Help needed in converting c++ code into R

[Mayank Singh]

Hi all,
Here is the code in c++ and i am new to coding world hence i need little help in converting this code into R

#include <iostream>
#include <cmath>               
#include <fstream>                
#include <string>                    

using namespace std;

int main(int argc, char *argv[])
{
std::string protein;
ifstream aa;
aa.open("aa.txt");        //we are getting the data from the file (we assume that we have aa.txt file) 
aa>>protein;                //the sequence should be in one letter code (uppercase letters)
aa.close();

int ProtLength;                       //now we are getting protein length
ProtLength = protein.length();

char Asp = 'D';
char Glu = 'E';
char Cys = 'C';
char Tyr = 'Y';
char His = 'H';
char Lys = 'K';
char Arg = 'R';

int AspNumber = 0;
int GluNumber = 0;
int CysNumber = 0;
int TyrNumber = 0;
int HisNumber = 0;
int LysNumber = 0;
int ArgNumber = 0;

int i=0;

for ( i = 0; i <= protein.length() - 1; ++i)              //  we are looking for charged amino acids
{
if (protein[i] == Asp)
 ++AspNumber;

if (protein[i] == Glu)
 ++GluNumber;

if (protein[i] == Cys)
 ++CysNumber;

if (protein[i] == Tyr)
 ++TyrNumber;

if (protein[i] == His)
 ++HisNumber;

if (protein[i] == Lys)
 ++LysNumber;

if (protein[i] == Arg)
 ++ArgNumber;
}

double NQ = 0.0; //net charge in given pH

double QN1=0;  //C-terminal charge
double QN2=0;  //D charge
double QN3=0;  //E charge
double QN4=0;  //C charge
double QN5=0;  //Y charge
double QP1=0;  //H charge
double QP2=0;  //NH2 charge
double QP3=0;  //K charge
double QP4=0;  //R charge

double pH = 0.0;           

for(;;)                //the infinite loop
{

// we are using pK values form Wikipedia as they give quite good approximation
// if you want you can change it

QN1=-1/(1+pow(10,(3.65-pH)));                                         
QN2=-AspNumber/(1+pow(10,(3.9-pH)));           
QN3=-GluNumber/(1+pow(10,(4.07-pH)));           
QN4=-CysNumber/(1+pow(10,(8.18-pH)));           
QN5=-TyrNumber/(1+pow(10,(10.46-pH)));        
QP1=HisNumber/(1+pow(10,(pH-6.04)));            
QP2=1/(1+pow(10,(pH-8.2)));                
QP3=LysNumber/(1+pow(10,(pH-10.54)));           
QP4=ArgNumber/(1+pow(10,(pH-12.48)));            

NQ=QN1+QN2+QN3+QN4+QN5+QP1+QP2+QP3+QP4;

//if you want to see how the program works step by step uncomment below line
//      cout<<"NQ="<<NQ<<"\tat pH ="<<pH<<"\ti:" <<i++<<endl;       

if (pH>=14.0)
{                                                 //you should never see this message
cout<<"Something is wrong - pH is higher than 14"<<endl;  //
break;                                            
}                                                 

if (NQ<=0)                            // if this condition is true we can stop calculate
break;

pH+=0.01;                            // if not increase pH

}

ofstream outfile;                //we are writing results to outfile.txt
outfile.open("outfile.txt");           
outfile << "Protein length: "<<ProtLength<<endl;
outfile << "Number of Asp = "<<AspNumber<<endl;   
outfile << "Number of Glu = "<<GluNumber<<endl; 
outfile << "Number of Cys = "<<CysNumber<<endl; 
outfile << "Number of Tyr = "<<TyrNumber<<endl; 
outfile << "Number of His = "<<HisNumber<<endl;
outfile << "Number of Lys = "<<LysNumber<<endl; 
outfile << "Number of Arg = "<<ArgNumber<<endl;
outfile << "Protein isoelectric point: "<<pH<<endl;
outfile.close();
cout << "Protein isoelectric point: "<<pH<<endl;

system("PAUSE");
return EXIT_SUCCESS;
  }

[rproffitt]

Just like any conversion you do this line by line. There is rarely a magic app to do your work for you.

But reading http://dirk.eddelbuettel.com/code/rcpp.html it seems there are tutorials and more to speed you on your way.