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Diffstat (limited to 'java/CustomDescriptors.java')
| -rw-r--r-- | java/CustomDescriptors.java | 252 |
1 files changed, 252 insertions, 0 deletions
diff --git a/java/CustomDescriptors.java b/java/CustomDescriptors.java new file mode 100644 index 0000000..6822100 --- /dev/null +++ b/java/CustomDescriptors.java @@ -0,0 +1,252 @@ +//package insilico.core.descriptor.nestle;
+
+import insilico.core.descriptor.Descriptor;
+import insilico.core.descriptor.weight.QuantumNumber;
+import insilico.core.molecule.InsilicoMolecule;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.Molecule;
+import org.openscience.cdk.RingSet;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+/**
+ * Custom descriptors and fixes (to be compliant with older Dragon version).
+ *
+ * @author Alberto Manganaro (a.manganaro@kode-solutions.net)
+ */
+public class CustomDescriptors {
+
+ public double nHM;
+ public double RBN;
+ public double Hy;
+ public double N_MlogP_Correction;
+
+
+ public CustomDescriptors(InsilicoMolecule mol) {
+
+ // Hydrophilic factor
+ Hy = Hy(mol);
+
+ // no. heavy atoms as in Dragon 5
+ nHM = 0;
+
+ // no. of rotatable bonds as in Dragon 5
+ RBN = 0;
+
+ // >n- correction for MLogP
+ N_MlogP_Correction = 0;
+
+
+ try {
+
+ for (IAtom CurAt : mol.GetStructure().atoms()) {
+ if (CurAt.getSymbol().equalsIgnoreCase("Si") ||
+ CurAt.getSymbol().equalsIgnoreCase("Cu") ||
+ CurAt.getSymbol().equalsIgnoreCase("Ag") ||
+ CurAt.getSymbol().equalsIgnoreCase("Cd") ||
+ CurAt.getSymbol().equalsIgnoreCase("Sn") ||
+ CurAt.getSymbol().equalsIgnoreCase("Hg") ||
+ CurAt.getSymbol().equalsIgnoreCase("Pb") ||
+ CurAt.getSymbol().equalsIgnoreCase("Bi") ||
+ CurAt.getSymbol().equalsIgnoreCase("As"))
+ nHM++;
+ }
+
+ } catch (Exception e) {
+ nHM = -999;
+ }
+
+ try {
+
+ double[][] ConnAugMatrix = mol.GetMatrixConnectionAugmented();
+ int nSK = ConnAugMatrix.length;
+
+ RingSet rings = mol.GetSSSR();
+
+ for (int i=0; i<nSK; i++)
+ for (int j=(i+1); j<nSK; j++) {
+ // only single bonds
+ if (ConnAugMatrix[i][j] == 1) {
+ // check non terminal
+ if (calculateVD(ConnAugMatrix, i) == 1)
+ continue;
+ if (calculateVD(ConnAugMatrix, j) == 1)
+ continue;
+
+ // check type of atoms
+ int[] numberL = QuantumNumber.getWeights(mol.GetStructure());
+ if ( (numberL[i] < 2) || (numberL[j] < 2))
+ continue;
+
+ // check amide
+ if (checkAmide(ConnAugMatrix, i, j))
+ continue;
+
+ // seems that D5 discard bonds where one atom is connected to a Cl
+ if ( (checkOtherConstraints(ConnAugMatrix, i)) || (checkOtherConstraints(ConnAugMatrix, j)))
+ continue;
+
+ // check rings
+ boolean inRing = false;
+ for (IAtomContainer curRing : rings.atomContainers())
+ if ( (curRing.contains(mol.GetStructure().getAtom(i))) &&
+ (curRing.contains(mol.GetStructure().getAtom(j))) ) {
+ inRing = true;
+ break;
+ }
+ if (inRing) continue;
+
+ RBN++;
+ }
+ }
+
+ for (int i=0; i<nSK; i++) {
+ // N
+ if (ConnAugMatrix[i][i] == 7) {
+ if (mol.GetStructure().getAtom(i).getFlag(CDKConstants.ISAROMATIC)) {
+ boolean nn = false;
+ int n_vd = 0;
+ for (int j=0; j<nSK; j++) {
+ if (i==j) continue;
+ if (ConnAugMatrix[i][j] > 0) {
+ n_vd++;
