public void SaturateRingSystems(IAtomContainer atomContainer)
{
var rs0 = Cycles.FindSSSR(atomContainer.Builder.NewAtomContainer(atomContainer)).ToRingSet();
var ringSets = RingPartitioner.PartitionRings(rs0);
IAtom atom = null;
foreach (var rs in ringSets)
{
var containers = RingSetManipulator.GetAllAtomContainers(rs);
foreach (var ac in containers)
{
var temp = new int[ac.Atoms.Count];
for (int g = 0; g < ac.Atoms.Count; g++)
{
atom = ac.Atoms[g];
temp[g] = atom.ImplicitHydrogenCount.Value;
atom.ImplicitHydrogenCount = (atomContainer.GetConnectedBonds(atom).Count() - ac.GetConnectedBonds(atom).Count() - temp[g]);
}
Saturate(ac);
for (int g = 0; g < ac.Atoms.Count; g++)
{
atom = ac.Atoms[g];
atom.ImplicitHydrogenCount = temp[g];
}
}
}
}
public virtual void saturateRingSystems(IAtomContainer atomContainer)
{
IRingSet rs = new SSSRFinder(atomContainer.Builder.newMolecule(atomContainer)).findSSSR();
System.Collections.ArrayList ringSets = RingPartitioner.partitionRings(rs);
IAtomContainer ac = null;
IAtom atom = null;
int[] temp;
for (int f = 0; f < ringSets.Count; f++)
{
rs = (IRingSet)ringSets[f];
ac = RingSetManipulator.getAllInOneContainer(rs);
temp = new int[ac.AtomCount];
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
temp[g] = atom.getHydrogenCount();
atom.setHydrogenCount(atomContainer.getBondCount(atom) - ac.getBondCount(atom) - temp[g]);
}
saturate(ac);
for (int g = 0; g < ac.AtomCount; g++)
{
atom = ac.getAtomAt(g);
atom.setHydrogenCount(temp[g]);
}
}
}
public void TestgetBitFingerprintIAtomContainerIRingSetList()
{
var fingerprinter = new ExtendedFingerprinter();
Assert.IsNotNull(fingerprinter);
var mol = TestMoleculeFactory.MakeIndole();
var rs = Cycles.FindSSSR(mol).ToRingSet();
var rslist = RingPartitioner.PartitionRings(rs);
var bs = fingerprinter.GetBitFingerprint(mol, rs, rslist).AsBitSet();
var frag1 = TestMoleculeFactory.MakePyrrole();
var bs1 = fingerprinter.GetBitFingerprint(frag1).AsBitSet();
Assert.IsTrue(FingerprinterTool.IsSubset(bs, bs1));
Assert.IsFalse(FingerprinterTool.IsSubset(bs1, bs));
}
public void TestMapTemplates_IAtomContainer_Double()
{
var ac = TestMoleculeFactory.MakeBicycloRings();
var th3d = TemplateHandler3D.Instance;
var ffc = new ForceFieldConfigurator();
ffc.SetForceFieldConfigurator("mm2");
var ringSetMolecule = ffc.AssignAtomTyps(ac);
var ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
var largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
var largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
th3d.MapTemplates(largestRingSetContainer, largestRingSetContainer.Atoms.Count);
for (int i = 0; i < ac.Atoms.Count; i++)
{
Assert.IsNotNull(ac.Atoms[i].Point3D);
}
ModelBuilder3DTest.CheckAverageBondLength(ac);
}
/// <summary>
/// Generates a fingerprint of the default size for the given
/// AtomContainer, using path and ring metrics. It contains the
/// informations from <see cref="Fingerprinter.GetBitFingerprint(IAtomContainer)"/> and bits which tell if the structure
/// has 0 rings, 1 or less rings, 2 or less rings ... 10 or less rings and
/// bits which tell if there is a fused ring system with 1,2...8 or more
/// rings in it. The RingSet used is passed via rs parameter. This must be
/// a smallesSetOfSmallestRings. The List must be a list of all ring
/// systems in the molecule.
