fix: update OCL to 2026.10.0

scripts/openchemlib/classes.js

@@ -61,7 +61,6 @@ const changedClasses = [
   ['chem/Molecule', changeMolecule],
   ['chem/MolfileParser', replaceStandardCharsets(1)],
   ['chem/Molecule3D', removeCloneInfos],
-  ['chem/PeriodicTable', replaceHashTable],
   ['chem/phesaflex/EvaluableFlexibleOverlap', changeEvaluableFlexibleOverlap],
   ['chem/prediction/IncrementTable', changeIncrementTable],
   ['chem/prediction/IncrementTableWithIndex', changeIncrementTableWithIndex],

scripts/openchemlib/removed.js

@@ -113,6 +113,7 @@ export const removedClasses = [
   'util/AnimatedGIFWriter.java',
   'util/Base64.java',
   'util/BinaryEncoder.java',
+  'util/BlockingPipe.java',
   'util/BrowserControl.java',
   'util/concurrent',
   'util/datamodel/IdentifiedObject.java',

src/com/actelion/research/gwt/chemlib/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.java

@@ -221,6 +221,8 @@ public static ModelMedianInteger getMedianForInteger(List<Integer> liScore) {
 		modelMedian.lowerQuartile = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.25) + 0.5);
 		modelMedian.median = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.5) + 0.5);
 		modelMedian.upperQuartile = (int)(MedianStatisticFunctions.getPercentileFromSortedInt(liScore, 0.75) + 0.5);
+		modelMedian.min = liScore.get(0);
+		modelMedian.max = liScore.get(liScore.size()-1);
 		modelMedian.size = liScore.size();
 		return modelMedian;
 	}

src/com/actelion/research/gwt/chemlib/com/actelion/research/calc/statistics/median/ModelMedianDouble.java

@@ -94,75 +94,55 @@ public double range(){
 
 
 	public String toString() {
-		StringBuilder sb = new StringBuilder(); 
-
+		StringBuilder sb = new StringBuilder();
 		sb.append(Formatter.format4(lowerQuartile));
 		sb.append("\t");
 		sb.append(Formatter.format4(median));
 		sb.append("\t");
 		sb.append(Formatter.format4(upperQuartile));
-
 		return sb.toString();
 	}
 
 	public static String toString(List<ModelMedianDouble> liModelMedian) {
 
-		StringBuilder sb = new StringBuilder(); 
-
+		StringBuilder sb = new StringBuilder();
 		int length = LENGTH;
-
 		int lengthText = 15;
 
 		sb.append(StringFunctions.format2DefinedLengthTrailing("Id", lengthText));
 		for (int i = 0; i < liModelMedian.size(); i++) {
 			ModelMedianDouble m = liModelMedian.get(i);
-
 			String s = StringFunctions.format2DefinedLengthLeading(Integer.toString(m.id), length);
-
 			sb.append(s);
 		}
 
 		sb.append("\n");
-
 		sb.append(StringFunctions.format2DefinedLengthTrailing("Upper quartile", lengthText));
 		for (int i = 0; i < liModelMedian.size(); i++) {
 			ModelMedianDouble m = liModelMedian.get(i);
-
 			String s = StringFunctions.format2DefinedLengthLeading(Formatter.format2(m.upperQuartile), length);
-
 			sb.append(s);
 		}
-
 		sb.append("\n");
-
 		sb.append(StringFunctions.format2DefinedLengthTrailing("Median", lengthText));
 		for (int i = 0; i < liModelMedian.size(); i++) {
 			ModelMedianDouble m = liModelMedian.get(i);
-
 			String s = StringFunctions.format2DefinedLengthLeading(Formatter.format2(m.median), length);
-
 			sb.append(s);
 		}
-
 		sb.append("\n");
-
 		sb.append(StringFunctions.format2DefinedLengthTrailing("Lower quartile", lengthText));
 		for (int i = 0; i < liModelMedian.size(); i++) {
 			ModelMedianDouble m = liModelMedian.get(i);
-
 			String s = StringFunctions.format2DefinedLengthLeading(Formatter.format2(m.lowerQuartile), length);
-
 			sb.append(s);
 		}
 
 		sb.append("\n");
-
 		sb.append(StringFunctions.format2DefinedLengthTrailing("Size", lengthText));
 		for (int i = 0; i < liModelMedian.size(); i++) {
 			ModelMedianDouble m = liModelMedian.get(i);
-
 			String s = StringFunctions.format2DefinedLengthLeading(Integer.toString(m.size), length);
-
 			sb.append(s);
 		}
 

src/com/actelion/research/gwt/chemlib/com/actelion/research/calc/statistics/median/ModelMedianInteger.java

@@ -45,7 +45,11 @@ public class ModelMedianInteger {
 	public int median;
 
 	public int upperQuartile;
-
+
+	public int min;
+
+	public int max;
+
 	public int id;
 
 	public int size;

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMolecule.java

@@ -3113,8 +3113,7 @@ else if (isAtomicNoElectropositive(mAtomicNo[connAtom])) {
 				state -= bondOrder;
 			}
 			else if (mAtomicNo[atom] != mAtomicNo[connAtom]) {
-				if (PeriodicTable.getElement(mAtomicNo[atom]).getElectronegativity()
-				  < PeriodicTable.getElement(mAtomicNo[connAtom]).getElectronegativity())
+				if (cElectronegativity[mAtomicNo[atom]] < cElectronegativity[mAtomicNo[connAtom]])
 					state += bondOrder;
 				else
 					state -= bondOrder;

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/ExtendedMoleculeFunctions.java

