Example #1
0
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;
  }    
Example #2
0
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;
}
Example #3
0
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);
}
Example #4
0
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);
}
Example #5
0
// 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");
}
Example #6
0
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);
}
Example #7
0
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);
}
Example #8
0
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);
}
Example #9
0
// 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;
}
Example #12
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;
}
Example #14
0
  bool FastSearchFormat::ObtainTarget(OBConversion* pConv, vector<OBMol>& patternMols, const string& indexname)
  {
    //Obtains an OBMol from:
    // the filename in the -s option or
    // the SMARTS string in the -s option or
    // by converting the file in the -S or -aS options (deprecated).
    // If there is no -s -S or -aS option, information on the index file is displayed.

    OBMol patternMol;
    patternMol.SetIsPatternStructure();

    const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);

    bool OldSOption=false;
    //If no -s option, make OBMol from file in -S option or -aS option (both deprecated)
    if(!p)
    {
      p = pConv->IsOption("S",OBConversion::GENOPTIONS);
      if(!p)
        p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly
      OldSOption = true;
    }
    if(p)
    {
      vector<string> vec;
      tokenize(vec, p);

      //ignore leading ~ (not relevant to fastsearch)
      if(vec[0][0]=='~')
        vec[0].erase(0,1);

      if(vec.size()>1 && vec[1]=="exact")
        pConv->AddOption("e", OBConversion::INOPTIONS);

      OBConversion patternConv;
      OBFormat* pFormat;
      //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;
  }
Example #15
0
///////////////////////////////////////////////////////////////////////////////
//! \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);
}
Example #16
0
int main(int argc,char *argv[])
{
  OBConversion Conv(&cin, &cout); //default input and output are console

  OBFormat* pInFormat = NULL;
  OBFormat* pOutFormat = NULL;
  bool inGzip = false;
  bool outGzip = false;
  vector<string> FileList, OutputFileList;
  string OutputFileName;

  // Parse commandline
  bool gotInType = false, gotOutType = false;
  bool SplitOrBatch=false;

  char *oext = NULL;
  char *iext = NULL;

  //load plugs to fully initialize option parameters
  OBPlugin::LoadAllPlugins();

  //Save name of program without its path (and .exe)
  string pn(argv[0]);
  string::size_type pos;
#ifdef _WIN32
  pos = pn.find(".exe");
  if(pos!=string::npos)
    argv[0][pos]='\0';
#endif
  pos = pn.find_last_of("/\\");
  if(pos==string::npos)
    program_name=argv[0];
  else
    program_name=argv[0]+pos+1;

  const char* p;
  int arg;
  for (arg = 1; arg < argc; ++arg)
    {
      if (argv[arg])
        {
          if (argv[arg][0] == '-')
            {
              switch (argv[arg][1])
                {

                case 'V':
                  {
                    cout << "Open Babel " << BABEL_VERSION << " -- "
                         << __DATE__ << " -- " << __TIME__ << endl;
                    exit(0);
                  }

                case 'i':
                  gotInType = true;
                  iext = argv[arg] + 2;
                  if(!*iext)
                    iext = argv[++arg]; //space left after -i: use next argument

                  if (strncasecmp(iext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      iext = argv[++arg];
                      pInFormat = Conv.FormatFromMIME(iext);
                    }
                  else
                    {
                      //The ID provided by the OBFormat class is used as the identifying file extension
                      pInFormat = Conv.FindFormat(iext);
                    }
                  if(pInFormat==NULL)
                    {
                      cerr << program_name << ": cannot read input format!" << endl;
                      usage();
                    }
                  break;

                case 'o':
                  gotOutType = true;
                  oext = argv[arg] + 2;
                  if(!*oext)
                    oext = argv[++arg]; //space left after -i: use next argument

                  if (arg >= argc)
                    usage(); // error in parsing command-line

                  if (strncasecmp(oext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      oext = argv[++arg];
                      pOutFormat = Conv.FormatFromMIME(oext);
                    }
                  else
                    pOutFormat = Conv.FindFormat(oext);

                  if(pOutFormat==NULL)
                    {
                      cerr << program_name << ": cannot write output format!" << endl;
                      usage();
                    }
                  break;

                case 'L': //display a list of plugin type or classes
                  {
                    const char* param=NULL;
                    if(argc>arg+1)
                      param = argv[arg+2];

                    // First assume first arg is a plugin type and
                    // param is a subtype, like babel -L ops gen3D
                    // or first arg is a plugin ID, like babel -L cml
                    OBPlugin* plugin;
                    if ((OBPlugin::GetPlugin("plugins", argv[arg+1]) &&
                         (plugin = OBPlugin::GetPlugin(argv[arg+1], param))) ||
                        (plugin = OBPlugin::GetPlugin(NULL, argv[arg+1])))
                    {
                      //Output details of subtype
                      string txt;
                      plugin->Display(txt, "verbose", argv[arg+1]);
                      cout << "One of the " << plugin->TypeID() << '\n' << txt << endl;
                      return 0;
                    }
                    //...otherwise assume it is a plugin type, like babel -L forcefields
                    //Output list of subtypes
                    OBPlugin::List(argv[arg+1], param);
                    return 0;
                  }
                case '?':
                case 'H':
                  if(isalnum(argv[arg][2]) || arg==argc-2)
                    {
                      if(strncasecmp(argv[arg]+2,"all",3))
                        {
                          const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2;
                          OBFormat* pFormat = Conv.FindFormat(pID);
                          if(pFormat)
                            {
                              cout << pID << "  " << pFormat->Description() << endl;
                              if(pFormat->Flags() & NOTWRITABLE)
                                cout << " This format is Read-only" << endl;
                              if(pFormat->Flags() & NOTREADABLE)
                                cout << " This format is Write-only" << endl;

                              if(strlen(pFormat->SpecificationURL()))
                                cout << "Specification at: " << pFormat->SpecificationURL() << endl;
                            }
                          else
                            cout << "Format type: " << pID << " was not recognized" <<endl;
                        }
                      else
                        {
                          OBPlugin::List("formats","verbose");
                        }
                    }
                  else
                    help();
                  return 0;

                case '-': //long option --name text
                  {
                    //Do nothing if name is empty
                    //Option's text is the next arg provided it doesn't start with -
                    char* nam = argv[arg]+2;
                    if(*nam != '\0')
                      {
                        string txt;
                        int i;
                        for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS)
                              && arg<argc-1 && argv[arg+1];++i) //removed  && *argv[arg+1]!='-'
                          {
                            if(!txt.empty()) txt+=' ';
                            txt += argv[++arg];
                          }
                        if(*nam=='-')
                          {
                            // Is a API directive, e.g.---errorlevel
                            //Send to the pseudoformat "obapi" (without any leading -)
                            OBConversion apiConv;
                            OBFormat* pAPI= OBConversion::FindFormat("obapi");
                            if(pAPI)
                              {
                                apiConv.SetOutFormat(pAPI);
                                apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
                                apiConv.Write(NULL, &std::cout);
                              }
                          }
                        else
                          // Is a long option name, e.g --addtotitle
                          Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
                      }
                  }
                  break;

                case 'm': //multiple output files
                  SplitOrBatch=true;
                  break;

                case 'a': //single character input option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
                  break;

                case 'x': //single character output option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
                  break;

                default: //single character general option
                  p = argv[arg]+1;
                  DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
                  break;
                }
            }
          else
            {
              //filenames
              if(!gotOutType)
                FileList.push_back(argv[arg]);
              else
                OutputFileName = argv[arg];
            }
        }
    }

  if(!gotOutType) //the last file is the output
    {
      if(FileList.empty())
        {
          cerr << "No output file or format spec!" << endl;
          usage();
        }
      OutputFileName = FileList.back();
      FileList.pop_back();
    }

