/// <inheritdoc />
protected override void AddWeakFingerprint(IFingerprinter fingerprinter, SealDirectory sealDirectory)
{
Contract.Requires(fingerprinter != null);
Contract.Requires(sealDirectory != null);
base.AddWeakFingerprint(fingerprinter, sealDirectory);
if (!ExcludeSemiStableHashOnFingerprintingSealDirectory && !sealDirectory.Kind.IsDynamicKind())
{
// A statically sealed directory can exist as multiple different instances, e.g., one can have partially sealed directories with the same root and member set.
// To distinguish those instances, we include the semi stable hash as part of the static fingerprint.
fingerprinter.Add("SemiStableHash", sealDirectory.SemiStableHash);
}
}
public virtual void TestBug934819()
{
// inlined molecules - note this test fails if implicit hydrogens are
// included. generally PubCheMFingerprint can't be used for substructure filter
IAtomContainer superStructure = Bug934819_2();
IAtomContainer subStructure = Bug934819_1();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(superStructure).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(subStructure).AsBitSet();
Assert.IsTrue(BitArrays.Equals(subBS, And(superBS, subBS)));
}
public virtual void TestBug706786()
{
// inlined molecules - note this test fails if implicit hydrogens are
// included. generally MACCS and ESTATE can't be used for substructure filter
// check those subclasses which check the bits are set
IAtomContainer superStructure = Bug706786_1();
IAtomContainer subStructure = Bug706786_2();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(superStructure);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(subStructure);
AddImplicitHydrogens(superStructure);
AddImplicitHydrogens(subStructure);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(superStructure).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(subStructure).AsBitSet();
Assert.IsTrue(BitArrays.Equals(subBS, And(superBS, subBS)));
}
/// <inheritdoc />
public void WriteFingerprintInputs(IFingerprinter writer)
{
using (var stream = new MemoryStream())
{
using (var buildXLWriter = new BuildXLWriter(
debug: false,
stream: stream,
leaveOpen: false,
logStats: false))
{
UnsafeOptions.Serialize(buildXLWriter);
writer.Add("SerializedUnsafeOptions", System.BitConverter.ToString(stream.ToArray()));
}
}
var thisRef = this;
writer.AddNested(ObservedPathEntryConstants.PathSet, w =>
{
foreach (var p in thisRef.PathEntries)
{
w.Add(ObservedPathEntryConstants.Path, p.Path);
if (p.Flags != ObservedPathEntryFlags.None)
{
w.Add(ObservedPathEntryConstants.Flags, p.Flags.ToString());
}
if (p.EnumeratePatternRegex != null)
{
w.Add(ObservedPathEntryConstants.EnumeratePatternRegex, p.EnumeratePatternRegex);
}
}
});
writer.AddCollection <StringId, ReadOnlyArray <StringId> >(
"ObservedAccessedFileNames",
ObservedAccessedFileNames,
(w, v) => w.Add(v));
// Observed inputs are included directly into the strong fingerprint hash computation,
// so they do not need to be serialized here
}
public void TestBug771485()
{
var builder = CDK.Builder;
var filename = "NCDK.Data.MDL.bug771485-1.mol";
var ins = ResourceLoader.GetAsStream(filename);
var reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure1 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
filename = "NCDK.Data.MDL.bug771485-2.mol";
ins = ResourceLoader.GetAsStream(filename);
reader = new MDLV2000Reader(ins, ChemObjectReaderMode.Strict);
IAtomContainer structure2 = (IAtomContainer)reader.Read(builder.NewAtomContainer());
// these molecules are different resonance forms of the same molecule
// make sure aromaticity is detected. although some fingerprinters do this
// one should not expected all implementations to do so.
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure1);
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(structure2);
Aromaticity.CDKLegacy.Apply(structure1);
Aromaticity.CDKLegacy.Apply(structure2);
AddImplicitHydrogens(structure1);
AddImplicitHydrogens(structure2);
Kekulization.Kekulize(structure1);
Kekulization.Kekulize(structure2);
// hydrogens loaded from MDL mol files if non-query. Structure 2 has
// query aromatic bonds and the hydrogen counts are not assigned - ensure
// this is done here.
