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 contingencyminimization(OBMol mol)
{
OBForceField uff = OBForceField.FindForceField("UFF");
//uff.ParseParamFile();
uff.SetLogLevel(1);
uff.Setup(mol);
uff.ConjugateGradients(10);
return(mol);
}
public void readMol(string file)
{
bool hideHydrogens = PlayerPrefs.GetString("hideHydrogens") == "True";
bool polarHydrogens = PlayerPrefs.GetString("polarHydrogens") == "True";
string ff = PlayerPrefs.GetString("forceField");
OpenBabel.OBConversion obconv = new OBConversion();
extension = file.Split('.')[1];
if (extension == "pdb")
{
obconv.SetInFormat("PDB");
}
else if (extension == "sdf")
{
obconv.SetInFormat("SDF");
}
else if (extension == "mol2")
{
obconv.SetInFormat("MOL2");
}
mol = new OBMol();
obconv.ReadFile(mol, file);
if (hideHydrogens)
{
mol.DeleteHydrogens();
}
else
{
mol.AddHydrogens();
}
if (polarHydrogens)
{
mol.DeleteNonPolarHydrogens();
}
if (ff != "") //a force field is selected
// Ghemical, MMFF94, UFF
{
OBForceField forceField = OBForceField.FindForceField(ff);
forceField.Setup(mol);
forceField.ConjugateGradients(1000);
}
}
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 List <int> moltoUFF(OBMol mol, string coefficientfilename, string datafilename, bool contingency, double padding)
{
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
if (contingency)
{
//if lammps fails to minimize, try minimization using openbabel as a starting point
OBForceField uff = OBForceField.FindForceField("UFF");
mol = lammpssetup.perturbator(mol, 2); //lammps crashes when atoms are on top of each other
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
obconv.WriteFile(mol, "badrun.cml");
uff.Setup(mol);
uff.SteepestDescent(1000);
}
lammpssetup.setupUFF(mol, coefficientfilename, datafilename, padding);
List <int> esequence = lammpssetup.getesequence();
return(esequence);
}
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);
}
public void designgraphtoUFF(designGraph host, string coefficientfilename, string datafilename, bool contingency)
{
OBMol mol = new OBMol();
OBFunctions.designgraphtomol(host, ref mol);
LAMMPSNow lammpssetup = new LAMMPSNow(parameters, atomtypes, periodictable);
if (contingency)
{
//if lammps fails to minimize, try minimization using openbabel as a starting point
OBForceField uff = OBForceField.FindForceField("UFF");
mol = lammpssetup.perturbator(mol, 2); //lammps crashes when atoms are on top of each other
OBConversion obconv = new OBConversion();
obconv.SetOutFormat("cml");
obconv.WriteFile(mol, "badrun.cml");
uff.Setup(mol);
uff.SteepestDescent(1000);
}
lammpssetup.setupUFF(mol, coefficientfilename, datafilename, 50);
//lammpssetup.setupUFFtest(mol);
//lammpssetup.reset();
}