#if defined(_WIN32) && defined(USING_DYNAMIC_LIBS)
  //Expand wildcards in input filenames and add to FileList
  vector<string> tempFileList(FileList);
  FileList.clear();
  vector<string>::iterator itr;
  for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
    DLHandler::findFiles (FileList, *itr);
#endif

  if (!gotInType)
    {
      if(FileList.empty())
        {
          cerr << "No input file or format spec!" <<endl;
          usage();
        }
    }

  if (!gotOutType)
    {
      pOutFormat = Conv.FormatFromExt(OutputFileName.c_str(), outGzip);
      if(pOutFormat==NULL)
        {
          cerr << program_name << ": cannot write output format!" << endl;
          usage();
        }
    }

    if(!Conv.SetInFormat(pInFormat))
    {
      cerr << "Invalid input format" << endl;
      usage();
    }
    if(!Conv.SetOutFormat(pOutFormat, outGzip))
    {
      cerr << "Invalid output format" << endl;
      usage();
    }

  if(SplitOrBatch)
    {
      //Put * into output file name before extension (or ext.gz)
      if(OutputFileName.empty())
        {
          OutputFileName = "*.";
          if (oext != NULL)
            OutputFileName += oext;
        }
      else
        {
          string::size_type pos = OutputFileName.rfind(".gz");
          if(pos==string::npos)
            pos = OutputFileName.rfind('.');
          else
            pos = OutputFileName.rfind('.',pos-1);
          if(pos==string::npos)
            OutputFileName += '*';
          else
            OutputFileName.insert(pos,"*");
        }
    }

  int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);

  Conv.ReportNumberConverted(count);

  if(OutputFileList.size()>1)
    {
      clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
    }

  std::string messageSummary = obErrorLog.GetMessageSummary();
  if (messageSummary.size())
    {
      clog << messageSummary << endl;
    }

#ifdef _DEBUG
  //CM keep window open
  cout << "Press any key to finish" <<endl;
  getch();
#endif

  return 0;
}
Example #17
0
  bool ReactionInChIFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if (pmol == NULL || !pmol->IsReaction())
      return false;
    ostream &ofs = *pConv->GetOutStream();

    OBFormat* pInChIFormat = OBConversion::FindFormat("inchi");
    if (!pInChIFormat)
      return false;

    bool isEquilibrium = pConv->IsOption("e");

    OBConversion inchiconv;
    inchiconv.SetOutFormat(pInChIFormat);
    stringstream ss;
    inchiconv.SetOutStream(&ss);

#define M_REACTANTS 0
#define M_PRODUCTS 1
#define M_AGENTS 2

    OBReactionFacade facade(pmol);

    std::vector<std::vector<std::string> > inchis(3);
    unsigned int nonInchi[3] = { 0, 0, 0 };
    bool hasNonInchi = false;
    OBMol mol;
    for (int part = 0; part <= 2; ++part) {
      unsigned int N;
      switch (part) {
      case M_REACTANTS: N = facade.NumComponents(REACTANT); break;
      case M_PRODUCTS: N = facade.NumComponents(PRODUCT); break;
      case M_AGENTS: N = facade.NumComponents(AGENT); break;
      }
      for (unsigned int i = 0; i < N; ++i) {
        mol.Clear();
        switch (part) {
        case M_REACTANTS: facade.GetComponent(&mol, REACTANT, i); break;
        case M_PRODUCTS: facade.GetComponent(&mol, PRODUCT, i); break;
        case M_AGENTS: facade.GetComponent(&mol, AGENT, i); break;
        }
        if (mol.NumAtoms() == 1 && mol.GetFirstAtom()->GetAtomicNum() == 0) {
          // This represents an unknown component
          nonInchi[part]++;
          hasNonInchi = true;
        }
        else {
          bool ok = inchiconv.Write(&mol);
          if (!ok) {
            nonInchi[part]++;
            hasNonInchi = true;
          }
          else {
            string inchi = ss.str();
            if (strncmp(inchi.c_str(), "InChI=1S/", 9) != 0)
              return false;
            inchis[part].push_back(TrimInChI(inchi.c_str()));
          }
          ss.str("");
        }
      }
    }

    std::sort(inchis[M_REACTANTS].begin(), inchis[M_REACTANTS].end());
    std::sort(inchis[M_PRODUCTS].begin(), inchis[M_PRODUCTS].end());
    std::sort(inchis[M_AGENTS].begin(), inchis[M_AGENTS].end());

    std::string reactants_string = "";
    const int rsize = inchis[M_REACTANTS].size();
    for (int i = 0; i < rsize; ++i) {
      if (i > 0)
        reactants_string += '!';
      reactants_string += inchis[M_REACTANTS][i];
    }
    std::string products_string = "";
    const int psize = inchis[M_PRODUCTS].size();
    for (int i = 0; i < psize; ++i) {
      if (i > 0)
        products_string += '!';
      products_string += inchis[M_PRODUCTS][i];
    }

    bool reactants_first = reactants_string <= products_string;

    ofs << RINCHI_VERSION_STRING;
    if (rsize > 0 || psize > 0 || !inchis[M_AGENTS].empty()) {
      ofs << (reactants_first ? reactants_string : products_string);
      ofs << "<>";
      ofs << (reactants_first ? products_string : reactants_string);
      if (!inchis[M_AGENTS].empty()) {
        ofs << "<>";
        for (std::vector<std::string>::const_iterator vit = inchis[M_AGENTS].begin(); vit != inchis[M_AGENTS].end(); ++vit) {
          if (vit != inchis[M_AGENTS].begin())
            ofs << '!';
          ofs << *vit;
        }
      }
    }
    ofs << "/d";
    if (isEquilibrium)
      ofs << '=';
    else
      ofs << (reactants_first ? '+' : '-');
    if (hasNonInchi) {
      ofs << "/u" << (reactants_first ? nonInchi[M_REACTANTS] : nonInchi[M_PRODUCTS]) << '-'
        << (reactants_first ? nonInchi[M_PRODUCTS] : nonInchi[M_REACTANTS]) << '-'
        << nonInchi[M_AGENTS];
    }

    ofs << '\n';
    return true;
  }
Example #18
0
// This function will call the Babel library to add 
// hydrogens to the residues
void PDB::addHydrogensToPair(AminoAcid& a, AminoAcid& b, int cd1, int cd2)
{
  OBMol mol;
  string addedH;
  istringstream tempss;
  bool ligand;
  if(b.atom[0]->line.find("HETATM") != string::npos)
    {
      ligand = true;
    }
  else
    {
      ligand = false;
    }

