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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 ConstraintContainer_H_
#define ConstraintContainer_H_
//#include "BiopolymerClass.h"
#include "Utils.h"
#include <vector>
#include <iostream>
class BiopolymerClassContainer; // trying a forward declaration
class MMB_EXPORT ConstraintToGroundContainer {
private:
std::vector <ConstraintClass> constraintClassVector;
std::vector <ChainResidueToGround> constrainChainRigidSegmentsVector;
public:
InterfaceContainer interfaceContainer;
void clear() {constraintClassVector.clear(); constrainChainRigidSegmentsVector .clear();};
const ConstraintClass getConstraintClass(int constraintToGroundIndex) const {
return constraintClassVector[constraintToGroundIndex]; };
std::vector<ConstraintClass> & getConstraintClassVector() { return constraintClassVector;}
// Constrain rigid segments in chain to either ground or a given residue on same chain. First step: storing in constrainChainRigidSegmentsVector to queue them:
void queueConstrainChainRigidSegments (ChainResidueToGround chainResidue){constrainChainRigidSegmentsVector.push_back(chainResidue); };
// This will take the ChainResidueToGround's in constrainChainRigidSegmentsVector and apply them.
void applyConstrainChainRigidSegments (BiopolymerClassContainer & biopolymerClassContainer, CompoundSystem & system, SimbodyMatterSubsystem & matter,State & state);
void printConstraintClass(int constraintToGroundIndex) const;
void validateConstraintClass(const ConstraintClass & myConstraintClass, BiopolymerClassContainer & myBiopolymerClassContainer) ;
void validateConstraintClassVector(BiopolymerClassContainer & myBiopolymerClassContainer);
void pruneCoordinateCouplers(BiopolymerClassContainer & myBiopolymerClassContainer, DuMMForceFieldSubsystem & _dumm);
void addConstraintClassToVector(ConstraintClass myConstraintClass);
void addConstraintClassToVector(String myChain, ResidueID myResidueID, String atomName);
void addConstraintToVector(String myChain, ResidueID myResidueID, String atomName,
String myChain2, ResidueID myResidueID2, String atomName2);
void deleteConstraintClass(int index);
void updateConstraintToVector(
int index,
String myChain, ResidueID myResidueID, String atomName,
BiopolymerClassContainer& biopolymerClassContainer);
void updateConstraintToVector(
int index,
String myChain, ResidueID myResidueID, String atomName,
String myChain2, ResidueID myResidueID2, String atomName2,
BiopolymerClassContainer& biopolymerClassContainer);
const int numConstraintClasses(){return constraintClassVector.size();};
void printConstraintClasses();
bool hasConstraintClass(String myChainID, ResidueID myResidueID);
bool hasConstraintClass(SimTK::String chain1, SimTK::String chain2); // This checks whether there is any constraint at all, of any type, between two chains.
void addSingleWeldConstraintPerInterfaceChainPair( BiopolymerClassContainer & myBiopolymerClassContainer);
};
#endif
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