IOEntries["molGen"] = optarg; // std::cout << "The input files are in " // << IOEntries["inFileDir"] << std::endl; break; case 'n': IOEntries["NBDepth"] = optarg; // std::cout << "The input files are in " // << IOEntries["inFileDir"] << std::endl; break; case 'o': IOEntries["userOutName"] = optarg; // std::cout << "output root input " << optarg << std::endl; break; case 'p': IOEntries["inPdbName"] = optarg; //std::cout << "Input PDB file is : " // << IOEntries["inPdbName"] << std::endl; break; case 'q': IOEntries["CoordToDict"] = optarg; // std::cout << "Cooord to Dict " // << IOEntries["inFileDir"] << std::endl; break; case 'r': IOEntries["monoRootName"] = optarg; //if (IOEntries["monoRootName"].size() > 3) //{ // IOEntries["monoRootName"] = IOEntries["monoRootName"].substr(0,3); //} //else if (IOEntries["monoRootName"].size() > 3) //{ // IOEntries["monoRootName"] ="UNL"; //} //std::cout << "Monomer root name is : " // << IOEntries["monoRootName"] << std::endl; break; case 's': IOEntries["inSdfName"] = optarg; //std::cout << "Monomer root name is : " // << IOEntries["monoRootName"] << std::endl; break; case 't': IOEntries["tabGen"] = optarg; std::cout << "Table generator mode : " << IOEntries["tabGen"] << std::endl; break; case 'u': IOEntries["inMC"] = optarg; std::cout << "inPut MC : " << IOEntries["inMC"] << std::endl; break; case 'w': IOEntries["BandC"] = optarg; break; case 'x': IOEntries["KandC"] = optarg; break; case 'y': IOEntries["transCoords"] = optarg; StrLower(IOEntries["transCoords"]); break; case 'z': IOEntries["transAngles"] = optarg; StrLower(IOEntries["transAngles"]); break; case 'A': IOEntries["AtomTypeOutName"] = optarg; break; case 'C': IOEntries["PeptidesOnly"] = optarg; break; case 'D': IOEntries["libMolTabDir"] = optarg; //std::cout << "Libmol table directory is : " // << IOEntries["libMolTabDir"] // << std::endl; break; case 'H': IOEntries["HBondDetect"] = optarg; break; case 'L': IOEntries["MetalRange"] = optarg; break; case 'M': IOEntries["MetalEnable"] = optarg; break; case 'N': IOEntries["OrgOnlyEnable"] = optarg; break; case 'O': IOEntries["NoGeoOpt"] = optarg; StrLower(IOEntries["NoGeoOpt"]); break; case 'P': IOEntries["UserParaFile"] = optarg; std::cout << "The param file from the user : " << IOEntries["UserParaFile"] << std::endl; break; case 'Q': IOEntries["MolGenParaFile"] = optarg; std::cout << "The param file for MolGen : " << IOEntries["MolGenParaFile"] << std::endl; break; case 'R': IOEntries["addProtCol"] = optarg; std::cout << "Job to add proton distances : " << IOEntries["addProtCol"] << std::endl; break; case 'S': IOEntries["codAtomStr"] = optarg; //std::cout << "COD atom types are output to : " // << IOEntries["AtomTypeOutName"] << std::endl; break; case 'T': IOEntries["GraphTests"] = optarg; StrLower(IOEntries["GraphTests"]); //std::cout << "COD atom types are output to : " // << IOEntries["AtomTypeOutName"] << std::endl; break; case 'U': IOEntries["TempTests"] = optarg; std::cout << "You are in temporally test mode " << IOEntries["TempTests"] << std::endl; break; case 'W': IOEntries["modifiedPl"] = optarg; std::cout << "Atoms attached to a plane removed : " << IOEntries["modifiedPl"] << std::endl; break; case 'X': IOEntries["Type1"] = optarg; std::cout << "The file containing atom type set A is " << IOEntries["Type1"] << std::endl; break; case 'Y': IOEntries["Type2"] = optarg; std::cout << "The file containing atom type set B is " << IOEntries["Type1"] << std::endl; break; case 'Z': IOEntries["HUMO"] = optarg; break; case '1': IOEntries["uBS"] = optarg; std::cout << "Upper bound for b " << IOEntries["uBS"] << std::endl; break; case '2': IOEntries["lBS"] = optarg; std::cout << "low bound for b " << IOEntries["lBS"] << std::endl; break; case '3': IOEntries["uAS"] = optarg; std::cout << "Upper bound for a " << IOEntries["uAS"] << std::endl; break; case '4': IOEntries["lAS"] = optarg; std::cout << "low bound for a " << IOEntries["lAS"] << std::endl; break; case '?': if (std::isprint(optopt)) { std::cerr << "command line arguments are not match at " << char(optopt) << std::endl; } else { std::cerr << "Unknown option character: " << optopt << std::endl; } default: continue; } } // Non-option arguments remained for (index = optind; index < numArg; index++) { std::cout << "Non-option argument " << ArgVars[index] << std::endl; } if(IOEntries.find("NBDepth") == IOEntries.end()) { IOEntries["NBDepth"] = "1"; } std::map::iterator iKeyFinder; iKeyFinder = IOEntries.find("monoRootName"); if (iKeyFinder ==IOEntries.end()) { IOEntries["monoRootName"] ="UNL"; } else { if (IOEntries["monoRootName"].empty()) { IOEntries["monoRootName"] ="UNL"; } } setBandASiga(); SetWorkMode(); } CheckEnvAndGetMode::~CheckEnvAndGetMode() { } void CheckEnvAndGetMode::parseArgs(int numArg, char** argVars) { static int verbose_flag; static struct option longOptions[] = { /* These options set a flag. */ {"verbose", noArgument, &verbose_flag, 1}, {"brief", noArgument, &verbose_flag, 0}, /* These options don't set a flag. We distinguish them by their indices. {"add", noArgument, 0, 'a'}, */ {"help", noArgument, 0, 'h'}, /* input files, keys are self-explained */ {"cifin", optionalArgument, 0, 'c'}, {"pdbin", optionalArgument, 0, 'p'}, {"sdfin", optionalArgument, 0, 'd'}, {"smiin", optionalArgument, 0, 'i'}, // the input smile string /* output files, output pdb has the same name * root as that of output cif */ {"cifout", optionalArgument, 0, 'o'}, /* monomer name in output files */ {"monout", optionalArgument, 0, 'r'}, {"codatm", optionalArgument, 0, 'A'}, {0, 0, 0, 0} }; int c=0; while (c !=-1) { int optIndex=0; c = getopt_long(numArg, argVars, "c:d:h:i:o:p:r:A:", longOptions, &optIndex); switch (c) { case 'h': printManual(); break; case 'c': IOEntries["inCifName"] = optarg; break; case 'p': IOEntries["inPdbName"] = optarg; break; case 'd': IOEntries["inSdfName"] = optarg; break; case 'i': IOEntries["inSmiStr"] = optarg; break; case 'o': IOEntries["userOutName"] = optarg; //IOEntries["outCifName"] = optarg; // should be that break; case 'r': IOEntries["monoRootName"] = optarg; break; case 'A': IOEntries["AtomTypeOutName"] = optarg; break; case '?': if (std::isprint(optopt)) { std::cerr << "command line arguments are not match at " << char(optopt) << std::endl; } else { std::cerr << "Unknown option character: " << optopt << std::endl; } default: std::abort(); } } } void CheckEnvAndGetMode::printManual() { } void CheckEnvAndGetMode::setBandASiga() { if (IOEntries.find("uBS")==IOEntries.end()) { IOEntries["uBS"] = "0.02"; } if (IOEntries.find("lBS")==IOEntries.end()) { IOEntries["lBS"] = "0.01"; } if (IOEntries.find("uAS")==IOEntries.end()) { IOEntries["uAS"] = "3.00"; } if (IOEntries.find("lAS")==IOEntries.end()) { IOEntries["lAS"] = "1.5"; } upperBondSig = StrToReal(IOEntries["uBS"]); lowBondSig = StrToReal(IOEntries["lBS"]); upperAngleSig = StrToReal(IOEntries["uAS"]); lowAngleSig = StrToReal(IOEntries["lAS"]); } void CheckEnvAndGetMode::SetWorkMode() { if (IOEntries.find("TempTests") !=IOEntries.end()) { if (IOEntries.find("inCifName")!=IOEntries.end()) { workMode = 1001; } else if (IOEntries.find("inCifNameB")!=IOEntries.end()) { workMode = 1002; } else { workMode = 1000; } } else if (IOEntries.find("GraphTests") !=IOEntries.end()) { workMode = 900; } else if (IOEntries.find("CoordToDict") !