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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 ContactContainer_H_
#define ContactContainer_H_
#include "BiopolymerClass.h"
#include "ResidueStretchContainer.h"
class MMB_EXPORT ContactContainer : public ResidueStretchContainer <ContactStretch> {
private:
//vector <ContactStretch> contactStretchVector;
vector <ContactWithin> contactWithinVector;
//HuntCrossleyForce huntCrossleyForce;
public:
void clear();
void validateContact(ContactStretch, BiopolymerClassContainer & myBiopolymerClassContainer);
void addContactToVector(ContactStretch myContactStretch) ;
void addContactToVector(ContactStretch myContactStretch, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void addContactToVector(string myChain, int myStartResidue, int myEndResidue, string myContactScheme, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void deleteContact(int id);
void updateContact(int id, string myChain, int myStartResidue, int myEndResidue, string myContactScheme, BiopolymerClassContainer & myBiopolymerClassContainer);
vector <ContactWithin> & getContactWithinVector() { return contactWithinVector; }
void validateContactWithin(ContactWithin contactWithin , BiopolymerClassContainer & myBiopolymerClassContainer);
void pushContactWithin(ContactWithin contactWithin, BiopolymerClassContainer & myBiopolymerClassContainer);
void createContactsWithin( BiopolymerClassContainer & myBiopolymerClassContainer, State & state );
void deleteContactWithin(int id);
void updateContactWithin(int id, String chainID, int resID, double radius, String contactScheme, BiopolymerClassContainer & myBiopolymerClassContainer);
void listDistances( BiopolymerClassContainer & myBiopolymerClassContainer, State & state );
void printContact(ContactStretch contactStretch);
void printContact(int contactIndex) ;
void printContacts() ;
//void createHuntCrossleyForce(GeneralForceSubsystem & forces,GeneralContactSubsystem & contacts,ContactSetIndex contactSetLargeSpheres)
//HuntCrossleyForce & getHuntCrossleyForce();
void applyContactsToBiopolymers (BiopolymerClassContainer & myBiopolymerClassContainer,GeneralContactSubsystem & contacts,GeneralForceSubsystem & forces,SimbodyMatterSubsystem & matter, LeontisWesthofClass & myLeontisWesthofClass,double excludedVolumeRadius, double excludedVolumeStiffness);
ContactStretch getContact(int contactIndex);
int numContacts() ;
bool hasSharedContact(String chainID, ResidueID startResidueID, ResidueID endResidueID, String contactScheme) ;
bool hasSharedContact(ContactStretch contactStretch) ;
};
#endif
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