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C++ OBMol::GetExactMass方法代码示例

本文整理汇总了C++中OBMol::GetExactMass方法的典型用法代码示例。如果您正苦于以下问题:C++ OBMol::GetExactMass方法的具体用法?C++ OBMol::GetExactMass怎么用?C++ OBMol::GetExactMass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OBMol的用法示例。


在下文中一共展示了OBMol::GetExactMass方法的6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: GenerateFormulaReference

void GenerateFormulaReference()
{
  std::ifstream ifs;
  if (!SafeOpen(ifs, smilestypes_file.c_str()))
    return;

  std::ofstream ofs;
  if (!SafeOpen(ofs, results_file.c_str()))
    return;

  OBMol mol;
  OBConversion conv(&ifs, &cout);

  if(! conv.SetInAndOutFormats("SMI","SMI"))
    {
      cerr << "SMILES format is not loaded" << endl;
      return;
    }

  for (;ifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;

      //write out formula, molecular weight and exact mass
      ofs << mol.GetFormula() << " " << mol.GetMolWt() << " " 
          << mol.GetExactMass() << endl;
    }

	cerr << " Molecular formula results written successfully" << endl;
  return;
}
开发者ID:candycode,项目名称:openbabel,代码行数:34,代码来源:formula.cpp

示例2: WriteReport

bool WriteReport(ostream &ofs,OBMol &mol)
{
  char buffer[BUFF_SIZE];
  ofs << "FILENAME: " << mol.GetTitle() << endl;
  ofs << "MASS: ";
  sprintf(buffer, "%5.4f", mol.GetMolWt());
  ofs << buffer << endl;
  ofs << "EXACT MASS: ";
  sprintf(buffer, "%5.7f", mol.GetExactMass());
  ofs << buffer << endl;
  if (mol.GetTotalCharge() != 0)
    {
      ofs << "TOTAL CHARGE: ";
      sprintf(buffer, "%d", mol.GetTotalCharge());
      ofs << buffer << endl;
    }
  if (mol.GetTotalSpinMultiplicity() != 1)
    {
      ofs << "TOTAL SPIN: ";
      sprintf(buffer, "%d", mol.GetTotalSpinMultiplicity());
      ofs << buffer << endl;
    }
  ofs << "INTERATOMIC DISTANCES" << endl;
  WriteDistanceMatrix(ofs, mol);
  ofs << endl << endl << "ATOMIC CHARGES" << endl;
  WriteCharges(ofs, mol);
  ofs << endl << endl << "BOND ANGLES" << endl;
  WriteAngles(ofs, mol);
  ofs << endl << endl << "TORSION ANGLES" << endl;
  WriteTorsions(ofs, mol);
  if (mol.IsChiral())
    {
      ofs << endl << endl << "CHIRAL ATOMS" << endl;
      WriteChiral(ofs, mol);
    }
  if (mol.HasData(obCommentData)) {
    ofs << endl << endl << "COMMENTS" << endl;
    OBCommentData *cd = (OBCommentData*)mol.GetData(obCommentData);
    ofs << cd->GetData() << endl;
  }
  ofs << endl << endl;
  return(true);
}
开发者ID:daju1,项目名称:winlibghemical,代码行数:43,代码来源:report.cpp

示例3: main


//.........这里部分代码省略.........
	// A third file is created to store information on the memory allocation of data structures
	// from the MMFF94 calculation routines. breakdown of memory allocated for each calculation type
	char filepath3[1100];
	std::ofstream output3;
	sprintf(filepath3, "%s/%s_%s_t%d_malloc.mat", cwd, statsfile, ff.c_str(), nthreads);
	std::cout << "Writing memory allocation breakdown detail file to: " << filepath3 << std::endl;
	output3.open(filepath3, ios::out | ios::app ); // The file is open in append mode