  // This section is just to suppress all of the 
  // warning message that aren't important to us
  {
    OBConversion apiConv;
    OBFormat* pAPI = OBConversion::FindFormat("obapi");
    if(pAPI)
      {
        apiConv.SetOutFormat(pAPI);
        apiConv.AddOption("errorlevel", OBConversion::GENOPTIONS, "0");
        apiConv.Write(NULL, &std::cout);
      }
  }

  // Now, let's pack up the information into a string
  string packedFile="";
  for(unsigned int i=0; i < a.altlocs[cd1].size(); i++)
    {
      if( !a.altlocs[cd1][i]->skip )
        {
          packedFile += a.altlocs[cd1][i]->line + "\n";
        }
    }
  
  int cd2_al = cd2;
  if(b.residue == "ASP" || b.residue == "GLU")
    {
      cd2_al = cd2%(b.altlocs.size());
    }

  for(unsigned int i=0; i < b.altlocs[cd2_al].size(); i++)
    {
      if( !b.altlocs[cd2_al][i]->skip )
        {
            packedFile += b.altlocs[cd2_al][i]->line + "\n";
        }
    }
  packedFile += a.makeConect(cd1);
  packedFile += b.makeConect(cd2_al);


  // Now, let's set up some Babel information
  // First, we get the PDB format to tell
  // Babel how to read the information and 
  // how to output it
  OBFormat* pdbformat = this->conv.FindFormat("pdb");
  this->conv.SetInFormat(pdbformat);
  this->conv.SetOutFormat(pdbformat);

  // Here is where Babel reads everything
  // and adds hydrogens to the pair
  // TO ADD: option to set pH
  this->conv.ReadString(&mol,packedFile);
  mol.AddHydrogens(false,true,PH_LEVEL);

  // Let's write the newly written hydrogens to 
  // a string and parse it
  addedH = this->conv.WriteString(&mol);
  tempss.str(addedH);

  // This ensures that the ligand hydrogens are labeled as
  // HETATM instead of ATOM just for the sake of STAAR. 
  // This may be wrong, but it should be fine since we are
  // stripping out that information later when we write 
  // the GAMESS inp files
  if( ligand )
    {
      string line;
      string f = "";
      while( getline(tempss,line) )
        {
          if( line.find(b.residue) != string::npos )
            {
              line.replace(0,6,"HETATM");
            }
          f += line + "\n";
        }
      tempss.seekg(ios_base::beg);
      tempss.clear();
      tempss.str(f);
    }

  this->failure = false;
  this->parsePDB(tempss,99999.99);

  // This is just to ensure that all of the atoms
  // are grouped together because Babel just 
  // appends the H to the end of the file
  if( !ligand )
      this->sortAtoms();

  // Split the atoms up into amino acids and chains
  this->populateChains(true);
}
Example #19
0
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
              continue;
            }

            index[currentCAN] = 1; // don't ever write this ring fragment again

            // OK, now retrieve the canonical ordering for the fragment
            vector<string> canonical_order;
            if (fragments[i].HasData("Canonical Atom Order")) {
              OBPairData *data = (OBPairData*)fragments[i].GetData("Canonical Atom Order");
              tokenize(canonical_order, data->GetValue().c_str());
            }

            // Write out an XYZ-style file with the CANSMI as the title
            cout << fragments[i].NumAtoms() << '\n';
            cout << currentCAN << '\n'; // endl causes a flush

            vector<string>::iterator can_iter;
            unsigned int order;
            OBAtom *atom;

            fragments[i].Center();
            fragments[i].ToInertialFrame();

            for (unsigned int index = 0; index < canonical_order.size(); 
                 ++index) {
              order = atoi(canonical_order[index].c_str());
              atom = fragments[i].GetAtom(order);
              
              snprintf(buffer, BUFF_SIZE, "C%8.3f%8.3f%8.3f\n",
                       atom->x(), atom->y(), atom->z());
              cout << buffer;
            }

          }
        fragments.clear();
        if (index.size() > fragmentCount) {
          fragmentCount = index.size();
          cerr << " Fragments: " << fragmentCount << endl;
        }

      } // while reading molecules (in this file)
    ifs.close();
    ifs.clear();
  } // while reading files

  // loop through the map and output frequencies
  map<string, int>::const_iterator indexItr;
  for (indexItr = index.begin(); indexItr != index.end(); ++indexItr) {
    cerr << (*indexItr).second << " INDEX " << (*indexItr).first << "\n";
  }
    
  return(0);
}
Example #20
0
bool OpNewS::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
  OBMol* pmol = dynamic_cast<OBMol*>(pOb);
  if(!pmol)
    return false;

  // The SMARTS and any other parameters are extracted on the first molecule
  // and stored in the member variables. The parameter is cleared so that
  // the original -s option in transform.cpp is inactive

  //string txt(pmap->find(GetID())->second); // ID can be "s" or "v"

  vector<OBQuery*>::iterator qiter;
  if(OptionText && *OptionText)//(!pConv || pConv->IsFirstInput())
  {
    //Set up on first call
    queries.clear();
    query=NULL;
    nPatternAtoms=0;
    inv=false;

    tokenize(vec, OptionText);
    inv = GetID()[0]=='v';
    if(vec[0][0]=='~')
    {
      inv = true;
      vec[0].erase(0,1);
    }

    //Do not filter out any molecules if there is a parameter "showall";
    //allows -s option to be used for highlighting substructures (--highlight also does this)
    vector<string>::iterator it = std::remove(vec.begin(), vec.end(),"showall");
    showAll = it != vec.end();
    if(showAll)
      vec.erase(it);

    //Store the number of matches required, if as a number in the second parameter, else 0.
    nmatches = 0;
    comparechar = '\0';
    if(vec.size()>1)
    {
      comparechar = vec[1][0];
      if(comparechar=='>' || comparechar=='<')
        vec[1].erase(0,1);
      else
        comparechar = '\0';
      nmatches = atoi(vec[1].c_str());
      if(nmatches) //remove this parameter to still allow coloring
        vec.erase(vec.begin()+1);
    }

    //Interpret as a filename if possible
    MakeQueriesFromMolInFile(queries, vec[0], &nPatternAtoms, strstr(OptionText,"noH"));
    vec.erase(remove(vec.begin(),vec.end(),"noH"),vec.end());//to prevent "noH2" being seen as a color
    
     
    if(queries.empty())
    {
      //SMARTS supplied
    
      // Explicit H in SMARTS requires explicit H in the molecule.
      // Calling AddHydrogens() on a copy of the molecule  is done in parsmart.cpp
      // only when SMARTS contains [H]. Doing more has complications with atom typing,
      // so AddHydrogens here on the molecule (not a copy) when #1 detected.
      addHydrogens = (vec[0].find("#1]")!=string::npos);

