/// <summary>
/// GetMolFormulaDotDisconnect
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public String GetMolFormulaDotDisconnect(
ICdkMol mol)
{
string mf = GetMolFormula(mol as CdkMol, includeSpaces: false, separateFragments: true);
return(mf);
}
/// <summary>
/// Get list of RNumbers and a count of instances for each
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static void GetCoreRGroupInfo(
ICdkMol mol,
out SortedDictionary <int, int> rgCounts,
out SortedDictionary <int, int> rgBufferStartingPos)
{
throw new NotImplementedException();
}
/// <summary>
/// Check if substructure query matches target molecule
/// </summary>
/// <param name="queryMol"></param>
/// <param name="targetMol"></param>
/// <returns></returns>
public bool IsSSSMatch(
ICdkMol queryMol,
ICdkMol targetMol)
{
SetSSSQueryMolecule(queryMol as CdkMol);
return(IsSSSMatch(targetMol as CdkMol));
}
/// <summary>
/// Prepare for FSS matching of supplied query molecule
/// </summary>
/// <param name="queryMol"></param>
public void SetFSSQueryMolecule(
ICdkMol queryMol,
string FullStructureSearchType = null)
{
FSSQueryMolecule = queryMol as CdkMol;
return;
}
/// <summary>
/// Hilight a target molecule using mapped atoms and bonds
/// </summary>
/// <param name="targetMol"></param>
/// <param name="mappedAtoms"></param>
/// <param name="mappedBonds"></param>
/// <returns></returns>
public ICdkMol HilightSSSMatchGMap(
ICdkMol targetMol,
int[] mappedAtoms,
int[] mappedBonds)
{
throw new NotImplementedException();
}
/// <summary>
/// GetFolFormula
/// </summary>
/// <param name="mol"></param>
/// <param name="includeSpaces"></param>
/// <param name="separateFragments"></param>
/// <param name="use2Hand3HforHydrogenIsotopes"></param>
/// <param name="ignoreIsotopes"></param>
/// <returns></returns>
public String GetMolFormula(
ICdkMol mol,
bool includeSpaces = false,
bool separateFragments = false,
bool use2Hand3HforHydrogenIsotopes = false,
bool ignoreIsotopes = false)
{
throw new NotImplementedException();
}
/// <summary>
/// Prepare for SSS matching of supplied query molecule
/// </summary>
/// <param name="queryMol"></param>
public void SetSSSQueryMolecule(
ICdkMol queryMol)
{
try
{
throw new NotImplementedException();
}
catch (Exception ex)
{
throw new Exception(ex.Message, ex);
}
}
/// <summary>
/// Get mapping of current query against supplied target
/// </summary>
/// <param name="targetMol"></param>
/// <param name="queryIndex"></param>
/// <param name="mappedAtoms"></param>
/// <param name="mappedBonds"></param>
/// <returns></returns>
public bool GetSSSMapping(
ICdkMol targetMol,
out int queryIndex,
out int[] mappedAtoms,
out int[] mappedBonds)
{
queryIndex = -1;
mappedAtoms = mappedBonds = null;
try
{
throw new NotImplementedException();
}
catch (Exception ex)
{
return(false); // just say false if exception encountered
}
}
/// <summary>
/// Perform a full structure search
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <param name="switches"></param>
/// <returns></returns>
public bool FullStructureMatch(
ICdkMol query,
ICdkMol target,
string FullStructureSearchType = null)
{
CdkMol q = query as CdkMol;
CdkMol t = target as CdkMol;
var fs = new UniversalIsomorphismTester();
if (fs.isIsomorph(q.NativeMol, t.NativeMol))
{
return(true);
}
else
{
return(false);
}
}
public static int ProcessTargetMolecule(ICdkMol mol)
{
throw new NotImplementedException();
}
public static void SetCoreStructure(ICdkMol mol, bool PromptUser)
{
throw new NotImplementedException();
}
/// <summary>
/// Map current query against supplied target molecule
/// </summary>
/// <param name="targetMol"></param>
/// <returns></returns>
public bool IsSSSMatch(
ICdkMol targetMol)
{
throw new NotImplementedException();
}
/// <summary>
/// Map current query against supplied target molecule
/// </summary>
/// <param name="targetMol"></param>
/// <returns></returns>
public bool IsFSSMatch(
ICdkMol targetMol)
{
return(FullStructureMatch(FSSQueryMolecule, targetMol));
}