private static void CheckFPSmartsForMolecule(string moleculeSmiles, string[][] expectedFPSmarts)
{
var expected = new HashSet <string>();
foreach (var strs in expectedFPSmarts)
{
foreach (var str in strs)
{
expected.Add(str);
}
}
// expectedFPSmarts[][] is a double array because for each smarts
// several equivalent variants
// of the smarts are given e.g. CCC C(C)C
var mol = parser.ParseSmiles(moleculeSmiles);
CircularFingerprinter circ = new CircularFingerprinter();
circ.Calculate(mol);
var subsmarts = new SmartsFragmentExtractor(mol);
subsmarts.SetMode(SubstructureSelectionMode.JCompoundMapper);
var numFP = circ.FPCount;
var actual = new HashSet <string>();
for (int i = 0; i < numFP; i++)
{
var fp = circ.GetFP(i);
actual.Add(subsmarts.Generate(fp.Atoms));
}
Assert.IsTrue(expected.IsSupersetOf(actual));
}
public static string CircularFpToString(CircularFingerprinter cfp)
{
CircularFingerprint fp = null;
string s = "fp\thashCode\titeration\tatoms\r\n";
int fpCount = cfp.FPCount;
for (int fpi = 0; fpi < fpCount; fpi++)
{
fp = cfp.GetFP(fpi);
s += fpi.ToString() + "\t" + fp.Hash + "\t" + fp.Iteration + "\t(" + string.Join(", ", fp.Atoms) + ")\r\n";
}
return(s);
}
/// <summary>
/// Appends a new row to the model source data, which consists of a molecule and whether or not it
/// is considered active.
/// </summary>
/// <param name="mol">molecular structure, which must be non-blank</param>
/// <param name="active">whether active or not</param>
public void AddMolecule(IAtomContainer mol, bool active)
{
if (mol == null || mol.Atoms.Count == 0)
{
throw new CDKException("Molecule cannot be blank or null.");
}
var circ = new CircularFingerprinter(ClassType)
{
PerceiveStereo = this.PerceiveStereo
};
circ.Calculate(mol);
// gather all of the (folded) fingerprints into a sorted set
int AND_BITS = Folding - 1; // e.g. 1024/0x400 -> 1023/0x3FF: chop off higher order bits
var hashset = new SortedSet <int>();
for (int n = circ.FPCount - 1; n >= 0; n--)
{
int code = circ.GetFP(n).Hash;
if (Folding > 0)
{
code &= AND_BITS;
}
hashset.Add(code);
}
// convert the set into a sorted primitive array
var hashes = new int[hashset.Count];
int p = 0;
foreach (var h in hashset)
{
hashes[p++] = h;
}
// record the processed information for model building purposes
if (active)
{
numActive++;
}
training.Add(hashes);
activity.Add(active);
foreach (var h in hashes)
{
if (!inHash.TryGetValue(h, out int[] stash))
public void TestGetBitFingerprint()
{
Assert.IsTrue(trivialMol != null);
var circ = new CircularFingerprinter();
var result = circ.GetBitFingerprint(trivialMol);
BitArray wantBits = new BitArray(0), gotBits = result.AsBitSet();
int[] REQUIRE_BITS = { 19, 152, 293, 340, 439, 480, 507, 726, 762, 947, 993 };
foreach (var b in REQUIRE_BITS)
{
BitArrays.SetValue(wantBits, b, true);
}
if (!BitArrays.Equals(wantBits, gotBits))
{
throw new CDKException("Got " + gotBits + ", wanted " + wantBits);
}
}
public void TestUseStereoElements()
{
const string smiles1 = "CC[C@@H](C)O";
const string smiles2 = "CC[C@H](O)C";
const string molfile = "\n"
+ " CDK 10121722462D \n"
+ "\n"
+ " 5 4 0 0 0 0 999 V2000\n"
+ " -4.1837 2.6984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
+ " -3.4692 3.1109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
+ " -2.7547 2.6984 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n"
+ " -2.0403 3.1109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
+ " -2.7547 1.8734 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n"
+ " 1 2 1 0 0 0 0\n"
+ " 2 3 1 0 0 0 0\n"
+ " 3 4 1 0 0 0 0\n"
+ " 3 5 1 1 0 0 0\n"
+ "M END\n";
IChemObjectBuilder bldr = CDK.Builder;
MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(molfile));
SmilesParser smipar = new SmilesParser(bldr);
var mol1 = smipar.ParseSmiles(smiles1);
var mol2 = smipar.ParseSmiles(smiles2);
IAtomContainer mol3 = mdlr.Read(bldr.NewAtomContainer());
var fpr = new CircularFingerprinter
{
// when stereo-chemistry is perceived we don't have coordinates from the
// SMILES and so get a different fingerprint
PerceiveStereo = true
};
