C++ OBConversion::FindFormat方法代码示例

本文整理汇总了C++中OBConversion::FindFormat方法的典型用法代码示例。如果您正苦于以下问题：C++ OBConversion::FindFormat方法的具体用法？C++ OBConversion::FindFormat怎么用？C++ OBConversion::FindFormat使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类OBConversion的用法示例。

在下文中一共展示了OBConversion::FindFormat方法的7个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: main

int main(int argc,char *argv[])
{
  // turn off slow sync with C-style output (we don't use it anyway).
  std::ios::sync_with_stdio(false);

  OBConversion conv;
  OBFormat *inFormat, *canFormat;
  OBMol mol;
  ifstream ifs;
  vector<OBMol> fragments;
  unsigned int fragmentCount = 0; // track how many in library -- give a running count
  map<string, int> index; // index of cansmi
  string currentCAN;
  unsigned int size;
  OBAtom *atom;
  OBBond *bond;
  bool nonRingAtoms, nonRingBonds;
  char buffer[BUFF_SIZE];

  canFormat = conv.FindFormat("can");
  conv.SetOutFormat(canFormat);

  if (argc < 2)
    {
      cout << "Usage: obfragment <file>" << endl;
      return(-1);
    }

  for (int i = 1; i < argc; i++) {
    cerr << " Reading file " << argv[i] << endl;

    inFormat = conv.FormatFromExt(argv[i]);
    if(inFormat==NULL || !conv.SetInFormat(inFormat))
      {
        cerr << " Cannot read file format for " << argv[i] << endl;
        continue; // try next file
      }
    
    ifs.open(argv[i]);
    
    if (!ifs)
      {
        cerr << "Cannot read input file: " << argv[i] << endl;
        continue;
      }
    
    
    while(ifs.peek() != EOF && ifs.good())
      {
        conv.Read(&mol, &ifs);
        if (!mol.Has3D()) continue; // invalid coordinates!
        mol.DeleteHydrogens(); // remove these before we do anything else
        
        do {
          nonRingAtoms = false;
          size = mol.NumAtoms();
          for (unsigned int i = 1; i <= size; ++i)
            {
              atom = mol.GetAtom(i);
              if (!atom->IsInRing()) {
                mol.DeleteAtom(atom);
                nonRingAtoms = true;
                break; // don't know how many atoms there are
              } 
              // Previously, we changed atoms to carbon here.
              // Now we perform this alchemy in terms of string-rewriting
              // once the canonical SMILES is generated
            }
        } while (nonRingAtoms);
        
        if (mol.NumAtoms() < 3)
          continue;
        
        if (mol.NumBonds() == 0)
          continue;
        
        do {
          nonRingBonds = false;
          size = mol.NumBonds();
          for (unsigned int i = 0; i < size; ++i)
            {
              bond = mol.GetBond(i);
              if (!bond->IsInRing()) {
                mol.DeleteBond(bond);
                nonRingBonds = true;
                break; // don't know how many bonds there are
              }
            }        
        } while (nonRingBonds);

        fragments = mol.Separate();
        for (unsigned int i = 0; i < fragments.size(); ++i)
          {
            if (fragments[i].NumAtoms() < 3) // too small to care
              continue;
              
            currentCAN = conv.WriteString(&fragments[i], true);
            currentCAN = RewriteSMILES(currentCAN); // change elements to "a/A" for compression
            if (index.find(currentCAN) != index.end()) { // already got this
              index[currentCAN] += 1; // add to the count for bookkeeping
//.........这里部分代码省略.........

开发者ID:annulen，项目名称:openbabel，代码行数:101，代码来源:obfragment.cpp

示例2: main

///////////////////////////////////////////////////////////////////////////////
//! \brief  Generate rough 3D coordinates for SMILES (or other 0D files).
//
int main(int argc,char **argv)
{
  char *program_name= argv[0];
  int c;
  string basename, filename = "", option, option2, ff = "MMFF94";

  list<string> argl(argv+1, argv+argc);

  list<string>::iterator optff = find(argl.begin(), argl.end(), "-ff");
  if (optff != argl.end()) {
    list<string>::iterator optffarg = optff;
    ++optffarg;

    if (optffarg != argl.end()) {
      ff = *optffarg;

