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 UInt_Vect GetConnectivityInvariants(ROMol mol, bool includeRingMembership)
{
var invars = new UInt_Vect((int)mol.getNumAtoms());
RDKFuncs.getConnectivityInvariants(mol, invars, includeRingMembership);
return(invars);
}
public static ROMol Parse(string smarts)
{
if (smarts == null)
{
throw new ArgumentNullException(nameof(smarts));
}
var pattern = SmartsCache.GetOrAdd(smarts, a_smarts =>
{
ROMol query = Chem.MolFromSmarts(a_smarts);
if (query == null)
{
return(nullSmarts);
}
query.setProp("source", "SMARTS");
return(query);
});
if (object.ReferenceEquals(pattern, nullSmarts))
{
return(null);
}
return(pattern);
}
public static string MolFragmentToSmiles(ROMol mol, Int_Vect atomsToUse, Int_Vect bondsToUse = null,
Str_Vect atomSymbols = null, Str_Vect bondSymbols = null,
bool isomericSmiles = true, bool kekuleSmiles = false, int rootedAtAtom = -1, bool canonical = true,
bool allBondsExplicit = false, bool allHsExplicit = false)
{
return(RDKFuncs.MolFragmentToSmiles(mol, atomsToUse, bondsToUse, atomSymbols, bondSymbols, isomericSmiles, kekuleSmiles, rootedAtAtom, canonical));
}
public static UInt_Vect GetFeatureInvariants(ROMol mol)
{
var invars = new UInt_Vect((int)mol.getNumAtoms());
RDKFuncs.getFeatureInvariants(mol, invars);
return(invars);
}
public static ROMol StripMol(ROMol mol)
{
foreach (var query in saltPatterns)
{
mol = RDKFuncs.deleteSubstructs(mol, query, true);
}
return(mol);
}
public static Double_Vect SlogP_VSA_(ROMol mol, Double_Vect bins = null, bool force = false)
{
if (bins == null)
{
bins = new Double_Vect(0);
}
return(RDKFuncs.calcSlogP_VSA(mol, bins, force));
}
public static ExplicitBitVect RDKFingerprint(ROMol mol,
int minPath = 1, int maxPath = 7, int fpSize = 2048, int nBitsPerHash = 2,
bool useHs = true, double tgtDensity = 0, int minSize = 128, bool branchedPaths = true,
bool useBondOrder = true, UInt_Vect atomInvariants = null, UInt_Vect fromAtoms = null,
SWIGTYPE_p_std__vectorT_std__vectorT_uint32_t_t_t atomBits = null,
SWIGTYPE_p_std__mapT_unsigned_int_std__vectorT_std__vectorT_int_t_t_std__lessT_unsigned_int_t_t bitInfo = null)
{
return(RDKFuncs.RDKFingerprintMol(mol, (uint)minPath, (uint)maxPath, (uint)fpSize, (uint)nBitsPerHash, useHs, tgtDensity, (uint)minSize, branchedPaths, useBondOrder, atomInvariants, fromAtoms, atomBits, bitInfo));
}
public static SparseIntVectu32 GetMorganFingerprint(ROMol mol, int radius, UInt_Vect invariants = null, UInt_Vect fromAtoms = null, bool useChirality = false, bool useBondTypes = true, bool onlyNonzeroInvariants = false, bool useCounts = true, BitInfoMap atomsSettingBits = null)
{
if (invariants == null)
{
invariants = new UInt_Vect(0);
}
if (fromAtoms == null)
{
fromAtoms = new UInt_Vect(0);
}
return(RDKFuncs.MorganFingerprintMol(mol, (uint)radius, invariants, fromAtoms, useChirality, useBondTypes, useCounts, onlyNonzeroInvariants, atomsSettingBits));
}
public static ExplicitBitVect GetMorganFingerprintAsBitVect(ROMol mol, int radius, int nBits = 2048, UInt_Vect invariants = null, UInt_Vect fromAtoms = null, bool useChirality = false, bool useBondTypes = true, bool onlyNonzeroInvariants = false, BitInfoMap atomsSettingBits = null)
{
if (invariants == null)
{
invariants = new UInt_Vect(0);
}
if (fromAtoms == null)
{
fromAtoms = new UInt_Vect(0);
}
return(RDKFuncs.getMorganFingerprintAsBitVect(mol, (uint)radius, (uint)nBits, invariants, fromAtoms, useChirality, useBondTypes, onlyNonzeroInvariants, atomsSettingBits));
}
static void BulkMemoryLeakTest()
{
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();
}
}
public static string MolToSVG(ROMol mol, int width = 300, int height = 300,
Int_Vect highlightAtoms = null, bool kekulize = true, int lineWidthMult = 1, int fontSize = 12,
bool includeAtomCircles = true, int confId = -1)
{
// See Code\GraphMol\Wrap\MolOps.cpp
var drawer = new MolDraw2DSVG(width, height);