Assert.IsTrue(Compares.AreEqual(fpr.GetFingerprint(mol1), fpr.GetFingerprint(mol2)));
Assert.IsFalse(Compares.AreEqual(fpr.GetFingerprint(mol2), fpr.GetFingerprint(mol3)));
fpr.PerceiveStereo = false;
Assert.IsTrue(Compares.AreEqual(fpr.GetFingerprint(mol1), fpr.GetFingerprint(mol2)));
Assert.IsTrue(Compares.AreEqual(fpr.GetFingerprint(mol2), fpr.GetFingerprint(mol3)));
}
public void TestGetCountFingerprint()
{
Assert.IsTrue(trivialMol != null);
var circ = new CircularFingerprinter();
var result = circ.GetCountFingerprint(trivialMol);
int[] ANSWER_KEY = { -414937772, 1, -1027418143, 1, 1627608083, 1, -868007456, 1, -1006701866, 1,
-1059145289, 1, -801752141, 1, 790592664, 1, -289109509, 1, -1650154758, 1,1286833445, 1 };
int wantBits = ANSWER_KEY.Length >> 1;
bool fail = result.GetNumberOfPopulatedBins() != wantBits;
for (int n = 0; !fail && n < result.GetNumberOfPopulatedBins(); n++)
{
int gotHash = result.GetHash(n), gotCount = result.GetCount(n);
bool found = false;
for (int i = 0; i < wantBits; i++)
{
int wantHash = ANSWER_KEY[i * 2], wantCount = ANSWER_KEY[i * 2 + 1];
if (gotHash == wantHash)
{
found = true;
if (gotCount != wantCount)
{
throw new CDKException("For hash " + gotHash + " got count " + gotCount + " but wanted " + wantCount);
}
}
}
if (!found)
{
fail = true;
break;
}
}
if (fail)
{
throw new CDKException("Hash values do not match.");
}
}
/// <summary>
/// BuildTest
/// </summary>
public static void BuildTest()
{
CircularFingerprinter cfp = null;
CircularFingerprinterClass FpClass = CircularFingerprinterClass.ECFP6; // FP diameter
int FpLen = 2048; // folded binary fp length
IAtomContainer mol, mol2;
//string molfile = FileUtil.ReadFile(@"C:\Download\CorpId-12345.mol");
//java.io.StringReader sr = new java.io.StringReader(molfile);
//if (Lex.Contains(molfile, "v2000"))
// cor = new MDLV2000Reader(sr);
//else
// cor = new MDLV3000Reader(sr);
//cor.setReaderMode(IChemObjectReader.Mode.RELAXED);
//ac = (IAtomContainer)cor.read(new AtomContainer());
//cor.close();
FpClass = CircularFingerprinterClass.ECFP4; // debug
cfp = new CircularFingerprinter(FpClass, FpLen);
StreamReader reader = new StreamReader(@"C:\Download\CorpId-12345.mol");
//FileReader FileReader = new FileReader(@"C:\Download\V3000 Mols.sdf");
EnumerableSDFReader rdr = new EnumerableSDFReader(reader.BaseStream, ChemObjectBuilder.Instance);
rdr.ReaderMode = ChemObjectReaderMode.Relaxed;
IEnumerator <IAtomContainer> cursor = rdr.GetEnumerator();
while (cursor.MoveNext())
{
mol = cursor.Current;
mol = CdkMol.GetLargestMoleculeFragment(mol);
ICountFingerprint cfp1 = cfp.GetCountFingerprint(mol); // get hash values and counts for each
cfp.Calculate(mol);
int fpCount = cfp.FPCount;
for (int fpi = 0; fpi < fpCount; fpi++) // gets
{
CircularFingerprint cfp2 = cfp.GetFP(fpi); // gets hash, iteration and lists of atoms (dups appear multiple times)
}
IBitFingerprint bfp = cfp.GetBitFingerprint(mol);
BitArray bs = bfp.AsBitSet();
int bsCard = bfp.Cardinality;
long bsSize = bfp.Length;
continue;
}
reader.Close();
return;
//java.io.StringReader sr = new java.io.StringReader(molfile);
//AtomContainer mol = new AtomContainer();
//mol.addAtom(new Atom("C"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addAtom(new Atom("H"));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(1)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(2)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(3)));
//mol.addBond(new Bond(mol.getAtom(0), mol.getAtom(4)));
//FileReader FileReader = new FileReader(@"C:\Download\CorpId-12345.mol");
//MolReader mr = new MolReader(FileReader, DefaultChemObjectBuilder.getInstance());
//java.io.StringReader sr = new java.io.StringReader(molfile);
//IMol m = (IMol)mr.next();
//FileReader.close();
}
/// <summary>
/// Build fingerprint
/// </summary>
/// <param name="mol"></param>
public static BitSetFingerprint BuildBitSetFingerprint(
IAtomContainer mol,
FingerprintType fpType,
int fpSubtype = -1,
int fpLen = -1)
{
// Data for Tanimoto similarity using various fingerprint types for CorpId 123456 query.