      argl.erase(optff,++optffarg);
    } else {
      argl.erase(optff);
    }
  }

  if (argl.empty()) {
    cout << "Usage: obgen <filename> [options]" << endl;
    cout << endl;
    cout << "options:      description:" << endl;
    cout << endl;
    cout << "  -ff         select a forcefield" << endl;
    cout << endl;
    OBPlugin::List("forcefields", "verbose");
    exit(-1);
  }

  basename = filename = *argl.begin();
  size_t extPos = filename.rfind('.');

  if (extPos!= string::npos) {
    basename = filename.substr(0, extPos);
  }

  // Find Input filetype
  OBConversion conv;
  OBFormat *format_in = conv.FormatFromExt(filename.c_str());
  OBFormat *format_out = conv.FindFormat("sdf");

  if (!format_in || !format_out || !conv.SetInAndOutFormats(format_in, format_out)) {
    cerr << program_name << ": cannot read input/output format!" << endl;
    exit (-1);
  }

  ifstream ifs;
  ofstream ofs;

  // Read the file
  ifs.open(filename.c_str());
  if (!ifs) {
    cerr << program_name << ": cannot read input file!" << endl;
    exit (-1);
  }

  OBMol mol;

  for (c=1;;c++) {
      mol.Clear();
      if (!conv.Read(&mol, &ifs))
        break;
      if (mol.Empty())
        break;

      OBForceField* pFF = OBForceField::FindForceField(ff);
      if (!pFF) {
        cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
        exit (-1);
      }

      //mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called

      pFF->SetLogFile(&cerr);
      pFF->SetLogLevel(OBFF_LOGLVL_LOW);

      //pFF->GenerateCoordinates();
      OBBuilder builder;
      builder.Build(mol);

      mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
      if (!pFF->Setup(mol)) {
        cerr << program_name << ": could not setup force field." << endl;
        exit (-1);
      }

      pFF->SteepestDescent(500, 1.0e-4);
      pFF->WeightedRotorSearch(250, 50);
      pFF->SteepestDescent(500, 1.0e-6);

      pFF->UpdateCoordinates(mol);
      //pFF->ValidateGradients();
      //pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
//.........这里部分代码省略.........

开发者ID:Reinis，项目名称:openbabel，代码行数:101，代码来源:obgen.cpp

示例3: main

int main(int argc,char **argv)
{
  char *program_name= argv[0];
  int c;
  int steps = 2500;
  double crit = 1e-6;
  bool sd = false;
  bool cut = false;
  bool newton = false;
  bool hydrogens = false;
  double rvdw = 6.0;
  double rele = 10.0;
  int freq = 10;
  string basename, filename = "", option, option2, ff = "MMFF94";
  char *oext;
  OBConversion conv;
  OBFormat *format_out = conv.FindFormat("pdb"); // default output format

  if (argc < 2) {
    cout << "Usage: obminimize [options] <filename>" << endl;
    cout << endl;
    cout << "options:      description:" << endl;
    cout << endl;
    cout << "  -c crit     set convergence criteria (default=1e-6)" << endl;
    cout << endl;
    cout << "  -cg         use conjugate gradients algorithm (default)" << endl;
    cout << endl;
    cout << "  -sd         use steepest descent algorithm" << endl;
    cout << endl;
    cout << "  -newton     use Newton2Num linesearch (default=Simple)" << endl;
    cout << endl;
    cout << "  -ff ffid    select a forcefield:" << endl;
    cout << endl;
    cout << "  -h          add hydrogen atoms" << endl;
    cout << endl;
    cout << "  -n steps    specify the maximum numer of steps (default=2500)" << endl;
    cout << endl;
    cout << "  -cut        use cut-off (default=don't use cut-off)" << endl;
    cout << endl;
    cout << "  -rvdw rvdw  specify the VDW cut-off distance (default=6.0)" << endl;
    cout << endl;
    cout << "  -rele rele  specify the Electrostatic cut-off distance (default=10.0)" << endl;
    cout << endl;
    cout << "  -pf freq    specify the frequency to update the non-bonded pairs (default=10)" << endl;
    cout << endl;
    OBPlugin::List("forcefields", "verbose");
    exit(-1);
  } else {
    int ifile = 1;
    for (int i = 1; i < argc; i++) {
      option = argv[i];

