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metrics.cpp
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#include <iostream>
#include <fstream>
#include <vector>
#include <stdlib.h>
#include <sstream>
#include <algorithm>
#include <RInside.h> // for the embedded R via RInside
using namespace std;
int getAtoms(string &seq){
int num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 13; // A
num += std::count(seq.begin(), seq.end(), 'R') * 26; // R
num += std::count(seq.begin(), seq.end(), 'N') * 17; // N
num += std::count(seq.begin(), seq.end(), 'D') * 16; // D
num += std::count(seq.begin(), seq.end(), 'C') * 14; // C
num += std::count(seq.begin(), seq.end(), 'Q') * 20; // Q
num += std::count(seq.begin(), seq.end(), 'E') * 19; // E
num += std::count(seq.begin(), seq.end(), 'G') * 10; // H
num += std::count(seq.begin(), seq.end(), 'H') * 20; // H
num += std::count(seq.begin(), seq.end(), 'I') * 22; // I
num += std::count(seq.begin(), seq.end(), 'L') * 22; // L
num += std::count(seq.begin(), seq.end(), 'K') * 24; // K
num += std::count(seq.begin(), seq.end(), 'M') * 20; // M
num += std::count(seq.begin(), seq.end(), 'F') * 23; // F
num += std::count(seq.begin(), seq.end(), 'P') * 17; // P
num += std::count(seq.begin(), seq.end(), 'S') * 14; // S
num += std::count(seq.begin(), seq.end(), 'T') * 17; // T
num += std::count(seq.begin(), seq.end(), 'W') * 27; // W
num += std::count(seq.begin(), seq.end(), 'Y') * 24; // Y
num += std::count(seq.begin(), seq.end(), 'V') * 19; // V
return num;
}
double getCarbonAtoms(string &seq){
double num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 3;
num += std::count(seq.begin(), seq.end(), 'C') * 3;
num += std::count(seq.begin(), seq.end(), 'D') * 4;
num += std::count(seq.begin(), seq.end(), 'E') * 5;
num += std::count(seq.begin(), seq.end(), 'F') * 9;
num += std::count(seq.begin(), seq.end(), 'G') * 2;
num += std::count(seq.begin(), seq.end(), 'H') * 6;
num += std::count(seq.begin(), seq.end(), 'I') * 6;
num += std::count(seq.begin(), seq.end(), 'K') * 6;
num += std::count(seq.begin(), seq.end(), 'L') * 6;
num += std::count(seq.begin(), seq.end(), 'M') * 5;
num += std::count(seq.begin(), seq.end(), 'N') * 4;
num += std::count(seq.begin(), seq.end(), 'P') * 5;
num += std::count(seq.begin(), seq.end(), 'Q') * 5;
num += std::count(seq.begin(), seq.end(), 'R') * 6;
num += std::count(seq.begin(), seq.end(), 'S') * 3;
num += std::count(seq.begin(), seq.end(), 'T') * 4;
num += std::count(seq.begin(), seq.end(), 'V') * 5;
num += std::count(seq.begin(), seq.end(), 'W') * 11;
num += std::count(seq.begin(), seq.end(), 'Y') * 9;
return num;
}
double getHydrogenAtoms(string &seq){
double num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 7;
num += std::count(seq.begin(), seq.end(), 'C') * 7;
num += std::count(seq.begin(), seq.end(), 'D') * 7;
num += std::count(seq.begin(), seq.end(), 'E') * 9;
num += std::count(seq.begin(), seq.end(), 'F') * 11;
num += std::count(seq.begin(), seq.end(), 'G') * 5;
num += std::count(seq.begin(), seq.end(), 'H') * 9;
num += std::count(seq.begin(), seq.end(), 'I') * 13;
num += std::count(seq.begin(), seq.end(), 'K') * 14;
num += std::count(seq.begin(), seq.end(), 'L') * 13;
num += std::count(seq.begin(), seq.end(), 'M') * 11;
num += std::count(seq.begin(), seq.end(), 'N') * 8;
num += std::count(seq.begin(), seq.end(), 'P') * 9;
