Residue.h

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#ifndef RESIDUE_H
#define RESIDUE_H

#include <string>
#include <vector>
#include <set>
#include <map>
#include <string>
#include "Atom.h"
#include "tCycle.h"

using namespace std;

class Residue {
public:
        Residue():
          resName(""),
          resNumber(-1),
          hasCycle(false)
        {
                born[0][0] = born[0][1] = born[0][2] = born[1][0] = born[1][1] = born[1][2] = 0.0f;
                back[0][0] = back[0][1] = back[0][2] = back[1][0] = back[1][1] = back[1][2] = 0.0f;

        }

        unsigned int getNrStates(){
          map<string, int> nrStates  = { {"ARG", 2}, {"CTE", 2}, {"DPP", 3}, {"EPP", 3}, {"HSP", 3}, {"LYS", 2}, {"NTE", 2}, {"TYR", 2}, {"CYS", 2}};
          return nrStates.at(resName);
        }

        bool isTitGroup(){
                set<string> validGroups = {"ARG","DPP", "HSP", "NTE", "CTE", "EPP", "LYS", "TYR", "CYS"};
                if(validGroups.find(resName.c_str())!=validGroups.end()){
              return true;
                }
                return false;
        }

        void setResidueName(string _resName){
          resName = _resName;
        }

        string getResidueName(){
                return resName;
        }

        void setResidueNumber(int _resNumber){
            resNumber = _resNumber;
        }

        int getResidueNumber(){
                return resNumber;
        }

        void setAtomList(vector<Atom> &_atomList){
          atomList = _atomList;
        }

        vector<Atom>& getAtomList(){
                return atomList;
        }

        void setChainID(char _chainID){
            chainID = _chainID;
        }

        string getIdentifier(){
                stringstream result;
                result << resName << "-" << resNumber;
                if (chainID != ' ')
                        result << "_" << chainID;
                return result.str();
        }

        void setTCycle(tCycle &_cycle){
                cycle = _cycle;
                hasCycle = true;
        }
        
        bool haveCycle(){
          return hasCycle;
        }
        
        tCycle getTCycle(){
            return cycle;
        }

        void setBorn(float bornEner, unsigned int cycleNr, unsigned int stateNr){
                born[cycleNr][stateNr] = bornEner;
        }

        float getBorn(unsigned int cycleNr, unsigned int stateNr){
                return born[cycleNr][stateNr];
        }

        void setBack(float backEner, unsigned int cycleNr, unsigned int stateNr){
                back[cycleNr][stateNr] = backEner;
        }

        float getBack(unsigned int cycleNr, unsigned int stateNr){
                return back[cycleNr][stateNr];
        }

        void print(){
          for (unsigned int i = 0; i < atomList.size(); i++){
            Atom currentAtom = atomList.at(i);
            cout << currentAtom.pqrLine() << endl;
          }
        }

private:
        string resName;
        int resNumber;
        char chainID;
        vector<Atom> atomList;
        tCycle cycle;
        bool hasCycle;
        float born[2][3];
        float back[2][3];
};

#endif