      // If extra target mols have been supplied, make a composite SMARTS
      // to test for any of the targets.
      if(ExtraMols.size()>0)
      {
        for(unsigned i=0;i<ExtraMols.size();++i)
        {
          OBConversion extraConv;
          extraConv.AddOption("h");
          if(!extraConv.SetOutFormat("smi"))
            return false;
          // Add option which avoids implicit H being added to the SMARTS.
          // The parameter must be present but can be anything.
          extraConv.AddOption("h",OBConversion::OUTOPTIONS, "X");
          xsmarts += ",$(" + extraConv.WriteString(ExtraMols[i], true) + ")";
        }
      }

      string ysmarts = xsmarts.empty() ? vec[0] : "[$(" + vec[0] + ")" + xsmarts +"]";
      xsmarts.clear();
      if(!sp.Init(ysmarts))
      {
        string msg = ysmarts + " cannot be interpreted as either valid SMARTS "
          "or the name of a file with an extension known to OpenBabel "
          "that contains one or more pattern molecules.";
        obErrorLog.ThrowError(__FUNCTION__, msg, obError, onceOnly);
        delete pmol;
        pmol = NULL;
        pConv->SetOneObjectOnly(); //stop conversion
        return false;
      }
    }
    else
    {
      // Target is in a file. Add extra targets if any supplied
      for(unsigned i=0;i<ExtraMols.size();++i)
        queries.push_back(CompileMoleculeQuery(static_cast<OBMol*>(ExtraMols[i])));
      ExtraMols.clear();
    }

    if(vec.size()>1 && vec[1]=="exact")
    {
      if(queries.empty())
      {
        //Convert SMARTS to SMILES to count number of atoms
        OBConversion conv;
        OBMol patmol;
        if(!conv.SetInFormat("smi") || !conv.ReadString(&patmol, vec[0]))
        {
          obErrorLog.ThrowError(__FUNCTION__, "Cannot read the parameter of -s option, "
          "which has to be valid SMILES when the exact option is used.", obError, onceOnly);
          delete pmol;
          if(pConv)
            pConv->SetOneObjectOnly(); //stop conversion
          return false;
        }
        nPatternAtoms = patmol.NumHvyAtoms();
      }
    }
    else
      nPatternAtoms = 0;

    //disable old versions
    if(pConv)
      pConv->AddOption(GetID(), OBConversion::GENOPTIONS, "");
  }

  bool match = false;
  //These are a vector of each mapping, each containing atom indxs.
  vector<vector<int> > vecatomvec;
  vector<vector<int> >* pMappedAtoms = NULL;

  if(nPatternAtoms)
    if(pmol->NumHvyAtoms() != nPatternAtoms)
      return false;

  unsigned int imol=0; //index of mol in pattern file
  if(!queries.empty()) //filename supplied
  {
    //match is set true if any of the structures match - OR behaviour
    for(qiter=queries.begin();qiter!=queries.end();++qiter, ++imol)
    {
      OBIsomorphismMapper* mapper = OBIsomorphismMapper::GetInstance(*qiter);
      OBIsomorphismMapper::Mappings mappings;
      mapper->MapUnique(pmol, mappings);
      if( (match = !mappings.empty()) ) // extra parens to indicate truth value
      {
        OBIsomorphismMapper::Mappings::iterator ita;
        OBIsomorphismMapper::Mapping::iterator itb;
        for(ita=mappings.begin(); ita!=mappings.end();++ita)//each mapping
        {
          vector<int> atomvec;
          for(itb=ita->begin(); itb!=ita->end();++itb)//each atom index
            atomvec.push_back(itb->second+1);
          vecatomvec.push_back(atomvec);
          atomvec.clear();
        }
        pMappedAtoms = &vecatomvec;
        break;
      }
    }
  }
  else //SMARTS supplied
  {

    if(addHydrogens)
      pmol->AddHydrogens(false,false);

    if( (match = sp.Match(*pmol)) ) // extra parens to indicate truth value
    {
      pMappedAtoms = &sp.GetMapList();
      if(nmatches!=0)
      {
        int n = sp.GetUMapList().size();
        if(comparechar=='>')      match = (n > nmatches);
        else if(comparechar=='<') match = (n < nmatches);
        else                      match = (n == nmatches);
      }
    }
  }

  if((!showAll && (!match && !inv)) || (match && inv))
  {
    //delete a non-matching mol
    delete pmol;
    pmol = NULL;
    return false;
  }

  if(match)
    //Copy the idxes of the first match to a member variable so that it can be retrieved from outside
    firstmatch.assign(pMappedAtoms->begin()->begin(), pMappedAtoms->begin()->end());
  else
    firstmatch.clear();

  if(match && !inv && vec.size()>=2 && !vec[1].empty() && !nPatternAtoms)
  {
    vector<vector<int> >::iterator iter;

    if (vec[1]=="extract" || (vec.size()>3 && vec[2]=="extract"))
    {
      //Delete all unmatched atoms. Use only the first match
      ExtractSubstruct(pmol, *pMappedAtoms->begin());
      return true;
    }

    // color the substructure if there is a second parameter which is not "exact" or "extract" or "noH"
    // with multiple color parameters use the one corresponding to the query molecule, or the last
    if(imol>vec.size()-2)
      imol = vec.size()-2;
    for(iter=pMappedAtoms->begin();iter!=pMappedAtoms->end();++iter)//each match
       AddDataToSubstruct(pmol, *iter, "color", vec[imol+1]);
    return true;
  }

  if(pConv && pConv->IsLast())
  {
    for(qiter=queries.begin();qiter!=queries.end();++qiter)
      delete *qiter;
    queries.clear();
  }
  return true;
}
Example #21
0
void phmodel_test()
{
  OBMol mol;
  OBConversion conv;
  conv.SetInFormat("smi");
  conv.SetOutFormat("smi");

  unsigned int test = 0;

  // amine acid COOH pKa = 4.0 (carboxylic acid entry in phmodel.txt)
  // amino acid NH3+ pKa = 10.0 (amine entry in phmodel.txt)

  // 
  // Aspartic acid (sidechain COOH pKa = 3.8)
  //
  conv.ReadString(&mol, "NC(CC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH COOH
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 17, "Aspartic acid pH 1.0" );

  conv.ReadString(&mol, "NC(CC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 3.9); // NH3+ COOH COO-
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 16, "Aspartic acid pH 3.9" );

  conv.ReadString(&mol, "NC(CC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- COO-
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 15, "Aspartic acid pH 7.4" );

  conv.ReadString(&mol, "NC(CC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- COO-
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 14, "Aspartic acid pH 13.0" );

  // 
  // Glutamic acid (sidechain COOH pKa = 4.3)
  //
  conv.ReadString(&mol, "NC(CCC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH COOH
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 20, "Glutamic acid pH 1.0" );

  conv.ReadString(&mol, "NC(CCC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 4.15); // NH3+ COOH COO-
  //conv.Write(&mol, &cout);
 
