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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. *
* -------------------------------------------------------------------------- */
//#include "SimTKsimbody_aux.h"
#include <iostream>
#include <ostream>
#include <stdlib.h>// for MAX_PATH
#include "SimTKmolmodel.h"
#include "ParameterReader.h"
#include "BiopolymerClass.h"
using namespace SimTK;
using namespace std;
inline std::ostream& operator<<(std::ostream& o, const ParameterReader&) {
assert(false);
return o;
};
class AllTwoTransformLinearSprings : public Force::Custom::Implementation {
private:
SimbodyMatterSubsystem& matter;
ParameterReader& myParameterReader;
LeontisWesthofClass& myLeontisWesthofClass;
BiopolymerClassContainer & myBiopolymerClassContainer;
//Biopolymer * myChain;
mutable int parameterReaderIndex;
std::ostream& outputStream;
public:
AllTwoTransformLinearSprings (SimbodyMatterSubsystem& matter,ParameterReader& myParameterReader, LeontisWesthofClass& myLeontisWesthofClass, BiopolymerClassContainer & myBiopolymerClassContainer, std::ostream& outputStream ) ; // : matter(matter),myParameterReader(myParameterReader), myLeontisWesthofClass (myLeontisWesthofClass), myBiopolymerClassContainer(myBiopolymerClassContainer), outputStream(outputStream);
void calcAxes (const State& state ,LeontisWesthofBondRow myLeontisWesthofBondRow,ResidueID residueNumber1,ResidueID residueNumber2,String,String,Vec3 & xAxisVector1,Vec3 & yAxisVector1, Vec3 & zAxisVector1,Vec3 & xAxisVector2,Vec3 & yAxisVector2 , Vec3 & zAxisVector2,Vec3 & glycosidicNitrogenAtom1LocationInGround,Vec3 & glycosidicNitrogenAtom2LocationInGround, Vec3 & ring1CenterLocationInGround, Vec3 & ring2CenterLocationInGround) const ;
int isThisATwoTransformForce(String myBPEdge) const;
void calcForce(const State& state, Vector_<SpatialVec>& bodyForces,
Vector_<Vec3>& particleForces, Vector& mobilityForces) const ;
Real calcPotentialEnergy(const State& state) const;
bool dependsOnlyOnPositions() const;
};
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