/// </summary>
/// <param name="atomContainer">The AtomContainer for which a Fingerprint is generated</param>
/// <param name="ringSet">An SSSR RingSet of ac (if not available, use <see cref="GetBitFingerprint(IAtomContainer)"/>, which does the calculation)</param>
/// <param name="rslist">A list of all ring systems in ac</param>
/// <exception cref="CDKException">for example if input can not be cloned.</exception>
/// <returns>a BitArray representing the fingerprint</returns>
public IBitFingerprint GetBitFingerprint(IAtomContainer atomContainer, IRingSet ringSet, IEnumerable <IRingSet> rslist)
{
var container = (IAtomContainer)atomContainer.Clone();
var fingerprint = fingerprinter.GetBitFingerprint(container);
var size = this.Length;
var weight = MolecularFormulaManipulator.GetTotalNaturalAbundance(MolecularFormulaManipulator.GetMolecularFormula(container));
for (int i = 1; i < 11; i++)
{
if (weight > (100 * i))
{
fingerprint.Set(size - 26 + i); // 26 := RESERVED_BITS+1
}
}
if (ringSet == null)
{
ringSet = Cycles.FindSSSR(container).ToRingSet();
rslist = RingPartitioner.PartitionRings(ringSet);
}
for (int i = 0; i < 7; i++)
{
if (ringSet.Count > i)
{
fingerprint.Set(size - 15 + i); // 15 := RESERVED_BITS+1+10 mass bits
}
}
int maximumringsystemsize = 0;
foreach (var rs in rslist)
{
if (rs.Count > maximumringsystemsize)
{
maximumringsystemsize = rs.Count;
}
}
for (int i = 0; i < maximumringsystemsize && i < 9; i++)
{
fingerprint.Set(size - 8 + i - 3);
}
return(fingerprint);
}
public void TestMapTemplatesCyclicMol2()
{
TemplateHandler3D tmphandler3d = TemplateHandler3D.Instance;
string cyclicMolSmi = "CC(C)(C)NC(=O)C1CN(CCN1CC(CC(Cc1ccccc1)C(=O)NC1c2ccccc2CC1O)O)Cc1cccnc1";
IChemObjectBuilder builder = ChemObjectBuilder.Instance;
SmilesParser smiparser = new SmilesParser(builder);
var molecule = smiparser.ParseSmiles(cyclicMolSmi);
ForceFieldConfigurator forcefconf = new ForceFieldConfigurator();
forcefconf.SetForceFieldConfigurator("mmff94");
IRingSet rings = forcefconf.AssignAtomTyps(molecule);
var ringSystems = RingPartitioner.PartitionRings(rings);
IRingSet largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer allAtomsInOneContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
tmphandler3d.MapTemplates(allAtomsInOneContainer, allAtomsInOneContainer.Atoms.Count);
for (int j = 0; j < allAtomsInOneContainer.Atoms.Count; j++)
{
Assert.IsNotNull(allAtomsInOneContainer.Atoms[j].Point3D);
}
}
public static void ExtractUniqueRingSystemsFromFile(string dataFile)
{
Console.Out.WriteLine("****** EXTRACT UNIQUE RING SYSTEMS ******");
Console.Out.WriteLine($"From file: {dataFile}");
Dictionary <string, string> hashRingSystems = new Dictionary <string, string>();
SmilesGenerator smilesGenerator = new SmilesGenerator();
int counterRings = 0;
int counterMolecules = 0;
int counterUniqueRings = 0;
IRingSet ringSet = null;
string key = "";
IAtomContainer ac = null;
string molfile = dataFile + "_UniqueRings";
try
{
using (var fout = new FileStream(molfile, FileMode.Create))
using (var mdlw = new MDLV2000Writer(fout))
{
try
{
Console.Out.WriteLine("Start...");
using (var fin = new StreamReader(dataFile))
using (var imdl = new EnumerableSDFReader(fin, builder))
{
Console.Out.WriteLine("Read File in..");
foreach (var m in imdl)
{
counterMolecules = counterMolecules + 1;
IRingSet ringSetM = Cycles.FindSSSR(m).ToRingSet();
if (counterMolecules % 1000 == 0)
{
Console.Out.WriteLine("Molecules:" + counterMolecules);
}
if (ringSetM.Count > 0)
{
var ringSystems = RingPartitioner.PartitionRings(ringSetM);
for (int i = 0; i < ringSystems.Count; i++)
{
ringSet = (IRingSet)ringSystems[i];
ac = builder.NewAtomContainer();
var containers = RingSetManipulator.GetAllAtomContainers(ringSet);
foreach (var container in containers)
{
ac.Add(container);
}
counterRings = counterRings + 1;
// Only connection is important
for (int j = 0; j < ac.Atoms.Count; j++)
{
(ac.Atoms[j]).Symbol = "C";
}
try
{
key = smilesGenerator.Create(builder.NewAtomContainer(ac));
}
catch (CDKException e)
{
Trace.TraceError(e.Message);
return;
}
if (hashRingSystems.ContainsKey(key))
{
}
else
{
counterUniqueRings = counterUniqueRings + 1; hashRingSystems[key] = "1";
try
{
mdlw.Write(builder.NewAtomContainer(ac));
}
catch (Exception emdl)
{
if (!(emdl is ArgumentException || emdl is CDKException))
{
throw;
}
}
}
}
}
}
}
}
catch (Exception exc)
{
Console.Out.WriteLine($"Could not read Molecules from file {dataFile} due to: {exc.Message}");
}
}
}
catch (Exception ex2)
{
Console.Out.WriteLine($"IOError:cannot write file due to: {ex2.ToString()}");
}
Console.Out.WriteLine($"READY Molecules:{counterMolecules} RingSystems:{counterRings} UniqueRingsSystem:{counterUniqueRings}");
Console.Out.WriteLine($"HashtableKeys:{hashRingSystems.Count}");
}
/// <summary>
/// Generate 3D coordinates with force field information.
