Parsing text file using getline and assigning parts of each line to different variables in an array

Question

I am writing a program in C++ with which I want to read and parse lines from a (.pdb) text file. The lines look like this:

ATOM # CHAR 0 FLOAT1 FLOAT2 FLOAT3 1.00 0.00 CHAR

Where # is an integer (the atom number) and CHAR is the atom symbol (in this case either O or Si). The FLOATs are x, y, and z coordinates respectively.

The first three lines are:

ATOM      1  O          0      0.024  8.489  10.490  1.00  0.00        O
ATOM      2  O          0     10.069  1.380  9.223   1.00  0.00        O
ATOM      3  O          0     20.066  11.249 2.652   1.00  0.00        O

So far I've managed to read the text line by line and scan the contents using sscanf . However, I'm unable store the data into an array of the Atom class that I've created. Here's what the class looks like which is included in my header file:

class Atom  {
public:
        Atom()
        {};'

        int atom_num;
        char atom_sym[2];
        float atom_x, atom_y, atom_z;
};

Here's the section of my program where I parse the lines:

int main()
{
    int i;
    int Linecount = 0;

    char ign_a, ign_t, ign_o, ign_m; // I use these to store the ATOM of each line
    int ign1;  // I use this to store the 0 that appears before the coordinates of each line

    std::string filename = "textfile.pdb"
    std::ifstream file;

    file.open (filename.c_str());
    if (file.is_open())  {
        std::string line;
        while (getline(file, line))
            ++Linecount;
    }
    file.close();

    Atom atomList[Linecount];

    file.open (filename.c_str());
    if (file.is_open())  {
        std::string line;
        int atom_num;
        char atom_sym[2];
        float atom_x, atom_y, atom_z;
        for (i = 1; i < Linecount; ++i)  { // I have tried this for loop in different sections of the program but nothing seems to work
            while (getline(file, line))  {
                if (line.find("ATOM") == 0)  {
                    sscanf(line.c_str(), "%c%c%c%c %d %s %d %f %f %f", &ign_a, &ign_t, &ign_o, &ign_m,
                            &atom_num, atom_sym, &ign1, &atom_x, &atom_y, &atom_z); //

                    atomList[i].atom_num = atom_num; // This is where I attempt to store the data into the array
                    strcpy(atomList[i].atom_sym, atom_sym);
                    atomList[i].atom_x = atom_x;
                    atomList[i].atom_y = atom_y;
                    atomList[i].atom_z = atom_z;
                }

                    printf("%d %s %.3f %.3f %.3f\n", atomList[i].atom_num, atomList[i].atom_sym,
                            atomList[i].atom_x, atomList[i].atom_y, atomList[i].atom_z); // Test parsing of lines
            }
    }
    file.close();

    int j = 10;
    printf("TEST: %d %s %.3f %.3f %.3f\n", atomList[j].atom_num, atomList[j].atom_sym,
            atomList[j].atom_x, atomList[j].atom_y, atomList[j].atom_z);  // Print function to test storing into array

return 0;
}

The first print function appears to work correctly although it prints three "garbage" lines which I assume are due to the header of the text file despite using the if (line.find("ATOM") == 0) statement. Here's the output up to the third line:

0 0.000 0.000 0.000
0 0.000 0.000 0.000
0 0.000 0.000 0.000
1 O 0.024 8.489 10.490
2 O 10.069 1.380 9.223
3 O 20.066 11.249 2.652

The second print function, however, prints zero values only which indicates that the data is not being stored into the array correctly. I have also tried using std::cin and std::cout for assigning and printing the data but that did not appear to help. Here's the output for the second print function:

TEST: 0 0.000 0.000 0.000

My main issue here is that I'm unable to store the data from the input file into the array atomList[i] of class Atom. I've tried moving the for loop around as well as scanning directly into the atomList[i] variables among other things but I'm stuck at this point. What would I need to change so that the lines are read one by one and the correct information stored into the array?

I would appreciate any help with this. Thanks!

Answer 1

Not sure if this will answer any of your questions, but here's a way to do it. It doesn't use any of the old C-type idioms like scanf and raw arrays.

#include <iostream>
#include <fstream>
#include <iomanip>
#include <vector>
#include <string>
#include <sstream>

// Overloaded extraction operator
std::istream& operator>>(std::istream& i, Atom& a)
{
    std::string temp;
    int temp2;

    if (i >> temp
          >> a.atom_num
          >> a.atom_sym
          >> temp2
          >> a.atom_x
          >> a.atom_y
          >> a.atom_z) {
        i.ignore(256, '\n'); // Discard rest
    }

    return i;
}
// Overloaded insertion operator
std::ostream& operator<<(std::ostream& o, const Atom& a)
{
    o << a.atom_num << " "
      << a.atom_sym << " "
      << std::setprecision(3) << a.atom_x << " "
      << std::setprecision(3) << a.atom_y << " "
      << std::setprecision(3) << a.atom_z;

    return o;
}

int main()
{
    std::string filename = "textfile.pdb";
    std::ifstream file(filename);

    std::vector<Atom> atomList;

    if (file) {
        std::string line;
        while (std::getline(file, line)) {
            if (line.find("ATOM") == 0) {
                std::stringstream ss(line);
                Atom temp;
                if (ss >> temp) {
                    atomList.push_back(temp);
                }
            }
        }
    }

    if (atomList.size() > 10) {
        std::cout << atomList[10] << '\n';
    }

    return 0;
}