C++ OBConversion::SetOutFormat方法代码示例

int main() {  
   
     OBAtom a, b, c;
      a.SetAtomicNum(8);
      b.SetAtomicNum(6);
      c.SetAtomicNum(8);

     OBMol mol;
     mol.AddAtom(a);
     mol.AddAtom(b);
     mol.AddAtom(c);
     
     mol.AddBond(1,2,2);
     mol.AddBond(2,3,2);

      OBConversion conv;
      conv.SetOutFormat("SMI");
      cout << conv.WriteString(&mol,1) << endl;
      
     OBSmartsPattern sp;
     
     sp.Init ("C~*");
     
     sp.Match (mol,false);
     
       cout << sp.NumMatches() << endl;
       
        cout << sp.GetUMapList().size() << endl;
      
      return EXIT_SUCCESS;
  }    

bool OpExtraOut::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
  /*
    OptionText contains an output filename with a format extension.
    Make an OBConversion object with this as output destination.
    Make a copy the current OBConversion and replace the output format by
    an instance of ExtraFormat. This then does all the subsequent work.
  */
  if(!pConv || !OptionText || *OptionText=='\0')
    return true; //silent no-op. false would prevent the main output

  if(pConv->IsFirstInput())
  {
    OBConversion* pExtraConv = new OBConversion(*pConv); //copy ensures OBConversion::Index>-1
    std::ofstream* ofs;
    if( (ofs = new std::ofstream(OptionText)) ) // extra parens to indicate truth value
      pExtraConv->SetOutStream(ofs);
    if(!ofs || !pExtraConv->SetOutFormat(OBConversion::FormatFromExt(OptionText)))
    {
      obErrorLog.ThrowError(__FUNCTION__, "Error setting up extra output file", obError);
      return true;
    }
    OBConversion* pOrigConv = new OBConversion(*pConv);

    //Make an instance of ExtraFormat and divert the output to it. It will delete itself.
    pConv->SetOutFormat(new ExtraFormat(pOrigConv, pExtraConv));
  }
  return true;
}

void testPdbOccupancies()
{
  // See https://github.com/openbabel/openbabel/pull/1558
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("pdb");
  conv.ReadFile(&mol, GetFilename("test08.cif"));

  string pdb = conv.WriteString(&mol);
  conv.AddOption("o", OBConversion::OUTOPTIONS);
  pdb = conv.WriteString(&mol);

  OB_ASSERT(pdb.find("HETATM    1 NA   UNL     1       0.325   0.000   4.425  0.36") != string::npos);
  OB_ASSERT(pdb.find("HETATM   17  O   UNL     8       1.954   8.956   3.035  1.00") != string::npos);

  OBMol mol_pdb;
  conv.SetInFormat("pdb");
  conv.ReadFile(&mol_pdb, GetFilename("test09.pdb"));

  pdb = conv.WriteString(&mol_pdb);
  OB_ASSERT(pdb.find("HETATM    1 NA   UNL     1       0.325   0.000   4.425  0.36") != string::npos);
  OB_ASSERT(pdb.find("HETATM    2 NA   UNL     1       0.002   8.956   1.393  0.10") != string::npos);
  OB_ASSERT(pdb.find("HETATM   17  O   UNL     8       1.954   8.956   3.035  1.00") != string::npos);
}

void testSpaceGroupClean()
{
  // See https://github.com/openbabel/openbabel/pull/254
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("pdb");
  conv.ReadFile(&mol, GetFilename("test02.cif"));
  OBUnitCell* pUC = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
  const SpaceGroup* pSG = pUC->GetSpaceGroup();
  SpaceGroup* sg = new SpaceGroup(*pSG);
  pSG = SpaceGroup::Find(sg);
  OB_ASSERT( pSG != NULL );

  // Check also for errors and warnings
  string summary = obErrorLog.GetMessageSummary();
  OB_ASSERT( summary.find("error") == string::npos);
  OB_ASSERT( summary.find("warning") == string::npos);

  OB_ASSERT( pSG->GetId() == 166 );

  string pdb = conv.WriteString(&mol);
  pdb = conv.WriteString(&mol);