  // known bug
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 19, "Glutamic acid pH 4.15" );

  conv.ReadString(&mol, "NC(CCC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- COO-
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 18, "Glutamic acid pH 7.4" );

  conv.ReadString(&mol, "NC(CCC(O)=O)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- COO-
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 17, "Glutamic acid pH 13.0" );

  // 
  // Histidine (sidechain nH+ pKa = 6.08)
  //
  conv.ReadString(&mol, "NC(Cc1ncnc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH nH+
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 22, "Histidine pH 1.0" );
  
  conv.ReadString(&mol, "NC(Cc1ncnc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 5.0); // NH3+ COO- nH+
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 21, "Histidine pH 5.0" );

  conv.ReadString(&mol, "NC(Cc1ncnc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- n:
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 20, "Histidine pH 7.4" );

  conv.ReadString(&mol, "NC(Cc1ncnc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- n:
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 19, "Histidine pH 13.0" );

  // 
  // Lysine (sidechain NH3+ pKa = 8.28)
  //
  conv.ReadString(&mol, "NC(CCCCN)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH NH3+
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 26, "Lysine pH 1.0" );

  conv.ReadString(&mol, "NC(CCCCN)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- NH3+
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 25, "Lysine pH 7.4" );

  conv.ReadString(&mol, "NC(CCCCN)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 9.0); // NH3+ COO- NH2
  //conv.Write(&mol, &cout);
  
  // known bug
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 24, "Lysine pH 9.0" );

  conv.ReadString(&mol, "NC(CCCCN)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- NH2
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 23, "Lysine pH 13.0" );

  // 
  // Tyrosine (sidechain OH pKa = 10.1)
  //
  conv.ReadString(&mol, "NC(Cc1ccc(O)cc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH NH3+
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 25, "Tyrosine pH 1.0" );

  conv.ReadString(&mol, "NC(Cc1ccc(O)cc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- NH3+
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 24, "Tyrosine pH 7.4" );

  conv.ReadString(&mol, "NC(Cc1ccc(O)cc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 10.05); // NH3+ COO- NH2
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 23, "Tyrosine pH 10.05" );

  conv.ReadString(&mol, "NC(Cc1ccc(O)cc1)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- NH2
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 22, "Tyrosine pH 13.0" );

  // 
  // Arginine (sidechain =NH2+ pKa = 12.0)
  //
  conv.ReadString(&mol, "NC(CCCNC(N)=N)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH =NH2+
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 28, "Arginine pH 1.0" );

  conv.ReadString(&mol, "NC(CCCNC(N)=N)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- NH3+
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 27, "Arginine pH 7.4" );

  conv.ReadString(&mol, "NC(CCCNC(N)=N)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 11.0); // NH3+ COO- NH2
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 26, "Arginine pH 11.0" );

  conv.ReadString(&mol, "NC(CCCNC(N)=N)C(O)=O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- NH2
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 25, "Arginine pH 13.0" );

  // 
  // Gly-Gly (terminal NH3+, COOH and the amide bond)
  //
  conv.ReadString(&mol, "NCC(=O)NCC(=O)O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 1.0); // NH3+ COOH =NH2+
  //conv.Write(&mol, &cout);
  
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 18, "Gly-Gly pH 1.0" );

  conv.ReadString(&mol, "NCC(=O)NCC(=O)O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 7.4); // NH3+ COO- NH3+
  //conv.Write(&mol, &cout);
 
  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 17, "Gly-Gly pH 7.4" );

  conv.ReadString(&mol, "NCC(=O)NCC(=O)O");
  mol.SetAutomaticFormalCharge(true);
  mol.AddHydrogens(false, true, 13.0); // NH2 COO- NH2
  //conv.Write(&mol, &cout);

  BOOST_CHECK_MESSAGE( mol.NumAtoms() == 16, "Gly-Gly pH 13.0" );

}
Example #22
0
void genericSmilesCanonicalTest(const std::string &smiles)
{
  cout << "Testing generic smiles <-> canonical smiles" << endl;
  // read a smiles string
  OBMol mol;
  OBConversion conv;
  OB_REQUIRE( conv.SetInFormat("smi") );
  OB_REQUIRE( conv.SetOutFormat("can") );
  cout << "smiles: " << smiles << endl;
  // read a smiles string
  OB_REQUIRE( conv.ReadString(&mol, smiles) );

  // store the stereo data for the smiles string using unique symmetry ids
  std::vector<OBTetrahedralStereo::Config> tetrahedral1;
  std::vector<OBCisTransStereo::Config> cistrans1;
  std::vector<OBSquarePlanarStereo::Config> squareplanar1;

  // get the stereo data
  OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
  std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);

  std::vector<unsigned int> canlbls;
  std::vector<unsigned int> symclasses;
  OBGraphSym gs1(&mol);
  gs1.GetSymmetry(symclasses);
  CanonicalLabels(&mol, symclasses, canlbls);
  cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
  for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
    if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
      // convert to tetrahedral data
      OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
      OB_REQUIRE( ts );
      OB_ASSERT( ts->IsValid() );
      if (!ts->IsValid())
        continue;

      OBTetrahedralStereo::Config config = ts->GetConfig();
      // convert atom ids to symmetry ids
     if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.from))
        config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      tetrahedral1.push_back(config);
    } else
    if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
      // convert to tetrahedral data
      OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
      OB_REQUIRE( ct );
      OB_ASSERT( ct->IsValid() );

      OBCisTransStereo::Config config = ct->GetConfig();
      // convert atom ids to symmetry ids
      config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
      config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      cistrans1.push_back(config);
    } else
    if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
      // convert to tetrahedral data
      OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
      OB_REQUIRE( sp );
      OB_ASSERT( sp->IsValid() );
      if (!sp->IsValid())
        continue;

      OBSquarePlanarStereo::Config config = sp->GetConfig();
      // convert atom ids to symmetry ids
     if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      squareplanar1.push_back(config);
    }


  }

  // write to can smiles
  std::string canSmiles = conv.WriteString(&mol);
  cout << "canSmiles: " << canSmiles;
  // read can smiles in again
  OB_REQUIRE( conv.ReadString(&mol, canSmiles) );

  // store the stereo data for the smiles string using unique symmetry ids
  std::vector<OBTetrahedralStereo::Config> tetrahedral2;
  std::vector<OBCisTransStereo::Config> cistrans2;
  std::vector<OBSquarePlanarStereo::Config> squareplanar2;

  // get the stereo data
  OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
  stereoData = mol.GetAllData(OBGenericDataType::StereoData);

  OBGraphSym gs2(&mol);
  gs2.GetSymmetry(symclasses);
  CanonicalLabels(&mol, symclasses, canlbls);
  cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
  for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
    if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
      // convert to tetrahedral data
      OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
      OB_REQUIRE( ts );
      OB_ASSERT( ts->IsValid() );

      OBTetrahedralStereo::Config config = ts->GetConfig();
      // convert atom ids to symmetry ids
      if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.from))
        config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      tetrahedral2.push_back(config);
    }
    if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
      // convert to tetrahedral data
      OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
      OB_REQUIRE( ct );
      OB_ASSERT( ct->IsValid() );