+ if (ConnAugMatrix[j][j] == 7)
+ if (mol.GetStructure().getAtom(j).getFlag(CDKConstants.ISAROMATIC))
+ nn = true;
+ }
+ }
+ if ( (n_vd == 3) && (!nn)) {
+ N_MlogP_Correction++;
+ }
+ }
+ }
+ }
+
+ } catch (Exception e) {
+ RBN = -999;
+ }
+
+ }
+
+
+ private int calculateVD(double[][] ConnAugMatrix, int Atom) {
+ int nSK = ConnAugMatrix.length;
+ int VD = 0;
+ for (int i=0; i<nSK; i++) {
+ if (i==Atom) continue;
+ if (ConnAugMatrix[Atom][i] > 0)
+ VD++;
+ }
+ return VD;
+ }
+
+ private boolean checkAmide(double[][] ConnAugMatrix, int Atom1, int Atom2) {
+ int nSK = ConnAugMatrix.length;
+
+ if ( ( (ConnAugMatrix[Atom1][Atom1] == 6) && (ConnAugMatrix[Atom2][Atom2] == 7) ) ||
+ ( (ConnAugMatrix[Atom1][Atom1] == 7) && (ConnAugMatrix[Atom2][Atom2] == 6) ) ){
+ int Carbon = ConnAugMatrix[Atom1][Atom1] == 6 ? Atom1 : Atom2;
+ for (int i=0; i<nSK; i++) {
+ if (i==Carbon) continue;
+ if (ConnAugMatrix[Carbon][i] == 2)
+ if ( (ConnAugMatrix[i][i] == 8) || (ConnAugMatrix[i][i] == 16) )
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+
+ private boolean checkOtherConstraints(double[][] ConnAugMatrix, int Atom) {
+ int nSK = ConnAugMatrix.length;
+
+ int nF=0, nCl=0, nBr=0, nI=0, VD=0;
+
+ for (int i=0; i<nSK; i++) {
+ if (i==Atom) continue;
+
+ if (ConnAugMatrix[Atom][i] > 0)
+ VD++;
+
+ // #*
+ if ( (ConnAugMatrix[Atom][i] == 3) )
+ return true;
+
+ // Cl,F,Br,I attach
+ if ( (ConnAugMatrix[Atom][i] == 1) && (ConnAugMatrix[i][i] == 17) )
+ nCl++;
+ if ( (ConnAugMatrix[Atom][i] == 1) && (ConnAugMatrix[i][i] == 9) )
+ nF++;
+ if ( (ConnAugMatrix[Atom][i] == 1) && (ConnAugMatrix[i][i] == 35) )
+ nBr++;
+ if ( (ConnAugMatrix[Atom][i] == 1) && (ConnAugMatrix[i][i] == 53) )
+ nI++;
+ }
+
+ if ( (VD-1) == (nCl+nF+nBr+nI)) return true;
+
+ return false;
+ }
+
+
+ private double Hy(InsilicoMolecule mol) {
+
+ try {
+
+ double[][] ConnAugMatrix = mol.GetMatrixConnectionAugmented();
+
+ Molecule CurMol = mol.GetStructure();
+ int nSK = CurMol.getAtomCount();
+
+ int Nhy = 0; // hydrophilic groups
+ int nC = 0; // number of carbons
+
+ for (int At=0; At<nSK; At++) {
+
+ int nH = CurMol.getAtom(At).getImplicitHydrogenCount();
+
+ // hydrophilic groups (-OH, -SH, -NH)
+ if ( (ConnAugMatrix[At][At] == 7) || (ConnAugMatrix[At][At] == 8) ||
+ (ConnAugMatrix[At][At] == 16) ) {
+
+ // WRONG COUNT! but consistent with Dragon 7 and 5
+ Nhy += nH;
+
+ // correct count of hydrophilic groups
+
+// int nSng=0, nDbl=0, nTrp=0, nAr=0;
+// for (int j=0; j<nSK; j++) {
+// if (j==At) continue;
+// if (ConnAugMatrix[At][j] > 0) {
+// if (ConnAugMatrix[At][j] == 1) nSng++;
+// if (ConnAugMatrix[At][j] == 2) nDbl++;
+// if (ConnAugMatrix[At][j] == 3) nTrp++;
+// if (ConnAugMatrix[At][j] == 1.5) nAr++;
+// }
+// }
+// if ( ((nSng+nDbl+nTrp+nAr)==1) && (nSng==1) && (nH==1))
+// Nhy++;
+ }
+
+ // nC
+ if ( (ConnAugMatrix[At][At] == 6) ) {
+ nC++;
+ }
+
+ }
+
+ return ( (1 + Nhy) * Log2(1 + Nhy) + nC * ( (1.0/nSK) * Log2(1.0/nSK) ) + Math.sqrt( Nhy / (nSK*nSK)) ) / Log2(1 + nSK);
+
+ } catch (Throwable e) {
+ return Descriptor.MISSING_VALUE;
+ }
+
+ }
+
+
+ private double Log2(double val) {
+ return (Math.log(val) / Math.log(2));
+ }
+
+}
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