num += std::count(seq.begin(), seq.end(), 'Q') * 10;
num += std::count(seq.begin(), seq.end(), 'R') * 14;
num += std::count(seq.begin(), seq.end(), 'S') * 7;
num += std::count(seq.begin(), seq.end(), 'T') * 9;
num += std::count(seq.begin(), seq.end(), 'V') * 11;
num += std::count(seq.begin(), seq.end(), 'W') * 12;
num += std::count(seq.begin(), seq.end(), 'Y') * 11;
return num;
}
double getNitrogenAtoms(string &seq){
double num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 1;
num += std::count(seq.begin(), seq.end(), 'C') * 1;
num += std::count(seq.begin(), seq.end(), 'D') * 1;
num += std::count(seq.begin(), seq.end(), 'E') * 1;
num += std::count(seq.begin(), seq.end(), 'F') * 1;
num += std::count(seq.begin(), seq.end(), 'G') * 1;
num += std::count(seq.begin(), seq.end(), 'H') * 3;
num += std::count(seq.begin(), seq.end(), 'I') * 1;
num += std::count(seq.begin(), seq.end(), 'K') * 2;
num += std::count(seq.begin(), seq.end(), 'L') * 1;
num += std::count(seq.begin(), seq.end(), 'M') * 1;
num += std::count(seq.begin(), seq.end(), 'N') * 2;
num += std::count(seq.begin(), seq.end(), 'P') * 1;
num += std::count(seq.begin(), seq.end(), 'Q') * 2;
num += std::count(seq.begin(), seq.end(), 'R') * 4;
num += std::count(seq.begin(), seq.end(), 'S') * 1;
num += std::count(seq.begin(), seq.end(), 'T') * 1;
num += std::count(seq.begin(), seq.end(), 'V') * 1;
num += std::count(seq.begin(), seq.end(), 'W') * 2;
num += std::count(seq.begin(), seq.end(), 'Y') * 1;
return num;
}
double getOxygenAtoms(string &seq){
double num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 2;
num += std::count(seq.begin(), seq.end(), 'C') * 2;
num += std::count(seq.begin(), seq.end(), 'D') * 4;
num += std::count(seq.begin(), seq.end(), 'E') * 4;
num += std::count(seq.begin(), seq.end(), 'F') * 2;
num += std::count(seq.begin(), seq.end(), 'G') * 2;
num += std::count(seq.begin(), seq.end(), 'H') * 2;
num += std::count(seq.begin(), seq.end(), 'I') * 2;
num += std::count(seq.begin(), seq.end(), 'K') * 2;
num += std::count(seq.begin(), seq.end(), 'L') * 2;
num += std::count(seq.begin(), seq.end(), 'M') * 2;
num += std::count(seq.begin(), seq.end(), 'N') * 3;
num += std::count(seq.begin(), seq.end(), 'P') * 2;
num += std::count(seq.begin(), seq.end(), 'Q') * 3;
num += std::count(seq.begin(), seq.end(), 'R') * 2;
num += std::count(seq.begin(), seq.end(), 'S') * 3;
num += std::count(seq.begin(), seq.end(), 'T') * 3;
num += std::count(seq.begin(), seq.end(), 'V') * 2;
num += std::count(seq.begin(), seq.end(), 'W') * 2;
num += std::count(seq.begin(), seq.end(), 'Y') * 3;
return num;
}
double getSulfurAtoms(string &seq){
double num = 0;
num += std::count(seq.begin(), seq.end(), 'A') * 0 ;
num += std::count(seq.begin(), seq.end(), 'C') * 1 ;
num += std::count(seq.begin(), seq.end(), 'D') * 0 ;
num += std::count(seq.begin(), seq.end(), 'E') * 0 ;
num += std::count(seq.begin(), seq.end(), 'F') * 0 ;
num += std::count(seq.begin(), seq.end(), 'G') * 0 ;
num += std::count(seq.begin(), seq.end(), 'H') * 0 ;
num += std::count(seq.begin(), seq.end(), 'I') * 0 ;
num += std::count(seq.begin(), seq.end(), 'K') * 0 ;
num += std::count(seq.begin(), seq.end(), 'L') * 0 ;
num += std::count(seq.begin(), seq.end(), 'M') * 1 ;
num += std::count(seq.begin(), seq.end(), 'N') * 0 ;
num += std::count(seq.begin(), seq.end(), 'P') * 0 ;
num += std::count(seq.begin(), seq.end(), 'Q') * 0 ;
