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 bool averagepairwiseangle(OBMol mol, ref double avgangle)
{
VectorVecInt mapping = new VectorVecInt();
if (findcarboxylates(mol, ref mapping))
{
double sum = 0;
List <double> angles = new List <double>();
if (mapping.Count > 1)
{
OBAtom c1 = mol.GetAtom(mapping[0][1]);
OBAtom a1 = mol.GetAtom(mapping[0][3]);
OBAtom c2 = mol.GetAtom(mapping[1][1]);
OBAtom a2 = mol.GetAtom(mapping[1][3]);
double pangle = pairwiseangle(c1, a1, c2, a2);
angles.Add(pangle);
sum += pangle;
OBForceField MMFF94 = OBForceField.FindForceField("MMFF94");
MMFF94.Setup(mol);
for (int i = 0; i < 300; i++)
{
MMFF94.MolecularDynamicsTakeNSteps(1, 300, 1.2, 1);
MMFF94.GetCoordinates(mol);
pangle = pairwiseangle(c1, a1, c2,
a2); //this function is sufficiently fast that it does not need to be optimized, molecular dynamics takes about 15 milliseconds per step, this take practically nothing
angles.Add(pangle);
sum += pangle;
}
avgangle = sum / angles.Count;
return(true);
}
else
{
return(false);
}
}
else
{
return(false);
}
}
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);
}