static Residue::eAtomClassification ClassifyAtom(const Residue *residue, const CAtom& atom)
{
if (!atom.IsSetIupac_code()) return Residue::eUnknownAtom;
string code = atom.GetIupac_code().front();
CAtom::EElement element = atom.GetElement();
if (residue->IsAminoAcid()) {
// amino acid C-alpha
if (element==CAtom::eElement_c && code==" CA ")
return Residue::eAlphaBackboneAtom;
// amino acid partial backbone
if (
(element==CAtom::eElement_c && code==" C ") ||
(element==CAtom::eElement_n && code==" N ")
)
return Residue::ePartialBackboneAtom;
// amino acid complete backbone (all backbone that's not part of "partial")
// including both GLY alpha hydrogens and terminal COOH and NH3+
if (
(element==CAtom::eElement_o &&
(code==" O " || code==" OXT")) ||
(element==CAtom::eElement_h &&
(code==" H " || code==" HA " || code=="1HA " || code=="2HA " ||
code==" HXT" || code=="1H " || code=="2H " || code=="3H "))
)
return Residue::eCompleteBackboneAtom;
// anything else is side chain
return Residue::eSideChainAtom;
} else if (residue->IsNucleotide()) {
// nucleic acid Phosphorus
if (element==CAtom::eElement_p && code==" P ")
return Residue::eAlphaBackboneAtom;
// nucleic acid partial backbone
if (
(element==CAtom::eElement_c && (code==" C5*" || code==" C4*" || code==" C3*")) ||
(element==CAtom::eElement_o && (code==" O5*" || code==" O3*")) ||
(element==CAtom::eElement_h && (code==" H3T" || code==" H5T"))
)
return Residue::ePartialBackboneAtom;
// nucleic acid complete backbone (all backbone that's not part of "partial")
if (
(element==CAtom::eElement_o &&
(code==" O1P" || code==" O2P" || code==" O4*" || code==" O2*")) ||
(element==CAtom::eElement_c && (code==" C2*" || code==" C1*")) ||
(element==CAtom::eElement_h &&
(code=="1H5*" || code=="2H5*" || code==" H4*" || code==" H3*" ||
code==" H2*" || code==" H1*" || code==" H1P" || code==" H2P" ||
code==" HO2" || code=="1H2*" || code=="2H2*"))
)
return Residue::eCompleteBackboneAtom;
// anything else is side chain
return Residue::eSideChainAtom;
}
return Residue::eUnknownAtom;
}
