/// <summary>
/// GetMaxCorpId
/// </summary>
/// <returns></returns>
public static int GetMaxDestMolId()
{
int molId, maxMolId = 0;
FingerprintDao fpd = new FingerprintDao(Database, FingerprintType);
List <string> ids = new List <string>();
if (!fpd.DataFilesExist())
{
return(maxMolId);
}
fpd.OpenReaders();
while (true)
{
FingerprintRec rec = fpd.ReadFingerprintRec();
if (rec == null)
{
break;
}
//CorpIds.Add(rec.Cid); // debug
if (CorpDatabase)
{
int.TryParse(rec.Cid, out molId);
}
else
{
molId = rec.molId;
}
if (molId > maxMolId)
{
maxMolId = molId;
}
}
fpd.CloseReaders();
return(maxMolId);
}
/// <summary>
/// ExecuteSearch
/// </summary>
/// <param name="queryMol"></param>
public List <StructSearchMatch> ExecuteSearch(
IAtomContainer queryMol)
{
AssertMx.IsTrue(FingerprintType == FingerprintType.MACCS || FingerprintType == FingerprintType.Circular,
"Invalid FingerprintType: " + FingerprintType);
QueryMol = queryMol;
BitSetFingerprint fp = // generate a fingerprint
CdkMol.BuildBitSetFingerprintForLargestFragment(queryMol, FingerprintType);
QueryFpCardinality = fp.cardinality();
QueryFpLongArray = fp.asBitSet().toLongArray();
MatchList = new List <StructSearchMatch>();
ThreadException = null;
foreach (string databaseName in FingerprintDbMx.Databases) // loop on all databases
{
int srcId = -1;
if (Lex.Contains(databaseName, "corp"))
{
if (!GetCorpSim)
{
continue;
}
srcId = StructSearchMatch.CorpDbId;
}
else if (Lex.Contains(databaseName, "chembl"))
{
if (!GetChemblSim)
{
continue;
}
srcId = StructSearchMatch.ChemblDbId;
}
if (Debug)
{
DebugLog.Message("Starting sim search on " + databaseName + " database");
}
FpDao = new FingerprintDao(databaseName, FingerprintType);
if (!FpDao.DataFilesExist())
{
continue; // no files for this database
}
FileStreamReaders = FpDao.OpenReaders();
FileMatchLists = new List <StructSearchMatch> [FileStreamReaders.Length];
for (int i1 = 0; i1 < FileMatchLists.Length; i1++)
{
FileMatchLists[i1] = new List <StructSearchMatch>();
}
DateTime t0 = DateTime.Now;
if (UseMultipleThreads)
{
ExecuteMultiThreadSearch();
}
else
{
ExecuteSingleThreadSearch();
}
double et = TimeOfDay.Delta(ref t0);
FpDao.CloseReaders();
List <StructSearchMatch> matchList = MergeIndividualFileMatchLists();
if (KeysToExclude != null || SearchKeySubset != null) // filter by any allowed/disallowed keys
{
List <StructSearchMatch> matchList2 = new List <StructSearchMatch>();
foreach (StructSearchMatch m0 in matchList)
{
if (KeysToExclude != null && KeysToExclude.Contains(m0.SrcCid))
{
continue;
}
if (SearchKeySubset != null && !SearchKeySubset.Contains(m0.SrcCid))
{
continue;
}
matchList2.Add(m0);
}
matchList = matchList2;
}
matchList.Sort(StructSearchMatch.CompareByMatchQuality);
//int removeCount = matchList.Count - MaxHits; // limit to maxhits per database
//if (removeCount > 0)
// matchList.RemoveRange(MaxHits, removeCount);
//foreach (StructSearchMatch ssm0 in matchList)
// if (ssm0.SrcId != srcId) ssm0.SrcId = srcId; // debug
MatchList.AddRange(matchList);
double et2 = TimeOfDay.Delta(ref t0);
string msg =
string.Format("Search complete (" + databaseName + ").Time : {0:0.00} ", et) +
string.Format("{0} Hits: ", FileMatchLists[0].Count);
if (Debug)
{
DebugLog.Message(msg);
}
for (int hi = 0; hi < 5 && hi < FileMatchLists[0].Count; hi++)
{
StructSearchMatch sm = FileMatchLists[0][hi];
msg += sm.SrcCid + string.Format(" = {0:0.00}, ", sm.MatchScore);
}
} // database loop
if (ThreadException != null)
{
throw new Exception(ThreadException.Message, ThreadException);
}
MatchList.Sort( // sort by decreasing sim value
delegate(StructSearchMatch p1, StructSearchMatch p2)
{ return(p2.MatchScore.CompareTo(p1.MatchScore)); });
if (MaxHits > 0 && MatchList.Count > MaxHits) // remove hits beyond maximum if defined
{
MatchList.RemoveRange(MaxHits, MatchList.Count - MaxHits);
}
//ShowProgress(msg);
//Thread.Sleep(10000000);
return(MatchList);
}