std::vector<PDBAtom> extractAtomsFromXYZ(std::string filename) {
std::vector<PDBAtom> atoms;
std::ifstream xyz_file(filename.c_str());
if (xyz_file.is_open() && xyz_file.good()) {
// Read for 2 data lines.
std::string comment_line;
int number_of_atoms;
xyz_file >> number_of_atoms;
std::getline(xyz_file, comment_line);
std::string atomic_symbol, x, y, z;
for (int i = 0; i < number_of_atoms; ++i) {
xyz_file >> atomic_symbol >> x >> y >> z;
atoms.push_back(PDBAtom(atomic_symbol, atof(x.c_str()), atof(y.c_str()), atof(z.c_str())));
}
}
void PDB::read(const char* filename){
printf("Reading %s.\n", filename);
this->is_xyz = (!strcmp(filename + strlen(filename)-4, ".xyz"));
if (this->is_xyz) {
this->readXYZ(filename);
return;
}
char buffer[BUF_SIZE];
FILE* file = safe_fopen(filename, "r");
while(fgets(buffer, BUF_SIZE, file) != NULL){
if(strncmp(buffer,"SSBOND",6) == 0){
this->ssbonds.push_back(PDBSSBond(buffer));
}
if(strncmp(buffer, "ATOM", 4) == 0){
this->atoms.push_back(PDBAtom(buffer));
}
}
printf("Found %zu atoms and %zu SS-bonds.\n", this->atoms.size(), this->ssbonds.size());
printf("Done reading '%s'.\n", filename);
fclose(file);
}