      // steps
      if ((option == "-n") && (argc > (i+1))) {
        steps = atoi(argv[i+1]);
        ifile += 2;
      }
      // vdw cut-off
      if ((option == "-rvdw") && (argc > (i+1))) {
        rvdw = atof(argv[i+1]);
        ifile += 2;
      }
      // ele cut-off
      if ((option == "-rele") && (argc > (i+1))) {
        rele = atof(argv[i+1]);
        ifile += 2;
      }
      // pair update frequency
      if ((option == "-pf") && (argc > (i+1))) {
        freq = atoi(argv[i+1]);
        ifile += 2;
      }
      // steepest descent
      if (option == "-sd") {
        sd = true;
        ifile++;
      }
      // enable cut-off
      if (option == "-cut") {
        cut = true;
        ifile++;
      }
      // enable Newton2Num
      if (option == "-newton") {
        newton = true;
        ifile++;
      }

      if (strncmp(option.c_str(), "-o", 2) == 0) {
        oext = argv[i] + 2;
        if(!*oext) {
          oext = argv[++i]; //space left after -o: use next argument
          ifile++;
        }

        format_out = conv.FindFormat(oext);
        ifile++;
      }

      if (option == "-h") {
//.........这里部分代码省略.........

开发者ID:Reinis，项目名称:openbabel，代码行数:101，代码来源:obminimize.cpp

示例4: residue_test

void residue_test()
{
  cout << "# Unit tests for OBResidue \n";

  // OBResidue isolation tests
  OBResidue emptyResidue, testRes1;

  // chains parser tests

  // PR#1515198
  static const string loopTest1("C1(C(NC(C(N1C(C(NC(C=Cc1ccccc1)=O)C)=O)Cc1ccccc1)=O)Cc1ccccc1)=O");
  OBConversion conv;
  OBMol mol;
  OBFormat *inFormat = conv.FindFormat("SMI");
  
  conv.SetInFormat(inFormat);
  conv.ReadString(&mol, loopTest1);
  chainsparser.PerceiveChains(mol);

  // parse common residues
  unsigned int testCount = 3;
  static const string ala("NC(C)C(O)(=O)");
  CheckValidResidue(conv, ala, ++testCount);
  static const string arg("NC(CCCNC(N)=N)C(O)(=O)");
  CheckValidResidue(conv, arg, ++testCount);
  static const string asn("NC(CC(N)=O)C(O)(=O)");
  CheckValidResidue(conv, asn, ++testCount);
  static const string asp("NC(CC(O)=O)C(O)(=O)");
  CheckValidResidue(conv, asp, ++testCount);
  static const string cys("NC(CS)C(O)(=O)");
  CheckValidResidue(conv, cys, ++testCount);
  static const string glu("NC(CCC(O)=O)C(O)(=O)");
  CheckValidResidue(conv, glu, ++testCount);
  static const string gln("NC(CCC(N)=O)C(O)(=O)");
  CheckValidResidue(conv, gln, ++testCount);
  static const string gly("NC([H])C(O)(=O)");
  CheckValidResidue(conv, gly, ++testCount);
  static const string his("NC(CC1=CNC=N1)C(O)(=O)");
  CheckValidResidue(conv, his, ++testCount);
  static const string ile("NC(C(CC)C)C(O)(=O)");
  CheckValidResidue(conv, ile, ++testCount);
  static const string leu("NC(CC(C)C)C(O)(=O)");
  CheckValidResidue(conv, leu, ++testCount);
  static const string lys("NC(CCCCN)C(O)(=O)");
  CheckValidResidue(conv, lys, ++testCount);
  static const string met("NC(CCSC)C(O)(=O)");
  CheckValidResidue(conv, met, ++testCount);
  static const string phe("NC(CC1=CC=CC=C1)C(O)(=O)");
  CheckValidResidue(conv, phe, ++testCount);
  static const string pro("OC(C1CCCN1)(=O)");
  CheckValidResidue(conv, pro, ++testCount);
  static const string ser("NC(CO)C(O)(=O)");
  CheckValidResidue(conv, ser, ++testCount);
  static const string thr("NC(C(C)O)C(O)(=O)");
  CheckValidResidue(conv, thr, ++testCount);
  static const string trp("NC(CC1=CNC2=C1C=CC=C2)C(O)(=O)");
  CheckValidResidue(conv, trp, ++testCount);
  static const string tyr("NC(CC1=CC=C(O)C=C1)C(O)(=O)");
  CheckValidResidue(conv, tyr, ++testCount);
  static const string val("NC(C(C)C)C(O)(=O)");
  CheckValidResidue(conv, val, ++testCount);

