Residue ResidueSubstitutionTable::replaceResidue(Residue &_res) {
// If this residue isn't in our list of residues to be replaced,
// just return it!
if( !isResidueInSubstitutionTable(_res) )
return _res;
// Clone the current residue, and find the replacement info.
Residue newRes;
ReplacementInfo ri = find( _res.getResidueName() )->second;
string newName = ri.first;
AtomHash ah = ri.second;
// Loop over all of the atoms in the residue.
for(int i=0; i < _res.size(); ++i ){
Atom &currAtom = _res.getAtom(i);
string currAtomName = currAtom.getName();
// If the current atom is in the list of atoms we should keep,
// add it.
if( ah.find(currAtomName) != ah.end() )
newRes.addAtom( currAtom );
}
// Set the new name of the residue.
newRes.setResidueNumber( _res.getResidueNumber() );
newRes.setResidueIcode( _res.getResidueIcode() );
newRes.setChainId( _res.getChainId() );
newRes.setResidueName( newName );
return newRes;
}
AtomPointerVector PDBTopology::getBackboneAtoms(Residue &_res){
AtomPointerVector results;
map<string,bool>::iterator it;
for (it = backboneAtoms.begin();it != backboneAtoms.end();it++){
if (it->second && _res.atomExists(it->first)){
results.push_back(&_res.getAtom(it->first));
} else {
if (it->second){
MSLOUT.stream() << " getBackboneAtoms(Residue) , residue "<<_res.toString()<<" does not have backbone atom '"<<it->second<<"'"<<endl;
}
}
}
return results;
}
