void checkStructures()
{
// fragment DB
if (frag_db == 0)
{
frag_db = new FragmentDB;
}
Log.info() << "system contains " << S.countAtoms() << " atoms." << endl;
// building bonds
S.apply(frag_db->build_bonds);
// checking residues
Log.info() << "checking system" << endl;
ResidueChecker check(*frag_db);
S.apply(check);
// Check residue energies
double energy_limit = 500.0;
S.deselect();
amber.setup(S);
ResidueIterator it = S.beginResidue();
for (; +it; ++it)
{
it->select();
amber.updateEnergy();
double residue_energy = amber.getStretchEnergy() + amber.getBendEnergy()
+ amber.getVdWEnergy();
if (residue_energy > energy_limit)
{
Log.info() << "suspicious energies in residue " << it->getFullName() << ":" << it->getID() << " " << residue_energy
<< " kJ/mol (bend: " << amber.getBendEnergy() << " kJ/mol, stretch: " << amber.getStretchEnergy()
<< " kJ/mol, vdW: " << amber.getVdWEnergy() << " kJ/mol)" << endl;
}
it->deselect();
double quality = std::max(0.0, std::min(1.0, (energy_limit - residue_energy) / energy_limit));
for (PDBAtomIterator ai = it->beginPDBAtom(); +ai; ++ai)
{
ai->setOccupancy(quality);
}
}
}
void singlePoint()
{
double energy = amber.updateEnergy();
amber.updateForces();
Gradient grad;
grad.set(amber.getAtoms());
grad.normalize();
Log.info() << "single point energy: " << energy << " kJ/mol" << endl;
Log.info() << " - stretch :" << amber.getStretchEnergy() << " kJ/mol" << endl;
Log.info() << " - bend :" << amber.getBendEnergy() << " kJ/mol" << endl;
Log.info() << " - torsion :" << amber.getTorsionEnergy() << " kJ/mol" << endl;
Log.info() << " - VdW :" << amber.getVdWEnergy() << " kJ/mol" << endl;
Log.info() << " - electrostatic:" << amber.getESEnergy() << " kJ/mol" << endl;
Log.info() << "grad: " << grad.rms << endl;
}