/// <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);
}
/// <summary>
/// Merge existing .bin files with new records
/// 1. Copy .bin files to .mrg files filtering out cids that have been updated
/// 2. Append new records to .mrg files
/// 3. Rename .bin files to .bak files and .mrg files to new .bin files
/// </summary>
static void MergeRecordsIntoFiles(
List <FingerprintRec> fpRecList)
{
string date1, date2;
Progress.Show("Merging existing and new files...");
// Copy existing bin file entries filtering out cids that were updated
FpDao.OpenReaders("bin"); // open existing .bin files for input
FpDao.OpenWriters("mrg", FileMode.Create); // open new merge files for output
HashSet <string> fpRecHash = new HashSet <string>(); // build a hash of cids that shouldn't be copied
foreach (FingerprintRec fpr in fpRecList)
{
fpRecHash.Add(fpr.Cid);
}
int replacementCnt = 0;
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++) // copy each file
{
BinaryWriter bw = FpDao.BinaryWriters[fi];
while (true)
{
FingerprintRec fpr = FpDao.ReadFingerprintRec(fi);
if (fpr == null)
{
break;
}
if (fpRecHash.Contains(fpr.Cid))
{
//Log("Removing " + fpr.Cid); // debug
replacementCnt++;
continue; // skip if this cid is was updated in the incoming list
}
FpDao.WriteFingerprintRec(bw, fpr);
}
}
FpDao.CloseReaders();
// Append the new records to the merge files
foreach (FingerprintRec fpr in fpRecList) // write out buffered recs
{
FpDao.WriteFingerprintRec(fpr);
}
FpDao.CloseWriters();
// Backup old files and activate new files
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++) // check that we can backup all bin files
{
string fileName = FpDao.GetFpFileName(fi) + ".bin";
bool backupOk = FileUtil.CanRename(fileName);
if (!backupOk)
{
throw new Exception("Unable to rename file: " + fileName + ", aborting update");
}
}
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++)
{
string fileName = FpDao.GetFpFileName(fi);
bool backupOk = FileUtil.BackupAndReplaceFile(fileName + ".bin", fileName + ".bak", fileName + ".mrg");
if (!backupOk)
{
throw new Exception("Error replacing file: " + fileName + ".bin");
}
}
if (ByCheckpoint)
{
string checkPointDate = String.Format("{0:dd-MMM-yyyy HHmmss}", MoleculeDateTime); // format last new/updated date time in a format that works with Oracle
FpDao.WriteFingerPrintSimMxDataUpdateCheckpointDate(checkPointDate); // update checkpoint
}
Progress.Show("Merging complete...");
int cnt = fpRecList.Count;
string cid1 = fpRecList[0].Cid;
string cid2 = fpRecList[cnt - 1].Cid;
if (CidUpdateDateDict.ContainsKey(cid1))
{
date1 = CidUpdateDateDict[cid1].ToString();
}
else
{
date1 = "Missing";
}
if (CidUpdateDateDict.ContainsKey(cid2))
{
date2 = CidUpdateDateDict[cid1].ToString();
}
else
{
date2 = "Missing";
}
Log("Records stored: " + cnt + ", Adds: " + (cnt - replacementCnt) + ", Replacements: " + replacementCnt +
", Date range: " + date1 + " - " + date2 + ", CIDs: First = " + cid1 + ", Last = " + cid2);
return;
}