  OB_ASSERT(pdb.find("H -3 m") != string::npos);
}

// Reading an InChI and then adding hydrogens messed up the structure
void test_Issue134_InChI_addH()
{
  OBConversion conv;
  conv.SetInFormat("inchi");
  OBMol mol;
  conv.ReadString(&mol, "InChI=1S/C2H7NO/c1-2(3)4/h2,4H,3H2,1H3/t2-/m0/s1");
  OB_ASSERT(!mol.HasData(OBGenericDataType::VirtualBondData));
  mol.AddHydrogens();
  conv.SetOutFormat("smi");
  std::string res = conv.WriteString(&mol, true);
  OB_COMPARE(res, "C[[email protected]@H](N)O");
}

void testCIFMolecules()
{
  // See https://github.com/openbabel/openbabel/pull/1558
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("smi"); // check for disconnected fragments
  conv.ReadFile(&mol, GetFilename("1519159.cif"));

  string smi = conv.WriteString(&mol);
  // never, never disconnected fragments from a molecule
  OB_ASSERT(smi.find(".") == string::npos);
}

void testPdbRemSpacesHMName()
{
  // See https://github.com/openbabel/openbabel/pull/1558
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("pdb");
  conv.ReadFile(&mol, GetFilename("test07.cif"));

  string pdb = conv.WriteString(&mol);
  conv.AddOption("o", OBConversion::OUTOPTIONS);
  pdb = conv.WriteString(&mol);

  OB_ASSERT(pdb.find("I41/amd:2") != string::npos);
}

void testPdbOutHexagonalAlternativeOrigin2()
{
  // See https://github.com/openbabel/openbabel/pull/1558
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("pdb");
  conv.ReadFile(&mol, GetFilename("test06.cif"));

  string pdb = conv.WriteString(&mol);
  conv.AddOption("o", OBConversion::OUTOPTIONS);
  pdb = conv.WriteString(&mol);

  OB_ASSERT(pdb.find("H -3 m") != string::npos);
}

// A segfault was occuring when a Universal SMILES was output after an InChIfied SMILES.
// This was due to short-circuit caching of InChIs on reading. The fix was to limit
// the situations when the cached value was used, but also to delete the cached value
// in this particular instance.
void test_Issue135_UniversalSmiles()
{
  // Test writing U smiles after I smiles
  OBConversion conv;
  conv.SetInFormat("smi");
  OBMol mol;
  conv.ReadString(&mol, "C(=O)([O-])C(=O)O");
  conv.SetOutFormat("smi");
  conv.SetOptions("I", OBConversion::OUTOPTIONS);
  std::string res = conv.WriteString(&mol, true);
  OB_COMPARE(res, "C(=O)(C(=O)O)[O-]");
  conv.SetOptions("U", OBConversion::OUTOPTIONS);
  res = conv.WriteString(&mol, true);
  OB_COMPARE(res, "C(=O)(C(=O)[O-])O");
}

int main(int argc, char **argv)
{
  if (argc < 2) {
    std::cout << "Usage: " << argv[0] << " <filename>" << std::endl;
    return 1;
  }

  // Read the file
  shared_ptr<OBMol> mol = GetMol(argv[1]);

  // Create the OBConformerSearch object
  OBConformerSearch cs;
  
  // Setup 
  std::cout << "Setting up conformer searching..." << std::endl
            << "   conformers:  30" << std::endl
            << "   children:    5" << std::endl
            << "   mutability:  5" << std::endl
            << "   convergence: 25" << std::endl;
  cs.Setup(*mol.get(),
           30, // numConformers
           5, // numChildren
           5, // mutability
           25); // convergence

  // Perform searching
  cs.Search();

  // Print the rotor keys
  RotorKeys keys = cs.GetRotorKeys();
  for (RotorKeys::iterator key = keys.begin(); key != keys.end(); ++key) {
    for (unsigned int i = 1; i < key->size(); ++i)
      std::cout << key->at(i) << " ";
    std::cout << std::endl;
  }

  // Get the conformers
  cs.GetConformers(*mol.get());

  std::cout << mol->NumConformers() << std::endl;
  OBConversion conv;
  conv.SetOutFormat("sdf");
  for (unsigned int c = 0; c < mol->NumConformers(); ++c) {
    mol->SetConformer(c);
    conv.Write(mol.get(), &std::cerr);
  }

}

int main(int argc, char **argv)
{
  // Define location of file formats for testing
#ifdef FORMATDIR
    char env[BUFF_SIZE];
    snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
    putenv(env);
#endif  

  std::ifstream ifs(GetFilename("canonstable.can").c_str());
  OB_REQUIRE( ifs );


  OBMol mol;
  OBConversion conv;
  conv.SetInFormat("smi");
  conv.SetOutFormat("can");

  std::string line;
  while (std::getline(ifs, line)) {
    OB_REQUIRE( conv.ReadString(&mol, line.c_str()) );

    std::vector<OBAtom*> atoms;
    FOR_ATOMS_OF_MOL(atom, mol)
      atoms.push_back(&*atom);

    for (int i = 0; i < 5; ++i) {
      // shuffle the atoms
      std::random_shuffle(atoms.begin(), atoms.end());
      mol.RenumberAtoms(atoms);