// Cart - Standard MDL Oracle Cartridge scores
//
// Similarity Score
// ------------------------------------------------
// Size -> 192 896 1024 1024 128 1024 320
// CorpId Cart MACCS PbChm ECFP4 EXT EState Basic Sbstr
// ------ ---- ---- ---- ---- ---- ---- ---- ----
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.95 1.00
// 123456 0.99 0.98 0.96 0.77 0.95 1.00 0.94 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.99 0.91 1.00 0.81 1.00 1.00 1.00 1.00
// 123456 0.98 0.95 1.00 0.74 0.92 1.00 0.93 0.94
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00
// 123456 0.98 1.00 0.83 0.76 0.77 0.90 0.76 0.94
// LSH Bin Count - The number of LSH bins (of 25) that match the query bin values
//--------------
// CorpId MAC PbC ECFP EX
// ------ --- --- --- ---
// 123456 25 25 25 25
// 123456 25 20 7 16
// 123456 25 20 9 19
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 20 25 9 25
// 123456 21 25 11 17
// 123456 25 25 25 25
// 123456 25 25 25 25
// 123456 25 9 6 11
// Data for Tanimoto similarity using various Circular fingerprint types.
// Using 2 molecules where the 2nd just has an added methyl group.
//
// Measure Score
// -------- -----
// ECFP0 1.00
// ECFP2 .88
// ECFP4 .75
// ECFP6 .64
// FCFP0 1.00
// FCFP2 .92
// FCFP4 .84
// FCFP6 .74
IFingerprinter ifptr = null;
IBitFingerprint ibfp = null;
BitSetFingerprint bfp = null;
IAtomContainer mol2;
string s = "";
DateTime t0 = DateTime.Now;
double getFptrTime = 0, buildFpTime = 0;
if (fpType == FingerprintType.Basic) // size = 1024
{
ifptr = new Fingerprinter();
}
else if (fpType == FingerprintType.Circular) // size variable
{
CircularFingerprinterClass cfpClass = (CircularFingerprinterClass)fpSubtype;
if (cfpClass < CircularFingerprinterClass.ECFP0 || cfpClass > CircularFingerprinterClass.ECFP6)
{
cfpClass = (CircularFingerprinterClass)CircularFingerprintType.DefaultCircularClass; // default class
}
if (fpLen < 0)
{
fpLen = CircularFingerprintType.DefaultCircularLength; // default length
}
ifptr = new CircularFingerprinter(cfpClass, fpLen);
//CircularFingerprinter cfp = (CircularFingerprinter)ifptr;
//ICountFingerprint cntFp = cfp.getCountFingerprint(mol); // debug
//s = CircularFpToString(cfp); // debug
}
else if (fpType == FingerprintType.Extended) // size = 1024
{
ifptr = new ExtendedFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.EState) // size = 128
{
ifptr = new EStateFingerprinter(); // use DEFAULT_SIZE and DEFAULT_SEARCH_DEPTH
}
else if (fpType == FingerprintType.MACCS) // size = 192
{
if (MACCSFp == null)
{
MACCSFp = new MACCSFingerprinter();
}
ifptr = MACCSFp;
}
else if (fpType == FingerprintType.PubChem) // size = 896
{
//IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
ifptr = new PubchemFingerprinter();
}
else if (fpType == FingerprintType.ShortestPath) // size =
{
ifptr = new ShortestPathFingerprinter(); // fails with atom type issue for many structures (e.g. 123456)
}
else if (fpType == FingerprintType.Signature) // size =
{
ifptr = new SignatureFingerprinter(); // can't convert array fingerprint to bitsetfingerprint
}
else if (fpType == FingerprintType.Substructure) // size = 320
{
ifptr = new SubstructureFingerprinter();
}
else
{
throw new Exception("Invalid CdkFingerprintType: " + fpType);
}
getFptrTime = TimeOfDay.Delta(ref t0);
ibfp = ifptr.GetBitFingerprint(mol);
bfp = (BitSetFingerprint)ibfp;
buildFpTime = TimeOfDay.Delta(ref t0);
//long size = bfp.size();
//int card = bfp.Cardinality;
return(bfp);
}
