/// <summary>
/// Prepare for FSS matching of supplied query molecule
/// </summary>
/// <param name="queryMol"></param>
public void SetFSSQueryMolecule(
INativeMolMx queryMol,
string FullStructureSearchType = null)
{
FSSQueryMolecule = queryMol as CdkMol;
return;
}
/// <summary>
/// GetMolFormulaDotDisconnect
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public String GetMolFormulaDotDisconnect(
INativeMolMx mol)
{
string mf = GetMolFormula(mol as CdkMol, includeSpaces: false, separateFragments: true);
return(mf);
}
/// <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 INativeMolMx HilightSSSMatchGMap(
INativeMolMx targetMol,
int[] mappedAtoms,
int[] mappedBonds)
{
throw new NotImplementedException();
}
/// <summary>
/// Get list of RNumbers and a count of instances for each
/// </summary>
/// <param name="mol"></param>
/// <returns></returns>
public static void GetCoreRGroupInfo(
INativeMolMx 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(
INativeMolMx queryMol,
INativeMolMx targetMol)
{
SetSSSQueryMolecule(queryMol as CdkMol);
return(IsSSSMatch(targetMol as CdkMol));
}
/// <summary>
/// Set substructure search query molecule
/// </summary>
/// <param name="cs"></param>
public void SetSSSQueryMolecule(
MoleculeMx cs)
{
QueryMol = cs.Clone();
SSSQueryMol = CdkMolFactory.NewCdkMol(cs);
CdkMolUtil.SetSSSQueryMolecule(SSSQueryMol);
return;
}
/// <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(
INativeMolMx 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(
INativeMolMx queryMol)
{
try
{
throw new NotImplementedException();
}
catch (Exception ex)
{
throw new Exception(ex.Message, ex);
}
}
/// <summary>
/// Do a SSS using the predefined query molecule and supplied target molecule
/// </summary>
/// <returns></returns>
public bool IsSSSMatch(MoleculeMx cs)
{
if (QueryMol == null || cs.IsBiopolymerFormat) // fix later
{
return(false);
}
TargetMol = cs;
SSSTargetMol = CdkMolFactory.NewCdkMol(cs);
bool b = CdkMolUtil.IsSSSMatch(SSSTargetMol);
return(b);
}
/// <summary>
/// Set full structure search query molecule
/// </summary>
/// <param name="cs"></param>
public void SetFSSQueryMolecule(
MoleculeMx cs)
{
if (cs.IsBiopolymerFormat) // fix later
{
QueryMol = cs;
return;
}
QueryMol = cs.Clone();
FSSQueryMol = CdkMolFactory.NewCdkMol(cs);
CdkMolUtil.SetFSSQueryMolecule(FSSQueryMol);
return;
}
/// <summary>
/// Perform a substructure search
/// </summary>
/// <param name="query"></param>
/// <param name="target"></param>
/// <returns></returns>
public bool IsSSSMatch(
MoleculeMx query,
MoleculeMx target)
{
if (query.IsBiopolymerFormat || target.IsBiopolymerFormat) // fix later
{
return(false);
}
QueryMol = query;
SSSQueryMol = CdkMolFactory.NewCdkMol(query);
SSSTargetMol = CdkMolFactory.NewCdkMol(target);
bool b = CdkMolUtil.IsSSSMatch(SSSQueryMol, SSSTargetMol);
return(b);
}
/// <summary>
/// Do a SSS using the predefined query molecule and supplied target molecule
/// </summary>
/// <returns></returns>
public bool IsFSSMatch(MoleculeMx cs)
{
if (MoleculeMx.IsUndefined(QueryMol) || MoleculeMx.IsUndefined(cs))
{
return(false);
}
if (cs.IsBiopolymerFormat)
{
return(IsFSSMatch(QueryMol, cs));
}
TargetMol = cs;
FSSTargetMol = CdkMolFactory.NewCdkMol(cs);
bool b = CdkMolUtil.IsFSSMatch(FSSTargetMol);
return(b);
}
/// <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(
INativeMolMx 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(
INativeMolMx query,
INativeMolMx target,
string FullStructureSearchType = null)
{
if (query == null || target == null)
{
return(false);
}
CdkMol q = query as CdkMol;
q.UpdateNativeMolecule(); // be sure up to date
if (q?.NativeMol == null)
{
return(false);
}
CdkMol t = target as CdkMol;
t.UpdateNativeMolecule();
if (t?.NativeMol == null)
{
return(false);
}
var fs = new UniversalIsomorphismTester();
