public static OBMol obminimizeUFF(OBMol mol, double crit, int steps)
{
bool sd = false;
bool cut = false;
bool newton = false;
bool hydrogens = true;
double rvdw = 6.0;
double rele = 10.0;
int freq = 10;
//var watch = Stopwatch.StartNew();
OBForceField ff = OBForceField.FindForceField("UFF");
//watch.Stop();
//watch.Start();
ff.Setup(mol);
ff.SetVDWCutOff(rvdw);
ff.SetElectrostaticCutOff(rele);
ff.SetUpdateFrequency(freq);
ff.EnableCutOff(cut);
ff.ConjugateGradientsInitialize(steps, crit);
bool done = true;
while (done)
{
done = ff.ConjugateGradientsTakeNSteps(1);
//ff.GetCoordinates(mol);
}
ff.GetCoordinates(mol);
//watch.Stop();//doesn't look like there is much I can do to optimize this, energy minimization just takes time
return(mol);
}
public static OBMol conformersearch(OBMol mol, int steps)
{
bool cut = false;
bool newton = false;
bool hydrogens = true;
double rvdw = 6.0;
double rele = 10.0;
int freq = 10;
OBForceField rotsearch = OBForceField.FindForceField("MMFF94");
rotsearch.Setup(mol);
rotsearch.SetVDWCutOff(rvdw);
rotsearch.SetElectrostaticCutOff(rele);
rotsearch.SetUpdateFrequency(freq);
rotsearch.EnableCutOff(cut);
rotsearch.RandomRotorSearch((uint)steps);
//rotsearch.WeightedRotorSearch(3,10);//this is very computationally expensive
rotsearch.GetCoordinates(mol);
return(mol);
}