num += std::count(seq.begin(), seq.end(), 'R') * 0 ;
num += std::count(seq.begin(), seq.end(), 'S') * 0 ;
num += std::count(seq.begin(), seq.end(), 'T') * 0 ;
num += std::count(seq.begin(), seq.end(), 'V') * 0 ;
num += std::count(seq.begin(), seq.end(), 'W') * 0 ;
num += std::count(seq.begin(), seq.end(), 'Y') * 0 ;
return num;
}
double percentResidue1(string &seq, int length){
double weight = 0;
weight += (double) std::count(seq.begin(), seq.end(), 'L') * 100 / (double) length; // L
weight += (double) std::count(seq.begin(), seq.end(), 'R') * 100 / (double) length; // R
return weight;
}
double percentResidue2(string &seq, int length){
double weight = 0;
weight += (double) std::count(seq.begin(), seq.end(), 'L') * 100 / (double) length; // L
weight += (double) std::count(seq.begin(), seq.end(), 'R') * 100 / (double) length; // R
weight += (double) std::count(seq.begin(), seq.end(), 'H') * 100 / (double) length; // H
return weight;
}
double getMolWeight(string &seq){
double weight = 0;
weight += (double) std::count(seq.begin(), seq.end(), 'A') * 71.0788; // A
weight += (double) std::count(seq.begin(), seq.end(), 'R') * 156.1875; // R
weight += (double) std::count(seq.begin(), seq.end(), 'N') * 114.1038; // N
weight += (double) std::count(seq.begin(), seq.end(), 'D') * 115.0886; // D
weight += (double) std::count(seq.begin(), seq.end(), 'C') * 103.1388; // C
weight += (double) std::count(seq.begin(), seq.end(), 'Q') * 128.1307; // Q
weight += (double) std::count(seq.begin(), seq.end(), 'E') * 129.1155; // E
weight += (double) std::count(seq.begin(), seq.end(), 'G') * 57.0519; // H
weight += (double) std::count(seq.begin(), seq.end(), 'H') * 137.1411; // H
weight += (double) std::count(seq.begin(), seq.end(), 'I') * 113.1594; // I
weight += (double) std::count(seq.begin(), seq.end(), 'L') * 113.1594; // L
weight += (double) std::count(seq.begin(), seq.end(), 'K') * 128.1741; // K
weight += (double) std::count(seq.begin(), seq.end(), 'M') * 131.1926; // M
weight += (double) std::count(seq.begin(), seq.end(), 'F') * 147.1766; // F
weight += (double) std::count(seq.begin(), seq.end(), 'P') * 97.1167; // P
weight += (double) std::count(seq.begin(), seq.end(), 'S') * 87.0782; // S
weight += (double) std::count(seq.begin(), seq.end(), 'T') * 101.1051; // T
weight += (double) std::count(seq.begin(), seq.end(), 'W') * 186.2132; // W
weight += (double) std::count(seq.begin(), seq.end(), 'Y') * 163.1760; // Y
weight += (double) std::count(seq.begin(), seq.end(), 'V') * 99.1326; // V
return weight;
}
vector<double> getAAPercent(string &seq, int size){
vector<double> v;
v.push_back((double) std::count(seq.begin(), seq.end(), 'A') * 100 / (double) size); // A
v.push_back((double) std::count(seq.begin(), seq.end(), 'R') * 100 / (double) size); // R
v.push_back((double) std::count(seq.begin(), seq.end(), 'N') * 100 / (double) size); // N
v.push_back((double) std::count(seq.begin(), seq.end(), 'D') * 100 / (double) size); // D
v.push_back((double) std::count(seq.begin(), seq.end(), 'C') * 100 / (double) size); // C
v.push_back((double) std::count(seq.begin(), seq.end(), 'Q') * 100 / (double) size); // Q
v.push_back((double) std::count(seq.begin(), seq.end(), 'E') * 100 / (double) size); // E
v.push_back((double) std::count(seq.begin(), seq.end(), 'G') * 100 / (double) size); // H