CDK.HydrogenAdder.AddImplicitHydrogens(structure1);
CDK.HydrogenAdder.AddImplicitHydrogens(structure2);
IFingerprinter fingerprinter = GetBitFingerprinter();
BitArray superBS = fingerprinter.GetBitFingerprint(structure2).AsBitSet();
BitArray subBS = fingerprinter.GetBitFingerprint(structure1).AsBitSet();
bool isSubset = FingerprinterTool.IsSubset(superBS, subBS);
Assert.IsTrue(isSubset);
}
/// <inheritdoc />
protected override void AddWeakFingerprint(IFingerprinter fingerprinter, SealDirectory sealDirectory)
{
Contract.Requires(fingerprinter != null);
Contract.Requires(sealDirectory != null);
base.AddWeakFingerprint(fingerprinter, sealDirectory);
// For non-composite shared opaque directories, contents and composed directories are always empty, and therefore the static fingerprint
// is not strong enough, i.e. multiple shared opaques can share the same directory root. So in this case we need to add the fingerprint of the producer
if (sealDirectory.Kind == SealDirectoryKind.SharedOpaque && !sealDirectory.IsComposite)
{
DirectoryArtifact directory = sealDirectory.Directory;
fingerprinter.Add(directory, m_directoryProducerFingerprintLookup(directory).Hash);
}
if (!ExcludeSemiStableHashOnFingerprintingSealDirectory && !sealDirectory.Kind.IsDynamicKind())
{
// A statically sealed directory can exist as multiple different instances, e.g., one can have partially sealed directories with the same root and member set.
// To distinguish those instances, we include the semi stable hash as part of the static fingerprint.
fingerprinter.Add("SemiStableHash", sealDirectory.SemiStableHash);
}
}
/// <summary>
/// Compute fingerprint associated with this unsafe options.
/// </summary>
public void ComputeFingerprint(IFingerprinter fingerprinter)
{
fingerprinter.Add(nameof(UnsafeConfiguration.SandboxKind), UnsafeConfiguration.SandboxKind.ToString());
fingerprinter.Add(nameof(UnsafeConfiguration.ExistingDirectoryProbesAsEnumerations), getBoolString(UnsafeConfiguration.ExistingDirectoryProbesAsEnumerations));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreGetFinalPathNameByHandle), getBoolString(UnsafeConfiguration.IgnoreGetFinalPathNameByHandle));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreNonCreateFileReparsePoints), getBoolString(UnsafeConfiguration.IgnoreNonCreateFileReparsePoints));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreReparsePoints), getBoolString(UnsafeConfiguration.IgnoreReparsePoints));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreSetFileInformationByHandle), getBoolString(UnsafeConfiguration.IgnoreSetFileInformationByHandle));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreZwOtherFileInformation), getBoolString(UnsafeConfiguration.IgnoreZwOtherFileInformation));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreZwRenameFileInformation), getBoolString(UnsafeConfiguration.IgnoreZwRenameFileInformation));
fingerprinter.Add(nameof(UnsafeConfiguration.MonitorFileAccesses), getBoolString(UnsafeConfiguration.MonitorFileAccesses));
fingerprinter.Add(nameof(UnsafeConfiguration.MonitorNtCreateFile), getBoolString(UnsafeConfiguration.MonitorNtCreateFile));
fingerprinter.Add(nameof(UnsafeConfiguration.MonitorZwCreateOpenQueryFile), getBoolString(UnsafeConfiguration.MonitorZwCreateOpenQueryFile));
fingerprinter.Add(nameof(UnsafeConfiguration.PreserveOutputs), UnsafeConfiguration.PreserveOutputs.ToString());
fingerprinter.Add(nameof(UnsafeConfiguration.UnexpectedFileAccessesAreErrors), getBoolString(UnsafeConfiguration.UnexpectedFileAccessesAreErrors));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnorePreloadedDlls), getBoolString(UnsafeConfiguration.IgnorePreloadedDlls));
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreDynamicWritesOnAbsentProbes), UnsafeConfiguration.IgnoreDynamicWritesOnAbsentProbes.ToString());
fingerprinter.Add(nameof(UnsafeConfiguration.DoubleWritePolicy), UnsafeConfiguration.DoubleWritePolicy.HasValue ? UnsafeConfiguration.DoubleWritePolicy.Value.ToString() : string.Empty);
fingerprinter.Add(nameof(UnsafeConfiguration.IgnoreUndeclaredAccessesUnderSharedOpaques), getBoolString(UnsafeConfiguration.IgnoreUndeclaredAccessesUnderSharedOpaques));
if (m_preservedOutputInfo.HasValue)
{
fingerprinter.AddNested("PreserveOutputInfo", fp => m_preservedOutputInfo.Value.ComputeFingerprint(fp));
}
/// <summary>
/// Computes fingerprint.
/// </summary>
public void ComputeFingerprint(IFingerprinter fingerprinter)
{
fingerprinter.Add(nameof(Salt), Salt.ToHex());
fingerprinter.Add(nameof(PreserveOutputTrustLevel), PreserveOutputTrustLevel);
}
/// <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);
}
