/// <summary>
/// Performs a mol copy and adds explicit hydrogens to each heavy atom to the copy
/// </summary>
/// <param name="mol"></param>
/// <returns>Copy of original mol with explicit hydrogens</returns>
public static OBMol AddExplicitHydrogens(this OBMol mol)
{
var newMol = new OBMol(mol);
foreach (var atom in newMol.Atoms())
{
newMol.AddHydrogens(atom);
}
return(newMol);
}
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);
}
}