drawer.setFontSize(fontSize / 24.0);
drawer.setLineWidth(drawer.lineWidth() * lineWidthMult);
drawer.drawOptions().circleAtoms = includeAtomCircles;
drawer.drawMolecule(mol, highlightAtoms, null, null, confId);
drawer.finishDrawing();
return(drawer.getDrawingText());
}
// static void rxnTest() {
// Console.WriteLine( "Reaction tests" );
// var rxn = ChemicalReaction.ReactionFromSmarts("[N:1][C:2].[OH][C:3]=[O:4]>>[C:2][N:1][C:3]=[O:4]");
// var amine = RWMol.MolFromSmiles("CCCN");
// var acid = RWMol.MolFromSmiles("C1CC1CC(=O)O");
// ROMol[] rs = {amine,acid};
// ROMol_Vect rv = new ROMol_Vect(rs);
// for(var i=0;i<100000;i++){
// var ps=rxn.runReactants(rv);
// if(i%100 == 0) {
// Console.WriteLine( "\t{0}", i );
// }
// }
// Console.WriteLine( "Goodbye" );
// }
// static void smiTest() {
// Console.WriteLine( "repeatedly from smiles" );
// for(var i=0;i<1000000;i++){
// ROMol m1=RDKFuncs.MolFromSmiles("c1ccccc1");
// if(i%1000 == 0) {
// Console.WriteLine( "\t{0}", i );
// }
// }
// Console.WriteLine( "Goodbye" );
// }
static void morganTest()
{
// ----- Object creation -----
Console.WriteLine("Creating some objects:");
ROMol m1 = RWMol.MolFromSmiles("c1ccccc1");
Console.WriteLine(" mol: " + m1 + " " + m1.getNumAtoms());
ROMol m2 = RWMol.MolFromSmiles("c1ccccn1");
var fp1 = RDKFuncs.MorganFingerprintMol(m1, 2);
var fp2 = RDKFuncs.MorganFingerprintMol(m2, 2);
Console.WriteLine(" sim: " + RDKFuncs.DiceSimilarity(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 int GetNumAtoms(ROMol mol, bool onlyExplicit = true)
{
return((int)mol.getNumAtoms(onlyExplicit));
}
public static MolSanitizeException_Vect DetectChemistryProblems(ROMol mol, SanitizeFlags sanitizeOps = SanitizeFlags.SANITIZE_ALL)
{
return(RDKFuncs.detectChemistryProblems(mol, (int)sanitizeOps));
}
public static void DetectBondStereochemistry(ROMol mol, int confId = -1)
{
RDKFuncs.detectBondStereochemistry(mol, confId);
}
public static ROMol DeleteSubstructs(ROMol mol, ROMol query, bool onlyFrags = false, bool useChirality = false)
{
return(RDKFuncs.deleteSubstructs(mol, query, onlyFrags, useChirality));
}
public static void AssignStereochemistry(ROMol mol,
bool cleanIt = false, bool force = false, bool flagPossibleStereoCenters = false)
{
RDKFuncs.assignStereochemistry(mol, cleanIt, force, flagPossibleStereoCenters);
}
public static void AssignChiralTypesFromBondDirs(ROMol mol, int confId = -1, bool replaceExistingTags = true)
{
RDKFuncs.assignChiralTypesFromBondDirs(mol, confId, replaceExistingTags);
}
public static void AddRecursiveQueries(ROMol mol, StringMolMap queries, string propName)
{
RDKFuncs.addRecursiveQueries(mol, queries, propName);
}
public static int GetNumBonds(ROMol mol, bool onlyHeavy = true)
{
return((int)mol.getNumBonds(onlyHeavy));
}
//
// rdChem
//
public static int GetNumHeavyAtoms(ROMol mol)
{
return((int)mol.getNumHeavyAtoms());
}
public static void MolToPDBFile(ROMol mol, string filename, int confId = -1, PDBFlavors flavor = 0)
{
RDKFuncs.MolToPDBFile(mol, filename, confId, (uint)flavor);
}
public static string MolToCXSmiles(ROMol mol, bool isomericSmiles = true,
bool kekuleSmiles = false, int rootedAtAtom = -1, bool canonical = true,
bool allBondsExplicit = false, bool allHsExplicit = false, bool doRandom = false)
{
return(RDKFuncs.MolToCXSmiles(mol, isomericSmiles, kekuleSmiles, rootedAtAtom, canonical, allHsExplicit, doRandom));
}
public static void MolToXYZFile(ROMol mol, string filename, int confId = -1)
{
RDKFuncs.MolToXYZFile(mol, filename, confId);
}
public static string MolToXYZBlock(ROMol mol, int confId = -1)
{
return(RDKFuncs.MolToXYZBlock(mol, confId));
}
public static string MolToInchi(ROMol mol, string options = "", ExtraInchiReturnValues ex = null)
{
return(RDKFuncs.MolToInchi(mol, ex ?? new ExtraInchiReturnValues(), options));
}
public static string MolToInchiKey(ROMol mol, string options = "")
{
return(RDKFuncs.MolToInchiKey(mol, options));
}