      // get can smiles
      mol.SetTitle("");
      std::string cansmi = conv.WriteString(&mol, true);
      // comapare with ref
      if (cansmi != line) {
        cout << "ref = " << line << endl;
        cout << "can = " << cansmi << endl;
        OB_ASSERT( cansmi == line );
      }
    }
  }
 
  return 0;
}

void testPdbOutAlternativeOrigin()
{
  // See https://github.com/openbabel/openbabel/pull/1558
  OBConversion conv;
  OBMol mol;
  conv.SetInFormat("cif");
  conv.SetOutFormat("pdb");
  conv.ReadFile(&mol, GetFilename("test04.cif"));

  string pdb = conv.WriteString(&mol);
  // ending space is needed to check that there is no origin set
  OB_ASSERT(pdb.find("P 4/n b m ") != string::npos);

  conv.AddOption("o", OBConversion::OUTOPTIONS);
  pdb = conv.WriteString(&mol);

  OB_ASSERT(pdb.find("P 4/n b m:1") != string::npos);
}

bool OpReadConformers::ProcessVec(std::vector<OBBase*>& vec)
{
  // DeferredFormat collects all the molecules, they are processed here, and Deferred Format outputs them
  OBConversion smconv;
  smconv.AddOption("n");
  if(!smconv.SetOutFormat("smi"))
  {
    obErrorLog.ThrowError(__FUNCTION__, "SmilesFormat is not loaded" , obError, onceOnly);
    return false;
  }

  std::string smiles, stored_smiles;
  OBMol* stored_pmol=NULL;
  std::vector<OBBase*>::iterator iter;
  for(iter= vec.begin();iter!=vec.end();++iter)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(*iter);
    if(!pmol)
      continue;
    smiles = smconv.WriteString(pmol);
    Trim(smiles);

    if(stored_smiles==smiles)
    {
      //add the coordinates of the current mol to the stored one as a conformer, and delete current mol
      double *confCoord = new double [pmol->NumAtoms() * 3];
      memcpy((char*)confCoord,(char*)pmol->GetCoordinates(),sizeof(double)*3*pmol->NumAtoms());
      stored_pmol->AddConformer(confCoord);
      delete pmol;
      *iter = NULL;
    }
    else
    {
      stored_pmol = pmol;
      stored_smiles = smiles;
    }
  }

  //erase the NULLS
  vec.erase(std::remove(vec.begin(),vec.end(), (void*)NULL), vec.end());
  return true;
}

//.........这里部分代码省略.........
      //Interpret as a filename if possible
      string& txt =vec [0];
      if( txt.empty() ||
          txt.find('.')==string::npos ||
          !(pFormat = patternConv.FormatFromExt(txt.c_str())) ||
          !patternConv.SetInFormat(pFormat) ||
          !patternConv.ReadFile(&patternMol, txt) ||
          patternMol.NumAtoms()==0)
        //if false, have a valid patternMol from a file
      {
        //is SMARTS/SMILES
        //Replace e.g. [#6] in SMARTS by C so that it can be converted as SMILES
        //for the fingerprint phase, but allow more generality in the SMARTS phase.
        for(;;)
        {
          string::size_type pos1, pos2;
          pos1 = txt.find("[#");
          if(pos1==string::npos)
            break;
          pos2 = txt.find(']');
          int atno;
          if(pos2!=string::npos &&  (atno = atoi(txt.substr(pos1+2, pos2-pos1-2).c_str())) && atno>0)
            txt.replace(pos1, pos2-pos1+1, etab.GetSymbol(atno));
          else
          {
            obErrorLog.ThrowError(__FUNCTION__,"Ill-formed [#n] atom in SMARTS", obError);
            return false;
          }
        }

        bool hasTildeBond;
        if( (hasTildeBond = (txt.find('~')!=string::npos)) ) // extra parens to indicate truth value
        {
          //Find ~ bonds and make versions of query molecule with a single and aromatic bonds
          //To avoid having to parse the SMILES here, replace ~ by $ (quadruple bond)
          //and then replace this in patternMol. Check first that there are no $ already
          //Sadly, isocynanides may have $ bonds.
          if(txt.find('$')!=string::npos)
          {
            obErrorLog.ThrowError(__FUNCTION__,
              "Cannot use ~ bonds in patterns with $ (quadruple) bonds.)", obError);
            return false;
          }
          replace(txt.begin(),txt.end(), '~' , '$');
        }

