openchemlib 9.20.0 → 9.20.1

package/dist/openchemlib.debug.js

@@ -11856,7 +11856,7 @@ function getExports($wnd) {
     return aromaticPi > 1;
   };
   _.idCodeCreate = function idCodeCreate() {
-    var EZCount, THCount, a, a$array, a$index, a$max, atom, atom0, atom1, atom10, atom11, atom2, atom3, atom4, atom5, atom6, atom7, atom8, atom9, atomList, base, bond, bond0, bond1, bond2, bond3, bond4, bondOrder, chargedAtoms, connBits, conns, count, customLabel, dbits, dif, enhancedCustomLabelCount, enhancedCustomLabelMaxChar, enhancedCustomLabelMaxLength, hIndex, i, i0, isAromaticSPBond, j, label_0, lbits, length_0, maxChar, maxLength, maxdif, mbits, nbits, nitrogens, otherAtoms, oxygens, parity;
+    var EZCount, THCount, a, a$array, a$index, a$max, atom, atom0, atom1, atom10, atom11, atom2, atom3, atom4, atom5, atom6, atom7, atom8, atom9, atomList, base, bond, bond0, bond1, bond2, bond3, bond4, bondOrder, chargedAtoms, connBits, conns, count, dbits, dif, enhancedCustomLabelCount, enhancedCustomLabelMaxChar, enhancedCustomLabelMaxLength, hIndex, i, i0, isAromaticSPBond, j, label_0, lbits, length_0, maxChar, maxLength, maxdif, mbits, nbits, nitrogens, otherAtoms, oxygens, parity;
     this.encodeBitsStart(false);
     this.encodeBits(9, 4);
     nbits = $wnd.Math.max(getNeededBits(this.mMol.getAtoms_0()), getNeededBits(this.mMol.getBonds_0()));
@@ -12212,13 +12212,13 @@ function getExports($wnd) {
       this.encodeBits(fromInt_0(lbits), 6);
       this.encodeBits(fromInt_0(mbits), 16);
       for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
-        customLabel = this.mMol.getAtomCustomLabel_0(this.mGraphAtom[atom]);
-        if (jsNotEquals(customLabel, null)) {
+        label_0 = this.mMol.getAtomCustomLabel_0(this.mGraphAtom[atom]);
+        if (jsNotEquals(label_0, null) && (length__I__devirtual$_0(label_0) > 15 || this.maxEnhancedCustomLabelCharCode(label_0) > 127)) {
           this.encodeBits(fromInt_0(atom), nbits);
-          length_0 = $wnd.Math.min(63, length__I__devirtual$_0(customLabel));
+          length_0 = $wnd.Math.min(63, length__I__devirtual$_0(label_0));
           this.encodeBits(fromInt_0(length_0), lbits);
           for (i = 0; i < length_0; i++)
-            this.encodeBits(fromInt_0(charAt_I_C__devirtual$_0(customLabel, i)), mbits);
+            this.encodeBits(fromInt_0(charAt_I_C__devirtual$_0(label_0, i)), mbits);
         }
       }
     }
@@ -14057,8 +14057,8 @@ function getExports($wnd) {
       return new TextDrawingObject_0(detail);
     return null;
   }
-  defineClass(846, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_DrawingObjectFactory_2_classLit = createForClass("com.actelion.research.chem", "DrawingObjectFactory", 846, Ljava_lang_Object_2_classLit);
+  defineClass(848, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_DrawingObjectFactory_2_classLit = createForClass("com.actelion.research.chem", "DrawingObjectFactory", 848, Ljava_lang_Object_2_classLit);
   function $clinit_Iterable() {
     $clinit_Iterable = emptyMethod;
   }
@@ -14792,8 +14792,8 @@ function getExports($wnd) {
   function $clinit_Element$1() {
     $clinit_Element$1 = emptyMethod;
   }
-  defineClass(847, 1, { 1: 1, 36: 1 });
-  var Lcom_actelion_research_chem_Element$1_2_classLit = createForClass("com.actelion.research.chem", "Element/1", 847, Ljava_lang_Object_2_classLit);
+  defineClass(849, 1, { 1: 1, 36: 1 });
+  var Lcom_actelion_research_chem_Element$1_2_classLit = createForClass("com.actelion.research.chem", "Element/1", 849, Ljava_lang_Object_2_classLit);
   function $clinit_ExtendedDepictor() {
     $clinit_ExtendedDepictor = emptyMethod;
     $clinit_Object();
@@ -22610,6 +22610,14 @@ function getExports($wnd) {
     this.$init_38();
     this.mMode = mode;
   }
+  function buildCustomLabel(cl, line) {
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SAL") && startsWith_Ljava_lang_String_I_Z__devirtual$(line, "  1", 10))
+      cl.atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 13, 17)));
+    else if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SDT"))
+      cl.isOCLCUstomLabel = startsWith_Ljava_lang_String__Z__devirtual$(substring_I_Ljava_lang_String___devirtual$(line, 11), "NOSEARCH_OCL_CUSTOM_LABEL");
+    else if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SED"))
+      cl.label_0 = trim__Ljava_lang_String___devirtual$(substring_I_Ljava_lang_String___devirtual$(line, 11));
+  }
   defineClass(150, 1, { 1: 1 }, MolfileParser, MolfileParser_0);
   _.$init_38 = function $init_38() {
   };
@@ -22618,6 +22626,14 @@ function getExports($wnd) {
       ($clinit_System(), out_0).println_0(s);
     }
   };
+  _.buildAtom = function buildAtom(line) {
+    var atom, x_0, y_0, z_0;
+    x_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 0, 10)));
+    y_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 10, 20)));
+    z_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 20, 30)));
+    atom = this.mMol.addAtom_1(x_0, -y_0, -z_0);
+    return atom;
+  };
   _.buildBond = function buildBond(atom1, atom2, bondType, stereo, topology) {
     var bond, isAtomESRAnd, queryFeatures, realBondType;
     realBondType = 1;
@@ -22747,6 +22763,213 @@ function getExports($wnd) {
     ui = isNull(this.mBondIndexMap) ? null : castTo(this.mBondIndexMap.get(valueOf_12(sourceBondIndex)), 35);
     return isNull(ui) ? sourceBondIndex - 1 : ui.intValue();
   };
+  _.handleAtomLists = function handleAtomLists(line) {
+    var aaa, atom, bNotList, k, no, sym, v;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  ALS")) {
+      atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 7, 10))) - 1;
+      if (atom >= 0) {
+        no = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 10, 13)));
+        bNotList = charAt_I_C__devirtual$_0(line, 14) == 84;
+        v = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, no, 15, 1);
+        aaa = 16;
+        for (k = 0; k < no; k++, aaa += 4) {
+          sym = trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 4));
+          v[k] = getAtomicNoFromLabel_0(sym, 1);
+        }
+        this.mMol.setAtomicNo_0(atom, 6);
+        this.mMol.setAtomList_1(atom, v, bNotList);
+      }
+    }
+  };
+  _.handleAtomMaps = function handleAtomMaps(atom, line) {
+    var mapNo;
+    mapNo = length__I__devirtual$_0(line) < 63 ? 0 : this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 60, 63)));
+    this.mMol.setAtomMapNo_0(atom, mapNo, false);
+  };
+  _.handleAtomQueryFeatures = function handleAtomQueryFeatures(atom, line) {
+    var hCount;
+    hCount = length__I__devirtual$_0(line) < 45 ? 0 : this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 42, 45)));
+    switch (hCount) {
+      case 0:
+        break;
+      case 1:
+        this.mMol.setAtomQueryFeature_0(atom, or_0(256, 512), true);
+        break;
+      case 2:
+        this.mMol.setAtomQueryFeature_0(atom, 128, true);
+        break;
+      case 3:
+        this.mMol.setAtomQueryFeature_0(atom, or_0(128, 256), true);
+        break;
+      default:
+        this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(128, 256), 512), true);
+        break;
+    }
+    if (length__I__devirtual$_0(line) >= 48 && charAt_I_C__devirtual$_0(line, 47) == 49) {
+      this.mMol.setAtomQueryFeature_0(atom, 8192, true);
+    }
+  };
+  _.handleCharge = function handleCharge(atom, line) {
+    var chargeDif;
+    chargeDif = this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 36, 39)));
+    if (chargeDif != 0) {
+      if (chargeDif == 4)
+        this.mMol.setAtomRadical_0(atom, 32);
+      else
+        this.mMol.setAtomCharge_0(atom, 4 - chargeDif);
+    }
+  };
+  _.handleCharge_0 = function handleCharge_0(line) {
+    var aaa, atom, charge, j, k, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  CHG")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          charge = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          this.mMol.setAtomCharge_0(atom, charge);
+        }
+      }
+    }
+  };
+  _.handleIsotops = function handleIsotops(line) {
+    var aaa, atom, j, k, mass, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  ISO")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          mass = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          this.mMol.setAtomMass_0(atom, mass);
+        }
+      }
+    }
+  };
+  _.handleMassDiff = function handleMassDiff(atom, line) {
+    var massDif;
+    massDif = this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 34, 36)));
+    if (massDif != 0) {
+      this.mMol.setAtomMass_0(atom, ($clinit_Molecule(), cRoundedMass)[this.mMol.getAtomicNo_0(atom)] + massDif);
+    }
+  };
+  _.handleQueryAtoms = function handleQueryAtoms(atom, line) {
+    var atomicNo, label_0, list;
+    label_0 = trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 31, 34));
+    if (equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "A") || equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "*")) {
+      this.mMol.setAtomQueryFeature_0(atom, 1, true);
+    } else if (equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "Q")) {
+      list = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, 1, 15, 1);
+      list[0] = 6;
+      this.mMol.setAtomList_1(atom, list, true);
