biolccc.h

#ifndef BIOLCCC_H
#define BIOLCCC_H
 
#include "auxiliary.h"
#include "biolcccexception.h"
#include "chemicalbasis.h"
#include "chromoconditions.h"
#include "parsing.h"
#include "chain_model.h"
#include "rod_model.h"
 
namespace BioLCCC
{
 
const ChromoConditions standardChromoConditions = ChromoConditions();
 
const ChemicalBasis rpAcnTfaChain =
    ChemicalBasis(RP_ACN_TFA_CHAIN);
 
const ChemicalBasis rpAcnFaRod =
    ChemicalBasis(RP_ACN_FA_ROD);
 
 
double calculateRT(const std::string &sequence,
                   const ChemicalBasis & chemBasis,
                   const ChromoConditions & conditions =
                       standardChromoConditions,
                   const int numInterpolationPoints = 0,
                   const bool continueGradient = true,
                   const bool backwardCompatibility = false);
 
 
double calculateAverageMass(const std::string &sequence,
                            const ChemicalBasis &chemBasis);
 
double calculateMonoisotopicMass(const std::string &sequence,
                                 const ChemicalBasis &chemBasis);
 
 
double calculateKd(const std::string &sequence,
                   const double secondSolventConcentration,
                   const ChemicalBasis &chemBasis,
                   const double columnPoreSize = 100.0,
                   const double columnRelativeStrength = 1.0,
                   const double temperature = 293.0);
}
#endif