/// </summary>
public IAtomContainer Generate3DCoordinates(IAtomContainer molecule, bool clone)
{
var originalAtomTypeNames = molecule.Atoms.Select(n => n.AtomTypeName).ToArray();
Debug.WriteLine("******** GENERATE COORDINATES ********");
foreach (var atom in molecule.Atoms)
{
atom.IsPlaced = false;
atom.IsVisited = false;
}
//CHECK FOR CONNECTIVITY!
Debug.WriteLine($"#atoms>{molecule.Atoms.Count}");
if (!ConnectivityChecker.IsConnected(molecule))
{
throw new CDKException("Molecule is NOT connected, could not layout.");
}
// setup helper classes
AtomPlacer atomPlacer = new AtomPlacer();
AtomPlacer3D ap3d = new AtomPlacer3D(parameterSet);
AtomTetrahedralLigandPlacer3D atlp3d = new AtomTetrahedralLigandPlacer3D(parameterSet);
if (clone)
{
molecule = (IAtomContainer)molecule.Clone();
}
atomPlacer.Molecule = molecule;
if (ap3d.NumberOfUnplacedHeavyAtoms(molecule) == 1)
{
Debug.WriteLine("Only one Heavy Atom");
ap3d.GetUnplacedHeavyAtom(molecule).Point3D = new Vector3(0.0, 0.0, 0.0);
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message,
ex3);
}
return(molecule);
}
//Assing Atoms to Rings,Aliphatic and Atomtype
IRingSet ringSetMolecule = ffc.AssignAtomTyps(molecule);
IRingSet largestRingSet = null;
int numberOfRingAtoms = 0;
IReadOnlyList <IRingSet> ringSystems = null;
if (ringSetMolecule.Count > 0)
{
if (templateHandler == null)
{
throw new CDKException("You are trying to generate coordinates for a molecule with rings, but you have no template handler set. Please do SetTemplateHandler() before generation!");
}
ringSystems = RingPartitioner.PartitionRings(ringSetMolecule);
largestRingSet = RingSetManipulator.GetLargestRingSet(ringSystems);
IAtomContainer largestRingSetContainer = RingSetManipulator.GetAllInOneContainer(largestRingSet);
numberOfRingAtoms = largestRingSetContainer.Atoms.Count;
templateHandler.MapTemplates(largestRingSetContainer, numberOfRingAtoms);
if (!CheckAllRingAtomsHasCoordinates(largestRingSetContainer))
{
throw new CDKException("RingAtomLayoutError: Not every ring atom is placed! Molecule cannot be layout.");
}
SetAtomsToPlace(largestRingSetContainer);
SearchAndPlaceBranches(molecule, largestRingSetContainer, ap3d, atlp3d, atomPlacer);
largestRingSet = null;
}
else
{
//Debug.WriteLine("****** Start of handling aliphatic molecule ******");
IAtomContainer ac = AtomPlacer.GetInitialLongestChain(molecule);
SetAtomsToUnVisited(molecule);
SetAtomsToUnplaced(molecule);
ap3d.PlaceAliphaticHeavyChain(molecule, ac);
//ZMatrixApproach
ap3d.ZMatrixChainToCartesian(molecule, false);
SearchAndPlaceBranches(molecule, ac, ap3d, atlp3d, atomPlacer);
}
LayoutMolecule(ringSystems, molecule, ap3d, atlp3d, atomPlacer);
//Debug.WriteLine("******* PLACE SUBSTITUENTS ******");
try
{
atlp3d.Add3DCoordinatesForSinglyBondedLigands(molecule);
}
catch (CDKException ex3)
{
Trace.TraceError($"PlaceSubstitutensERROR: Cannot place substitutents due to:{ex3.Message}");
Debug.WriteLine(ex3);
throw new CDKException("PlaceSubstitutensERROR: Cannot place substitutents due to:" + ex3.Message, ex3);
}
// restore the original atom type names
for (int i = 0; i < originalAtomTypeNames.Length; i++)
{
molecule.Atoms[i].AtomTypeName = originalAtomTypeNames[i];
}
return(molecule);
}