+    } else {
+      atomicNo = getAtomicNoFromLabel_0(label_0, 67);
+      this.mMol.setAtomicNo_0(atom, atomicNo);
+    }
+  };
+  _.handleRGroupLablelLocation = function handleRGroupLablelLocation(line) {
+    var aaa, atom, j, k, rno, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RGP")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          rno = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          if (rno >= 1 && rno <= 20) {
+            this.mMol.setAtomicNo_0(atom, getAtomicNoFromLabel_0("R" + rno, 2));
+          }
+        }
+      }
+    }
+  };
+  _.handleRadicals = function handleRadicals(line) {
+    var aaa, atom, j, k, radical, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RAD")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          radical = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          switch (radical) {
+            case 1:
+              this.mMol.setAtomRadical_0(atom, 16);
+              break;
+            case 2:
+              this.mMol.setAtomRadical_0(atom, 32);
+              break;
+            case 3:
+              this.mMol.setAtomRadical_0(atom, 48);
+              break;
+          }
+        }
+      }
+    }
+  };
+  _.handleRingBondCount = function handleRingBondCount(line) {
+    var aaa, atom, j, k, ringState, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RBC") || startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RBD")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          ringState = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          switch (ringState) {
+            case -1:
+              this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(16, 32), 64), true);
+              break;
+            case 1:
+              this.mMol.setAtomQueryFeature_0(atom, 8, true);
+              break;
+            case 2:
+              this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(8, 32), 64), true);
+              break;
+            case 3:
+              this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(16, 32), 64), true);
+              break;
+            case 4:
+              this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(8, 16), 32), true);
+              break;
+          }
+        }
+      }
+    }
+  };
+  _.handleSubstitutionCount = function handleSubstitutionCount(line) {
+    var aaa, atom, bond, j, k, substitution, substitutionCount, vvv;
+    if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SUB")) {
+      j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
+      if (j > 0) {
+        aaa = 10;
+        vvv = 14;
+        for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
+          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
+          substitution = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
+          if (substitution == -2) {
+            this.mMol.setAtomQueryFeature_0(atom, 2048, true);
+          } else if (substitution > 0) {
+            substitutionCount = 0;
+            for (bond = 0; bond < this.mMol.getAllBonds_0(); bond++) {
+              if (this.mMol.getBondAtom_0(0, bond) == atom || this.mMol.getBondAtom_0(1, bond) == atom) {
+                substitutionCount++;
+              }
+            }
+            if (substitution > substitutionCount) {
+              this.mMol.setAtomQueryFeature_0(atom, 4096, true);
+            }
+          }
+        }
+      }
+    }
+  };
   _.handleValences = function handleValences(valence) {
     var atom, chargeCorrection;
     if (jsNotEquals(valence, null)) {
@@ -22815,7 +23038,7 @@ function getExports($wnd) {
     return null;
   };
   _.interpretV3AtomLine = function interpretV3AtomLine(line) {
-    var atom, atomIndex, bNotList, bond, field, index_0, index1, index2, l, label_0, list, mapNo, specifier, substitutionCount, v, value_0, x_0, y_0, z_0;
+    var atom, atomIndex, bNotList, bond, field, index_0, index1, index2, l, label_0, list, mapNo, matcher, pattern, rgLabel, specifier, substitutionCount, v, value_0, x_0, y_0, z_0;
     index1 = 0;
     index2 = this.endOfItem(line, index1);
     atomIndex = parseInt_2(substring_II_Ljava_lang_String___devirtual$(line, index1, index2));
@@ -22867,10 +23090,11 @@ function getExports($wnd) {
       specifier = substring_II_Ljava_lang_String___devirtual$(line, index1, index2);
       index_0 = indexOf_I_I__devirtual$(specifier, 61);
       field = substring_II_Ljava_lang_String___devirtual$(specifier, 0, index_0);
-      value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
       if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "CHG")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         this.mMol.setAtomCharge_0(atom, value_0);
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "RAD")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         switch (value_0) {
           case 1:
             this.mMol.setAtomRadical_0(atom, 16);
@@ -22884,10 +23108,13 @@ function getExports($wnd) {
         }
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "CFG")) {
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "MASS")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         this.mMol.setAtomMass_0(atom, value_0);
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "VAL")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         this.mMol.setAtomAbnormalValence_0(atom, value_0 == -1 ? 0 : value_0 == 0 ? -1 : value_0);
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "HCOUNT")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         switch (value_0) {
           case 0:
             break;
@@ -22905,6 +23132,7 @@ function getExports($wnd) {
             break;
         }
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "SUBST")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         if (value_0 == -1) {
           this.mMol.setAtomQueryFeature_0(atom, 2048, true);
         } else if (value_0 > 0) {
@@ -22919,6 +23147,7 @@ function getExports($wnd) {
           }
         }
       } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "RBCNT")) {
+        value_0 = parseInt_2(substring_I_Ljava_lang_String___devirtual$(specifier, index_0 + 1));
         switch (value_0) {
           case -1:
             this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(16, 32), 64), true);
@@ -22936,6 +23165,13 @@ function getExports($wnd) {
             this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(8, 16), 32), true);
             break;
         }
+      } else if (equals_Ljava_lang_Object__Z__devirtual$_2(field, "RGROUPS")) {
+        pattern = compile("RGROUPS=\\((\\d+) (\\d+).*\\)");
+        matcher = pattern.matcher(line);
+        if (matcher.find_0()) {
+          rgLabel = "R" + matcher.group_0(2);
+          this.mMol.setAtomCustomLabel_0(atom, rgLabel);
+        }
       } else {
         this.TRACE("Warning MolfileParser: Unused version 3 atom specifier:" + field + "\n");
       }
@@ -23221,7 +23457,7 @@ function getExports($wnd) {
     return this.indexOfNextItem(line, end);
   };
   _.readMoleculeFromBuffer = function readMoleculeFromBuffer(reader) {
-    var aaa, atom, atom1, atom2, atomicNo, bNotList, bond, bondType, charge, chargeDif, cl, cl$iterator, customLabelMap, e, hCount, i, i0, i1, j, k, label_0, line, list, mapNo, mass, massDif, name_0, natoms, nbonds, nlists, no, radical, res, ringState, rno, sgroupNo, stereo, substitution, substitutionCount, sym, topology, v, valence, vvv, x_0, y_0, z_0;
+    var atom, atom1, atom2, bondType, cl, cl$iterator, customLabelMap, e, i, i0, i1, line, name_0, natoms, nbonds, nlists, res, sgroupNo, stereo, topology, v, valence;
     valence = null;
     customLabelMap = null;
     try {
@@ -23289,54 +23525,12 @@ function getExports($wnd) {
           this.TRACE("Error [readMoleculeFromBuffer]: No Atom Line\n");
           return false;
         }
-        x_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 0, 10)));
-        y_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 10, 20)));
-        z_0 = parseFloat_0(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 20, 30)));
-        atom = this.mMol.addAtom_1(x_0, -y_0, -z_0);
-        label_0 = trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 31, 34));
-        if (equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "A") || equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "*")) {
-          this.mMol.setAtomQueryFeature_0(atom, 1, true);
-        } else if (equals_Ljava_lang_Object__Z__devirtual$_2(label_0, "Q")) {
-          list = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, 1, 15, 1);
-          list[0] = 6;
-          this.mMol.setAtomList_1(atom, list, true);
-        } else {
-          atomicNo = getAtomicNoFromLabel_0(label_0, 67);
-          this.mMol.setAtomicNo_0(atom, atomicNo);
-        }
-        massDif = this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 34, 36)));
-        if (massDif != 0) {
-          this.mMol.setAtomMass_0(atom, ($clinit_Molecule(), cRoundedMass)[this.mMol.getAtomicNo_0(atom)] + massDif);
-        }
-        chargeDif = this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 36, 39)));
-        if (chargeDif != 0) {
-          if (chargeDif == 4)
-            this.mMol.setAtomRadical_0(atom, 32);