=IOEntries.end()) { workMode = 350; } else if (IOEntries.find("HUMO")!=IOEntries.end()) { if (IOEntries.find("inCifName")!=IOEntries.end()) { workMode = 910; } else if (IOEntries.find("inCifNameB")!=IOEntries.end()) { workMode = 311; } } else if (IOEntries.find("MetalEnable")!=IOEntries.end()) { if (IOEntries.find("inCifName")!=IOEntries.end()) { workMode = 912; } else if (IOEntries.find("inCifNameB")!=IOEntries.end()) { if (IOEntries.find("MetalRange")!=IOEntries.end()) { workMode = 313; } else { workMode = 312; } } } else if (IOEntries.find("OrgOnlyEnable")!=IOEntries.end()) { if (IOEntries.find("inCifNameB")!=IOEntries.end()) { if (IOEntries.find("UserParaFile")!=IOEntries.end()) { workMode = 314; } } } else if (IOEntries.find("HBondDetect")!=IOEntries.end()) { if (IOEntries.find("inCifNameB")!=IOEntries.end()) { workMode = 315; } } else if (IOEntries.find("addProtCol") != IOEntries.end() ) { workMode = 800; } else if (IOEntries.find("KandC") !=IOEntries.end()) { workMode = 920; } else if (IOEntries.find("BandC") !=IOEntries.end()) { workMode = 930; } else if ( IOEntries.find("inCifName")!=IOEntries.end() ) { if (!IOEntries["inCifName"].empty()) { if (IOEntries.find("molGen") != IOEntries.end()) { workMode =32; } else if ( IOEntries.find("inPdbName")!=IOEntries.end()) { if (IOEntries.find("transCoords") != IOEntries.end()) { if (!IOEntries["inPdbName"].empty() && IOEntries["transCoords"] =="y" ) { // This mode read the input cif file and PDB file // replace the coordinates in the cif with the corresponding ones in the PDB // which have been refined workMode = 21; std::cout << "Coords transforming mode " << std::endl; } else { std::cout << "You need to enter a output PDB name " << std::endl; } } if (IOEntries.find("transAngles") != IOEntries.end()) { if (!IOEntries["inPdbName"].empty() && IOEntries["transAngles"] =="y" ) { // This mode read the input cif file and PDB file // replace the angles in the cif with the ones calculated from PDB workMode = 22; } else { std::cout << "You need to enter a output PDB name " << std::endl; } } } else { if ( IOEntries.find("AtomTypeOutName")!=IOEntries.end()) { if (!IOEntries["AtomTypeOutName"].empty()) { // This mode outputs COD atom type only workMode =41; } else { std::cout << "You need to enter the name of the output file containing COD atom type" << std::endl; } } else { // This is default restraint generation mode workMode = 11; if (IOEntries.find("userOutName") ==IOEntries.end()) { IOEntries["userOutName"] = "libmol.out"; } } } } } else if (IOEntries.find("inCifNameB") !=IOEntries.end()) { if (IOEntries.find("molGen") != IOEntries.end()) { // This mode takes a general cif file and generate a whole molecule // and unique bonds and angles within the molecule if (IOEntries.find("enableNeu") != IOEntries.end()) { workMode = 3111; } else { workMode = 31; } } else if (IOEntries.find("tabGen") != IOEntries.end()) { workMode = 33; } else if ( IOEntries.find("AtomTypeOutName")!=IOEntries.end()) { if (!IOEntries["AtomTypeOutName"].empty()) { // This mode outputs COD atom type only workMode =42; } else { std::cout << "You need to enter the name of" << " the output file containing atom types" << std::endl; } } } else if (IOEntries.find("inSdfName") !=IOEntries.end()) { if(IOEntries.find("AtomTypeOutName") !=IOEntries.end()) { if (!IOEntries["AtomTypeOutName"].empty()) { // This mode outputs COD atom type only workMode =43; } } else { workMode =13; } } else if (IOEntries.find("inSmiName") !=IOEntries.end()) { if (IOEntries.find("monoRootName") != IOEntries.end()) { workMode =12; } else if(IOEntries.find("AtomTypeOutName") !=IOEntries.end()) { if (!IOEntries["AtomTypeOutName"].empty()) { // This mode outputs COD atom type only workMode =42; } } } else if (IOEntries.find("inMol2Name") !