obmolecformat.h

Go to the documentation of this file.

/**********************************************************************
obmolecformat.h - Subclass of OBFormat for conversion of OBMol.

Copyright (C) 2005 Chris Morley

This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_MOLECULEFORMAT_H
#define OB_MOLECULEFORMAT_H

#include "mol.h"
#include "obconversion.h"

namespace OpenBabel {

class OBMoleculeFormat : public OBFormat
{
public:

        OBMoleculeFormat()
        {
                OBConversion::RegisterOptionParam("b", this, 0, OBConversion::INOPTIONS);
                OBConversion::RegisterOptionParam("s", this, 0, OBConversion::INOPTIONS);
                //The follow are OBMol options, which should not be in OBConversion.
                //But here isn't entirely appropriate either, since could have
                //OBMol formats loaded but none of them derived from this class.
                //However, this possibility is remote.
                OBConversion::RegisterOptionParam("s", NULL, 1,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("v", NULL, 1,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("h", NULL, 0,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("d", NULL, 0,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("b", NULL, 0,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("c", NULL, 0,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("p", NULL, 0,OBConversion::GENOPTIONS); 
                OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS);
                OBConversion::RegisterOptionParam("j", NULL, 0,OBConversion::GENOPTIONS);
        };

        virtual bool ReadChemObject(OBConversion* pConv)
        {
          std::istream &ifs = *pConv->GetInStream();
          if (ifs.peek() == EOF || !ifs.good())
            return false;

                static OBMol* pmol;

                    std::string auditMsg = "OpenBabel::Read molecule ";
                    std::string description(Description());
                    auditMsg += description.substr(0,description.find('\n'));
                    obErrorLog.ThrowError(__FUNCTION__,
                                          auditMsg,
                                          obAuditMsg);

                //With j option, reuse pmol except for the first mol
                if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsFirstInput())
                        pmol = new OBMol;
                
                bool ret=ReadMolecule(pmol,pConv);
                if(ret && pmol->NumAtoms() > 0) //Do transformation and return molecule
                        pConv->AddChemObject(pmol->DoTransformations(pConv->GetOptions(OBConversion::GENOPTIONS)));
                else
                        pConv->AddChemObject(NULL);

                return ret;
        };
        
        virtual bool WriteChemObject(OBConversion* pConv)
        {
                //Retrieve the target OBMol
                OBBase* pOb = pConv->GetChemObject();
                OBMol* pmol = dynamic_cast<OBMol*> (pOb);
                bool ret=false;
                if(pmol)
                {       
                        if(pmol->NumAtoms()==0)
                        {
                                std::string auditMsg = "OpenBabel::Molecule ";
                                auditMsg += pmol->GetTitle();
                                auditMsg += " has 0 atoms";
                                obErrorLog.ThrowError(__FUNCTION__,
                                                auditMsg,
                                                obInfo);
                        }
                        ret=true;

                        std::string auditMsg = "OpenBabel::Write molecule ";
                        std::string description(Description());
                        auditMsg += description.substr(0,description.find('\n'));
                        obErrorLog.ThrowError(__FUNCTION__,
                                              auditMsg,
                                              obAuditMsg);

                        if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsLast()) //With j option, output only at end
                        {
                                ret=WriteMolecule(pmol,pConv);
                                delete pOb;
                        }
                }
                return ret;
        };

        const std::type_info& GetType()
        {
                return typeid(OBMol*);
        };

};

}
#endif //OB_MOLECULEFORMAT_H

---

This file is part of the documentation for Open Babel, version 2.0.2.

Documentation copyright © 1998-2005, the Open Babel Developers.
Open Babel is hosted by:
Generated on Thu Nov 30 20:18:01 2006 by  1.5.1.