-          else
-            this.mMol.setAtomCharge_0(atom, 4 - chargeDif);
-        }
-        mapNo = length__I__devirtual$_0(line) < 63 ? 0 : this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 60, 63)));
-        this.mMol.setAtomMapNo_0(atom, mapNo, false);
-        hCount = length__I__devirtual$_0(line) < 45 ? 0 : this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 42, 45)));
-        switch (hCount) {
-          case 0:
-            break;
-          case 1:
-            this.mMol.setAtomQueryFeature_0(atom, or_0(256, 512), true);
-            break;
-          case 2:
-            this.mMol.setAtomQueryFeature_0(atom, 128, true);
-            break;
-          case 3:
-            this.mMol.setAtomQueryFeature_0(atom, or_0(128, 256), true);
-            break;
-          default:
-            this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(128, 256), 512), true);
-            break;
-        }
-        if (length__I__devirtual$_0(line) >= 48 && charAt_I_C__devirtual$_0(line, 47) == 49) {
-          this.mMol.setAtomQueryFeature_0(atom, 8192, true);
-        }
+        atom = this.buildAtom(line);
+        this.handleQueryAtoms(atom, line);
+        this.handleMassDiff(atom, line);
+        this.handleCharge(atom, line);
+        this.handleAtomMaps(atom, line);
+        this.handleAtomQueryFeatures(atom, line);
         v = length__I__devirtual$_0(line) < 51 ? 0 : this.parseIntOrSpaces(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 48, 51)));
         if (v != 0) {
           if (jsEquals(valence, null))
@@ -23374,133 +23568,13 @@ function getExports($wnd) {
         return true;
       }
       while (jsNotEquals(line, null) && !(equals_Ljava_lang_Object__Z__devirtual$_2(line, "M  END") || equals_Ljava_lang_Object__Z__devirtual$_2(line, "$$$$"))) {
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  CHG")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              charge = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              this.mMol.setAtomCharge_0(atom, charge);
-            }
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  ISO")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              mass = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              this.mMol.setAtomMass_0(atom, mass);
-            }
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RAD")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              radical = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              switch (radical) {
-                case 1:
-                  this.mMol.setAtomRadical_0(atom, 16);
-                  break;
-                case 2:
-                  this.mMol.setAtomRadical_0(atom, 32);
-                  break;
-                case 3:
-                  this.mMol.setAtomRadical_0(atom, 48);
-                  break;
-              }
-            }
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RBC") || startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RBD")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              ringState = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              switch (ringState) {
-                case -1:
-                  this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(16, 32), 64), true);
-                  break;
-                case 1:
-                  this.mMol.setAtomQueryFeature_0(atom, 8, true);
-                  break;
-                case 2:
-                  this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(8, 32), 64), true);
-                  break;
-                case 3:
-                  this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(16, 32), 64), true);
-                  break;
-                case 4:
-                  this.mMol.setAtomQueryFeature_0(atom, or_0(or_0(8, 16), 32), true);
-                  break;
-              }
-            }
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  ALS")) {
-          atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 7, 10))) - 1;
-          if (atom >= 0) {
-            no = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 10, 13)));
-            bNotList = charAt_I_C__devirtual$_0(line, 14) == 84;
-            v = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, no, 15, 1);
-            aaa = 16;
-            for (k = 0; k < no; k++, aaa += 4) {
-              sym = trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 4));
-              v[k] = getAtomicNoFromLabel_0(sym, 1);
-            }
-            this.mMol.setAtomicNo_0(atom, 6);
-            this.mMol.setAtomList_1(atom, v, bNotList);
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SUB")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              substitution = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              if (substitution == -2) {
-                this.mMol.setAtomQueryFeature_0(atom, 2048, true);
-              } else if (substitution > 0) {
-                substitutionCount = 0;
-                for (bond = 0; bond < this.mMol.getAllBonds_0(); bond++) {
-                  if (this.mMol.getBondAtom_0(0, bond) == atom || this.mMol.getBondAtom_0(1, bond) == atom) {
-                    substitutionCount++;
-                  }
-                }
-                if (substitution > substitutionCount) {
-                  this.mMol.setAtomQueryFeature_0(atom, 4096, true);
-                }
-              }
-            }
-          }
-        }
-        if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  RGP")) {
-          j = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 6, 9)));
-          if (j > 0) {
-            aaa = 10;
-            vvv = 14;
-            for (k = 1; k <= j; k++, aaa += 8, vvv += 8) {
-              atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, aaa, aaa + 3))) - 1;
-              rno = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, vvv, vvv + 3)));
-              if (rno >= 1 && rno <= 20) {
-                this.mMol.setAtomicNo_0(atom, getAtomicNoFromLabel_0("R" + rno, 2));
-              }
-            }
-          }
-        }
+        this.handleCharge_0(line);
+        this.handleIsotops(line);
+        this.handleRadicals(line);
+        this.handleRingBondCount(line);
+        this.handleAtomLists(line);
+        this.handleSubstitutionCount(line);
+        this.handleRGroupLablelLocation(line);
         if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SAL") && length__I__devirtual$_0(line) >= 17 || startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SDT") && length__I__devirtual$_0(line) >= 12 || startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SED") && length__I__devirtual$_0(line) >= 12) {
           if (isNull(customLabelMap))
             customLabelMap = new TreeMap();
@@ -23510,12 +23584,7 @@ function getExports($wnd) {
             cl = new MolfileParser$CustomLabel();
             customLabelMap.put(sgroupNo, cl);
           }
-          if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SAL") && startsWith_Ljava_lang_String_I_Z__devirtual$(line, "  1", 10))
-            cl.atom = parseInt_2(trim__Ljava_lang_String___devirtual$(substring_II_Ljava_lang_String___devirtual$(line, 13, 17)));
-          else if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SDT"))
-            cl.isOCLCUstomLabel = startsWith_Ljava_lang_String__Z__devirtual$(substring_I_Ljava_lang_String___devirtual$(line, 11), "NOSEARCH_OCL_CUSTOM_LABEL");
-          else if (startsWith_Ljava_lang_String__Z__devirtual$(line, "M  SED"))
-            cl.label_0 = trim__Ljava_lang_String___devirtual$(substring_I_Ljava_lang_String___devirtual$(line, 11));
+          buildCustomLabel(cl, line);
         }
         line = reader.readLine();
       }
@@ -26918,7 +26987,7 @@ function getExports($wnd) {
         throw toJs(new Exception_1("SmilesParser: Unknown atom label. position:" + (position - 1)));
       return true;
     }
-    if (smiles[position] == 65 && smiles[position + 1] == 115 || smiles[position] == 83 && smiles[position + 1] == 101) {
+    if (smiles[position] == 97 && smiles[position + 1] == 115 || smiles[position] == 115 && smiles[position + 1] == 101) {
       info.labelLength = 2;
       info.atomicNo = getAtomicNoFromLabel($create_10(smiles, position, info.labelLength, ($clinit_StandardCharsets(), UTF_8)));
       info.mayBeAliphatic = false;
@@ -29432,9 +29501,9 @@ function getExports($wnd) {
     this.$init_61();
     this.mBondLengthSet = isNull(set_0) ? new BondLengthSet(mol) : set_0;
     this.mMol = mol;
-    this.mBondAngle = initUnidimensionalArray(F_classLit, { 4: 1, 1: 1, 7: 1 }, 873, this.mMol.getAtoms_0(), 0, 3);
+    this.mBondAngle = initUnidimensionalArray(F_classLit, { 4: 1, 1: 1, 7: 1 }, 875, this.mMol.getAtoms_0(), 0, 3);
     for (atom0 = 0; atom0 < this.mMol.getAtoms_0(); atom0++) {
-      this.mBondAngle[atom0] = initUnidimensionalArray(F_classLit, { 873: 1, 4: 1, 1: 1, 7: 1 }, 44, this.mMol.getAllConnAtoms_0(atom0), 0, 2);
+      this.mBondAngle[atom0] = initUnidimensionalArray(F_classLit, { 875: 1, 4: 1, 1: 1, 7: 1 }, 44, this.mMol.getAllConnAtoms_0(atom0), 0, 2);
       for (i = 1; i < this.mMol.getAllConnAtoms_0(atom0); i++)
