C++ OBConversion::AddOption方法代码示例

extern "C" char *
ob_mol_to_canonical_smiles (char *molfile, int omit_iso_and_chiral_markings)
{
  OBMol mol;
  OBConversion conv;
  string tmpStr (molfile);
  string outstring;
  istringstream molstream (tmpStr);
  ostringstream smilesstream;
  char *tmpSmiles;

  conv.SetInAndOutFormats ("MDL", "CAN");
  conv.AddOption ("n", OBConversion::OUTOPTIONS);
  //conv.AddOption ("c", OBConversion::OUTOPTIONS);
  if (omit_iso_and_chiral_markings != 0)
    {
      conv.AddOption ("i", OBConversion::OUTOPTIONS);
    }

  conv.Read (&mol, &molstream);

  if (mol.Empty ())
    return NULL;

  conv.Write (&mol, &smilesstream);

  outstring = smilesstream.str ();

  outstring = outstring.substr (0, outstring.length () - 1);

  tmpSmiles = strdup (outstring.c_str ());

  return (tmpSmiles);
}

void DoOption(const char* p, OBConversion& Conv,
	      OBConversion::Option_type typ, int& arg, int argc, char *argv[])
{
  while(p && *p) //can have multiple single char options
  {
    char ch[2]="?";
    *ch = *p++;
    const char* txt=NULL;
    //Get the option text if needed
    int nParams = Conv.GetOptionParams(ch, typ);
    if(nParams)
    {
      if(*p)
      {
        txt = p; //use text immediately following the option letter
        p=NULL; //no more single char options
      }
      else if(arg<argc-1)
      {
        txt = argv[++arg]; //use text from next arg
        if(*txt=='-')
        {
          //...unless it is another option
          cerr << "Option -" << ch << " takes a parameter" << endl;
          exit(0);
        }
      }
    }
    Conv.AddOption(ch, typ, txt);
  }
}

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 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);
}

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;
}

void DoOption(const char* p, OBConversion& Conv,
	      OBConversion::Option_type typ, int& arg, int argc, char *argv[]) 
{
  //Unlike babel, cannot have multiple concatenated single char options
  //accepts: -sCCC -s CCC -s"CCC" -s CCC red -sCCC red
  char ch[2]="?";
  *ch = *p++;
  std::string txt;
  //Get the option text
  if(*p)
    txt = p; //use text immediately following the option letter, and keep looking

  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]; 
  }
  Conv.AddOption(ch, typ, txt.c_str());
}

//.........这里部分代码省略.........
                    }
                  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);

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
//.........这里部分代码省略.........

// 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);
//.........这里部分代码省略.........

//.........这里部分代码省略.........
                      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
            {