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obmolecformat.h - Subclass of OBFormat for conversion of OBMol. |
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Copyright (C) 2005 Chris Morley |
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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#ifndef OB_MOLECULEFORMAT_H |
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#define OB_MOLECULEFORMAT_H |
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#include "mol.hpp" |
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#include "obconversion.hpp" |
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namespace OpenBabel { |
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//! \brief An OBFormat convenience subclass for conversion to/from OBMol data |
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//! |
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//! An OBFormat which converts to and/or from OBMol can derive from this class |
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//! to save duplicating the ReadChemObject() and/or WriteChemObject() methods. |
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//! Derive directly from OBFormat if the object converted is not OBMol or |
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//! if interaction with the framework is required during the execution |
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//! of ReadMolecule() or WriteMolecule(), as for example in CMLFormat |
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class OBMoleculeFormat : public OBFormat |
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{ |
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public: |
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OBMoleculeFormat() |
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{ |
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OBConversion::RegisterOptionParam("b", this, 0, OBConversion::INOPTIONS); |
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OBConversion::RegisterOptionParam("s", this, 0, OBConversion::INOPTIONS); |
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//The follow are OBMol options, which should not be in OBConversion. |
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//But here isn't entirely appropriate either, since could have |
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//OBMol formats loaded but none of them derived from this class. |
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//However, this possibility is remote. |
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OBConversion::RegisterOptionParam("s", NULL, 1,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("v", NULL, 1,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("h", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("d", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("b", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("c", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("p", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS); |
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OBConversion::RegisterOptionParam("j", NULL, 0,OBConversion::GENOPTIONS); |
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}; |
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/// The "Convert" interface functions |
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virtual bool ReadChemObject(OBConversion* pConv) |
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{ |
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std::istream &ifs = *pConv->GetInStream(); |
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if (ifs.peek() == EOF || !ifs.good()) |
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return false; |
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static OBMol* pmol; |
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std::string auditMsg = "OpenBabel::Read molecule "; |
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std::string description(Description()); |
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auditMsg += description.substr(0,description.find('\n')); |
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obErrorLog.ThrowError(__FUNCTION__, |
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auditMsg, |
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obAuditMsg); |
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//With j option, reuse pmol except for the first mol |
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if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsFirstInput()) |
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pmol = new OBMol; |
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bool ret=ReadMolecule(pmol,pConv); |
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if(ret && pmol->NumAtoms() > 0) //Do transformation and return molecule |
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pConv->AddChemObject(pmol->DoTransformations(pConv->GetOptions(OBConversion::GENOPTIONS))); |
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else |
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pConv->AddChemObject(NULL); |
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return ret; |
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}; |
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virtual bool WriteChemObject(OBConversion* pConv) |
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{ |
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//Retrieve the target OBMol |
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OBBase* pOb = pConv->GetChemObject(); |
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OBMol* pmol = dynamic_cast<OBMol*> (pOb); |
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bool ret=false; |
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if(pmol) |
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{ |
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if(pmol->NumAtoms()==0) |
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{ |
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std::string auditMsg = "OpenBabel::Molecule "; |
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auditMsg += pmol->GetTitle(); |
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auditMsg += " has 0 atoms"; |
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obErrorLog.ThrowError(__FUNCTION__, |
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auditMsg, |
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obInfo); |
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} |
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ret=true; |
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std::string auditMsg = "OpenBabel::Write molecule "; |
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std::string description(Description()); |
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auditMsg += description.substr(0,description.find('\n')); |
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obErrorLog.ThrowError(__FUNCTION__, |
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auditMsg, |
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obAuditMsg); |
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if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsLast()) //With j option, output only at end |
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{ |
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ret=WriteMolecule(pmol,pConv); |
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delete pOb; |
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} |
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} |
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return ret; |
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}; |
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const std::type_info& GetType() |
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{ |
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return typeid(OBMol*); |
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}; |
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}; |
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} |
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#endif //OB_MOLECULEFORMAT_H |
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//! \file obmolecformat.h |
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//! \brief Subclass of OBFormat for conversion of OBMol. |