v.push_back((double) std::count(seq.begin(), seq.end(), 'H') * 100 / (double) size); // H
v.push_back((double) std::count(seq.begin(), seq.end(), 'I') * 100 / (double) size); // I
v.push_back((double) std::count(seq.begin(), seq.end(), 'L') * 100 / (double) size); // L
v.push_back((double) std::count(seq.begin(), seq.end(), 'K') * 100 / (double) size); // K
v.push_back((double) std::count(seq.begin(), seq.end(), 'M') * 100 / (double) size); // M
v.push_back((double) std::count(seq.begin(), seq.end(), 'F') * 100 / (double) size); // F
v.push_back((double) std::count(seq.begin(), seq.end(), 'P') * 100 / (double) size); // P
v.push_back((double) std::count(seq.begin(), seq.end(), 'S') * 100 / (double) size); // S
v.push_back((double) std::count(seq.begin(), seq.end(), 'T') * 100 / (double) size); // T
v.push_back((double) std::count(seq.begin(), seq.end(), 'W') * 100 / (double) size); // W
v.push_back((double) std::count(seq.begin(), seq.end(), 'Y') * 100 / (double) size); // Y
v.push_back((double) std::count(seq.begin(), seq.end(), 'V') * 100 / (double) size); // V
return v;
}
int main(int argc, const char* argv[])
{
RInside R(argc, argv); // create an embedded R instance
R.parseEvalQ("library(seqinr)");
ifstream input;
input.open(argv[1]);
vector<vector<string> > table;
vector<string> curr;
for (string row; getline(input, row, '\n'); ){
curr.clear();
istringstream ss(row);
for (string word; getline(ss, word, '\t'); )
curr.push_back(word);
table.push_back(curr);
}
input.close();
ofstream output;
output.open("protein_metrics.csv");
int size = table.size();
string seq = "";
int length = 0;
vector<double> aaPercent;
output << "function\tlength\tmol weight\ttheortical pI";
output << "\tpercent A";
output << "\tpercent R";
output << "\tpercent N";
output << "\tpercent D";
output << "\tpercent C";
output << "\tpercent Q";
output << "\tpercent E";
output << "\tpercent G";
output << "\tpercent H";
output << "\tpercent I";
output << "\tpercent L";
output << "\tpercent K";
output << "\tpercent M";
output << "\tpercent F";
output << "\tpercent P";
output << "\tpercent S";
output << "\tpercent T";
output << "\tpercent W";
output << "\tpercent Y";
output << "\tpercent V";
output << "\tpercent residue 1";
output << "\tpercent residue 2";
output << "\tnumber atoms";
output << "\tnumber carbon";
output << "\tnumber nitrogen";
output << "\tnumber oxygen";
output << "\tnumber sulphur";
output << endl;
for (int i = 0; i < size; ++i){
seq = table[i].at(2);
length = seq.length();
output << table[i].at(1);
// print length
output << "\t" << length;
// print mol weight
output << "\t" << getMolWeight(seq);
// print theoretical pI
R["v"] = seq;
R.parseEvalQ("prot <- s2c(v)");
R.parseEvalQ("pi <- computePI(prot)");
Rcpp::NumericVector p = R.parseEval("print(pi); pi");
output << "\t" << p[0];
// print composition AA
aaPercent = getAAPercent(seq, length);
for (int aa = 0; aa < 20; ++aa)
output << "\t" << aaPercent[aa];
// print residue 1
output << "\t" << percentResidue1(seq, length);
// print residue 2
output << "\t" << percentResidue2(seq, length);
// print num atoms
output << "\t" << getAtoms(seq);
// print num carbon
output << "\t" << getCarbonAtoms(seq);
// print num nitrogen
output << "\t" << getNitrogenAtoms(seq);
// print num oxygen
output << "\t" << getOxygenAtoms(seq);
// print num sulphur
output << "\t" << getSulfurAtoms(seq);
output << endl;
}
return 0;
}