	//           1     2      3       4        5         6     7     8      9      10      11       12        13    14    15
	output3 << "#METHOD: " << ff << " THREADS: " << nthreads << " DATASET: " << filename.c_str() << std::endl;
	output3 << "#ATOMS M_BOND M_ANGLE M_STRBND M_TORSION M_OOP M_VDW M_ELEC C_BOND C_ANGLE C_STRBND C_TORSION C_OOP C_VDW C_ELEC" << std::endl;

  double bondCalcTime, angleCalcTime, strbndCalcTime, torsionCalcTime, oopCalcTime, vdwCalcTime, electrostaticCalcTime;
  int numPairsVDW, numPairsElectrostatic;

  OBMol mol;
  double energy;
  for (c=1;;c++) {
    mol.Clear();

    totalTimer.start();
    readTimer.start();

    if (!conv.Read(&mol, &ifs))
      break;
    if (mol.Empty())
      break;

    if (hydrogens)
      mol.AddHydrogens();
       
    readTime = readTimer.get();
    setupTimer.start();


    if (!pFF->Setup(mol)) {
      cerr << program_name << ": could not setup force field." << endl;
      exit (-1);
    }

    setupTime = setupTimer.get();
    computeTimer.start();
    
    energy = pFF->Energy(false);

    computeTime = computeTimer.get();
    totalTime = totalTimer.get();

    // THREADS  ENERGY  MOL_MASS  NUM_ATOMS  NUM_ROTORS  NUM_CONF  TOT_TIME  TIME_READ  TIME_SETUP  TIME_COMPUTE STEPS  #MOL_NAME
    output << nthreads << " " << energy << " " << mol.GetExactMass() << " " << mol.NumAtoms()
    		<< " " << mol.NumRotors() << "  " <<  mol.NumConformers() << " "
    		<< totalTime <<  " " << readTime << " " << " " << setupTime << " " << computeTime << " "
    		<< totalSteps << " #" << mol.GetTitle()  // comment added to avoid errors when reading matrix in Octave
    		<< std::endl;

    map<string, double> timings = pFF->getTimings();
    map<string, size_t> memalloc = pFF->getAllocatedMemory();
    MapKeys mk;
    // 1      2       3        4         5     6     7      8       9         10         11      12
    // E_BOND E_ANGLE E_STRBND E_TORSION E_OOP E_VDW E_ELEC N_ATOMS PAIRS_VDW PAIRS_ELEC MEM_VDW MEM_ELEC
    output2 << timings[mk.TIME_BOND_CALCULATIONS] << " "  // 1
    		<< timings[mk.TIME_ANGLE_CALCULATIONS] << " " // 2
    		<< timings[mk.TIME_STRBND_CALCULATIONS] << " " // 3
    		<< timings[mk.TIME_TORSION_CALCULATIONS] << " " // 4
    		<< timings[mk.TIME_OOP_CALCULATIONS] << " " // 5
    		<< timings[mk.TIME_VDW_CALCULATIONS] << " " // 6
    		<< timings[mk.TIME_ELECTROSTATIC_CALCULATIONS] << " " // 7
    		<< mol.NumAtoms() << " " // 8
    		<< timings[mk.TOTAL_VDW_CALCULATIONS] << " " // 9
    		<< timings[mk.TOTAL_ELECTROSTATIC_CALCULATIONS] << " " // 10
    		<< memalloc[mk.MEM_VDW_CALCULATIONS] << " " // 11
    		<< memalloc[mk.MEM_ELECTROSTATIC_CALCULATIONS] << std::endl; // 12

