infile.fasta:
>seq01 some description protein
AGCTAC GTACAT
CAGTCGTGT GAT
CGAGC GGG
>seq02 another chloropyll_Rubisco subunit
AGCTAG AGTAG
CGCGCTAGCTAG
CGATGC AA
CGCGGTCGT
>seq03 some other description protein
AGCTAC GTACATG
CAGTCGTGT GATG
CGAGC GGGA

output:
>seq01 AGCTACGTACATCAGTCGTGTGATCGAGCGGG
>seq02 AGCTAGAGTAGCGCGCTAGCTAGCGATGCAACGCGGTCGT
>seq03 AGCTACGTACATGCAGTCGTGTGATGCGAGCGGGA

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

using namespace std;

int main()
{
    ifstream inFILE("infile.fasta");
    int inGuard = 1;               //using a guard variable
    while (inFILE.good()) {
    string line;        //declare string for each line

    getline(inFILE, line);    //Read the whole line

    char *sPtr;        //Declare char pointer sPtr for tokens
    //Initialize char pointer sArray for conversion of the string to char*
    char *sArray = new char[line.length() + 1];
    strcpy(sArray, line.c_str());

    if (sArray[0] == '>') {
        sPtr = strtok(sArray, " ");    //Using space as delimiter get the first token.
        cout << sPtr << " ";       //Print the first token only
        continue;
    } 
    else 
    {
        sPtr = strtok(sArray, " ");    //Get all the tokens with " " as delimiter.
        //For all tokens
        while (sPtr != NULL) {
        cout << sPtr;
        sPtr = strtok(NULL, " ");
        }
    }
    }

    cout << endl;
    inFILE.close();

    return 0;
}

>seq01 AGCTACGTACATCAGTCGTGTGATCGAGCGGG>seq02anotherchloropyll_RubiscosubunitAGCTAGAGTAGCGCGCTAGCTAGCGATGCAACGCGGTCGT>seq03 AGCTACGTACATGCAGTCGTGTGATGCGAGCGGGA

    if (sArray[0] == '>') {
 sPtr = strtok(sArray, " ");    //Using space as delimiter get the first token.
if (inGuard == 1) {
cout << sPtr << " ";
inGuard++;
} 
else
  { 
     cout << endl << sPtr << " ";      //Print the first token on a new line
    }       
        continue;

output:

>seq01 AGCTACGTACATCAGTCGTGTGATCGAGCGGG
>seq02 AGCTAGAGTAGCGCGCTAGCTAGCGATGCAACGCGGTCGT
>seq03 AGCTACGTACATGCAGTCGTGTGATGCGAGCGGGA