Residue* PeptideBuilder::createResidue_(const String& type, const int id)
{
Residue* res = new Residue(type, String(id));
PDBAtom* nitrogen = new PDBAtom(PTE[Element::N], "N");
PDBAtom* carbona = new PDBAtom(PTE[Element::C], "CA");
PDBAtom* carbon = new PDBAtom(PTE[Element::C], "C");
// put CA into the starting position
carbona->setPosition(Vector3( 0.00, 0.00, 0.0));
// insert N and C
nitrogen->setPosition(Vector3(-1 * BOND_LENGTH_N_CA, 0.00, 0.00));
carbon->setPosition
(Vector3(BOND_LENGTH_C_CA * (cos(Constants::PI * 71./180.)),
0.00,
BOND_LENGTH_C_CA * (sin(Constants::PI * 71. / 180.))));
// insert atomes into residue/chain/protein
res->insert(*nitrogen);
res->insert(*carbona);
res->insert(*carbon);
// flag as an amino acid
res->setProperty(Residue::PROPERTY__AMINO_ACID);
// create the bonds
nitrogen->createBond(*carbona)->setOrder(Bond::ORDER__SINGLE);
carbona->createBond(*carbon)->setOrder(Bond::ORDER__SINGLE);
return res;
}
void PeptideBuilder::peptide_(Residue& resold, Residue& resnew)
{
PDBAtom* poxygen = new PDBAtom(PTE[Element::O], "O");
// dynamic_cast<PDBAtom*>(resold->getAtom("C")); ?????
PDBAtom* pcarbon = getAtomByName_(resold, "C");
PDBAtom* pcarbona = getAtomByName_(resold, "CA");
PDBAtom* pnitrogen_n = getAtomByName_(resnew, "N");
Vector3 CA_C_axis =(pcarbon->getPosition() - pcarbona->getPosition()).normalize();
Vector3 C_NN_axis =(pnitrogen_n->getPosition() - pcarbon->getPosition()).normalize();
Matrix4x4 mat;
mat.setRotation(Angle(Constants::PI), CA_C_axis);
Vector3 newpos = mat * C_NN_axis;
// newpos = mat * newpos;
newpos = newpos.normalize() * BOND_LENGTH_C_O + pcarbon->getPosition();
//newpos= pcarbon->getPosition();
poxygen->setPosition(newpos);
//set C-O-bond
(pcarbon->createBond(*poxygen))->setOrder(Bond::ORDER__DOUBLE);
resold.insert(*poxygen);
//----------set hydrogen. We can't do this for proline,
// since in this case, this hydrogen doesn't exist
if (!is_proline_)
{
PDBAtom* phydrogen = new PDBAtom(PTE[Element::H], "H");
pcarbon = getAtomByName_(resold, "C");
pnitrogen_n = getAtomByName_(resnew, "N");
poxygen = getAtomByName_(resold, "O");
newpos = (pcarbon->getPosition() - poxygen->getPosition()).normalize();
newpos = newpos * BOND_LENGTH_N_H + pnitrogen_n->getPosition();
phydrogen->setPosition(newpos);
phydrogen->createBond(*pnitrogen_n)->setOrder(Bond::ORDER__SINGLE);;
resnew.insert(*phydrogen);
}
return;
}