         this.mBondAngle[atom0][i] = initUnidimensionalArray(F_classLit, { 44: 1, 4: 1, 1: 1 }, 5, i, 15, 1);
     }
@@ -32248,9 +32317,9 @@ function getExports($wnd) {
             atomIndex2 = temp;
           }
           if (jsEquals(fa, null))
-            fa = initUnidimensionalArray(Lcom_actelion_research_chem_coords_FragmentAssociation_2_classLit, { 4: 1, 1: 1, 7: 1 }, 869, this.mFragmentList.size(), 0, 2);
+            fa = initUnidimensionalArray(Lcom_actelion_research_chem_coords_FragmentAssociation_2_classLit, { 4: 1, 1: 1, 7: 1 }, 871, this.mFragmentList.size(), 0, 2);
           if (jsEquals(fa[f2], null))
-            setCheck(fa, f2, initUnidimensionalArray(Lcom_actelion_research_chem_coords_FragmentAssociation_2_classLit, { 869: 1, 4: 1, 1: 1, 7: 1 }, 116, f2, 0, 1));
+            setCheck(fa, f2, initUnidimensionalArray(Lcom_actelion_research_chem_coords_FragmentAssociation_2_classLit, { 871: 1, 4: 1, 1: 1, 7: 1 }, 116, f2, 0, 1));
           if (isNotNull(fa[f2][f1]))
             fa[f2][f1].add_6(atomIndex1, atomIndex2);
           else {
@@ -33694,7 +33763,7 @@ function getExports($wnd) {
   function $clinit_InventorDefaultTemplateList() {
     $clinit_InventorDefaultTemplateList = emptyMethod;
     $clinit_ArrayList();
-    DEFAULT_TEMPLATE = stampJavaTypeInfo(getClassLiteralForArray(Ljava_lang_String_2_classLit, 1), { 4: 1, 1: 1, 7: 1, 9: 1 }, 2, 6, ["gkvt@@@@LddTTTrbTRTRTRRRRRRRRRRRRRrVRrIh\\IAaQxlY@gRHdJCJcRXlv_CfJx|A\\hRHejiLaQjTje^kSjtFcIhvXmVKMjt{lN{Kavy\\^wGjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjh@@vo@HBC@PhLN@bPhtFKCcpDbILaRhtzCIbsX\\nOO`JDbqDjSKdJeJmQjtz}Ahr[LVkMnpz\\nwGj{PBhBdBlBBBjBfBnBaBiBeBmBcBkBgBoB`bhbdblbbbjbfbnbabibebmbcbkbgbob`RhRdRlRbRjRfRnRaRiReRmRcRkRgRoR`rhrdrlrbrjrfrnrarirermrcrkrgror`JhJdJlJbJjJfJnJaJiJeJmJcJkJgJoJ`jhjdjljbjjjfjnjajijej` !BnkjyVwsVr|iQn|Q|goTZWPIJwbudnRkVYBez]siZymNJZUqNFBqZWxS~iCXVU]SeRjwrtSPAjkvXLpBAZauDPzq]PfMlecrMnkv|@\\SFD`m|mWiEoCXp`SIe_J[l|[XCbloTV`[Gc@FJGopyyoOlFQfUy^w\\Bgz|", "gcrt@@@@LdbbbbTRbRbRbRRRRRRRRRRRRVRrVQIA`HtRGAaIxZAHfShTjCIbqylQGKgqdBaXeQJeruBiPitZmFoPZLFSYbvZlVGMnsZ]vWSmr{]UUUUUUUUUUUUUUUUUUUUUUUUUUUUUT@@[G`DAA`HTFG@QHTZCEaqxBQDfPiTZ]AdqYlNWGgpEBQXbUIerEReVhuZ]^`tYMfKUfwX]NW[jkPBhBdBlBbBjBfBnBaBiBeBmBcBkBgBoB`bhbdblbbbjbfbnbabibebmbcbkbgbob`RhRdRlRbRjRfRnRaRiReRmRcRkRgRoR`rhrdrlrbrjrfrnrarirermrcrkrgror`JhJdJlJbJjJfJnJaJiJeJmJcJkJgJoJ`jhjdjljbjjjfjnjajij` !B^cR]`]Fm]QkfljE\\p\x7FUVfgOmFXsQe_gXPyXis_wF|vUUX_XbxpzU]HUFgYViwFo~@uemc@}~T\x7FIEPioYVwr]JnM~[ZEC\\g}~o_pUfdo~irsklTLiyVJshnw^iVAsZ`_~}PYkckURH{FYMImFaRaccUlCZSHMfP", "dml@@Dje^VGiyZjjjh@vtHSBinFU@ !BPTCTy[skMzUPF`AJbBixEZHS[Il", "dml@@DjYVvGiyZjjjh@vtHSBinFU@ !BwLo~BJ~UquhXBinZ\\ykA@F_eMrT", "dml@@LdfbbQX^fUZjjj`C[PaLJfxYT !BzxIHVc{OiJVRpprePho~]}y\x7FwLl", "deL@@DjUYkfEijjjj@MeBDpj[ad !B\x7FaA\x7FMVr[AvkKzm_jKvVbD{sk", "dil@@LddTQRl[NX^Fjjjj@MiBDpj[a@ !BPfL@\x7Fox@M~T@\x7Fox@\x7F`C~@@", "daL@@DjYtKJqjynjjjj@MaBDpj[` !B`bL@_gx@@Gy~@Gx@_`@"]);
+    DEFAULT_TEMPLATE = stampJavaTypeInfo(getClassLiteralForArray(Ljava_lang_String_2_classLit, 1), { 4: 1, 1: 1, 7: 1, 9: 1 }, 2, 6, ["gkvt@@@@LddTTTrbTRTRTRRRRRRRRRRRRRrVRrIh\\IAaQxlY@gRHdJCJcRXlv_CfJx|A\\hRHejiLaQjTje^kSjtFcIhvXmVKMjt{lN{Kavy\\^wGjjjjjjjjjjjjjjjjjjjjjjjjjjjjjjh@@vo@HBC@PhLN@bPhtFKCcpDbILaRhtzCIbsX\\nOO`JDbqDjSKdJeJmQjtz}Ahr[LVkMnpz\\nwGj{PBhBdBlBBBjBfBnBaBiBeBmBcBkBgBoB`bhbdblbbbjbfbnbabibebmbcbkbgbob`RhRdRlRbRjRfRnRaRiReRmRcRkRgRoR`rhrdrlrbrjrfrnrarirermrcrkrgror`JhJdJlJbJjJfJnJaJiJeJmJcJkJgJoJ`jhjdjljbjjjfjnjajijej` !BnkjyVwsVr|iQn|Q|goTZWPIJwbudnRkVYBez]siZymNJZUqNFBqZWxS~iCXVU]SeRjwrtSPAjkvXLpBAZauDPzq]PfMlecrMnkv|@\\SFD`m|mWiEoCXp`SIe_J[l|[XCbloTV`[Gc@FJGopyyoOlFQfUy^w\\Bgz|", "gcrt@@@@LdbbbbTRbRbRbRRRRRRRRRRRRVRrVQIA`HtRGAaIxZAHfShTjCIbqylQGKgqdBaXeQJeruBiPitZmFoPZLFSYbvZlVGMnsZ]vWSmr{]UUUUUUUUUUUUUUUUUUUUUUUUUUUUUT@@[G`DAA`HTFG@QHTZCEaqxBQDfPiTZ]AdqYlNWGgpEBQXbUIerEReVhuZ]^`tYMfKUfwX]NW[jkPBhBdBlBbBjBfBnBaBiBeBmBcBkBgBoB`bhbdblbbbjbfbnbabibebmbcbkbgbob`RhRdRlRbRjRfRnRaRiReRmRcRkRgRoR`rhrdrlrbrjrfrnrarirermrcrkrgror`JhJdJlJbJjJfJnJaJiJeJmJcJkJgJoJ`jhjdjljbjjjfjnjajij` !B^cR]`]Fm]QkfljE\\p?UVfgOmFXsQe_gXPyXis_wF|vUUX_XbxpzU]HUFgYViwFo~@uemc@}~T?IEPioYVwr]JnM~[ZEC\\g}~o_pUfdo~irsklTLiyVJshnw^iVAsZ`_~}PYkckURH{FYMImFaRaccUlCZSHMfP", "dml@@Dje^VGiyZjjjh@vtHSBinFU@ !BPTCTy[skMzUPF`AJbBixEZHS[Il", "dml@@DjYVvGiyZjjjh@vtHSBinFU@ !BwLo~BJ~UquhXBinZ\\ykA@F_eMrT", "dml@@LdfbbQX^fUZjjj`C[PaLJfxYT !BzxIHVc{OiJVRpprePho~]}y?wLl", "deL@@DjUYkfEijjjj@MeBDpj[ad !B?aA?MVr[AvkKzm_jKvVbD{sk", "dil@@LddTQRl[NX^Fjjjj@MiBDpj[a@ !BPfL@?ox@M~T@?ox@?`C~@@", "daL@@DjYtKJqjynjjjj@MaBDpj[` !B`bL@_gx@@Gy~@Gx@_`@"]);
   }
   function InventorDefaultTemplateList() {
     $clinit_InventorDefaultTemplateList();
@@ -33705,6 +33774,7 @@ function getExports($wnd) {
     for (idcode$array = DEFAULT_TEMPLATE, idcode$index = 0, idcode$max = idcode$array.length; idcode$index < idcode$max; ++idcode$index) {
       idcode = idcode$array[idcode$index];
       fragment = new IDCodeParserWithoutCoordinateInvention().getCompactMolecule(idcode);
+      fragment.ensureHelperArrays_0(31);
       ffp = searcher.createLongIndex(fragment);
       template = new InventorTemplate(fragment, ffp, false);
       template.normalizeCoordinates();
@@ -34153,8 +34223,8 @@ function getExports($wnd) {
   function $clinit_AbstractDescriptorHandlerLongFP() {
     $clinit_AbstractDescriptorHandlerLongFP = emptyMethod;
   }
-  defineClass(837, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_descriptor_AbstractDescriptorHandlerLongFP_2_classLit = createForClass("com.actelion.research.chem.descriptor", "AbstractDescriptorHandlerLongFP", 837, Ljava_lang_Object_2_classLit);
+  defineClass(839, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_descriptor_AbstractDescriptorHandlerLongFP_2_classLit = createForClass("com.actelion.research.chem.descriptor", "AbstractDescriptorHandlerLongFP", 839, Ljava_lang_Object_2_classLit);
   function $clinit_ForceField() {
     $clinit_ForceField = emptyMethod;
   }
@@ -34650,8 +34720,8 @@ function getExports($wnd) {
         newtable[i][j] = castTo(table[i][j], 35).intValue();
     return newtable;
   }
-  defineClass(845, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_forcefield_mmff_Csv_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "Csv", 845, Ljava_lang_Object_2_classLit);
+  defineClass(847, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_forcefield_mmff_Csv_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "Csv", 847, Ljava_lang_Object_2_classLit);
   function $clinit_Electrostatic() {
     $clinit_Electrostatic = emptyMethod;
     $clinit_Object();
@@ -35009,8 +35079,8 @@ function getExports($wnd) {
       row *= 10;
     return row;
   }
-  defineClass(844, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_forcefield_mmff_PeriodicTable_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "PeriodicTable", 844, Ljava_lang_Object_2_classLit);
+  defineClass(846, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_forcefield_mmff_PeriodicTable_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "PeriodicTable", 846, Ljava_lang_Object_2_classLit);
   function $clinit_RingBoolean() {
     $clinit_RingBoolean = emptyMethod;
     $clinit_Enum();
@@ -35098,8 +35168,8 @@ function getExports($wnd) {
     $clinit_Search();
     return a;
   }
-  defineClass(842, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_forcefield_mmff_Search_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "Search", 842, Ljava_lang_Object_2_classLit);
+  defineClass(844, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_forcefield_mmff_Search_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff", "Search", 844, Ljava_lang_Object_2_classLit);
   function $clinit_Searchable() {
     $clinit_Searchable = emptyMethod;
   }
@@ -36546,8 +36616,8 @@ function getExports($wnd) {
     }
     return false;
   }
-  defineClass(852, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_forcefield_mmff_type_Angle_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Angle", 852, Ljava_lang_Object_2_classLit);
+  defineClass(854, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_forcefield_mmff_type_Angle_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Angle", 854, Ljava_lang_Object_2_classLit);
   function $clinit_Atom_0() {
     $clinit_Atom_0 = emptyMethod;
     $clinit_Object();
@@ -37645,8 +37715,8 @@ function getExports($wnd) {
       }
     return 0;
   }
-  defineClass(843, 1, { 1: 1 });
-  var Lcom_actelion_research_chem_forcefield_mmff_type_Torsion_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Torsion", 843, Ljava_lang_Object_2_classLit);
+  defineClass(845, 1, { 1: 1 });
+  var Lcom_actelion_research_chem_forcefield_mmff_type_Torsion_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Torsion", 845, Ljava_lang_Object_2_classLit);
   function $clinit_CompoundFileParser() {
     $clinit_CompoundFileParser = emptyMethod;
     $clinit_Object();
@@ -38240,9 +38310,9 @@ function getExports($wnd) {
     $clinit_StructureNameResolver();
     return sResolver;
   }
-  defineClass(848, 1, { 1: 1 });
+  defineClass(850, 1, { 1: 1 });
   var sResolver;
-  var Lcom_actelion_research_chem_name_StructureNameResolver_2_classLit = createForClass("com.actelion.research.chem.name", "StructureNameResolver", 848, Ljava_lang_Object_2_classLit);