=IOEntries.end()) { if (IOEntries.find("monoRootName") != IOEntries.end()) { workMode =14; } else if(IOEntries.find("AtomTypeOutName") !=IOEntries.end()) { if (!IOEntries["AtomTypeOutName"].empty()) { // This mode outputs COD atom type only workMode =44; } } } else { std::cout << "what is the input file ? " << std::endl; } printVarAndMode(); } void CheckEnvAndGetMode::printVarAndMode() { std::cout << "||=====================Job description====================================||" << std::endl; if (workMode==11 || workMode==12) { std::cout << "You will get an output cif file for a list of dictionary restraints" << std::endl << "based on the input cif file" << std::endl << "Your input cif file : " << IOEntries["inCifName"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output dictionary file(cif) : " << IOEntries["userOutName"] << std::endl; } else if (workMode==12) { std::cout << "You will get an output cif file for a list of dictionary restraints" << std::endl << "based on the input SMILE file" << std::endl << "Your input SMILE file : " << IOEntries["inSmiStr"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output dictionary file(cif) : " << IOEntries["userOutName"] << std::endl; } else if (workMode==13) { std::cout << "You will get an output cif file for a list of dictionary restraints" << std::endl << "based on the input MOL/SDF file" << std::endl << "Your input MOL/SDF file : " << IOEntries["inSdfName"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output dictionary file(cif) : " << IOEntries["userOutName"] << std::endl; } else if (workMode==2) { std::cout << "Your job is get a full library description based on input cif and PDB files " << std::endl << "Your input cif file : " << IOEntries["inCifName"] << std::endl << "Your input PDB file : " << IOEntries["inPdbName"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output dictionary file(cif) : " << IOEntries["userOutName"] << std::endl; } else if (workMode==21) { std::cout << "The current job is coordinate transform in the dictionary file " << std::endl; } else if (workMode==31 || workMode==311 || workMode==312 || workMode==32) { std::cout << "Your job is to deduce values of bond and bond-angle" << " and build molecules from your input cif file " << std::endl << "Your input cif file : " << IOEntries["inCifNameB"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output dictionary file(cif) : " << IOEntries["userOutName"] << std::endl; if (workMode==311) { std::cout << "Huckel's MO will be used in the calculations to " << "decide aromaticity in bonds " << std::endl; } else if (workMode == 312) { std::cout << "The job will handle with atoms of metal elements" << std::endl; } } else if (workMode==41) { std::cout << "Your job is to look at atom types of COD format" << std::endl << "for atoms in the input cif file" << std::endl << "Your input cif file : " << IOEntries["inCifName"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output atom type file(txt) : " << IOEntries["AtomTypeOutName"] << std::endl; } else if (workMode==42) { std::cout << "Your job is to look at atom types of COD format" << std::endl << "for atoms in the input mol/sdf file" << std::endl << "Your input mol/sdf file : " << IOEntries["inSdfName"] << std::endl << "Your monomer name : " << IOEntries["monoRootName"] << std::endl << "The output atom type file(txt) : " << IOEntries["AtomTypeOutName"] << std::endl; } else if (workMode==910) { std::cout << "The Mode for HUMO applications is activated " << std::endl; } std::cout << "||========================================================================||" << std::endl; } }