	// 1     2      3       4        5         6     7     8      9      10      11       12        13    14    15
    // ATOMS M_BOND M_ANGLE M_STRBND M_TORSION M_OOP M_VDW M_ELEC C_BOND C_ANGLE C_STRBND C_TORSION C_OOP C_VDW C_ELEC
    output3 << mol.NumAtoms() << " " // 1
    		<< memalloc[mk.MEM_BOND_CALCULATIONS] << " " // 2
    		<< memalloc[mk.MEM_ANGLE_CALCULATIONS] << " " // 3
    		<< memalloc[mk.MEM_STRBND_CALCULATIONS] << " " // 4
    		<< memalloc[mk.MEM_TORSION_CALCULATIONS] << " " // 5
    		<< memalloc[mk.MEM_OOP_CALCULATIONS] << " " // 6
    		<< memalloc[mk.MEM_VDW_CALCULATIONS] << " " // 7
    		<< memalloc[mk.MEM_ELECTROSTATIC_CALCULATIONS] << " " // 8
    		<< timings[mk.TOTAL_BOND_CALCULATIONS] << " " // 9
    		<< timings[mk.TOTAL_ANGLE_CALCULATIONS] << " " // 10
    		<< timings[mk.TOTAL_STRBND_CALCULATIONS] << " " // 11
    		<< timings[mk.TOTAL_TORSION_CALCULATIONS] << " " // 12
    		<< timings[mk.TOTAL_OOP_CALCULATIONS] << " " // 13
    		<< timings[mk.TOTAL_VDW_CALCULATIONS] << " " // 14
    		<< timings[mk.TOTAL_ELECTROSTATIC_CALCULATIONS] << " " // 15
    		<< std::endl;

    if (!isfinite(energy)) {
      cerr << " Title: " << mol.GetTitle() << endl;
      FOR_ATOMS_OF_MOL(atom, mol) {
        cerr << " x: " << atom->x() << " y: " << atom->y() << " z: " << atom->z() << endl;
      }
    }

  } // end for loop
开发者ID:ovalerio,项目名称:ocl_openbabel,代码行数:101,代码来源:obenergyx.cpp

示例4: 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)
    {
      if (strncmp(argv[1], "-g", 2))
        {
          cout << "Usage: formula" << endl;
          cout << "   Tests Open Babel molecular formula, weight, and exact mass." << endl;
          return 0;
        }
      else
        {
          GenerateFormulaReference();
          return 0;
        }
    }

  cout << "# Testing molecular formulas..." << endl;

  std::ifstream mifs;
  if (!SafeOpen(mifs, smilestypes_file.c_str()))
    {
      cout << "Bail out! Cannot read file " << smilestypes_file << endl;
      return -1; // test failed
    }

  std::ifstream rifs;
  if (!SafeOpen(rifs, results_file.c_str()))
    {
      cout << "Bail out! Cannot read file " << results_file << endl;
      return -1; // test failed
    }

  char buffer[BUFF_SIZE];
  vector<string> vs;
  OBMol mol;
  OBConversion conv(&mifs, &cout);
  unsigned int currentTest = 0;
  // double mass;

  if(! conv.SetInAndOutFormats("SMI","SMI"))
    {
      cout << "Bail out! SMILES format is not loaded" << endl;
      return -1;
    }

  for (;mifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;
      if (!rifs.getline(buffer,BUFF_SIZE))
        {
          cout << "Bail out! error reading reference data" << endl;
          return -1; // test failed
        }

      tokenize(vs,buffer);
      if (vs.size() != 3)
        {
          cout << "Bail out! Reference data has incorrect format" << endl;
          return -1; // test failed
        }

      if (vs[0] != mol.GetFormula())
        {
          cout << "not ok " << ++currentTest << " # molecular formula incorrect"
               << " for molecule " << mol.GetTitle() << "\n";
        }
      else
        cout << "ok " << ++currentTest << " # molecular formula\n";

      if ( fabs(atof(vs[1].c_str()) - mol.GetMolWt() ) > 1.0e-3)
        {
          cout << "not ok " << ++currentTest << " # molecular weight incorrect"
               << " for molecule " << mol.GetTitle() << "\n";
          cout << "# Expected " << atof(vs[1].c_str()) << " found " <<
            mol.GetMolWt() << "\n";
        }
      else
        cout << "ok " << ++currentTest << " # molecular weight\n";

      if ( fabs(atof(vs[2].c_str()) - mol.GetExactMass() ) > 1.0e-3)
        {
          cout << "not ok " << ++currentTest << " # exact mass incorrect"
               << " for molecule " << mol.GetTitle() << "\n";
          cout << "# Expected " << atof(vs[2].c_str()) << " found " <<
            mol.GetExactMass() << "\n";
        }
      else
        cout << "ok " << ++currentTest << " # molecular exact mass\n";