  // nucleics
  static const string a("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1cnc2c(ncnc12)N");
  CheckValidResidue(conv, a, ++testCount);
  static const string g("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1c(nc(cc1)N)=O");
  CheckValidResidue(conv, g, ++testCount);
  static const string c("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1cnc2c([nH]c(nc12)N)=O");
  CheckValidResidue(conv, c, ++testCount);
  static const string t("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1c([nH]c(c(c1)C)=O)=O");
  CheckValidResidue(conv, t, ++testCount);
  static const string u("OC[[email protected]]1O[[email protected]]([[email protected]@H]([[email protected]@H]1O)O)n1c([nH]c(cc1)=O)=O");
  CheckValidResidue(conv, u, ++testCount);

  // invalid residues
  static const string benzene("c1ccccc1");
  CheckInvalidResidue(conv, benzene, ++testCount);
  static const string pyrrole("c1cccn[H]1");
  CheckInvalidResidue(conv, pyrrole, ++testCount);
  static const string amine("CC(=O)CCN");
  CheckInvalidResidue(conv, amine, ++testCount);

  // check some dipeptides
  static const string ala_val("NC(C)C(=O)NC(C(C)C)C(=O)O");
  CheckValidDipeptide(conv, ala_val, ++testCount);
  static const string cys_leu("NC(CS)C(=O)NC(CC(C)C)C(=O)O");
  CheckValidDipeptide(conv, cys_leu, ++testCount);
 
}

开发者ID:arebzanipro，项目名称:contributed，代码行数:89，代码来源:residue.cpp

示例5: main

int main(int argc,char *argv[])
{
  // turn off slow sync with C-style output (we don't use it anyway).
  std::ios::sync_with_stdio(false);

  if (argc != 1)
    {
      cout << "Usage: residue" << endl;
      cout << " Unit tests for OBResidue " << endl;
      return(-1);
    }

  cout << "# Unit tests for OBResidue \n";

  cout << "ok 1\n"; // for loading tests

  // OBResidue isolation tests
  OBResidue emptyResidue, testRes1;
  cout << "ok 2\n"; // ctor works

  // chains parser tests

  // PR#1515198
  static const string loopTest1("C1(C(NC(C(N1C(C(NC(C=Cc1ccccc1)=O)C)=O)Cc1ccccc1)=O)Cc1ccccc1)=O");
  OBConversion conv;
  OBMol mol;
  OBFormat *inFormat = conv.FindFormat("SMI");
  
  conv.SetInFormat(inFormat);
  conv.ReadString(&mol, loopTest1);
  chainsparser.PerceiveChains(mol);

  // OK if it doesn't crash
  cout << "ok 3\n";

  // parse common residues
  unsigned int testCount = 3;
  static const string ala("NC(C)C(O)(=O)");
  CheckValidResidue(conv, ala, ++testCount);
  static const string arg("NC(CCCNC(N)=N)C(O)(=O)");
  CheckValidResidue(conv, arg, ++testCount);
  static const string asn("NC(CC(N)=O)C(O)(=O)");
  CheckValidResidue(conv, asn, ++testCount);
  static const string asp("NC(CC(O)=O)C(O)(=O)");
  CheckValidResidue(conv, asp, ++testCount);
  static const string cys("NC(CS)C(O)(=O)");
  CheckValidResidue(conv, cys, ++testCount);
  static const string glu("NC(CCC(O)=O)C(O)(=O)");
  CheckValidResidue(conv, glu, ++testCount);
  static const string gln("NC(CCC(N)=O)C(O)(=O)");
  CheckValidResidue(conv, gln, ++testCount);
  static const string gly("NC([H])C(O)(=O)");
  CheckValidResidue(conv, gly, ++testCount);
  static const string his("NC(CC1=CNC=N1)C(O)(=O)");
  CheckValidResidue(conv, his, ++testCount);
  static const string ile("NC(C(CC)C)C(O)(=O)");
  CheckValidResidue(conv, ile, ++testCount);
  static const string leu("NC(CC(C)C)C(O)(=O)");
  CheckValidResidue(conv, leu, ++testCount);
  static const string lys("NC(CCCCN)C(O)(=O)");
  CheckValidResidue(conv, lys, ++testCount);
  static const string met("NC(CCSC)C(O)(=O)");
  CheckValidResidue(conv, met, ++testCount);
  static const string phe("NC(CC1=CC=CC=C1)C(O)(=O)");
  CheckValidResidue(conv, phe, ++testCount);
  static const string pro("OC(C1CCCN1)(=O)");
  CheckValidResidue(conv, pro, ++testCount);
  static const string ser("NC(CO)C(O)(=O)");
  CheckValidResidue(conv, ser, ++testCount);
  static const string thr("NC(C(C)O)C(O)(=O)");
  CheckValidResidue(conv, thr, ++testCount);
  static const string trp("NC(CC1=CNC2=C1C=CC=C2)C(O)(=O)");
  CheckValidResidue(conv, trp, ++testCount);
  static const string tyr("NC(CC1=CC=C(O)C=C1)C(O)(=O)");
  CheckValidResidue(conv, tyr, ++testCount);
  static const string val("NC(C(C)C)C(O)(=O)");
  CheckValidResidue(conv, val, ++testCount);