      OBCisTransStereo::Config config = ct->GetConfig();
      // convert atom ids to symmetry ids
      config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
      config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      cistrans2.push_back(config);
    } else
    if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
      // convert to tetrahedral data
      OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
      OB_REQUIRE( sp );
      OB_ASSERT( sp->IsValid() );

      OBSquarePlanarStereo::Config config = sp->GetConfig();
      // convert atom ids to symmetry ids
      if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      squareplanar2.push_back(config);
    }

  }

  // compare the tetrahedral structs
  OB_ASSERT( tetrahedral1.size() == tetrahedral2.size() );
  for (unsigned int i = 0; i < tetrahedral1.size(); ++i) {
    for (unsigned int j = 0; j < tetrahedral2.size(); ++j) {
      if (tetrahedral1[i].center == tetrahedral2[j].center)
        OB_ASSERT( tetrahedral1[i] == tetrahedral2[j] );
        if ( tetrahedral1[i] != tetrahedral2[j] ) {
          cout << "1 = " << tetrahedral1[i] << endl;
          cout << "2 = " << tetrahedral2[j] << endl;
        }
    }
  }
  // compare the cistrans structs
  OB_ASSERT( cistrans1.size() == cistrans2.size() );
  for (unsigned int i = 0; i < cistrans1.size(); ++i) {
    for (unsigned int j = 0; j < cistrans2.size(); ++j) {
      if ((cistrans1[i].begin == cistrans2[j].begin) && (cistrans1[i].end == cistrans2[j].end))
        OB_ASSERT( cistrans1[i] == cistrans2[j] );
      if ((cistrans1[i].begin == cistrans2[j].end) && (cistrans1[i].end == cistrans2[j].begin))
        OB_ASSERT( cistrans1[i] == cistrans2[j] );
    }
  }
  // compare the square-planar structs
  OB_ASSERT( squareplanar1.size() == squareplanar2.size() );
  for (unsigned int i = 0; i < squareplanar1.size(); ++i) {
    for (unsigned int j = 0; j < squareplanar2.size(); ++j) {
      if (squareplanar1[i].center == squareplanar2[j].center)
        OB_ASSERT( squareplanar1[i] == squareplanar2[j] );
        if ( squareplanar1[i] != squareplanar2[j] ) {
          cout << "1 = " << squareplanar1[i] << endl;
          cout << "2 = " << squareplanar2[j] << endl;
        }
    }
  }

  cout << "." << endl << endl;
}
Example #23
0
int main(int argc,char **argv)
{
  OBForceField* pFF = OBForceField::FindForceField("Ghemical");
  pFF->SetLogFile(&cout);
  pFF->SetLogLevel(OBFF_LOGLVL_LOW);

  OBMol mol;
  mol.Clear();

  char commandline[100];
  vector<string> vs;

  cout << endl;
  cout << "openbabel                            " << endl;
  cout << "M O L E C U L A R   M E C H A N I C S" << endl;
  cout << "                              program" << endl;
  cout << "                v 0.1                " << endl << endl;

  while (1) {

    cout << "command > ";
    cin.getline(commandline, 100);

    //
    // commands with no parameters
    //
    if (EQn(commandline, "quit", 4) || cin.eof()) {
      cout << "bye." << endl;
      exit(0);
    }
    
    if (EQn(commandline, "help", 4) || cin.eof()) {
      cout << endl;
      cout << "commands:            description:" << endl;
      cout << "load <filename>      load a molecule from filename" << endl;
      cout << "save <filename>      save currently loaded molecule to filename" << endl;
      cout << "ff <forcefield>      select the force field" << endl;
      cout << "forcefields          print the available forcefields" << endl;
      cout << endl;
      cout << "energy               calculate the energy" << endl;
      cout << "ebond                calculate the bond stretching energy" << endl;
      cout << "eangle               calculate the angle bending energy" << endl;
      cout << "estrbnd              calculate the stretch-bending enregy" << endl;
      cout << "eoop                 calculate the out-of-plane bending energy" << endl;
      cout << "etorsion             calculate the torsional energy" << endl;
      cout << "evdw                 calculate the Van der Waals energy" << endl;
      cout << "eeq                  calculate the electrostatic energy" << endl;
      cout << endl;
      cout << "sd <n>               steepest descent energy minimization for n steps" << endl;
      cout << "cg <n>               conjugate gradients energy minimization for n steps" << endl;
      cout << "" << endl;
      cout << "addH                 add hydrogens" << endl;
      cout << "delH                 delete hydrogens" << endl;
      cout << endl;
      cout << "gen                  generate/minimize a (random) structure" << endl;
      cout << "rs                   rotate around all rotatable bonds" << endl;
      cout << "nconf                print the number of conformers" << endl;
      cout << "conf <n>             select conformer n" << endl;
      cout << endl;
      cout << "quit                 quit" << endl;
      cout << endl;
      continue;
    }

    // calculate the energy
    if (EQn(commandline, "energy", 6)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  total energy = " << pFF->Energy() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "ebond", 5)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  bond stretching energy = " << pFF->E_Bond() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "eangle", 6)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  angle bending energy = " << pFF->E_Angle() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "estrbnd", 7)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  stretch-bending energy = " << pFF->E_StrBnd() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "eoop", 4)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  out-of-plane bending energy = " << pFF->E_OOP() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "etorsion", 8)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  torsional energy = " << pFF->E_Torsion() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }

    if (EQn(commandline, "evdw", 4)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  Van der Waals energy = " << pFF->E_VDW() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }
    
    if (EQn(commandline, "eeq", 3)) {
      if (mol.Empty()) {
        cout << "no molecule loaded." << endl;
        continue;
      }
      cout << endl << "  electrostatic energy = " << pFF->E_Electrostatic() << " " << pFF->GetUnit() << endl << endl;
      continue;
    }
    
    if (EQn(commandline, "addH", 4)) {
      int num1, num2;
      num1 = mol.NumAtoms();
      mol.AddHydrogens(false, true);
      num2 = mol.NumAtoms();
      cout << (num2 - num1) << " hydrogens added." << endl;
      
      if (!pFF->Setup(mol)) {
        cout << "error while initializing the force field for this molecule." <<endl;
        continue;
      }
      continue;
    }
    
    if (EQn(commandline, "delH", 4)) {
      int num1, num2;
      num1 = mol.NumAtoms();
      mol.DeleteHydrogens();
      num2 = mol.NumAtoms();
      cout << (num1 - num2) << " hydrogens deleted." << endl;
      
      if (!pFF->Setup(mol)) {
        cout << "error while initializing the force field for this molecule." <<endl;
        continue;
      }
      continue;
    }
    
    if (EQn(commandline, "gen", 3)) {
      //pFF->GenerateCoordinates();
      pFF->UpdateCoordinates(mol);
      continue;
    }
    
    if (EQn(commandline, "rs", 2)) {
      pFF->SystematicRotorSearch();
      pFF->UpdateCoordinates(mol);
      continue;
    }
    
    if (EQn(commandline, "nconf", 5)) {
      cout << endl << "  number of conformers = " << mol.NumConformers() << endl << endl;
      continue;
    }