+  var Lcom_actelion_research_chem_name_StructureNameResolver_2_classLit = createForClass("com.actelion.research.chem.name", "StructureNameResolver", 850, Ljava_lang_Object_2_classLit);
   function $clinit_CLogPPredictor() {
     $clinit_CLogPPredictor = emptyMethod;
     $clinit_Object();
@@ -40876,7 +40946,7 @@ function getExports($wnd) {
         }
       }
     }
-    this.mRuleBonds = castTo(bondList.toArray_1(initUnidimensionalArray(Lcom_actelion_research_chem_reaction_mapping_ChemicalRuleBond_2_classLit, { 874: 1, 4: 1, 1: 1, 7: 1 }, 149, 0, 0, 1)), 874);
+    this.mRuleBonds = castTo(bondList.toArray_1(initUnidimensionalArray(Lcom_actelion_research_chem_reaction_mapping_ChemicalRuleBond_2_classLit, { 876: 1, 4: 1, 1: 1, 7: 1 }, 149, 0, 0, 1)), 876);
     count = 0;
     for (atom3 = 0; atom3 < this.mReactant.getAtoms_0(); atom3++)
       if (this.mReactant.getAtomMapNo_0(atom3) == 0 && !this.mReactant.isExcludeGroupAtom(atom3))
@@ -50294,7 +50364,7 @@ function getExports($wnd) {
     JSComponent.call(this, jsCheckBox);
     this.$init_194();
   }
-  defineClass(858, 191, { 1: 1 }, JSCheckBox);
+  defineClass(860, 191, { 1: 1 }, JSCheckBox);
   _.$init_194 = function $init_194() {
   };
   _.isSelected_0 = function isSelected_1() {
@@ -50305,7 +50375,7 @@ function getExports($wnd) {
     var component = this.getJsComponent();
     return component.setSelected(b);
   };
-  var Lcom_actelion_research_gwt_js_api_generic_internal_JSCheckBox_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSCheckBox", 858, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
+  var Lcom_actelion_research_gwt_js_api_generic_internal_JSCheckBox_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSCheckBox", 860, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
   function $clinit_JSClipboardHandler() {
     $clinit_JSClipboardHandler = emptyMethod;
     $clinit_Object();
@@ -50358,7 +50428,7 @@ function getExports($wnd) {
     JSComponent.call(this, jsComboBox);
     this.$init_196();
   }
-  defineClass(859, 191, { 1: 1 }, JSComboBox);
+  defineClass(861, 191, { 1: 1 }, JSComboBox);
   _.$init_196 = function $init_196() {
   };
   _.addItem_0 = function addItem(item_0) {
@@ -50389,7 +50459,7 @@ function getExports($wnd) {
     var component = this.getJsComponent();
     return component.setSelectedItem(item_0);
   };
-  var Lcom_actelion_research_gwt_js_api_generic_internal_JSComboBox_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSComboBox", 859, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
+  var Lcom_actelion_research_gwt_js_api_generic_internal_JSComboBox_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSComboBox", 861, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
   function $clinit_JSDialog() {
     $clinit_JSDialog = emptyMethod;
     $clinit_Object();
@@ -50662,14 +50732,14 @@ function getExports($wnd) {
     JSComponent.call(this, jsLabel);
     this.$init_201();
   }
-  defineClass(857, 191, { 1: 1 }, JSLabel);
+  defineClass(859, 191, { 1: 1 }, JSLabel);
   _.$init_201 = function $init_201() {
   };
   _.setText_0 = function setText_0(text_0) {
     var component = this.getJsComponent();
     return component.setText(text_0);
   };
-  var Lcom_actelion_research_gwt_js_api_generic_internal_JSLabel_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSLabel", 857, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
+  var Lcom_actelion_research_gwt_js_api_generic_internal_JSLabel_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSLabel", 859, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
   function $clinit_JSMouseHandler() {
     $clinit_JSMouseHandler = emptyMethod;
     $clinit_GenericEventHandler();
@@ -50715,7 +50785,7 @@ function getExports($wnd) {
     JSComponent.call(this, jsTextField);
     this.$init_204();
   }
-  defineClass(860, 191, { 1: 1 }, JSTextField);
+  defineClass(862, 191, { 1: 1 }, JSTextField);
   _.$init_204 = function $init_204() {
   };
   _.getText_0 = function getText_0() {
@@ -50726,7 +50796,7 @@ function getExports($wnd) {
     var component = this.getJsComponent();
     return component.setText(text_0);
   };
-  var Lcom_actelion_research_gwt_js_api_generic_internal_JSTextField_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSTextField", 860, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
+  var Lcom_actelion_research_gwt_js_api_generic_internal_JSTextField_2_classLit = createForClass("com.actelion.research.gwt.js.api.generic.internal", "JSTextField", 862, Lcom_actelion_research_gwt_js_api_generic_internal_JSComponent_2_classLit);
   function $clinit_MoleculeQueryFeatures() {
     $clinit_MoleculeQueryFeatures = emptyMethod;
     $clinit_Object();
@@ -51286,9 +51356,9 @@ function getExports($wnd) {
     b.append_9(ZEROS[i]);
     return b.toString_0();
   }
-  defineClass(841, 1, { 1: 1 });
+  defineClass(843, 1, { 1: 1 });
   var ROUNDING_MODE_CODE, ROUNDING_MODE_MULTIPLE_OF = 2, ROUNDING_MODE_NONE = 0, ROUNDING_MODE_SIGNIFICANT_DIGITS = 1, ROUNDING_MODE_TEXT, ZEROS;
-  var Lcom_actelion_research_util_DoubleFormat_2_classLit = createForClass("com.actelion.research.util", "DoubleFormat", 841, Ljava_lang_Object_2_classLit);
+  var Lcom_actelion_research_util_DoubleFormat_2_classLit = createForClass("com.actelion.research.util", "DoubleFormat", 843, Ljava_lang_Object_2_classLit);
   function $clinit_IntArrayComparator() {
     $clinit_IntArrayComparator = emptyMethod;
     $clinit_Object();
@@ -51480,10 +51550,10 @@ function getExports($wnd) {
     this.$init_210();
     this.reason = ($clinit_CodeDownloadException$Reason(), TERMINATED);
   }
-  defineClass(863, 24, { 4: 1, 12: 1, 1: 1, 24: 1, 18: 1 }, CodeDownloadException);
+  defineClass(865, 24, { 4: 1, 12: 1, 1: 1, 24: 1, 18: 1 }, CodeDownloadException);
   _.$init_210 = function $init_210() {
   };
-  var Lcom_google_gwt_core_client_CodeDownloadException_2_classLit = createForClass("com.google.gwt.core.client", "CodeDownloadException", 863, Ljava_lang_RuntimeException_2_classLit);
+  var Lcom_google_gwt_core_client_CodeDownloadException_2_classLit = createForClass("com.google.gwt.core.client", "CodeDownloadException", 865, Ljava_lang_RuntimeException_2_classLit);
   function $clinit_CodeDownloadException$Reason() {
     $clinit_CodeDownloadException$Reason = emptyMethod;
     $clinit_Enum();
@@ -51510,9 +51580,9 @@ function getExports($wnd) {
     $clinit_CodeDownloadException$Reason$Map = emptyMethod;
     $MAP_3 = createValueOfMap(values_4());
   }
-  defineClass(864, 1, { 1: 1 });
+  defineClass(866, 1, { 1: 1 });
   var $MAP_3;
-  var Lcom_google_gwt_core_client_CodeDownloadException$Reason$Map_2_classLit = createForClass("com.google.gwt.core.client", "CodeDownloadException/Reason/Map", 864, Ljava_lang_Object_2_classLit);
+  var Lcom_google_gwt_core_client_CodeDownloadException$Reason$Map_2_classLit = createForClass("com.google.gwt.core.client", "CodeDownloadException/Reason/Map", 866, Ljava_lang_Object_2_classLit);
   function $clinit_Duration() {
     $clinit_Duration = emptyMethod;
     $clinit_Object();
@@ -51703,14 +51773,14 @@ function getExports($wnd) {
   function nativeTopWindow() {
     return $wnd;
   }
-  defineClass(861, 1, { 1: 1 });
+  defineClass(863, 1, { 1: 1 });
   var TOP_WINDOW;
-  var Lcom_google_gwt_core_client_ScriptInjector_2_classLit = createForClass("com.google.gwt.core.client", "ScriptInjector", 861, Ljava_lang_Object_2_classLit);
+  var Lcom_google_gwt_core_client_ScriptInjector_2_classLit = createForClass("com.google.gwt.core.client", "ScriptInjector", 863, Ljava_lang_Object_2_classLit);
   function $clinit_ScriptInjector$FromString() {
     $clinit_ScriptInjector$FromString = emptyMethod;
   }
-  defineClass(862, 1, { 1: 1 });
-  var Lcom_google_gwt_core_client_ScriptInjector$FromString_2_classLit = createForClass("com.google.gwt.core.client", "ScriptInjector/FromString", 862, Ljava_lang_Object_2_classLit);
+  defineClass(864, 1, { 1: 1 });
+  var Lcom_google_gwt_core_client_ScriptInjector$FromString_2_classLit = createForClass("com.google.gwt.core.client", "ScriptInjector/FromString", 864, Ljava_lang_Object_2_classLit);
   function $clinit_ScriptInjector$FromUrl() {
     $clinit_ScriptInjector$FromUrl = emptyMethod;
     $clinit_Object();
@@ -54485,11 +54555,11 @@ function getExports($wnd) {
   function $clinit_BufferedWriter() {
     $clinit_BufferedWriter = emptyMethod;
   }
-  defineClass(850, 456, { 1: 1 });
+  defineClass(853, 456, { 1: 1 });
   _.newLine = function newLine() {
     throwUnimplemented();
   };
-  var Ljava_io_BufferedWriter_2_classLit = createForClass("java.io", "BufferedWriter", 850, Ljava_io_Writer_2_classLit);
+  var Ljava_io_BufferedWriter_2_classLit = createForClass("java.io", "BufferedWriter", 853, Ljava_io_Writer_2_classLit);
   function $clinit_File() {
     $clinit_File = emptyMethod;
   }
@@ -57458,8 +57528,8 @@ function getExports($wnd) {
     }
     return allZero;
   }
-  defineClass(854, 1, { 1: 1 });
-  var Ljava_math_BitLevel_2_classLit = createForClass("java.math", "BitLevel", 854, Ljava_lang_Object_2_classLit);
+  defineClass(856, 1, { 1: 1 });
+  var Ljava_math_BitLevel_2_classLit = createForClass("java.math", "BitLevel", 856, Ljava_lang_Object_2_classLit);
