chemicalbasis.h

#ifndef CHEMICALBASIS_H
#define CHEMICALBASIS_H
 
#include <map>
#include <vector>
#include "biolcccexception.h"
#include "chemicalgroup.h"
 
namespace BioLCCC
{
 
class ChemicalBasisException : public BioLCCCException
{
public:
    ChemicalBasisException(std::string message);
};
 
 
enum PolymerModel
{
    ROD,
 
    CHAIN
};
 
 
enum PredefinedChemicalBasis
{
 
    RP_ACN_TFA_CHAIN, 
 
    RP_ACN_FA_ROD 
};
 
 
class ChemicalBasis
{
public:
    ChemicalBasis();
 
    ChemicalBasis(PredefinedChemicalBasis predefinedChemicalBasisId);
 
 
    std::map<std::string, ChemicalGroup> & chemicalGroups();
 
 
    const std::map<std::string, ChemicalGroup> & chemicalGroups() const;
 
    const ChemicalGroup & defaultNTerminus() const;
 
    const ChemicalGroup & defaultCTerminus() const;
 
 
    void addChemicalGroup(ChemicalGroup newChemicalGroup);
 
 
    void removeChemicalGroup(std::string label);
 
    void clearChemicalGroups();
 
    //    Throws ChemicalBasisException if the chemical group is not found.
    //    \param label The label of the chemical group to be modified.
    //    \param newBindEnergy The new value of the bind energy.
    //*/
    //void setChemicalGroupBindEnergy(std::string label, double newBindEnergy);
 
 
    double secondSolventBindEnergy() const;
 
 
    void setSecondSolventBindEnergy(double newEnergy);
 
    void setPolymerModel(PolymerModel newModel);
 
    const PolymerModel polymerModel() const;
 
 
    double monomerLength() const;
 
 
    void setMonomerLength(double newMonomerLength);
 
 
    double kuhnLength() const;
 
 
    void setKuhnLength(double newKuhnLength);
 
 
    double adsorptionLayerWidth() const;
 
 
    void setAdsorptionLayerWidth(double newAdsorptionLayerWidth);
 
 
    const std::vector<double> & adsorptionLayerFactors() const;
 
 
    void setAdsorptionLayerFactors(
        std::vector<double> newAdsorptionLayerFactors);
 
 
    bool snyderApproximation() const;
 
 
    void setSnyderApproximation(bool flag);
 
    bool specialRodModel() const;
    
 
    void setSpecialRodModel(bool flag);
    
    bool neglectPartiallyDesorbedStates() const;
 
 
    void setNeglectPartiallyDesorbedStates(bool flag);
 
    double firstSolventDensity() const;
 
    void setFirstSolventDensity(double newFirstSolventDensity);
 
    double secondSolventDensity() const;
 
    void setSecondSolventDensity(double newSecondSolventDensity);
 
    double firstSolventAverageMass() const;
 
    void setFirstSolventAverageMass(double newFirstSolventAverageMass);
 
    double secondSolventAverageMass() const;
 
    void setSecondSolventAverageMass(double newSecondSolventAverageMass);
 
    ChemicalBasis setPredefinedChemicalBasis(
        PredefinedChemicalBasis predefinedChemicalBasisId);
 
private:
    std::map<std::string,ChemicalGroup> mChemicalGroups;
    double mSecondSolventBindEnergy;
    double mMonomerLength;
    double mKuhnLength;
    double mAdsorptionLayerWidth;
    std::vector<double> mAdsorptionLayerFactors;
    PolymerModel mPolymerModel;
    double mFirstSolventDensity;
    double mSecondSolventDensity;
    double mFirstSolventAverageMass;
    double mSecondSolventAverageMass;
    bool mSnyderApproximation;
    bool mSpecialRodModel;
    bool mNeglectPartiallyDesorbedStates;
};
 
}
 
#endif