Biomol/ControlParameterFunctions.hpp

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/* 
 * ControlParameterFunctions.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_BIOMOL_CONTROLPARAMETERFUNCTIONS_HPP
#define CDPL_BIOMOL_CONTROLPARAMETERFUNCTIONS_HPP
 
#include "CDPL/Biomol/APIPrefix.hpp"
#include "CDPL/Biomol/ResidueDictionary.hpp"
#include "CDPL/Biomol/MMCIFDataProcessingFunction.hpp"
 
 
namespace CDPL
{
 
    namespace Base
    {
 
        class ControlParameterContainer;
    }
 
    namespace Biomol
    {
 
        CDPL_BIOMOL_API bool getStrictErrorCheckingParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setStrictErrorCheckingParameter(Base::ControlParameterContainer& cntnr, bool strict);
 
        CDPL_BIOMOL_API bool hasStrictErrorCheckingParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearStrictErrorCheckingParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getCheckLineLengthParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setCheckLineLengthParameter(Base::ControlParameterContainer& cntnr, bool check);
 
        CDPL_BIOMOL_API bool hasCheckLineLengthParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearCheckLineLengthParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API const ResidueDictionary::SharedPointer& getResidueDictionaryParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setResidueDictionaryParameter(Base::ControlParameterContainer& cntnr, const ResidueDictionary::SharedPointer& dict);
 
        CDPL_BIOMOL_API bool hasResidueDictionaryParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearResidueDictionaryParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getApplyDictFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setApplyDictFormalChargesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasApplyDictFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearApplyDictFormalChargesParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getApplyDictAtomTypesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setApplyDictAtomTypesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasApplyDictAtomTypesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearApplyDictAtomTypesParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getCalcMissingFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setCalcMissingFormalChargesParameter(Base::ControlParameterContainer& cntnr, bool calc);
 
        CDPL_BIOMOL_API bool hasCalcMissingFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearCalcMissingFormalChargesParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getPerceiveMissingBondOrdersParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPerceiveMissingBondOrdersParameter(Base::ControlParameterContainer& cntnr, bool perceive);
 
        CDPL_BIOMOL_API bool hasPerceiveMissingBondOrdersParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPerceiveMissingBondOrdersParameter(Base::ControlParameterContainer& cntnr);
 
        
        CDPL_BIOMOL_API bool getCombineInterferingResidueCoordinatesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setCombineInterferingResidueCoordinatesParameter(Base::ControlParameterContainer& cntnr, bool comb);
 
        CDPL_BIOMOL_API bool hasCombineInterferingResidueCoordinatesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearCombineInterferingResidueCoordinatesParameter(Base::ControlParameterContainer& cntnr);
 
        
        CDPL_BIOMOL_API bool getPDBApplyDictAtomBondingToStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBApplyDictAtomBondingToStdResiduesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasPDBApplyDictAtomBondingToStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBApplyDictAtomBondingToStdResiduesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBApplyDictAtomBondingToNonStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBApplyDictAtomBondingToNonStdResiduesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasPDBApplyDictAtomBondingToNonStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBApplyDictAtomBondingToNonStdResiduesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBApplyDictBondOrdersToStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBApplyDictBondOrdersToStdResiduesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasPDBApplyDictBondOrdersToStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBApplyDictBondOrdersToStdResiduesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBApplyDictBondOrdersToNonStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBApplyDictBondOrdersToNonStdResiduesParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasPDBApplyDictBondOrdersToNonStdResiduesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBApplyDictBondOrdersToNonStdResiduesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBIgnoreConectRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBIgnoreConectRecordsParameter(Base::ControlParameterContainer& cntnr, bool ignore);
 
        CDPL_BIOMOL_API bool hasPDBIgnoreConectRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBIgnoreConectRecordsParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBDeduceBondOrdersFromCONECTRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBDeduceBondOrdersFromCONECTRecordsParameter(Base::ControlParameterContainer& cntnr, bool deduce);
 