   function $clinit_Conversion() {
     $clinit_Conversion = emptyMethod;
     $clinit_Object();
@@ -57772,9 +57842,9 @@ function getExports($wnd) {
     result1.append_9(toString_41(exponent));
     return result1.toString_0();
   }
-  defineClass(853, 1, { 1: 1 });
+  defineClass(855, 1, { 1: 1 });
   var bigRadices, digitFitInInt;
-  var Ljava_math_Conversion_2_classLit = createForClass("java.math", "Conversion", 853, Ljava_lang_Object_2_classLit);
+  var Ljava_math_Conversion_2_classLit = createForClass("java.math", "Conversion", 855, Ljava_lang_Object_2_classLit);
   function $clinit_Division() {
     $clinit_Division = emptyMethod;
     $clinit_Object();
@@ -57957,8 +58027,8 @@ function getExports($wnd) {
     a[start_0 + bLen] = toInt_0(carry1);
     return toInt_0(shr_0(carry1, 32));
   }
-  defineClass(855, 1, { 1: 1 });
-  var Ljava_math_Division_2_classLit = createForClass("java.math", "Division", 855, Ljava_lang_Object_2_classLit);
+  defineClass(857, 1, { 1: 1 });
+  var Ljava_math_Division_2_classLit = createForClass("java.math", "Division", 857, Ljava_lang_Object_2_classLit);
   function $clinit_Elementary() {
     $clinit_Elementary = emptyMethod;
     $clinit_Object();
@@ -58125,8 +58195,8 @@ function getExports($wnd) {
       borrow = shr_0(borrow, 32);
     }
   }
-  defineClass(856, 1, { 1: 1 });
-  var Ljava_math_Elementary_2_classLit = createForClass("java.math", "Elementary", 856, Ljava_lang_Object_2_classLit);
+  defineClass(858, 1, { 1: 1 });
+  var Ljava_math_Elementary_2_classLit = createForClass("java.math", "Elementary", 858, Ljava_lang_Object_2_classLit);
   function $clinit_MathContext() {
     $clinit_MathContext = emptyMethod;
     $clinit_Object();
@@ -58385,9 +58455,9 @@ function getExports($wnd) {
     $clinit_Multiplication();
     return add_20(add_20(mul_0(and_0(fromInt_0(a), 4294967295), and_0(fromInt_0(b), 4294967295)), and_0(fromInt_0(c), 4294967295)), and_0(fromInt_0(d), 4294967295));
   }
-  defineClass(849, 1, { 1: 1 });
+  defineClass(852, 1, { 1: 1 });
   var bigFivePows, bigTenPows, fivePows, tenPows, whenUseKaratsuba = 63;
-  var Ljava_math_Multiplication_2_classLit = createForClass("java.math", "Multiplication", 849, Ljava_lang_Object_2_classLit);
+  var Ljava_math_Multiplication_2_classLit = createForClass("java.math", "Multiplication", 852, Ljava_lang_Object_2_classLit);
   function $clinit_RoundingMode() {
     $clinit_RoundingMode = emptyMethod;
     $clinit_Enum();
@@ -58421,9 +58491,9 @@ function getExports($wnd) {
     $clinit_RoundingMode$Map = emptyMethod;
     $MAP_4 = createValueOfMap(values_5());
   }
-  defineClass(838, 1, { 1: 1 });
+  defineClass(840, 1, { 1: 1 });
   var $MAP_4;
-  var Ljava_math_RoundingMode$Map_2_classLit = createForClass("java.math", "RoundingMode/Map", 838, Ljava_lang_Object_2_classLit);
+  var Ljava_math_RoundingMode$Map_2_classLit = createForClass("java.math", "RoundingMode/Map", 840, Ljava_lang_Object_2_classLit);
   function $clinit_Charset() {
     $clinit_Charset = emptyMethod;
     $clinit_Object();
@@ -59930,8 +60000,8 @@ function getExports($wnd) {
   function $clinit_ArrayDeque$DescendingIteratorImpl() {
     $clinit_ArrayDeque$DescendingIteratorImpl = emptyMethod;
   }
-  defineClass(840, 1, { 1: 1, 39: 1 });
-  var Ljava_util_ArrayDeque$DescendingIteratorImpl_2_classLit = createForClass("java.util", "ArrayDeque/DescendingIteratorImpl", 840, Ljava_lang_Object_2_classLit);
+  defineClass(842, 1, { 1: 1, 39: 1 });
+  var Ljava_util_ArrayDeque$DescendingIteratorImpl_2_classLit = createForClass("java.util", "ArrayDeque/DescendingIteratorImpl", 842, Ljava_lang_Object_2_classLit);
   function $clinit_ArrayDeque$IteratorImpl() {
     $clinit_ArrayDeque$IteratorImpl = emptyMethod;
     $clinit_Object();
@@ -60235,7 +60305,7 @@ function getExports($wnd) {
   function Arrays$0methodref$compare$Type() {
     $clinit_Arrays$0methodref$compare$Type();
   }
-  defineClass(879, $wnd.Function, { 1: 1, 870: 1 }, Arrays$0methodref$compare$Type);
+  defineClass(881, $wnd.Function, { 1: 1, 872: 1 }, Arrays$0methodref$compare$Type);
   _.compare_7 = function compare_31(d1, d2) {
     return compare_24(d1, d2);
   };
@@ -60248,7 +60318,7 @@ function getExports($wnd) {
   function Arrays$1methodref$compare$Type() {
     $clinit_Arrays$1methodref$compare$Type();
   }
-  defineClass(880, $wnd.Function, { 1: 1, 881: 1 }, Arrays$1methodref$compare$Type);
+  defineClass(882, $wnd.Function, { 1: 1, 883: 1 }, Arrays$1methodref$compare$Type);
   _.compare_8 = function compare_32(d1, d2) {
     return compare_27(d1, d2);
   };
@@ -60327,7 +60397,7 @@ function getExports($wnd) {
   function Arrays$lambda$0$Type() {
     $clinit_Arrays$lambda$0$Type();
   }
-  defineClass(878, $wnd.Function, { 1: 1, 870: 1 }, Arrays$lambda$0$Type);
+  defineClass(880, $wnd.Function, { 1: 1, 872: 1 }, Arrays$lambda$0$Type);
   _.compare_7 = function compare_33(d1, d2) {
     return lambda$0_10(d1, d2);
   };
@@ -60526,7 +60596,7 @@ function getExports($wnd) {
   }
   function emptyListIterator() {
     $clinit_Collections();
-    return castTo(($clinit_Collections$EmptyListIterator(), INSTANCE_0), 865);
+    return castTo(($clinit_Collections$EmptyListIterator(), INSTANCE_0), 867);
   }
   function emptyMap() {
     $clinit_Collections();
@@ -60628,7 +60698,7 @@ function getExports($wnd) {
     Object_0.call(this);
     this.$init_341();
   }
-  defineClass(420, 1, { 1: 1, 39: 1, 865: 1 }, Collections$EmptyListIterator);
+  defineClass(420, 1, { 1: 1, 39: 1, 867: 1 }, Collections$EmptyListIterator);
   _.$init_341 = function $init_341() {
   };
   _.forEachRemaining_0 = function forEachRemaining_13(consumer) {
@@ -61293,7 +61363,7 @@ function getExports($wnd) {
     AbstractHashMap_0.call(this, ignored);
     this.$init_357();
   }
-  defineClass(70, 205, { 4: 1, 1: 1, 55: 1 }, HashMap, HashMap_0);
+  defineClass(71, 205, { 4: 1, 1: 1, 55: 1 }, HashMap, HashMap_0);
   _.$init_357 = function $init_357() {
   };
   _.equals_4 = function equals_47(value1, value2) {
@@ -61307,7 +61377,7 @@ function getExports($wnd) {
     hashCode = hashCode__I__devirtual$(key);
     return ensureInt(hashCode);
   };
-  var Ljava_util_HashMap_2_classLit = createForClass("java.util", "HashMap", 70, Ljava_util_AbstractHashMap_2_classLit);
+  var Ljava_util_HashMap_2_classLit = createForClass("java.util", "HashMap", 71, Ljava_util_AbstractHashMap_2_classLit);
   function $clinit_HashSet() {
     $clinit_HashSet = emptyMethod;
     $clinit_AbstractSet();
@@ -61327,7 +61397,7 @@ function getExports($wnd) {
     this.$init_358();
     this.map_0 = new HashMap_0(initialCapacity);
   }
-  defineClass(71, 101, { 4: 1, 1: 1, 30: 1, 71: 1, 58: 1 }, HashSet, HashSet_0);
+  defineClass(72, 101, { 4: 1, 1: 1, 30: 1, 72: 1, 58: 1 }, HashSet, HashSet_0);
   _.$init_358 = function $init_358() {
   };
   _.add = function add_30(o) {
@@ -61353,7 +61423,7 @@ function getExports($wnd) {
   _.size = function size_23() {
     return this.map_0.size();
   };
-  var Ljava_util_HashSet_2_classLit = createForClass("java.util", "HashSet", 71, Ljava_util_AbstractSet_2_classLit);
+  var Ljava_util_HashSet_2_classLit = createForClass("java.util", "HashSet", 72, Ljava_util_AbstractSet_2_classLit);
   function $clinit_InternalHashCodeMap() {
     $clinit_InternalHashCodeMap = emptyMethod;
     $clinit_Object();
@@ -63469,6 +63539,34 @@ function getExports($wnd) {
   }
   defineClass(649, 1, { 1: 1 });
   var Ljava_util_function_UnaryOperator$lambda$0$Type_2_classLit = createForClass("java.util.function", "UnaryOperator/lambda$0$Type", 649, Ljava_lang_Object_2_classLit);
+  function $clinit_Matcher() {
+    $clinit_Matcher = emptyMethod;
+  }
+  defineClass(838, 1, { 1: 1 });
+  _.find_0 = function find_0() {
+    throwUnimplemented();
+    return false;
+  };
+  _.group_0 = function group_0(group) {
+    throwUnimplemented();
+    return null;
+  };
+  var Ljava_util_regex_Matcher_2_classLit = createForClass("java.util.regex", "Matcher", 838, Ljava_lang_Object_2_classLit);
+  function $clinit_Pattern() {
+    $clinit_Pattern = emptyMethod;
+    $clinit_Object();
+  }
+  function compile(p) {
+    $clinit_Pattern();
+    throwUnimplemented();
+    return null;
+  }
+  defineClass(837, 1, { 1: 1 });
+  _.matcher = function matcher_0(input_0) {
+    throwUnimplemented();
+    return null;
+  };
+  var Ljava_util_regex_Pattern_2_classLit = createForClass("java.util.regex", "Pattern", 837, Ljava_lang_Object_2_classLit);
   function $clinit_BaseStream() {
     $clinit_BaseStream = emptyMethod;
   }
@@ -63612,14 +63710,14 @@ function getExports($wnd) {
   }
   function lambda$62(c1_0, c2_1) {
     $clinit_Collectors();
-    return castTo(addAll_9(c1_0, c2_1), 71);
+    return castTo(addAll_9(c1_0, c2_1), 72);
   }
   function lambda$63(s_0) {
     $clinit_Collectors();
     return s_0;
   }
   function mapping_0(mapper, downstream) {
-    return new CollectorImpl(downstream.supplier_0(), castTo(new Collectors$lambda$23$Type(downstream, mapper), 866), downstream.combiner_0(), downstream.finisher_0(), stampJavaTypeInfo(getClassLiteralForArray(Ljava_util_stream_Collector$Characteristics_2_classLit, 1), { 4: 1, 1: 1, 7: 1 }, 82, 0, []));
