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#ifndef BaseInteractionParameterReader_H_
#define BaseInteractionParameterReader_H_
/* -------------------------------------------------------------------------- *
* MMB (MacroMoleculeBuilder) *
* -------------------------------------------------------------------------- *
* *
* Copyright (c) 2011-12 by the Author. *
* Author: Samuel Flores *
* *
* See RNABuilder.cpp for the copyright and usage agreement. *
* -------------------------------------------------------------------------- */
#include "SimTKmolmodel.h"
//#include "SimTKsimbody_aux.h"
#include "SimTKsimbody.h"
#include <ios>
#include <fstream>
#include <vector>
#include <iostream>
#include <string>
#include "Utils.h"
using namespace std;
using namespace SimTK;
/**
*
*
* /param
* myPdbResidueName1,2 must be one of "A","C","G","U".
* bondingEdge1,2 must be one of "WatsonCrick","Hoogsteen","Sugar","Bifurcated".
* glycosidicBondOrientation must be either "Cis" or "Trans".
*
*/
struct LeontisWesthofBondRow {
String pdbResidueName1;
String bondingEdge1;
String pdbResidueName2;
String bondingEdge2;
String glycosidicBondOrientation;
String residue1Atom[4];
String residue2Atom[4];
double bondLength[4];
double springConstant[4];
double torqueConstant;
Vec3 attachmentPoint;
double rotationAngle;
Vec3 rotationAxis;
String isTwoTransformForce;
double distanceC1pC1p;
};
class LeontisWesthofBondKey {
public:
String pdbResidueName1;
String pdbResidueName2;
String bondingEdge1;
String bondingEdge2;
String glycosidicBondOrientation;
String isTwoTransformForce;
LeontisWesthofBondKey(
String myPdbResidueName1, String myPdbResidueName2,
String myBondingEdge1, String myBondingEdge2,
String myGlycosidicBondOrientation, String myIsTwoTransformForce
);
LeontisWesthofBondKey(LeontisWesthofBondRow myLeontisWesthofBondRow);
bool operator==(const LeontisWesthofBondKey &other) const noexcept;
};
struct LeontisWesthofBondMatrix {
vector<LeontisWesthofBondRow> myLeontisWesthofBondRow;
};
class LeontisWesthofClass {
public:
LeontisWesthofBondMatrix myLeontisWesthofBondMatrix;
void initialize(const String &inFileName);
Transform getLeontisWesthofTransform(LeontisWesthofBondRow myLeontisWesthofBondRow) const;
LeontisWesthofBondRow getNearestLeontisWesthofBondRow(String myPdbResidueName1, String myPdbResidueName2, Transform residue1Transform, Transform residue2Transform) const;
void printLeontisWesthofBondRows ();
int getLeontisWesthofBondRowIndex(
String myPdbResidueName1,
String myPdbResidueName2,
String myBondingEdge1,
String myBondingEdge2,
String myGlycosidicBondOrientation,
String myBasePairIsTwoTransformForce
) const;
LeontisWesthofBondRow getLeontisWesthofBondRow(ResidueID myResidueNumber1,ResidueID myResidueNumber2, String myPdbResidueName1, String myBondingEdge1, String myPdbResidueName2,String myBondingEdge2, String myGlycosidicBondOrientation,String myBasePairIsTwoTransformForce) const ;
};
bool isKnownBondingEdge(const std::string &edge);
#endif // BaseInteractionParameterReader_H_
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