Question

I have a file which holds protein coordinates as well as other information preceding it. My aim is to look for a certain line called “$PARAMETERS” and then copy from there every line succeeding it till the end of the file.

How can I get that done? This is the small code I wrote part of the entire program (that someone else wrote years ago, and I took over to upgrade his code for my research):

ifstream InFile;
InFile.open (DC_InFile.c_str(), ios::in);

while ( not InFile.eof() )
{
    Line = NextLine (&InFile);

    if (Line.find ("#") == 0) continue;   // skip lines starting with # (comments)
    if (Line.length()   == 0) continue;   // skip empty lines
    size_t pos = Line.find("$PARAMETERS");
    Line.copy(Line.begin("$PARAMETERS")+pos, Line.end("$END"));
    &Line.copy >> x_1 >> y_2 >> z_3;

}

Bearing in mind that I defined Line as string

Answer 1

I guess you need to read data between $PARAMETERS and $END, not from $PARAMETERS until end of file. If so, you can use the following code:

string str;
while (getline(InFile, str))
{
    if (str.find("#") == 0)
        continue;
    if (str.length() == 0)
        continue;
    if (str.find("$PARAMETERS") == 0)
    {
        double x_1, y_2, z_3; // you want to read numbers, i guess
        while (getline(InFile, str))
        {
            if (str.find("$END") == 0)
                break;
            stringstream stream(str);
            if (stream >> x_1 >> y_2 >> z_3)
            {
                // Do whatever you want with x_1, y_2 and z_3
            }
        }
    }
}

This will handle multiple sections of data; not sure if you really want this behavior.

For example:

# comment
$PARAMETERS
1 2 3
4 5 6
$END
#unrelated data
100 200 300
$PARAMETERS
7 8 9
10 11 12
$END