+    return new CollectorImpl(downstream.supplier_0(), castTo(new Collectors$lambda$23$Type(downstream, mapper), 868), downstream.combiner_0(), downstream.finisher_0(), stampJavaTypeInfo(getClassLiteralForArray(Ljava_util_stream_Collector$Characteristics_2_classLit, 1), { 4: 1, 1: 1, 7: 1 }, 82, 0, []));
   }
   function mergeAll(m1, m2, mergeFunction) {
     var entry, entry$iterator;
@@ -63872,7 +63970,7 @@ function getExports($wnd) {
   }
   defineClass(395, 1, { 1: 1 }, Collectors$30methodref$add$Type);
   _.accept_1 = function accept_5(arg0, arg1) {
-    castTo(arg0, 71).add(arg1);
+    castTo(arg0, 72).add(arg1);
   };
   var Ljava_util_stream_Collectors$30methodref$add$Type_2_classLit = createForClass("java.util.stream", "Collectors/30methodref$add$Type", 395, Ljava_lang_Object_2_classLit);
   function $clinit_Collectors$31methodref$requireNonNull$Type() {
@@ -63986,7 +64084,7 @@ function getExports($wnd) {
     this.downstream_0 = downstream_0;
     this.mapper_1 = mapper_1;
   }
-  defineClass(383, 1, { 1: 1, 866: 1 }, Collectors$lambda$23$Type);
+  defineClass(383, 1, { 1: 1, 868: 1 }, Collectors$lambda$23$Type);
   _.accept_1 = function accept_7(arg0, arg1) {
     lambda$23(this.downstream_0, this.mapper_1, arg0, arg1);
   };
@@ -64140,7 +64238,7 @@ function getExports($wnd) {
   }
   defineClass(396, 1, { 1: 1 }, Collectors$lambda$62$Type);
   _.apply_2 = function apply_19(arg0, arg1) {
-    return lambda$62(castTo(arg0, 71), castTo(arg1, 71));
+    return lambda$62(castTo(arg0, 72), castTo(arg1, 72));
   };
   var Ljava_util_stream_Collectors$lambda$62$Type_2_classLit = createForClass("java.util.stream", "Collectors/lambda$62$Type", 396, Ljava_lang_Object_2_classLit);
   function $clinit_Collectors$lambda$63$Type() {
@@ -64154,7 +64252,7 @@ function getExports($wnd) {
     return $andThen(this, after);
   };
   _.apply_1 = function apply_20(arg0) {
-    return lambda$63(castTo(arg0, 71));
+    return lambda$63(castTo(arg0, 72));
   };
   var Ljava_util_stream_Collectors$lambda$63$Type_2_classLit = createForClass("java.util.stream", "Collectors/lambda$63$Type", 397, Ljava_lang_Object_2_classLit);
   function $clinit_Collectors$lambda$7$Type() {
@@ -65136,8 +65234,8 @@ function getExports($wnd) {
     $clinit_ArrayStamper();
     return stampJavaTypeInfo_0(array, referenceType);
   }
-  defineClass(839, 1, { 1: 1 });
-  var Ljavaemul_internal_ArrayStamper_2_classLit = createForClass("javaemul.internal", "ArrayStamper", 839, Ljava_lang_Object_2_classLit);
+  defineClass(841, 1, { 1: 1 });
+  var Ljavaemul_internal_ArrayStamper_2_classLit = createForClass("javaemul.internal", "ArrayStamper", 841, Ljava_lang_Object_2_classLit);
   function $clinit_EmulatedCharset() {
     $clinit_EmulatedCharset = emptyMethod;
     $clinit_Charset();
@@ -65740,6 +65838,9 @@ function getExports($wnd) {
     }
     return this.mTorsion[bondIndex].length - 1;
   };
+  _.getMostLikelyTorsionIndexes = function getMostLikelyTorsionIndexes() {
+    return this.mBestTorsionIndex;
+  };
   _.getRotatableBonds = function getRotatableBonds() {
     return this.mRotatableBond;
   };
@@ -66540,6 +66641,18 @@ function getExports($wnd) {
     }
     return this.mConformerLikelihood.length - 1;
   };
+  _.getMostLikelyConformerIndex = function getMostLikelyConformerIndex() {
+    var highestIndex, highestLikelihood, t;
+    highestLikelihood = 0;
+    highestIndex = -1;
+    for (t = 0; t < this.mConformerLikelihood.length; t++) {
+      if (highestLikelihood < this.mConformerLikelihood[t]) {
+        highestLikelihood = this.mConformerLikelihood[t];
+        highestIndex = t;
+      }
+    }
+    return highestIndex;
+  };
   _.originalToExtendedAtom = function originalToExtendedAtom_0(originalAtom) {
     return this.mOriginalToExtendedAtom[originalAtom];
   };
@@ -66909,8 +67022,6 @@ function getExports($wnd) {
     var detail, prediction;
     Object_0.call(this);
     this.$init_415();
-    if (getTorsionFrequencies("gGP`@dfyjidNcGI[WQCP`<")[0] == -1)
-      ($clinit_System(), out_0).println_0("ERROR");
     this.mBond = bond;
     this.mTorsionAtom = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, 4, 15, 1);
     this.mRearAtom = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, 2, 15, 1);
@@ -66926,8 +67037,6 @@ function getExports($wnd) {
     this.mFragment1 = fragment[this.mFragmentNo1];
     this.mFragment2 = fragment[this.mFragmentNo2];
     this.mBondAtomsInFragmentOrder = fragmentNo[mol.getBondAtom_0(0, bond)] == this.mFragmentNo1;
-    if (getTorsionFrequencies("gGP`@dfyjidNcGI[WQCP`<")[0] == -1)
-      ($clinit_System(), out_0).println_0("ERROR");
     if (use60degreeSteps) {
       this.mDefaultTorsion = SIXTY_DEGREE_TORSION;
       this.mDefaultFrequency = SIXTY_DEGREE_FREQUENCY;
@@ -67184,11 +67293,11 @@ function getExports($wnd) {
     this.mConformerIndex = conformerIndex;
     this.mEncodedBits = encoder.encode_0(torsionIndex, conformerIndex);
   }
-  defineClass(72, 1, { 23: 1, 1: 1, 72: 1 }, TorsionSet, TorsionSet_0);
+  defineClass(70, 1, { 23: 1, 1: 1, 70: 1 }, TorsionSet, TorsionSet_0);
   _.$init_416 = function $init_416() {
   };
   _.compareTo_1 = function compareTo_45(ts) {
-    return this.compareTo_23(castTo(ts, 72));
+    return this.compareTo_23(castTo(ts, 70));
   };
   _.compareTo_23 = function compareTo_46(ts) {
     var i;
@@ -67198,7 +67307,7 @@ function getExports($wnd) {
     return 0;
   };
   _.equals_0 = function equals_51(ts) {
-    return this.compareTo_23(castTo(ts, 72)) == 0;
+    return this.compareTo_23(castTo(ts, 70)) == 0;
   };
   _.getCollisionStrainIfMatches = function getCollisionStrainIfMatches(er) {
     return this.matches(er.getMask(), er.getData()) ? this.mCollisionIntensitySum : 0;
@@ -67270,7 +67379,7 @@ function getExports($wnd) {
   _.mCollisionIntensitySum = 0;
   _.mContribution = 0;
   _.mIsUsed = false;
-  var Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit = createForClass("org.openmolecules.chem.conf.gen", "TorsionSet", 72, Ljava_lang_Object_2_classLit);
+  var Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit = createForClass("org.openmolecules.chem.conf.gen", "TorsionSet", 70, Ljava_lang_Object_2_classLit);
   function $clinit_TorsionSetEliminationRule() {
     $clinit_TorsionSetEliminationRule = emptyMethod;
     $clinit_Object();
@@ -67462,19 +67571,19 @@ function getExports($wnd) {
   }
   function TorsionSetStrategy(conformerGenerator) {
     $clinit_TorsionSetStrategy();
-    var count, f1, f10, f2, i, i0, rb, rb$array, rb$array0, rb$array1, rb$index, rb$index0, rb$index1, rb$max, rb$max0, rb$max1, rf, rf$array, rf$index, rf$max;
+    var count, f1, f10, f2, fragmentCount, i, i0, rb, rb$array, rb$array0, rb$array1, rb$index, rb$index0, rb$index1, rb$max, rb$max0, rb$max1, rf, rf$array, rf$index, rf$max;
     Object_0.call(this);
     this.$init_419();
     this.mConformerGenerator = conformerGenerator;
     this.mRotatableBond = conformerGenerator.getRotatableBonds();
     this.mRigidFragment = conformerGenerator.getRigidFragments();
     this.mTorsionSetEncoder = new TorsionSetEncoder(this.mRigidFragment, this.mRotatableBond);
-    this.mFragmentCount = 0;
+    fragmentCount = 0;
     for (rb$array0 = this.mRotatableBond, rb$index0 = 0, rb$max0 = rb$array0.length; rb$index0 < rb$max0; ++rb$index0) {
       rb = rb$array0[rb$index0];
-      this.mFragmentCount = $wnd.Math.max(this.mFragmentCount, $wnd.Math.max(1 + rb.getFragmentNo(0), 1 + rb.getFragmentNo(1)));
+      fragmentCount = $wnd.Math.max(fragmentCount, $wnd.Math.max(1 + rb.getFragmentNo(0), 1 + rb.getFragmentNo(1)));
     }
-    count = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mFragmentCount, 15, 1);
+    count = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, fragmentCount, 15, 1);
     for (rb$array1 = this.mRotatableBond, rb$index1 = 0, rb$max1 = rb$array1.length; rb$index1 < rb$max1; ++rb$index1) {
       rb = rb$array1[rb$index1];
       count[rb.getFragmentNo(0)]++;
@@ -67497,12 +67606,12 @@ function getExports($wnd) {
       count[f10]++;
       count[f2]++;
     }
-    this.mGraphFragment = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mFragmentCount, 15, 1);
-    this.mGraphBond = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mFragmentCount, 15, 1);
-    this.mGraphParent = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mFragmentCount, 15, 1);
-    this.mGraphFragmentHandled = initUnidimensionalArray(Z_classLit, { 10: 1, 4: 1, 1: 1 }, 5, this.mFragmentCount, 16, 1);
-    this.mBondsBetweenFragments = initUnidimensionalArray(I_classLit, { 4: 1, 1: 1, 7: 1 }, 26, this.mFragmentCount, 0, 3);
-    for (f1 = 1; f1 < this.mFragmentCount; f1++) {
+    this.mGraphFragment = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, fragmentCount, 15, 1);
+    this.mGraphBond = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, fragmentCount, 15, 1);
+    this.mGraphParent = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, fragmentCount, 15, 1);
+    this.mGraphFragmentHandled = initUnidimensionalArray(Z_classLit, { 10: 1, 4: 1, 1: 1 }, 5, fragmentCount, 16, 1);
+    this.mBondsBetweenFragments = initUnidimensionalArray(I_classLit, { 4: 1, 1: 1, 7: 1 }, 26, fragmentCount, 0, 3);
+    for (f1 = 1; f1 < fragmentCount; f1++) {
       this.mBondsBetweenFragments[f1] = initUnidimensionalArray(I_classLit, { 26: 1, 4: 1, 1: 1, 7: 1 }, 6, f1, 0, 2);