    //
    // commands with parameters
    //
    tokenize(vs, commandline);
    
    // select forcefield
    if (EQn(commandline, "ff", 2)) {
      if (vs.size() < 2) {
        cout << "no <forcefield> specified." << endl;
        continue;
      }
      
      pFF = OBForceField::FindForceField(vs[1]);

      if (!mol.Empty())
        if (!pFF->Setup(mol))
          cout << "error while initializing the force field (" << vs[1] << ") for this molecule." <<endl;

      continue;
    }

   
    // load <filename>
    if (EQn(commandline, "load", 4)) {
      if (vs.size() < 2) {
        cout << "no <filename> specified." << endl;
        continue;
      }
      
      ifstream ifs;
      OBConversion conv;
      OBFormat *format_in = conv.FormatFromExt(vs[1].c_str());
   
      if (!format_in || !conv.SetInFormat(format_in)) {
        cout << "could not detect format." << endl;
        continue;
      }
       
      ifs.open(vs[1].c_str());
      if (!ifs) {
        cout << "could not open '" << vs[1] << "'." <<endl;
        continue;
      }
      
      mol.Clear();
      if (!conv.Read(&mol, &ifs)) {
        cout << "could not read a molecule from '" << vs[1] << "'." <<endl;
        continue;
      }
      
      if (mol.Empty()) {
        cout << "this molecule is empty." <<endl;
        continue;
      }

      if (!pFF->Setup(mol)) {
        cout << "error while initializing the force field for this molecule." <<endl;
        continue;
      }

      cout << "molecule succesfully loaded." << endl;
      cout << "  " << mol.NumAtoms() << " atoms" << endl;
      cout << "  " << mol.NumBonds() << " bonds" << endl;

      ifs.close();
 
      continue;
    }
    
    // save <filename>
    if (EQn(commandline, "save", 4)) {
      if (vs.size() < 2) {
        cout << "no <filename> specified." << endl;
        continue;
      }
      
      ofstream ofs;
      OBConversion conv;
      OBFormat *format_out = conv.FormatFromExt(vs[1].c_str());
   
      if (!format_out || !conv.SetOutFormat(format_out)) {
        cout << "could not detect format." << endl;
        continue;
      }
       
      ofs.open(vs[1].c_str());
      if (!ofs) {
        cout << "could not open '" << vs[1] << "'." <<endl;
        continue;
      }
      
      if (!conv.Write(&mol, &ofs)) {
        cout << "could not read a molecule from '" << vs[1] << "'." <<endl;
        continue;
      }
      
      cout << "molecule succesfully saved." << endl;
      cout << "  " << mol.NumAtoms() << " atoms" << endl;
      cout << "  " << mol.NumBonds() << " bonds" << endl;

      ofs.close();
 
      continue;
    }

    // steepest descent
    if (EQn(commandline, "sd", 2)) {
      if (vs.size() < 2) {
        cout << "no <n> steps specified." << endl;
        continue;
      }

      pFF->SteepestDescent(atoi(vs[1].c_str()), OBFF_ANALYTICAL_GRADIENT);
      pFF->UpdateCoordinates(mol);

      continue;
    }

    // conjugate gradients
    if (EQn(commandline, "cg", 2)) {
      if (vs.size() < 2) {
        cout << "no <n> steps specified." << endl;
        continue;
      }

      pFF->ConjugateGradients(atoi(vs[1].c_str()), OBFF_ANALYTICAL_GRADIENT);
      pFF->UpdateCoordinates(mol);

      continue;
    }

    cout << "invalid command." << endl;
  }

  return(1);
}
Example #24
0
int main(int argc,char *argv[])
{
  OBConversion Conv(&cin, &cout); //default input and output are console 

  OBFormat* pInFormat = NULL;
  OBFormat* pOutFormat = NULL;
  vector<string> FileList, OutputFileList;
  string OutputFileName;

  // Parse commandline
  bool gotInType = false, gotOutType = false;
  bool SplitOrBatch=false;

  char *oext = NULL;
  char *iext = NULL;

  //Save name of program without its path (and .exe)
  string pn(argv[0]);
  string::size_type pos;
#ifdef _WIN32
  pos = pn.find(".exe");
  if(pos!=string::npos)
    argv[0][pos]='\0';
#endif
  pos = pn.find_last_of("/\\");
  if(pos==string::npos)
    program_name=argv[0];
  else
    program_name=argv[0]+pos+1;

  const char* p;
  int arg;
  for (arg = 1; arg < argc; ++arg)
    {
      if (argv[arg])
        {
          if (argv[arg][0] == '-')
            {
              char opchar[2]="?";
              opchar[0]=argv[arg][1];
              switch (opchar[0])
                {

                case 'V':
                  {
                    cout << "Open Babel " << BABEL_VERSION << " -- " 
                         << __DATE__ << " -- " << __TIME__ << endl;
                    exit(0);
                  }

                case 'i':
                  //Parameter is the input format which overrides any file extensions
                  gotInType = true;
                  iext = argv[arg] + 2;
                  if(!*iext)
                    iext = argv[++arg]; //space left after -i: use next argument

                  if (strncasecmp(iext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      iext = argv[++arg];
                      pInFormat = Conv.FormatFromMIME(iext);
                    }
                  else
                      pInFormat = Conv.FindFormat(iext);
                  if(pInFormat==NULL)
                    {
                      cerr << program_name << ": cannot read input format!" << endl;
                      usage();
                    }
                  break;

                case 'o':
                  //Parameter is the output format which overrides any file extension
                  gotOutType = true;
                  oext = argv[arg] + 2;
                  if(!*oext)
                    oext = argv[++arg]; //space left after -i: use next argument

                  if (strncasecmp(oext, "MIME", 4) == 0)
                    {
                      // get the MIME type from the next argument
                      oext = argv[++arg];
                      pOutFormat = Conv.FormatFromMIME(oext);
                    }
                  else
                    pOutFormat = Conv.FindFormat(oext);

                  if(pOutFormat==NULL)
                    {
                      cerr << program_name << ": cannot write output format!" << endl;
                      usage();
                    }
                  break;

                case 'O':
                  OutputFileName = argv[arg] + 2;
                  if(OutputFileName.size()<3)
                    OutputFileName = argv[++arg]; //space left after -O: use next argument
                  break;

                case 'L': //display a list of plugin type or classes
                  {
                    const char* param=NULL;
                    if(argc>arg+1)
                      param = argv[arg+2];

