include/biolccc.h
00001 #ifndef BIOLCCC_H
00002 #define BIOLCCC_H
00003 
00004 #include "auxiliary.h"
00005 #include "biolcccexception.h"
00006 #include "chemicalbasis.h"
00007 #include "chromoconditions.h"
00008 #include "parsing.h"
00009 #include "chain_model.h"
00010 #include "rod_model.h"
00011 
00013 namespace BioLCCC
00014 {
00015 
00017 const ChromoConditions standardChromoConditions = ChromoConditions();
00018 
00020 const ChemicalBasis rpAcnTfaChain =
00021     ChemicalBasis(RP_ACN_TFA_CHAIN);
00022 
00024 const ChemicalBasis rpAcnFaRod =
00025     ChemicalBasis(RP_ACN_FA_ROD);
00026 
00028 
00040 double calculateRT(const std::string &sequence,
00041                    const ChemicalBasis & chemBasis,
00042                    const ChromoConditions & conditions =
00043                        standardChromoConditions,
00044                    const int numInterpolationPoints = 0,
00045                    const bool continueGradient = true,
00046                    const bool backwardCompatibility = false) 
00047                    throw(BioLCCCException);
00048 
00050 
00054 double calculateAverageMass(const std::string &sequence,
00055                             const ChemicalBasis &chemBasis)
00056                             throw(BioLCCCException);
00058 
00062 double calculateMonoisotopicMass(const std::string &sequence,
00063                                  const ChemicalBasis &chemBasis)
00064                                  throw(BioLCCCException);
00065 
00067 
00079 double calculateKd(const std::string &sequence,
00080                    const double secondSolventConcentration,
00081                    const ChemicalBasis &chemBasis,
00082                    const double columnPoreSize = 100.0,
00083                    const double columnRelativeStrength = 1.0,
00084                    const double temperature = 293.0)
00085                    throw(BioLCCCException);
00086 }
00087 #endif
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