  // nucleics
  static const string a("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1cnc2c(ncnc12)N");
  CheckValidResidue(conv, a, ++testCount);
  static const string g("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1c(nc(cc1)N)=O");
  CheckValidResidue(conv, g, ++testCount);
  static const string c("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1cnc2c([nH]c(nc12)N)=O");
  CheckValidResidue(conv, c, ++testCount);
  static const string t("OC[[email protected]]1O[[email protected]](C[[email protected]@H]1O)n1c([nH]c(c(c1)C)=O)=O");
  CheckValidResidue(conv, t, ++testCount);
  static const string u("OC[[email protected]]1O[[email protected]]([[email protected]@H]([[email protected]@H]1O)O)n1c([nH]c(cc1)=O)=O");
  CheckValidResidue(conv, u, ++testCount);

  // invalid residues
  static const string benzene("c1ccccc1");
  CheckInvalidResidue(conv, benzene, ++testCount);
  static const string pyrrole("c1cccn[H]1");
  CheckInvalidResidue(conv, pyrrole, ++testCount);
  static const string amine("CC(=O)CCN");
  CheckInvalidResidue(conv, amine, ++testCount);

  // check some dipeptides
  static const string ala_val("NC(C)C(=O)NC(C(C)C)C(=O)O");
//.........这里部分代码省略.........

开发者ID:baoilleach，项目名称:obstereo-2-2-x，代码行数:101，代码来源:residue.cpp

示例6: mmff94_validate

void mmff94_validate()
{
  OBForceField* pFF = OBForceField::FindForceField("MMFF94");

  OBConversion conv;
  OBFormat *format_in = conv.FindFormat("mol2");
  vector<string> vs;
  vector<int> types;
  vector<double> fcharges, pcharges;
  vector<double> bond_lengths;
  char buffer[BUFF_SIZE], _logbuf[BUFF_SIZE];
  bool molfound, atomfound, bondfound, fchgfound, pchgfound;
  double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq;
  double termcount; //1=bond, 2=angle, 3=strbnd, 4=torsion, 5=oop
  int n = 0;

  BOOST_REQUIRE_MESSAGE( format_in && conv.SetInFormat(format_in), "Could not set mol2 input format" );

  ifstream ifs, ifs2;
  ofstream ofs;

  ifs.open("MMFF94_dative.mol2");
  BOOST_REQUIRE_MESSAGE( ifs, "Could not open ./MMFF94_dative.mol2" );
 
  ifs2.open("MMFF94_opti.log");
  BOOST_REQUIRE_MESSAGE( ifs2, "Could not open ./MMFF94_opti.log" );
    
  ofs.open("MMFF94_openbabel.log");
  BOOST_REQUIRE_MESSAGE( ofs, "Could not open ./MMFF94_openbabel.log" );
    
  pFF->SetLogFile(&ofs);
  pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
   
  OBMol mol;
  for (unsigned int c=1;; c++) {
    mol.Clear();
    types.clear();
    fcharges.clear();
    pcharges.clear();
    bond_lengths.clear();

    if (!conv.Read(&mol, &ifs))
      break;
    if (mol.Empty())
      break;
     
    BOOST_CHECK_MESSAGE( pFF->Setup(mol), "Could not setup calculations (missing parameters...)" );

    pFF->GetAtomTypes(mol);
    //pFF->GetFormalCharges(mol);
    pFF->GetPartialCharges(mol);

    termcount = 0;
    molfound = false;
    atomfound = false;
    bondfound = false;
    fchgfound = false;
    pchgfound = false;

    // Parse log file for types, charges, energies, ..
    while (ifs2.getline(buffer, 150)) {
      tokenize(vs, buffer);
      if (vs.size() == 0) {
        bondfound = false;
        continue;
      }
	
      string str(buffer);
      if (string::npos != str.find(mol.GetTitle(),0))
        molfound = true;

