/// <summary>
/// OpenFingerprintFilesForReading
/// </summary>
/// <returns></returns>
public FileStream[] OpenReaders(
string fileExtension = "bin")
{
if (Lex.IsUndefined(fileExtension))
{
fileExtension = ".bin";
}
if (!fileExtension.StartsWith("."))
{
fileExtension = "." + fileExtension;
}
FileStream[] fsa = new FileStream[FingerprintDao.FingerprintFileCount];
for (int fi = 0; fi < FingerprintDao.FingerprintFileCount; fi++)
{
string fileName = GetFpFileName(fi) + fileExtension;
int bufferSize = (int)Math.Pow(2, 20); // 2**20 = 1MB = 1048576;
FileStream fs = new FileStream(fileName, FileMode.Open, FileAccess.Read, FileShare.Read, bufferSize, FileOptions.SequentialScan);
fsa[fi] = fs;
}
ReadStreams = fsa;
Rfpa = null;
Rsi = -1;
return(fsa);
}
/// <summary>
/// Read next fingerprint rec from file
/// </summary>
/// <param name="fi"></param>
/// <returns></returns>
public FingerprintRec ReadFingerprintRec(
int fi)
{
if (Rfpa == null || Rfpa.reader != ReadStreams[fi]) // start reading file
{
Rfpa = new ReadFingerprintRecArgs();
Rfpa.Initialize(ReadStreams[fi], FpLengthInLongs);
}
if (!ReadRawFingerprintRec(Rfpa))
{
return(null); // end of file
}
FingerprintRec r = new FingerprintRec();
r.molId = Rfpa.uci;
r.SrcId = Rfpa.src;
string cid = ASCIIEncoding.ASCII.GetString(Rfpa.cidBytes, 0, Rfpa.cidLength);
r.Cid = CompoundIdNormalizeForDatabase(cid);
r.Cardinality = Rfpa.cardinality;
r.Fingerprint = (long[])Rfpa.fingerprint.Clone();
return(r);
}
/// <summary>
/// ReadFingerprintRec
/// </summary>
/// <returns></returns>
public FingerprintRec ReadFingerprintRec()
{
if (Rsi < 0)
{
Rsi = 0; // first file
}
FingerprintRec r = ReadFingerprintRec(Rsi);
while (r == null) // if end of file try going to next
{
if (Rsi + 1 >= ReadStreams.Length)
{
return(null);
}
Rsi++;
Rfpa = new ReadFingerprintRecArgs();
Rfpa.Initialize(ReadStreams[Rsi], FpLengthInLongs);
r = ReadFingerprintRec(Rsi);
}
r.molId = Rfpa.uci;
r.SrcId = Rfpa.src;
string cid = ASCIIEncoding.ASCII.GetString(Rfpa.cidBytes, 0, Rfpa.cidLength);
r.Cid = CompoundIdNormalizeForDatabase(cid);
r.Cardinality = Rfpa.cardinality;
r.Fingerprint = (long[])Rfpa.fingerprint.Clone();
return(r);
}
/// <summary>
/// ReadFingerprintRec
/// </summary>
/// <param name="reader"></param>
/// <param name="fileLength"></param>
/// <param name="uci"></param>
/// <param name="src"></param>
/// <param name="cidLength"></param>
/// <param name="cidBytes"></param>
/// <param name="cardinality"></param>
/// <param name="fingerprint"></param>
/// <returns></returns>
public bool ReadRawFingerprintRec(
ReadFingerprintRecArgs a)
{
unsafe // unsafe code, must be compiled with unsafe switch
{
int cidLength = 0, cidLongs, li, bi;
long *lp1, lp2;
byte[] buffer = a.buffer;
if (a.reader.Position >= a.fileLength)
{
return(false);
fixed(byte *bp = &(buffer[0])) // fix the buffer for low-level access
{
int readLen1 = 4 + 4 + 1; // UCI (4), src(4) and cid length(1)
a.reader.Read(buffer, 0, readLen1); // read UCI, src and cid length
cidLength = buffer[8];
int readLen2 = cidLength + 4 + 1 + a.fingerprint.Length * 8;