        //read as standard SMILES
        patternConv.SetInFormat("smi");
        if(!patternConv.ReadString(&patternMol, vec[0]))
        {
          obErrorLog.ThrowError(__FUNCTION__,"Cannot read the SMILES string",obError);
          return false;
        }
        if(hasTildeBond)
        {
          AddPattern(patternMols, patternMol, 0); //recursively add all combinations of tilde bond values
          return true;
        }
      }
      else
      {
        // target(s) are in a file
        patternMols.push_back(patternMol);
        while(patternConv.Read(&patternMol))
          patternMols.push_back(patternMol);
        return true;
      }
    }

    if(OldSOption) //only when using deprecated -S and -aS options
    {
      //make -s option for later SMARTS test
      OBConversion conv;
      if(conv.SetOutFormat("smi"))
      {
        string optiontext = conv.WriteString(&patternMol, true);
        pConv->AddOption("s", OBConversion::GENOPTIONS, optiontext.c_str());
      }
    }

    if(!p)
    {
      //neither -s or -S options provided. Output info rather than doing search
      const FptIndexHeader& header = fs.GetIndexHeader();
      string id(header.fpid);
      if(id.empty())
        id = "default";
      clog << indexname << " is an index of\n " << header.datafilename
           << ".\n It contains " << header.nEntries
           << " molecules. The fingerprint type is " << id << " with "
           << OBFingerprint::Getbitsperint() * header.words << " bits.\n"
           << "Typical usage for a substructure search:\n"
           << "obabel indexfile.fs -osmi -sSMILES\n"
           << "(-s option in GUI is 'Convert only if match SMARTS or mols in file')" << endl;
      return false;
    }

    patternMols.push_back(patternMol);
    return true;
  }

///////////////////////////////////////////////////////////////////////////////
//! \brief compute rms between chemically identical molecules
int main(int argc, char **argv)
{
	bool firstOnly = false;
	if (argc != 3 && argc != 4)
	{
		cerr << "Usage: " << argv[0]
				<< " [-firstonly] <reference structure(s)> <comparison structure(s)>\n";
		cerr << "Computes the heavy-atom RMSD of identical compound structures.\n";
		cerr << "Structures in multi-structure files are compared one-by-one unless -firstonly\n" 
		<< "is passed, in which case only the first structure in the reference file is used.\n";
		exit(-1);
	}

	char *fileRef = argv[1];
	char *fileTest = argv[2];

	if (argc == 4)
	{
		//if iterate is passed as first command, try to match structures in first file to strucutres in second
		if (strcmp("-firstonly", argv[1]) != 0)
		{
			cerr << "Usage: " << argv[0]
					<< " [-firstonly] <reference structure(s)> <comparison structure(s)>\n";
			exit(-1);
		}

		fileRef = argv[2];
		fileTest = argv[3];
		firstOnly = true;
	}

	//open mols
	OBConversion refconv;
	OBFormat *refFormat = refconv.FormatFromExt(fileRef);
	if (!refFormat || !refconv.SetInFormat(refFormat)
			|| !refconv.SetOutFormat("SMI"))
	{
		cerr << "Cannot read reference molecule format!" << endl;
		exit(-1);
	}

	OBConversion testconv;
	OBFormat *testFormat = testconv.FormatFromExt(fileTest);
	if (!testFormat || !testconv.SetInAndOutFormats(testFormat, testFormat))
	{
		cerr << "Cannot read reference molecule format!" << endl;
		exit(-1);
	}

	//read reference
	ifstream ifsref;
	OBMol molref;

	ifsref.open(fileRef);
	if (!ifsref)
	{
		cerr << "Cannot read fixed molecule file: " << fileRef << endl;
		exit(-1);
	}

	//check comparison file
	ifstream ifstest;
	ifstest.open(fileTest);
	if (!ifstest)
	{
		cerr << "Cannot read file: " << fileTest << endl;
		exit(-1);
	}

	while (refconv.Read(&molref, &ifsref))
	{
		processMol(molref);
		Matcher matcher(molref);// create the matcher
		OBMol moltest;
		while (testconv.Read(&moltest, &ifstest))
		{
			if (moltest.Empty())
				break;

			processMol(moltest);

			double rmsd = matcher.computeRMSD(moltest);

			cout << "RMSD " << moltest.GetTitle() << " " << rmsd << "\n";
			if (!firstOnly)
			{
				break;
			}
		}
	}
	return (0);
}