@@ -66,13 +66,10 @@
 package com.actelion.research.chem;
 
 import com.actelion.research.calc.ArrayUtilsCalc;
-import com.actelion.research.calc.statistics.StatisticsOverview;
 import com.actelion.research.calc.statistics.median.MedianStatisticFunctions;
-import com.actelion.research.chem.descriptor.DescriptorEncoder;
 import com.actelion.research.chem.descriptor.DescriptorHandler;
 import com.actelion.research.chem.descriptor.flexophore.redgraph.SubGraphIndices;
 import com.actelion.research.chem.mcs.ListWithIntVec;
-import com.actelion.research.util.BurtleHasher;
 import com.actelion.research.util.Formatter;
 import com.actelion.research.util.datamodel.IntegerDouble;
 
@@ -1063,7 +1060,7 @@ public static boolean isThioEther(StereoMolecule mol, int atom) {
 	}
 
 	public static boolean isWildcard(StereoMolecule mol, int atom) {
-		if(mol.getAtomicNo(atom) == PeriodicTable.ConnectionPoint){
+		if(mol.getAtomicNo(atom) == 0){
 			return true;
 		}
 		return false;

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/MolecularFormula.java

@@ -34,7 +34,7 @@
 package com.actelion.research.chem;
 
 public class MolecularFormula {
-	private static final double[] sRelativeMass = { 0.0,
+	public static final double[] sRelativeMass = { 0.0,
 	1.00794, 4.0026, 6.9410, 9.0122, 10.811, 12.011,    //  H , He, Li, Be, B , C , 
 	 14.007, 15.999, 18.998, 20.180, 22.990, 24.305,    //  N , O , F , Ne, Na, Mg, 
 	 26.982, 28.086, 30.974, 32.066, 35.453, 39.948,    //  Al, Si, P , S , Cl, Ar, 
@@ -68,7 +68,7 @@ public class MolecularFormula {
 	113.15934, 128.17428, 131.19846, 147.17646,  97.11658,  87.0777,  //  Leu,Lys,Met,Phe,Pro,Ser,
 	101.10458, 186.2134 , 163.17546,  99.13246 };                     //  Thr,Trp,Tyr,Val,
 
-	private static final double[] sAbsoluteMass = { 0.0, 
+	public static final double[] sAbsoluteMass = { 0.0,
 	   1.007825,   4.00260 ,   7.016003,   9.012182,	//  H, He,Li,Be
 	  11.009305,  12.000000,  14.003074,  15.994915,	//  B ,C ,N, O
 	  18.998403,  19.992435,  22.989767,  23.985042,	//  F ,Ne,Na,Mg

src/com/actelion/research/gwt/chemlib/com/actelion/research/chem/Molecule.java

@@ -462,6 +462,27 @@ public class Molecule implements Serializable {
 			{2,3}, {3}											//  No, Lr
 		};
 
+	// Allen scale (lanthanides,actinides from ReVEBE & Pauling scale)
+	public static final float[] cElectronegativity = new float[] { 2.544f,
+			2.300f, 4.160f, 0.912f, 1.576f, 2.051f, 2.544f,		//  H,  He, Li, Be, B,  C,
+			3.066f, 3.610f, 4.193f, 4.787f, 0.869f, 1.293f,		//  N,  O,  F,  Ne, Na, Mg,
+			1.613f, 1.916f, 2.253f, 2.589f, 2.869f, 3.242f,		//  Al, Si, P,  S,  Cl, Ar,
+			0.734f, 1.034f, 1.190f, 1.380f, 1.530f, 1.650f,		//  K,  Ca, Sc, Ti, V,  Cr,
+			1.750f, 1.800f, 1.840f, 1.880f, 1.850f, 1.588f,		//  Mn, Fe, Co, Ni, Cu, Zn,
+			1.756f, 1.994f, 2.211f, 2.424f, 2.685f, 2.966f,		//  Ga, Ge, As, Se, Br, Kr,
+			0.706f, 0.963f, 1.120f, 1.320f, 1.410f, 1.470f,		//  Rb, Sr, Y,  Zr, Nb, Mo,
+			1.510f, 1.540f, 1.560f, 1.580f, 1.870f, 1.521f,		//  Tc, Ru, Rh, Pd, Ag, Cd,
+			1.656f, 1.824f, 1.984f, 2.158f, 2.359f, 2.582f,		//  In, Sn, Sb, Te, I,  Xe,
+			0.659f, 0.881f, 1.02f,  1.04f,  0.92f,  0.95f, 		//  Cs, Ba, La ,Ce, Pr, Nd,
+			0.99f,  1.03f,  1.08f,  1.06f,  1.05f,  1.09f, 		//  Pm, Sm, Eu, Gd, Tb, Dy,
+			1.12f,  1.08f,  1.11f,  1.21f,  1.09f,  1.16f, 		//  Ho, Er, Tm, Yb, Lu, Hf,
+			1.34f,  1.47f,  1.60f,  1.65f,  1.68f,  1.72f, 		//  Ta, W,  Re, Os, Ir, Pt,
+			1.92f,  1.765f, 1.789f, 1.854f, 2.01f,  2.19f, 		//  Au, Hg, Tl, Pb, Bi, Po,
+			2.39f,  2.60f,  0.67f,  0.89f,  0.98f,  1.08f, 		//  At, Rn, Fr, Ra, Ac, Th,
+			1.5f,   1.38f,  1.36f,  1.28f,  1.3f,   1.3f, 		//  Pa, U,  Np, Pu, Am, Cm,
+			1.3f,   1.3f,   1.3f,   1.3f,   1.3f,   1.3f,  		//  Bk, Cf, Es, Fm, Md, No,
+	};
+
 	transient protected int mMaxAtoms;
 	transient protected int mMaxBonds;