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/* -------------------------------------------------------------------------- *
* MMB (MacroMoleculeBuilder) *
* -------------------------------------------------------------------------- *
* *
* Copyright (c) 2011-12 by the Author. *
* Author: Samuel Flores *
* *
* See RNABuilder.cpp for the copyright and usage agreement. *
* -------------------------------------------------------------------------- */
#ifndef BasePairContainer_H_
#define BasePairContainer_H_
#include "MMB_config.h"
#include "SimTKmolmodel.h"
#include "BiopolymerClass.h"
#include "Utils.h"
#include "ResidueStretchContainer.h"
#include "BaseInteractionParameterReader.h"
#include "NTC_PARAMETER_READER.h"
class MMB_EXPORT BasePairContainer {
public:
void clear() ;
BasePairContainer(){clear();} ;
void addBasePair(BiopolymerClassContainer & myBiopolymerClassContainer,
const LeontisWesthofClass & lhClass,
BaseInteraction myBasePair, bool helicalStacking=false);
void deleteBasePair(int basePairIndex );
void updateBasePair(int index,
String ch1, int res1, String edge1,
String ch2, int res2, String edge2,
String orient,
BiopolymerClassContainer& myBiopolymerClassContainer,
const LeontisWesthofClass& lhClass, bool helicalStacking=false);
void validateBasePair(BiopolymerClassContainer & myBiopolymerClassContainer,
const LeontisWesthofClass & lhClass,
BaseInteraction & myBasePair, bool helicalStacking=false);
const BaseInteraction & getBasePair(int basePairIndex) ;
//BaseInteraction & updBasePair(int);
int numBasePairs() ;
#ifdef MMB_NTC_ENABLED
void addHelicalStacking(BiopolymerClassContainer & myBiopolymerClassContainer, const LeontisWesthofClass & lhClass,const NTC_PAR_Class & ntc_par_class, NTC_Class_Container & my_ntc_class_container);
#else
void addHelicalStacking(BiopolymerClassContainer & myBiopolymerClassContainer, const LeontisWesthofClass & lhClass);
#endif // MMB_NTC_ENABLED
vector<BaseInteraction> myBasePairVector;
void printBasePairs();
void setBasePairSatisfied(int,bool);
vector<int> getSatisfiedBasePairs();
String getBasePairsStrings();
private:
bool hasWatsonCrickCisPair(String chainID ,ResidueID residueNumber) ;
const BaseInteraction getWatsonCrickCisPair(String chainID ,ResidueID residueNumber) ;
const String getWatsonCrickCisPairingChain(String chainID ,ResidueID residueNumber) ;
const ResidueID getWatsonCrickCisPairingResidue(String chainID ,ResidueID residueNumber) ;
const ResidueID getLastWatsonCrickCisPairingResidueOfRun(String chainID ,ResidueID firstResidueNumberInStack, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void generateHelicalStackingInteractions(String chainID,ResidueID firstResidue, ResidueID lastResidue,BiopolymerClassContainer & myBiopolymerClassContainer, const LeontisWesthofClass & lhClass);
}; // of class
#endif
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