                    // First assume first arg is a plugin type and
                    // param is a subtype, like babel -L ops gen3D
                    // or first arg is a plugin ID, like babel -L cml
                    OBPlugin* plugin;
                    if(OBPlugin::GetPlugin("plugins", argv[arg+1])
                      && (plugin = OBPlugin::GetPlugin(argv[arg+1], param))
                      || (plugin = OBPlugin::GetPlugin(NULL, argv[arg+1])))
                    {
                      //Output details of subtype
                      string txt;
                      plugin->Display(txt, "verbose", argv[arg+1]);
                      cout << "One of the " << plugin->TypeID() << '\n' << txt << endl;
                      return 0;
                    }
                    //...otherwise assume it is a plugin type, like babel -L forcefields
                    //Output list of subtypes
                    OBPlugin::List(argv[arg+1], param);
                    return 0;
                  }

                case '?':
                case 'H':
                  if(isalnum(argv[arg][2]) || arg==argc-2)
                    {
                      if(strncasecmp(argv[arg]+2,"all",3))
                        {
                          OBFormat* pFormat
                            = (arg==argc-2) ? Conv.FindFormat(argv[arg+1]) : Conv.FindFormat(argv[arg]+2);
                          if(pFormat)
                            {
                              cout << argv[arg]+2 << "  " << pFormat->Description() << endl;
                              if(pFormat->Flags() & NOTWRITABLE)
                                cout << " This format is Read-only" << endl;
                              if(pFormat->Flags() & NOTREADABLE)
                                cout << " This format is Write-only" << endl;

                              if(strlen(pFormat->SpecificationURL()))
                                cout << "Specification at: " << pFormat->SpecificationURL() << endl;
                            }
                          else
                            cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
                        }
                      else
                        {
                          OBPlugin::List("formats","verbose");
                        }
                    }
                  else
                    help();
                  return 0;

                case '-': //long option --name text
                  {
                    //Option's text is in the next and subsequent args, until one starts with -
                    char* nam = argv[arg]+2;
                    if(!strcasecmp(nam, "help")) //special case handled here
                    {
                      help();
                      return 0;
                    }
                    if(*nam != '\0') //Do nothing if name is empty
                      {
                        string txt;
                        while(arg<argc-1 && *argv[arg+1]!='-')
                          {
                            //use text from subsequent args
                            if(!txt.empty())txt += ' '; //..space separated if more than one
                            txt += argv[++arg]; 
                          }

                        // If a API directive, e.g.---errorlevel
                        // send to the pseudoformat "obapi" (without any leading -)
                        if(*nam=='-')
                          {
                            OBConversion apiConv;
                            OBFormat* pAPI= OBConversion::FindFormat("obapi");
                            if(pAPI)
                              {
                                apiConv.SetOutFormat(pAPI);
                                apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
                                apiConv.Write(NULL, &std::cout);
                              }
                          }
                        else
                          // Is a normal long option name, e.g --addtotitle
                          Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
                      }
                  }
                  break;
					
                case 'm': //multiple output files
                  SplitOrBatch=true;
                  break;
					
                case 'a': //single character input option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
                  break;

                case 'x': //single character output option
                  p = argv[arg]+2;
                  DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
                  break;

                //Not essential, but allows these options to be before input filenames
                //since we know they take one parameter, and are the most likely options to be misplaced
                case 'f':
                case 'l':
                  p = argv[arg] + 2;
                  if(!*p)
                    p = argv[++arg]; //space left after -f: use next argument
                  Conv.AddOption(opchar, OBConversion::GENOPTIONS, p);
                  break;
                
                case ':':
                  //e.g. -:c1ccccc1. SMILES passed as a file name and handled in OBConversion
                  FileList.push_back(argv[arg]);
                  break;

                default: //single character general option
                  p = argv[arg]+1;
                  DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
                  break;
                }
            }
          else //filenames
              FileList.push_back(argv[arg]);
        }
    }

#ifdef _WIN32
  //Expand wildcards in input filenames and add to FileList
  vector<string> tempFileList(FileList);
  FileList.clear();
  vector<string>::iterator itr;
  for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
  {
    if((*itr)[0]=='-')
      FileList.push_back(*itr);
    else
      DLHandler::findFiles (FileList, *itr);
  }
#endif
  
  if (!gotInType)
    {
      if(FileList.empty())
        {
          cerr << "No input file or format spec or possibly a misplaced option.\n"
            "Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
          usage();
        }
    }

  if (!gotOutType)
    {
      //check there is a valid output format, but the extension will be re-interpreted in OBConversion
      pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
      if(OutputFileName.empty() || pOutFormat==NULL)
        {
          cerr << "Missing or unknown output file or format spec or possibly a misplaced option.\n"
            "Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
          usage();
        }
    }
  
    if(!Conv.SetInFormat(pInFormat))
    {
      cerr << "Invalid input format" << endl;
      usage();
    }
    if(!Conv.SetOutFormat(pOutFormat))
    {
      cerr << "Invalid output format" << endl;
      usage();
    }

  if(SplitOrBatch)
    {
      //Put * into output file name before extension (or ext.gz)
      if(OutputFileName.empty())
        {
          OutputFileName = "*.";
          OutputFileName += oext;
        }
      else
        {
          string::size_type pos = OutputFileName.rfind(".gz");
          if(pos==string::npos)
            pos = OutputFileName.rfind('.');
          else
            pos = OutputFileName.rfind('.',pos-1);
          if(pos==string::npos)
            OutputFileName += '*';
          else
            OutputFileName.insert(pos,"*");
        }
    }

  int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
 
  Conv.ReportNumberConverted(count);

  if(OutputFileList.size()>1)
    {
      clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
    }

  //std::string messageSummary = obErrorLog.GetMessageSummary();
  //if (messageSummary.size())
  //  {
  //    clog << messageSummary << endl;
  //  }

#ifdef _DEBUG
  //CM keep window open
  cout << "Press any key to finish" <<endl;
  getch();
#endif
  
  return 0;
}
Example #25
0
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;

      string inchiString = "-";
      if (inchiFormat) {
        conv.SetOutFormat(inchiFormat);
        inchiString = conv.WriteString(&mol);
        if ( inchiString.length() == 0 )
        {
          inchiString = "-";
        }
      }
      cout << "InChI            " << inchiString << endl;

      cout << "num_atoms        " << mol.NumAtoms() << endl;
      cout << "num_bonds        " << mol.NumBonds() << endl;
      cout << "num_residues     " << mol.NumResidues() << endl;
      cout << "num_rotors       " << mol.NumRotors() << endl;
      if (mol.NumResidues() > 0)
        cout << "sequence         " << sequence(mol) << endl;
      else
        cout << "sequence         " << "-" << endl;

      cout << "num_rings        " << nrings(mol) << endl;

      OBDescriptor* pDesc;
      pDesc= OBDescriptor::FindType("logP");
      if(pDesc)
        cout << "logP             " << pDesc->Predict(&mol) << endl;

      pDesc = OBDescriptor::FindType("TPSA");
      if(pDesc)
        cout << "PSA              " << pDesc->Predict(&mol) << endl;

      pDesc = OBDescriptor::FindType("MR");
      if(pDesc)
        cout << "MR               " << pDesc->Predict(&mol) << endl;

      cout << "$$$$" << endl; // SDF like end of compound descriptor list
      
      //Other OBDescriptors could be output here, even ones that were rarely
      // used. Since these are plugin classes, they may not be loaded, but
      // then with code like the above they are just ignored.
    } // end for loop
  
  return(0);
}