const CHARMMAtomTopology &CHARMMResidueTopologyBase::get_atom(std::string name)
const {
base::Vector<CHARMMAtomTopology>::const_iterator it =
std::find_if(atoms_.begin(), atoms_.end(), atom_has_name(name));
if (it != atoms_.end()) {
return *it;
} else {
IMP_THROW("atom " << name << " not found in residue topology",
ValueException);
}
}
CHARMMAtomTopology &CHARMMResidueTopologyBase::get_atom(std::string name) {
// A map would be more elegant here (avoid linear lookup time) but
// a) atoms need to be ordered and b) residues rarely have more than ~30 atoms
base::Vector<CHARMMAtomTopology>::iterator it =
std::find_if(atoms_.begin(), atoms_.end(), atom_has_name(name));
if (it != atoms_.end()) {
return *it;
} else {
IMP_THROW("atom " << name << " not found in residue topology",
ValueException);
}
}
void CHARMMIdealResidueTopology::remove_atom(std::string name)
{
base::Vector<CHARMMAtomTopology>::iterator it
= std::find_if(atoms_.begin(), atoms_.end(), atom_has_name(name));
if (it != atoms_.end()) {
atoms_.erase(it);
} else {
IMP_THROW("atom " << name << " not found in residue topology",
ValueException);
}
// Remove any bonds that refer to this atom
bonds_.erase(std::remove_if(bonds_.begin(), bonds_.end(),
bond_has_atom<2>(name)), bonds_.end());
angles_.erase(std::remove_if(angles_.begin(), angles_.end(),
bond_has_atom<3>(name)), angles_.end());
dihedrals_.erase(std::remove_if(dihedrals_.begin(), dihedrals_.end(),
bond_has_atom<4>(name)), dihedrals_.end());
impropers_.erase(std::remove_if(impropers_.begin(), impropers_.end(),
bond_has_atom<4>(name)), impropers_.end());
}