      // now after adding explict hydrogens -- should be identical
      //  since we'll add hydrogens that were implicit before

//.........这里部分代码省略.........
开发者ID:candycode,项目名称:openbabel,代码行数:101,代码来源:formula.cpp

示例5: formula_test

void formula_test()
{
#ifdef TESTDATADIR
  string testdatadir = TESTDATADIR;
  string results_file = testdatadir + "formularesults.txt";
  string smilestypes_file = testdatadir + "attype.00.smi";
#else
  string results_file = "files/formularesults.txt";
  string smilestypes_file = "files/attype.00.smi";
#endif

  cout << "# Testing molecular formulas..." << endl;

  std::ifstream mifs;
  BOOST_REQUIRE_MESSAGE( SafeOpen(mifs, smilestypes_file.c_str()), "Bail out! Cannot read file " );

  std::ifstream rifs;
  BOOST_REQUIRE_MESSAGE( SafeOpen(rifs, results_file.c_str()), "Bail out! Cannot read file " );

  char buffer[BUFF_SIZE];
  char message[BUFF_SIZE];
  vector<string> vs;
  OBMol mol;
  OBConversion conv(&mifs, &cout);
  unsigned int currentTest = 0;
  // double mass;

  BOOST_REQUIRE_MESSAGE( conv.SetInAndOutFormats("SMI","SMI"), "Bail out! SMILES format is not loaded" );

  for (;mifs;)
    {
      mol.Clear();
      conv.Read(&mol);
      if (mol.Empty())
        continue;
      BOOST_REQUIRE_MESSAGE( rifs.getline(buffer,BUFF_SIZE), "Bail out! error reading reference data" );

      tokenize(vs,buffer);
      BOOST_REQUIRE_MESSAGE( vs.size() == 3, "Bail out! Reference data has incorrect format" );

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # molecular formula incorrect for molecule %s"
		                   " # Expected %s, found %s", currentTest, mol.GetTitle(),
				   vs[0].c_str(), mol.GetFormula().c_str());
      BOOST_CHECK_MESSAGE(vs[0] == mol.GetFormula(), message );

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # molecular weight incorrect for molecule %s"
		                   " # Expected %f, found %f ", currentTest, mol.GetTitle(),
				   atof(vs[1].c_str()), mol.GetMolWt());
      BOOST_CHECK_MESSAGE( fabs(atof(vs[1].c_str()) - mol.GetMolWt() ) < 1.0e-3, message );

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # exact mass incorrect for molecule %s"
		                   " # Expected %f, found %f ", currentTest, mol.GetTitle(),
				   atof(vs[2].c_str()), mol.GetExactMass());
      BOOST_CHECK_MESSAGE( fabs(atof(vs[2].c_str()) - mol.GetExactMass() ) < 1.0e-3, message );

      // now after adding explict hydrogens -- should be identical
      //  since we'll add hydrogens that were implicit before

      // PR#1485580
      BOOST_CHECK( mol.AddHydrogens() );

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # molecular formula incorrect for "
		                   "hydrogen-added molecule %s", currentTest, mol.GetTitle());
      BOOST_CHECK_MESSAGE(vs[0] == mol.GetFormula(), message);

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # molecular weight incorrect for hydrogen-added "
		                   "molecule %s # Expected %f, found %f ", currentTest, mol.GetTitle(),
				   atof(vs[1].c_str()), mol.GetMolWt());
      BOOST_CHECK_MESSAGE( fabs(atof(vs[1].c_str()) - mol.GetMolWt() ) < 1.0e-3, message);

      currentTest++;
      snprintf(message, BUFF_SIZE, "not ok %d # exact mass  incorrect for hydrogen-added "
		                   "molecule %s # Expected %f, found %f ", currentTest, mol.GetTitle(),
				   atof(vs[2].c_str()), mol.GetExactMass());
      BOOST_CHECK_MESSAGE( fabs(atof(vs[2].c_str()) - mol.GetExactMass() ) < 1.0e-3, message);

    }

}
开发者ID:arebzanipro,项目名称:contributed,代码行数:84,代码来源:formula.cpp

示例6: 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


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