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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 MobilizerContainer_H_
#define MobilizerContainer_H_
#include "ResidueStretchContainer.h"
class BiopolymerClassContainer;
class MMB_EXPORT MobilizerContainer : public ResidueStretchContainer <MobilizerStretch> {
private:
vector <MobilizerWithin> mobilizerWithinVector;
public:
void clear();
bool isEmpty();
MobilizerContainer(){clear();}
vector<SingleBondMobility> singleBondMobilityVector;
//InterfaceContainer mobilizerInterfaceContainer;
void validateMobilizerStretch(int mobilizerStretchIndex, BiopolymerClassContainer & myBiopolymerClassContainer);
void validateMobilizerStretch(MobilizerStretch & ms, BiopolymerClassContainer & myBiopolymerClassContainer);
void addMobilizerStretchToVector(MobilizerStretch myMobilizerStretch, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void addMobilizerStretchToVector(String myChain, ResidueID myStartResidue, ResidueID myEndResidue, String bondMobilityString, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void addMobilizerStretchToVector(String myChain, String bondMobilityString, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void updateMobilizerStretch(int id, String myChain, ResidueID myStartResidue, ResidueID myEndResidue, String bondMobilityString, BiopolymerClassContainer & myBiopolymerClassContainer);
void deleteMobilizerStretch(int id);
void printMobilizerStretch(int mobilizerStretchIndex);
void printMobilizerStretches();
int numMobilizerStretches() ;
String getChain(int mobilizerStretchIndex);
ResidueID getStartResidue(int mobilizerStretchIndex);
ResidueID getEndResidue(int mobilizerStretchIndex);
void setBiopolymerBondMobility (BiopolymerClassContainer & myBiopolymerClassContainer);
vector<MobilizerWithin> & getMobilizerWithinVector() { return mobilizerWithinVector; }
void createMobilizersWithin ( BiopolymerClassContainer & myBiopolymerClassContainer, State & state );
void pushMobilizerWithin ( MobilizerWithin mobilizerWithin, BiopolymerClassContainer & myBiopolymerClassContainer);
void validateMobilizerWithin(MobilizerWithin mobilizerWithin , BiopolymerClassContainer & myBiopolymerClassContainer);
int numMobilizerWithin();
void deleteMobilizerWithin(int id);
void updateMobilizerWithin(int id, String myChain, ResidueID myRes, double myRadius, String bondMobilityString, BiopolymerClassContainer & myBiopolymerClassContainer);
void addPhiPsiMobility(String chain, ResidueID startResidue, ResidueID endResidue, String bondMobilityString , BiopolymerClassContainer& biopolymerClassContainer );
void addPhiPsiMobility(String bondMobilityString , BiopolymerClassContainer& biopolymerClassContainer );
void addMobilizerStretchToVector(MobilizerStretch mobilizerStretch, String bondMobilityString , BiopolymerClassContainer & myBiopolymerClassContainer);
void addMobilizerStretchesToVector(vector <MobilizerStretch> residueStretchVector, String bondMobilityString , BiopolymerClassContainer & myBiopolymerClassContainer);
void addMobilizerStretchesToVector(BiopolymerClassContainer&);
//void addMobilizerStretchesToVector(BiopolymerClassContainer&, CompoundSystem&, State&);
void addMobilizerStretchesToVector(vector<MobilizerStretch>, BiopolymerClassContainer&);
void addSingleBondMobilityToAllChains(String bondMobilityString , BiopolymerClassContainer& biopolymerClassContainer );
void addMobilizerDomainsInterfacesToVector(const vector<MobilizerDomainsInterface> & mDIVector, BiopolymerClassContainer & myBiopolymerClassContainer);
void setMobilizerTypeForAllChains(const String myMobilizerString, BiopolymerClassContainer & myBiopolymerClassContainer);/*{
cout<<__FILE__<<":"<<__FUNCTION__<<":"<<__LINE__<<" myMobilizerString = >"<<myMobilizerString<<"< "<<endl;
for (int i = 0 ; i < myBiopolymerClassContainer.getNumBiopolymers(); i++) {
String myChainID = myBiopolymerClassContainer.updBiopolymerClass(i).getChainID();
//String myMobilizerString = parameterStringClass.getString(1);
cout<<__FILE__<<":"<<__LINE__<<" Adding mobilizer stretch to biopolymer index "<<i<<" , chain "<< myChainID<<endl;
addMobilizerStretchToVector(
myChainID,
myMobilizerString,
myBiopolymerClassContainer
);
} // of for
}*/
};
#endif
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