if (fs.IsIsomorph(q.NativeMol, t.NativeMol))
{
return(true);
}
else
{
return(false);
}
}
public static int ProcessTargetMolecule(INativeMolMx mol)
{
throw new NotImplementedException();
}
public static void SetCoreStructure(INativeMolMx mol, bool PromptUser)
{
throw new NotImplementedException();
}
/// <summary>
/// Do setup in preparation for decompose
/// </summary>
/// <param name="qt"></param>
/// <param name="q"></param>
public void PrepareForDecompose(
QueryTable qt,
Query q)
{
throw new NotImplementedException();
#if false
Stopwatch sw = Stopwatch.StartNew();
MetaTable mt = qt.MetaTable;
QueryColumn qc = qt.GetQueryColumnByName("core");
if (qc == null)
{
throw new UserQueryException("Core column not defined in rgroup_decomposition table");
}
string molfile = qc.MolString;
if (molfile == null || molfile == "")
{ // core not defined in Rgroup decomposition table, try to get from structure search in rest of query
foreach (QueryTable qt3 in q.Tables)
{
if (!qt3.MetaTable.IsRootTable)
{
continue;
}
MetaColumn mc3 = qt3.MetaTable.FirstStructureMetaColumn;
if (mc3 != null)
{
QueryColumn qc3 = qt3.GetQueryColumnByName(mc3.Name);
molfile = qc3.MolString;
break;
}
}
}
if (molfile == null || molfile == "")
{
throw new UserQueryException("R-group decomposition core structure is not defined");
}
bool allowHydrogenSubstituents = true;
qc = qt.GetQueryColumnByName("AllowHydrogenSubstituents");
if (Lex.Contains(qc?.Criteria, "'N'"))
{
allowHydrogenSubstituents = false; // set to false if "no" criteria specified
}
TerminateOptionString = "First mapping";
bool allowMultipleCoreMappings = false;
qc = qt.GetQueryColumnByName("Terminate_Option");
if (qc != null && qc.Criteria != "")
{
ParsedSingleCriteria psc = MqlUtil.ParseSingleCriteria(qc.Criteria);
TerminateOptionString = psc.Value;
allowMultipleCoreMappings = Lex.Contains(TerminateOptionString, "All");
}
MoleculeMx cs = new MoleculeMx(MoleculeFormat.Molfile, molfile);
cs.GetCoreRGroupInfo(out RgCounts, out RgTotalCount); // need to redefine these
RGroupDecomp.Initialize();
RGroupDecomp.SetAlignStructuresToCore(true);
RGroupDecomp.SetAllowMultipleCoreMappings(allowMultipleCoreMappings);
RGroupDecomp.SetIncludeHydrogenFragments(allowHydrogenSubstituents);
if (DebugMx.True) // debug
{
String coreSmiles = "[R1]c1cn2c3c(c1= O)cc(c(c3SC(C2)[R4])[R3])[R2]";
string coreChime = "CYAAFQwAUewQeV58YHemfM^EQqPRfIYlJGEkx6M7e4db95jjK5HrNFVP2e1qHphWPL98KvcvrsF7bP9bRcW4QH$si9PXkkuwre6Q5UkHZjciQqeAKVLSHNAeQTAMlkiXEBD$BePpbNQCPD3BkklFEaQqwokeI$FwUoS5cAixQXkMbLTWDaAK7t7cOkSmt3RhwQedbrba6OHKBq3OF4Dhlz$0BfLeKCUUo8ixle176M2aIzXUccTOU8Xy8ARwE3bTyMfjuI3UunZceJf4iZELvsj3PX2MHZG73baUvQGS4DaxUaBGps81PPiDljfvxwFv8OfdOyIRlOBeuEAvk2rT9SRT6oMZIV6UtLFvmCHdwKnu9WtrfV1rEctydNUVxW4qKVlV0rZtpK1oZXuKcv6WVdl6r2hrjVLxBhblTVKO7w1qGRoziquOnPQkKd9H4EQfV0rP6mzI8Au8ulti2fu3YKB94lPXftPGbwr5yA";
IMolLib coreMol = MolLibFactory.NewMolLib(MoleculeFormat.Molfile, molfile);
coreChime = MoleculeMx.MolfileStringToChimeString(molfile);
molfile = coreMol.MolfileString;
}
CoreMolecule = CdkMol.Util.MolfileStringToMolecule(molfile);
RGroupDecomp.SetCoreStructure(CoreMolecule, false);
CoreChemicalStructure = new MoleculeMx(MoleculeFormat.Molfile, molfile);
StrMatcher = null;
int msTime = (int)sw.ElapsedMilliseconds;
if (RGroupDecomp.Debug)
{
DebugLog.Message("Time(ms): " + msTime);
}
return;
#endif
}
/// <summary>
/// Map current query against supplied target molecule
/// </summary>
/// <param name="targetMol"></param>
/// <returns></returns>
public bool IsSSSMatch(
INativeMolMx targetMol)
{
throw new NotImplementedException();
}
/// <summary>
/// Map current query against supplied target molecule
/// </summary>
/// <param name="targetMol"></param>
/// <returns></returns>
public bool IsFSSMatch(
INativeMolMx targetMol)
{
return(FullStructureMatch(FSSQueryMolecule, targetMol));
}