      // read atom types
      if (atomfound) {
        if (n) {
          types.push_back(atoi(vs[2].c_str()));
          types.push_back(atoi(vs[5].c_str()));
          types.push_back(atoi(vs[8].c_str()));
          types.push_back(atoi(vs[11].c_str()));
        } else {
          if (vs.size() > 2)
            types.push_back(atoi(vs[2].c_str()));
          if (vs.size() > 5)
            types.push_back(atoi(vs[5].c_str()));
          if (vs.size() > 8)
            types.push_back(atoi(vs[8].c_str()));
   
          atomfound = false;
        }
        n--;
      }
        
      // read formal charges
      if (fchgfound) {
        if (n) {
          fcharges.push_back(atof(vs[2].c_str()));
          fcharges.push_back(atof(vs[5].c_str()));
          fcharges.push_back(atof(vs[8].c_str()));
          fcharges.push_back(atof(vs[11].c_str()));
        } else {
          if (vs.size() > 2)
//.........这里部分代码省略.........

开发者ID:arebzanipro，项目名称:contributed，代码行数:101，代码来源:mmff94validate.cpp

示例7: main

int main(int argc,char **argv)
{
  char *program_name= argv[0];
  int c;
  char *FileIn = NULL;

  if (argc != 2)
    {
      string err = "Usage: ";
      err += program_name;
      err += " <filename>\n"
      "Output format:\n"
        "name NAME\n"
        "formula  FORMULA\n"
        "mol_weight MOLECULAR_WEIGHT\n"
        "exact_mass ISOTOPIC MASS\n"
        "canonical_SMILES STRING\n"
        "InChI  STRING\n"
        "num_atoms  NUM\n"
        "num_bonds  NUM\n"
        "num_residues  NUM\n"
	"num_rotors NUM\n"
        "sequence RESIDUE_SEQUENCE\n"
        "num_rings NUMBER_OF_RING_(SSSR)\n"
        "logP   NUM\n"
        "PSA    POLAR_SURFACE_AREA\n"
        "MR     MOLAR REFRACTIVITY";
      err += "$$$$";
//      ThrowError(err); wasn't being output because error level too low
      cerr << err; //Why not do directly
      exit(-1);
    }
  else
    {
      FileIn  = argv[1];
    }

  // Find Input filetype
  OBConversion conv;
  OBFormat *format = conv.FormatFromExt(FileIn);
    
  if (!format || !conv.SetInFormat(format))
    {
      cerr << program_name << ": cannot read input format!" << endl;
      exit (-1);
    }

  ifstream ifs;

  // Read the file
  ifs.open(FileIn);
  if (!ifs)
    {
      cerr << program_name << ": cannot read input file!" << endl;
      exit (-1);
    }
  
  OBMol mol;
  OBFormat *canSMIFormat = conv.FindFormat("can");
  OBFormat *inchiFormat = conv.FindFormat("inchi");


  ////////////////////////////////////////////////////////////////////////////
  // List of properties
  // Name
  // Molecular weight (Standard molar mass given by IUPAC atomic masses)
  // Number of rings : the size of the smallest set of smallest rings (SSSR)
  
  //.....ADD YOURS HERE.....
  
  for (c = 1;; ++c)
    {
      mol.Clear();
      conv.Read(&mol, &ifs);
      if (mol.Empty())
        break;
      
      if (!mol.HasHydrogensAdded())
        mol.AddHydrogens();
      // Print the properties
      if (strlen(mol.GetTitle()) != 0)
        cout << "name             " << mol.GetTitle() << endl;
      else 
        cout << "name             " << FileIn << " " << c << endl;

      cout << "formula          " << mol.GetFormula() << endl;
      cout << "mol_weight       " << mol.GetMolWt() << endl;
      cout << "exact_mass       " << mol.GetExactMass() << endl;

      string smilesString = "-";
      if (canSMIFormat) {
        conv.SetOutFormat(canSMIFormat);
        smilesString = conv.WriteString(&mol);
        if ( smilesString.length() == 0 )
        {
          smilesString = "-";
        }
      }
      cout << "canonical_SMILES " << smilesString << endl;

//.........这里部分代码省略.........

开发者ID:Jsunseri，项目名称:openbabel，代码行数:101，代码来源:obprop.cpp

注：本文中的OBConversion::FindFormat方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。