        CDPL_BIOMOL_API bool hasPDBDeduceBondOrdersFromCONECTRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBDeduceBondOrdersFromCONECTRecordsParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBIgnoreFormalChargeFieldParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBIgnoreFormalChargeFieldParameter(Base::ControlParameterContainer& cntnr, bool ignore);
 
        CDPL_BIOMOL_API bool hasPDBIgnoreFormalChargeFieldParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBIgnoreFormalChargeFieldParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBEvaluateMASTERRecordParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBEvaluateMASTERRecordParameter(Base::ControlParameterContainer& cntnr, bool eval);
 
        CDPL_BIOMOL_API bool hasPDBEvaluateMASTERRecordParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBEvaluateMASTERRecordParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBTruncateLinesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBTruncateLinesParameter(Base::ControlParameterContainer& cntnr, bool trunc);
 
        CDPL_BIOMOL_API bool hasPDBTruncateLinesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBTruncateLinesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBWriteFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBWriteFormalChargesParameter(Base::ControlParameterContainer& cntnr, bool write);
 
        CDPL_BIOMOL_API bool hasPDBWriteFormalChargesParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBWriteFormalChargesParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBWriteCONECTRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBWriteCONECTRecordsParameter(Base::ControlParameterContainer& cntnr, bool write);
 
        CDPL_BIOMOL_API bool hasPDBWriteCONECTRecordsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBWriteCONECTRecordsParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBWriteCONECTRecordsForAllBondsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBWriteCONECTRecordsForAllBondsParameter(Base::ControlParameterContainer& cntnr, bool write);
 
        CDPL_BIOMOL_API bool hasPDBWriteCONECTRecordsForAllBondsParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBWriteCONECTRecordsForAllBondsParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API bool getPDBWriteCONECTRecordsReflectingBondOrderParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBWriteCONECTRecordsReflectingBondOrderParameter(Base::ControlParameterContainer& cntnr, bool write);
 
        CDPL_BIOMOL_API bool hasPDBWriteCONECTRecordsReflectingBondOrderParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBWriteCONECTRecordsReflectingBondOrderParameter(Base::ControlParameterContainer& cntnr);
 
 
        CDPL_BIOMOL_API unsigned int getPDBFormatVersionParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setPDBFormatVersionParameter(Base::ControlParameterContainer& cntnr, unsigned int ver);
 
        CDPL_BIOMOL_API bool hasPDBFormatVersionParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearPDBFormatVersionParameter(Base::ControlParameterContainer& cntnr);
        
        CDPL_BIOMOL_API bool getMMCIFApplyDictAtomBondingParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setMMCIFApplyDictAtomBondingParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasMMCIFApplyDictAtomBondingParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearMMCIFApplyDictAtomBondingParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getMMCIFApplyDictBondOrdersParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setMMCIFApplyDictBondOrdersParameter(Base::ControlParameterContainer& cntnr, bool apply);
 
        CDPL_BIOMOL_API bool hasMMCIFApplyDictBondOrdersParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearMMCIFApplyDictBondOrdersParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API bool getMMCIFOutputBiopolymersAsChemCompParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setMMCIFOutputBiopolymersAsChemCompParameter(Base::ControlParameterContainer& cntnr, bool output);
 
        CDPL_BIOMOL_API bool hasMMCIFOutputBiopolymersAsChemCompParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearMMCIFOutputBiopolymersAsChemCompParameter(Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API const MMCIFDataProcessingFunction& getMMCIFOutputDataPostprocFunctionParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void setMMCIFOutputDataPostprocFunctionParameter(Base::ControlParameterContainer& cntnr, const MMCIFDataProcessingFunction& func);
 
        CDPL_BIOMOL_API bool hasMMCIFOutputDataPostprocFunctionParameter(const Base::ControlParameterContainer& cntnr);
 
        CDPL_BIOMOL_API void clearMMCIFOutputDataPostprocFunctionParameter(Base::ControlParameterContainer& cntnr);
 
    } // namespace Biomol
} // namespace CDPL
 
#endif // CDPL_BIOMOL_CONTROLPARAMETERFUNCTIONS_HPP