Proteins constitute a class of molecules that are the primary drivers of all biochemical activity in living organisms on Earth. Every viable cell in every Earth-based life form has DNA molecules inside of its nucleus, and through the process of protein biosynthesis, cells transcribe DNA into RNA, then translate that RNA into protein products.

Protein biosynthesis involves assembling a chain of amino acids, each of which is coded for by a sequence of three RNA nucleotides. The resulting molecule is a form of polypeptide known as a protein. We refer to this sequence of amino acids as the primary structure of a protein. The secondary, ternary and quaternary structures refer to the complex shapes formed as hydrophobic interactions, intramolecular hydrogen bonds and van der Waals forces cause the primary structure of a protein to fold around itself and other proteins, giving the protein its essential biological functionality.

There are 20 proteogenic amino acids. We usually use single-letter abbreviations to refer to them (A for alanine, C for cysteine, etc.), constituting an alphabet for describing protein structure:

A C D E F G H I K L M N P Q R S T V W Y

File /srv/datasets/amino-monoisotopic-mass (also available via HTTP) contains a simple table of the monoisotopic masses (measured in daltons) of each of the 20 proteogenic amino acids, along with the letters that we usually use to refer to them. Here are the first five lines of the file:

A 71.03711
C 103.00919
D 115.02694
E 129.04259
F 147.06841

As in Rosalind problem PRTM, we can use this data to compute the weight/mass of a protein, given its primary structure. This information can be useful for the purposes of protein mass spectrometry, e.g. in the identification and categorization of proteins involved in diseases such as those produced by viruses like SARS-Cov-2, which is the foundation for developing mRNA vaccines such as those that were quickly developed in response to COVID-19.

Here is a small amount of code that uses assertions to test the constructors and the mass() function, then reads strings from stdin, assumes those strings are protein descriptors, and prints a couple of facts about each protein. I've also created a sample executable named cs19_protein that is a working version of this program, if you'd like to consult it for testing purposes.

#include <cassert>
#include <cmath>
#include <initializer_list>
#include <iostream>
#include <stdexcept>
#include <string>
#include "cs19_protein.h"
 
int main(int argc, char **argv) {
  // from Rosalind PRTM: https://rosalind.info/problems/prtm/
  const std::initializer_list<char> prtm_prot{'S', 'K', 'A', 'D', 'Y', 'E', 'K'};
  constexpr double prtm_mass = 821.392;
  assert(std::abs(cs19::Protein(prtm_prot).mass() - prtm_mass) < .001);
  assert(std::abs(cs19::Protein(std::string(prtm_prot)).mass() - prtm_mass) < .001);
  assert(std::abs(cs19::Protein(std::string(prtm_prot).c_str()).mass() - prtm_mass) < .001);
  assert(std::abs(cs19::Protein(prtm_prot.begin(), prtm_prot.end()).mass() - prtm_mass) < .001);
 
  cs19::Protein test;
  while (std::cin) {
    try {
      if (std::cin >> test)
        std::cout << test << ' ' << test.size() << ' ' << test.mass() << '\n';
    } catch (std::domain_error &error) {
      std::cerr << error.what() << '\n';
    }
  }
}

e.g. try running the sample executable and giving it some text on stdin or the name of a file (such as /srv/datasets/ebola_orf_products which contains 220 protein descriptors from the segments of the Ebola virus reference genome that constitute open reading frames, or potential protein products of Ebola:

% cs19_protein <<<SKADYEK
SKADYEK 7 821.392
 
% tail -5 /srv/datasets/ebola_orf_products | cs19_protein
MGHGKLSLRNYQS 13 1471.74
MQDSEVKLIERLTGLLSLFPDGLYRFD 27 3136.63
MSLTQHNKLRTLYN 14 1699.88
MLYQYLARWNSALVDNTTS 19 2227.07
MTVKSEIPSLQYSRLDNNLRVNDN 24 2787.4

Submit cs19_protein.h via turnin.