a.reader.Read(buffer, readLen1, readLen2); // read cid, card(4), fpLen(1) & fp
a.uci = *((int *)&(bp[0]));
a.src = *((int *)&(bp[4]));
a.cidLength = cidLength;
cidLongs = (cidLength + 7) / 8; // copy the cid in 8-byte chunks
fixed(byte *bp2 = &(a.cidBytes[0])) // fix the dest cid byte array
{
lp1 = (long *)&(bp[readLen1]); // start of cid in buffer
lp2 = (long *)&(bp2[0]); // start of a.cidLength
for (li = 0; li < cidLongs; li++) // copy the cid
{
*(&lp2[li]) = *(&lp1[li]);
}
}
bi = readLen1 + cidLength; // start of cardinality
a.cardinality = *((int *)&(bp[bi]));
byte fpLongs = buffer[bi + 4]; // number of longs in fp
lp1 = (long *)&(bp[bi + 5]); // position of fp in buffer
fixed(long *lpFp = &(a.fingerprint[0])) // fix the dest fingerprint
{
for (li = 0; li < fpLongs; li++) // copy it
{
*(&lpFp[li]) = *(&lp1[li]);
}
}
}
}
return(true);
}
StructSearchMatch ReadFingerprintRec_To_StructSearchMatch(
ReadFingerprintRecArgs a)
{
StructSearchMatch sm = new StructSearchMatch();
sm.SearchType = StructureSearchType.MolSim;
sm.SrcDbId = a.src;
sm.SrcCid = AsciiEncodingInstance.GetString(a.cidBytes, 0, a.cidLength);
if (sm.SrcDbId == 0)
{
sm.SrcCid = CompoundId.NormalizeForDatabase(sm.SrcCid); // be sure CorpIds are proper length
}
return(sm);
}
/// <summary>
/// Find Cid for debug purposes
/// </summary>
/// <param name="a"></param>
/// <returns></returns>
bool IsSrcCidMatch(
string cid,
ReadFingerprintRecArgs a)
{
StructSearchMatch sm = ReadFingerprintRec_To_StructSearchMatch(a);
if (Lex.Eq(sm.SrcCid, cid))
{
return(true);
}
else
{
return(false);
}
}
/// <summary>
/// Search a single file
/// </summary>
void SearchSingleFile(int fi)
{
StructSearchMatch sm = null;
AssertMx.IsNotNull(FpDao, "FpDao");
List <StructSearchMatch> matchList = FileMatchLists[fi];
AssertMx.IsNotNull(matchList, "matchList");
OpenBitSet queryObs = new OpenBitSet(QueryFpLongArray, QueryFpLongArray.Length);
AssertMx.IsNotNull(queryObs, "queryObs");
OpenBitSet dbObs = new OpenBitSet(QueryFpLongArray, QueryFpLongArray.Length); // gets set to DB fp for intersect
AssertMx.IsNotNull(dbObs, "dbObs");
FileStream fs = FileStreamReaders[fi];
AssertMx.IsNotNull(fs, "fs");
ReadFingerprintRecArgs a = new ReadFingerprintRecArgs();
a.Initialize(fs, QueryFpLongArray.Length);
try
{
while (true)
{
bool readOk = FpDao.ReadRawFingerprintRec(a);
if (!readOk)
{
break;
}
//if (IsSrcCidMatch("03435269", a)) a = a; // debug
dbObs.Bits = a.fingerprint;
dbObs.Intersect(queryObs);
int commonCnt = (int)dbObs.Cardinality();
float simScore = commonCnt / (float)(a.cardinality + QueryFpCardinality - commonCnt);
if (simScore >= MinimumSimilarity)
{
sm = ReadFingerprintRec_To_StructSearchMatch(a);
sm.SearchType = StructureSearchType.MolSim;
sm.MatchScore = simScore;
matchList.Add(sm);
}
}
}
catch (Exception ex)
{
string msg = ex.Message;
msg += string.Format("\r\nfi: {0}, fs.Name: {1}, sm: {2}", fi, fs.Name, sm != null ? sm.Serialize() : "");
DebugLog.Message(DebugLog.FormatExceptionMessage(ex, msg));
throw new Exception(msg, ex);
}
return;
}