       for (f2 = 0; f2 < f1; f2++)
         this.mBondsBetweenFragments[f1][f2] = this.getRotatableBondsBetween(f1, f2);
@@ -67529,7 +67638,7 @@ function getExports($wnd) {
   }
   function lambda$0_17(ts_0) {
     $clinit_TorsionSetStrategy();
-    return castTo(ts_0, 72).getCollisionStrainSum();
+    return castTo(ts_0, 70).getCollisionStrainSum();
   }
   defineClass(258, 1, { 1: 1 });
   _.$init_419 = function $init_419() {
@@ -67560,7 +67669,7 @@ function getExports($wnd) {
     if (this.mSecondChoiceList.size_1() == 0)
       return null;
     index_0 = instanceOf(this, 76) ? castTo(this, 76).getRandom().nextInt_0(this.mSecondChoiceList.size_1()) : 0;
-    ts = castTo(this.mSecondChoiceList.get_3(index_0), 72);
+    ts = castTo(this.mSecondChoiceList.get_3(index_0), 70);
     this.mSecondChoiceList.remove_0(index_0);
     return ts;
   };
@@ -67641,7 +67750,7 @@ function getExports($wnd) {
     if (isNull(ts)) {
       if (this.mSecondChoiceList.size_1() != 0) {
         this.mUsingSecondChoices = true;
-        while (this.mSecondChoiceList.size_1() != 0 && castTo(this.mSecondChoiceList.get_3(this.mSecondChoiceList.size_1() - 1), 72).getCollisionStrainSum() > this.mLowestCollisionStrain + 3)
+        while (this.mSecondChoiceList.size_1() != 0 && castTo(this.mSecondChoiceList.get_3(this.mSecondChoiceList.size_1() - 1), 70).getCollisionStrainSum() > this.mLowestCollisionStrain + 3)
           this.mSecondChoiceList.remove_0(this.mSecondChoiceList.size_1() - 1);
         ts = this.getBestSecondChoice();
       }
@@ -67749,7 +67858,6 @@ function getExports($wnd) {
     this.mMaxTotalCount = $wnd.Math.min(maxTotalCount, this.mPermutationCount);
   };
   _.mCollisionCount = 0;
-  _.mFragmentCount = 0;
   _.mLowestCollisionStrain = 0;
   _.mMaxTotalCount = 0;
   _.mPermutationCount = 0;
@@ -67765,7 +67873,7 @@ function getExports($wnd) {
   }
   defineClass(441, 1, { 1: 1 }, TorsionSetStrategy$lambda$0$Type);
   _.applyAsDouble = function applyAsDouble(arg0) {
-    return lambda$0_17(arg0);
+    return lambda$0_17(castTo(arg0, 70));
   };
   var Lorg_openmolecules_chem_conf_gen_TorsionSetStrategy$lambda$0$Type_2_classLit = createForClass("org.openmolecules.chem.conf.gen", "TorsionSetStrategy/lambda$0$Type", 441, Ljava_lang_Object_2_classLit);
   function $clinit_TorsionSetStrategyRandom() {
@@ -67783,6 +67891,9 @@ function getExports($wnd) {
   _.$init_420 = function $init_420() {
   };
   _.createTorsionSet = function createTorsionSet_0(previousTorsionSet) {
+    return this.createTorsionSet_1(this.mPreferLikelyTorsions);
+  };
+  _.createTorsionSet_1 = function createTorsionSet_1(startWithMostProbable) {
     var baseConformer, conformerIndex, count, j, j0, progress, rb, rf, torsionIndex, ts;
     if (this.getTorsionSetCount() == this.getPermutationCount_0())
       return null;
@@ -67792,7 +67903,13 @@ function getExports($wnd) {
     do {
       if (count++ == 64)
         return null;
-      if (this.mPreferLikelyTorsions) {
+      if (startWithMostProbable && this.getTorsionSetCount() == 0) {
+        for (rf = 0; rf < this.mRigidFragment.length; rf++)
+          conformerIndex[rf] = this.mRigidFragment[rf].getMostLikelyConformerIndex();
+        baseConformer = this.mConformerGenerator.getBaseConformer(conformerIndex);
+        for (rb = 0; rb < this.mRotatableBond.length; rb++)
+          torsionIndex[rb] = baseConformer.getMostLikelyTorsionIndexes()[rb];
+      } else if (this.mPreferLikelyTorsions) {
         progress = count / 64;
         for (rf = 0; rf < this.mRigidFragment.length; rf++)
           conformerIndex[rf] = this.mRigidFragment[rf].getLikelyRandomConformerIndex(this.mRandom.nextDouble(), progress);
@@ -67828,14 +67945,10 @@ function getExports($wnd) {
   defineClass(236, 76, { 1: 1, 76: 1 }, TorsionSetStrategyAdaptiveRandom);
   _.$init_421 = function $init_421() {
   };
-  _.createTorsionSet = function createTorsionSet_1(previousTorsionSet) {
+  _.createTorsionSet = function createTorsionSet_2(previousTorsionSet) {
     var collidingConformerIndex, collidingTorsionIndex, collisionIntensitySum, conformerIndex, count, i, i0, index_0, indexTried, j, random, rigidFragment, rigidFragment$array, rigidFragment$index, rigidFragment$max, torsionIndex, ts;
-    if (isNull(previousTorsionSet)) {
-      if (this.mStartWithMostProbable)
-        return this.createTorsionSet_0(initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRotatableBond.length, 15, 1), initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRigidFragment.length, 15, 1));
-      else
-        return getClassPrototype(76).createTorsionSet.call(this, null);
-    }
+    if (isNull(previousTorsionSet))
+      return getClassPrototype(76).createTorsionSet_1.call(this, this.mStartWithMostProbable);
     if (previousTorsionSet.getCollisionStrainSum() == 0)
       return getClassPrototype(76).createTorsionSet.call(this, previousTorsionSet);
     collisionIntensitySum = this.getBondAndFragmentCollisionIntensities(previousTorsionSet);
@@ -67908,7 +68021,7 @@ function getExports($wnd) {
     this.$init_422();
     this.mCurrentMaxTorsionIndex = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRotatableBond.length, 15, 1);
     this.mCurrentMaxConformerIndex = initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRigidFragment.length, 15, 1);
-    this.mAvailableTorsionSet = initUnidimensionalArray(Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit, { 4: 1, 1: 1, 7: 1 }, 72, 1, 0, 1);
+    this.mAvailableTorsionSet = initUnidimensionalArray(Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit, { 4: 1, 1: 1, 7: 1 }, 70, 1, 0, 1);
     setCheck(this.mAvailableTorsionSet, 0, this.createTorsionSet_0(initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRotatableBond.length, 15, 1), initUnidimensionalArray(I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mRigidFragment.length, 15, 1)));
     this.mAvailableTorsionSetIndex = -1;
   }
@@ -67957,7 +68070,7 @@ function getExports($wnd) {
     for (i1 = 0; i1 < this.mCurrentMaxConformerIndex.length; i1++)
       if (!isConformerIndex || i1 != bestIndex)
         count *= this.mCurrentMaxConformerIndex[i1] + 1;
-    this.mAvailableTorsionSet = initUnidimensionalArray(Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit, { 4: 1, 1: 1, 7: 1 }, 72, count, 0, 1);
+    this.mAvailableTorsionSet = initUnidimensionalArray(Lorg_openmolecules_chem_conf_gen_TorsionSet_2_classLit, { 4: 1, 1: 1, 7: 1 }, 70, count, 0, 1);
     if (isConformerIndex)
       this.mCurrentMaxConformerIndex[bestIndex]++;
     else
@@ -67993,7 +68106,7 @@ function getExports($wnd) {
     sort_7(this.mAvailableTorsionSet, new TorsionSetStrategyLikelySystematic$lambda$0$Type());
     this.mAvailableTorsionSetIndex = -1;
   };
-  _.createTorsionSet = function createTorsionSet_2(previousTorsionSet) {
+  _.createTorsionSet = function createTorsionSet_3(previousTorsionSet) {
     if (jsEquals(this.mAvailableTorsionSet, null))
       return null;
     if (this.mAvailableTorsionSetIndex + 1 == this.mAvailableTorsionSet.length)
@@ -68013,7 +68126,7 @@ function getExports($wnd) {
   }
   defineClass(450, 1, { 1: 1, 36: 1 }, TorsionSetStrategyLikelySystematic$lambda$0$Type);
   _.compare_0 = function compare_40(arg0, arg1) {
-    return lambda$0_18(castTo(arg0, 72), castTo(arg1, 72));
+    return lambda$0_18(castTo(arg0, 70), castTo(arg1, 70));
   };
   _.equals_0 = function equals_52(other) {
     return getClassPrototype(1).equals_0.call(this, other);
@@ -68970,9 +69083,9 @@ function getExports($wnd) {
     var angle, angle1, angle2, atom, atom0, atom1, atom2, atom3, atom4, bond, bond0, bondAngleSet, bondLength1, bondLength2, bondLengthSet, conn1, conn2, connAngle, connAtom, connAtom1, connAtom2, connBond, connBond1, connBond2, connIndex, distance, doubleBondOpponentIndex, dx, dy, dz, i, i0, i1, i2, i3, isE, j, j0, j1, notAtom, opponentIndex, outerAtom, rule;
     bondLengthSet = new BondLengthSet(mol);
     bondAngleSet = new BondAngleSet(mol, bondLengthSet);
-    rule = initUnidimensionalArray(Lorg_openmolecules_chem_conf_so_DistanceRule_2_classLit, { 4: 1, 1: 1, 7: 1 }, 871, mol.getAllAtoms_0(), 0, 2);
+    rule = initUnidimensionalArray(Lorg_openmolecules_chem_conf_so_DistanceRule_2_classLit, { 4: 1, 1: 1, 7: 1 }, 873, mol.getAllAtoms_0(), 0, 2);
     for (i0 = 1; i0 < mol.getAllAtoms_0(); i0++)
-      setCheck(rule, i0, initUnidimensionalArray(Lorg_openmolecules_chem_conf_so_DistanceRule_2_classLit, { 4: 1, 1: 1, 7: 1, 871: 1 }, 103, i0, 0, 1));
+      setCheck(rule, i0, initUnidimensionalArray(Lorg_openmolecules_chem_conf_so_DistanceRule_2_classLit, { 4: 1, 1: 1, 7: 1, 873: 1 }, 103, i0, 0, 1));
     for (bond0 = 0; bond0 < mol.getAllBonds_0(); bond0++) {
       atom0 = combineAtoms(mol.getBondAtom_0(0, bond0), mol.getBondAtom_0(1, bond0));
       setFixedDistance(rule, atom0, atom0, bondLengthSet.getLength_0(bond0), 10);
@@ -70831,7 +70944,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.20.0";
+  toReturn.version = "9.20.1";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -70976,8 +71089,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.20.0
- * @date 2026-02-13T13:13:15.774Z
+ * @version v9.20.1
+ * @date 2026-03-10T16:02:22.907Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */