/// <summary>
/// Assigns Gasteiger partial charges to molecule
/// </summary>
/// <returns>OBMol with Gasteiger partial charges assigned</returns>
public static OBMol AssignGasteigerCharges(this OBMol mol)
{
var newMol = mol.AddExplicitHydrogens();
newMol.UnsetPartialChargesPerceived();
foreach (var atom in newMol.Atoms())
{
atom.GetPartialCharge();
}
return(newMol);
}
/// <summary>
/// Calculates the Crippen SLogP VSA contributions from each atom
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static double[] CrippenSLogPVsaContributions(this OBMol mol, bool includeHydrogens)
{
var newMol = includeHydrogens ? mol.AddExplicitHydrogens() : mol;
var result = new List <double>();
foreach (var atom in newMol.Atoms())
{
var key = atom.GetCrippenKey();
if (!string.IsNullOrEmpty(key))
{
result.Add(CrippenConstants.GetLogP(key));
}
}
return(result.ToArray());
}
/// <summary>
/// Perform depth limited search of each atom to a depth of length
/// </summary>
/// <param name="mol"></param>
/// <param name="length"></param>
/// <param name="useHydrogens"></param>
/// <returns></returns>
public static IEnumerable <Path> PathsOfLengthN(this OBMol mol, int length, bool useHydrogens = false)
{
var newMol = useHydrogens ? mol.AddExplicitHydrogens() : mol;
var paths = new List <Path>();
foreach (var atom in newMol.Atoms())
{
var foundPaths = new List <IEnumerable <OBAtom> >();
var currentPath = new List <OBAtom>();
Search.DepthLimitedSearch(atom, length, currentPath, ref foundPaths);
foreach (var foundPath in foundPaths)
{
if (foundPath.Count() == length + 1)
{
paths.Add(new Path(foundPath));
}
}
}
return(paths.Distinct(new PathComparer()));
}
