public static ExplicitBitVect ToBitVectorOrNull(string fp)
{
var array = new List <int>();
for (int i = 0; i < fp.Length; i++)
{
switch (fp[i])
{
case '0':
break;
case '1':
array.Add(i);
break;
default:
return(null);
}
}
var o = new ExplicitBitVect((uint)fp.Length);
foreach (var i in array)
{
o.setBit((uint)i);
}
return(o);
}
static void Main()
{
// ----- Object creation -----
Console.WriteLine("Creating some objects:");
ROMol m1 = RWMol.MolFromSmiles("c1ccccc1");
Console.WriteLine(" mol: " + m1 + " " + m1.getNumAtoms());
ROMol m2 = RWMol.MolFromSmiles("c1ccccn1");
Console.WriteLine(" smi: " + m1 + " " + m1.MolToSmiles());
Console.WriteLine(" smi2: " + m2 + " " + m2.MolToSmiles());
ExplicitBitVect fp1 = RDKFuncs.LayeredFingerprintMol(m1);
ExplicitBitVect fp2 = RDKFuncs.LayeredFingerprintMol(m2);
Console.WriteLine(" sim: " + RDKFuncs.TanimotoSimilarityEBV(fp1, fp2));
//rxnTest();
//smiTest();
morganTest();
Console.WriteLine("Goodbye");
}
public static ExplicitBitVect FoldToTargetDensity(ExplicitBitVect fp, double density = 0.3, int minLength = 64)
{
while (fp.GetNumOnBits() / fp.Count() > density && fp.Count() / 2 > minLength)
{
fp = RDKFuncs.FoldFingerprint(fp, 2);
}
return(fp);
}
/// <summary>
/// Calculated similarity between two fingerprints,
/// handles any folding that may need to be done to ensure that they are compatible
/// </summary>
/// <param name="fp1"></param>
/// <param name="fp2"></param>
/// <param name="metric">Default is <see cref="TanimotoSimilarity(ExplicitBitVect, ExplicitBitVect)"/></param>
/// <returns>The calculated similarity</returns>
public static double FingerprintSimilarity(ExplicitBitVect fp1, ExplicitBitVect fp2, Func <ExplicitBitVect, ExplicitBitVect, double> metric = null)
{
metric = metric ?? TanimotoSimilarity;
var sz1 = fp1.GetNumBits();
var sz2 = fp2.GetNumBits();
if (sz1 < sz2)
{
fp2 = RDKFuncs.FoldFingerprint(fp2, (uint)(sz2 / sz1));
}
else if (sz2 < sz1)
{
fp1 = RDKFuncs.FoldFingerprint(fp1, (uint)(sz1 / sz2));
}
return(metric(fp1, fp2));
}
static void Main(string[] args)
{
// ----- Object creation -----
Console.WriteLine("Creating some objects:");
ROMol m1 = RWMol.MolFromSmiles("c1ccccc1");
Console.WriteLine(" mol: " + m1 + " " + m1.getNumAtoms());
ROMol m2 = RWMol.MolFromSmiles("c1ccccn1");
Console.WriteLine(" smi: " + m1 + " " + m1.MolToSmiles());
Console.WriteLine(" smi2: " + m2 + " " + m2.MolToSmiles());
ExplicitBitVect fp1 = RDKFuncs.LayeredFingerprintMol(m1);
ExplicitBitVect fp2 = RDKFuncs.LayeredFingerprintMol(m2);
Console.WriteLine(" sim: " + RDKFuncs.TanimotoSimilarityEBV(fp1, fp2));
//rxnTest();
//smiTest();
//morganTest();
ROMol m3 = RWMol.MolFromSmiles("c1ccccc1");
uint nAtoms = m3.getNumAtoms(true);
Console.WriteLine("Bulk memory leak test");
for (uint i = 0; i < 10000; ++i)
{
ROMol m4 = RWMol.MolFromSmiles("Clc1cccc(N2CCN(CCC3CCC(CC3)NC(=O)c3cccs3)CC2)c1Cl");
if ((i % 1000) == 0)
{
Console.WriteLine(" Done: " + i);
}
m4.Dispose();
//GC.Collect();
}
Console.WriteLine("Goodbye");
}
static void CreateSomeObjects()
{
// ----- Object creation -----
Console.WriteLine("Creating some objects:");
ROMol m1 = RWMol.MolFromSmiles("c1ccccc1");
Console.WriteLine(" mol: " + m1 + " " + m1.getNumAtoms());
ROMol m2 = RWMol.MolFromSmiles("c1ccccn1");
Console.WriteLine(" smi: " + m1 + " " + m1.MolToSmiles());
Console.WriteLine(" smi2: " + m2 + " " + m2.MolToSmiles());
ExplicitBitVect fp1 = RDKFuncs.LayeredFingerprintMol(m1);
ExplicitBitVect fp2 = RDKFuncs.LayeredFingerprintMol(m2);
Console.WriteLine(" sim: " + RDKFuncs.TanimotoSimilarityEBV(fp1, fp2));
const string SMILES_benzene = "c1ccccc1";
ROMol m3 = RWMol.MolFromSmiles(SMILES_benzene);
uint nAtoms = m3.getNumAtoms(true);
Console.WriteLine($"The number of atoms in {SMILES_benzene} is {nAtoms}.");
}
public static double AsymmetricSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.AsymmetricSimilarity(bv1, bv2);
public static double CosineSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.CosineSimilarity(bv1, bv2);
public static double TanimotoSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.TanimotoSimilarityEBV(bv1, bv2);
public static double SokalSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.SokalSimilarity(bv1, bv2);
public static double RusselSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.RusselSimilarity(bv1, bv2);
public static double McConnaugheySimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.McConnaugheySimilarity(bv1, bv2);
public static double KulczynskiSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.KulczynskiSimilarity(bv1, bv2);
public static double DiceSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.DiceSimilarity(bv1, bv2);
public static ExplicitBitVect LayeredFingerprint(ROMol mol,
LayerFlags layerFlags = (LayerFlags)(-1), int minPath = 1, int maxPath = 7, int fpSize = 2048,
UInt_Vect atomCounts = null, ExplicitBitVect setOnlyBits = null, bool branchedPaths = true, UInt_Vect fromAtoms = null)
{
return(RDKFuncs.LayeredFingerprintMol(mol, (uint)layerFlags, (uint)minPath, (uint)maxPath, (uint)fpSize, atomCounts, setOnlyBits, branchedPaths, fromAtoms));
}
public static ExplicitBitVect PatternFingerprint(ROMol mol,
int fpSize = 2048, UInt_Vect atomCounts = null, ExplicitBitVect setOnlyBits = null)
{
return(RDKFuncs.PatternFingerprintMol(mol, (uint)fpSize, atomCounts, setOnlyBits));
}
public static double TverskySimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2, double a, double b) => RDKFuncs.TverskySimilarity(bv1, bv2, a, b);
public static double AllBitSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.AllBitSimilarity(bv1, bv2);
public static double BraunBlanquetSimilarity(ExplicitBitVect bv1, ExplicitBitVect bv2) => RDKFuncs.BraunBlanquetSimilarity(bv1, bv2);