Residue CG6p::to_cg(const Residue &r) const {
auto foo = [this](const Residue &res, auto && names) {
Residue r;
r.m_cg = m_cg;
r.name = res.name;
for (auto &&name : names) {
auto it = std::find_if(res.begin(), res.end(), [&name](auto &&atom) {
return atom.name == name;
});
std::ostringstream stream;
stream << "jian::CG6p::to_cg error! Atom '" << name << "' not found";
if (it == res.end()) throw stream.str();
r.push_back(*it);
}
return r;
};
const CompleteResidue &complete = CompleteResidue::instance();
if (is_cg(r)) {
return r;
}
else {
if (complete.lack_atoms(r)) {
Residue res = r;
complete(res);
return foo(res, m_basic_atoms);
}
else {
return foo(r, m_basic_atoms);
}
}
}
Residue make_residue(const string &name, const Mat &coords) {
Residue residue;
residue.name = name;
for (int i = 0; i < coords.rows(); i++) {
residue.push_back(Atom(_atom_names[name][i], coords(i, 0), coords(i, 1), coords(i, 2)));
}
return residue;
}
void read(Residue &res) {
char c;
read(res.name, res.num, res.m_cg);
while (true) {
read(c);
if (c == 'r') {
return;
}
else if (c == 'A') {
res.push_back(Atom{});
read(res.back());
}
else {
throw "This is not a standard '.jn' file! Illegal " + c;
}
}
}
