openchemlib 8.16.0 → 8.17.0

package/dist/openchemlib-full.pretty.js

@@ -1,7 +1,7 @@
 /**
  * openchemlib - Manipulate molecules
- * @version v8.16.0
- * @date 2024-10-17T16:04:00.262Z
+ * @version v8.17.0
+ * @date 2024-11-06T15:08:55.165Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */
@@ -6364,11 +6364,11 @@ _.mpDrawAtom = function mpDrawAtom(atom, esrGroupMemberCount){
   if ((this.mDisplayMode & 8192) == 0) {
     if (this.mMol.isFragment_0()) {
       if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 2048), 0))
-        hydrogensToAdd = this.mMol.getImplicitHydrogens_0(atom);
+        hydrogensToAdd = this.mMol.getImplicitHydrogens_1(atom);
     }
      else {
       if (this.mMol.getAtomicNo_0(atom) != 6 || this.mMol.getAtomMass_0(atom) != 0 || !this.mAtomIsConnected[atom] || this.mMol.getAtomRadical_0(atom) != 0)
-        hydrogensToAdd = this.mMol.getImplicitHydrogens_0(atom);
+        hydrogensToAdd = this.mMol.getImplicitHydrogens_1(atom);
     }
   }
   largeIsoString = false;
@@ -8896,7 +8896,6 @@ carc2.Canonizer = function Canonizer(mol){
 ;
 carc2.Canonizer_0 = function Canonizer_0(mol, mode){
   carc2.$clinit_Canonizer();
-  var i;
   Object_0.call(this);
   this.$init_6();
   this.mMol = mol;
@@ -8906,16 +8905,7 @@ carc2.Canonizer_0 = function Canonizer_0(mol, mode){
   if ((this.mMode & 2048) == 0)
     this.canFindNitrogenQualifyingForParity();
   this.mZCoordinatesAvailable = (mode & 64) != 0 || this.mMol.is3D_0();
-  this.mAllHydrogensAreExplicit = false;
-  if (this.mMol.getAllAtoms_0() > this.mMol.getAtoms_0() && !this.mMol.isFragment_0()) {
-    this.mAllHydrogensAreExplicit = true;
-    for (i = 0; i < this.mMol.getAtoms_0(); i++) {
-      if (this.mMol.getImplicitHydrogens_0(i) != 0) {
-        this.mAllHydrogensAreExplicit = false;
-        break;
-      }
-    }
-  }
+  this.mAllHydrogensAreExplicit = this.mMol.getImplicitHydrogens_0() == 0;
   if ((this.mMode & 2048) == 0) {
     this.mTHParity = initUnidimensionalArray(cggl.B_classLit, {8:1, 4:1, 1:1}, 5, this.mMol.getAtoms_0(), 15, 1);
     this.mTHParityIsPseudo = initUnidimensionalArray(cggl.Z_classLit, {13:1, 4:1, 1:1}, 5, this.mMol.getAtoms_0(), 16, 1);
@@ -9041,7 +9031,7 @@ _.canBreakTiesRandomly = function canBreakTiesRandomly(){
   var atom, atom0, atom1, rank, rankCount;
   for (atom0 = 0; atom0 < this.mMol.getAtoms_0(); atom0++) {
     this.mCanBase[atom0].init_0(atom0);
-    this.mCanBase[atom0].add_0(this.mAtomBits + 1, fromInt_0(2 * this.mCanRank[atom0]));
+    this.mCanBase[atom0].add_0(this.mAtomBits + 1, mul_0(fromInt_0(2), fromInt_0(this.mCanRank[atom0])));
   }
   rankCount = initUnidimensionalArray(cggl.I_classLit, {6:1, 4:1, 1:1}, 5, this.mNoOfRanks + 1, 15, 1);
   for (atom1 = 0; atom1 < this.mMol.getAtoms_0(); atom1++)
@@ -10205,7 +10195,7 @@ _.canRecursivelyFindAllParities = function canRecursivelyFindAllParities(){
         thParityInfo |= this.mTHESRType[atom] << 5;
         thParityInfo |= this.mTHESRGroup[atom];
       }
-      this.mCanBase[atom].add_0(2 * 9, fromInt_0(thParityInfo << 9));
+      this.mCanBase[atom].add_0(2 * 9, shl_0(fromInt_0(thParityInfo), 9));
     }
     for (bond = 0; bond < this.mMol.getBonds_0(); bond++) {
       ezParityInfo = this.mEZParity[bond] << 2 + 5;
@@ -10822,7 +10812,7 @@ _.encodeCoordinates = function encodeCoordinates(keepPositionAndScale, coords){
   this.mEncodingBuffer.append_4(includeHydrogenCoordinates?35:33);
   this.encodeBits(fromInt_0(this.mZCoordinatesAvailable?1:0), 1);
   this.encodeBits(fromInt_0(keepPositionAndScale?1:0), 1);
-  this.encodeBits(fromInt_0(narrow_int(resolutionBits / 2)), 4);
+  this.encodeBits(fromInt_0(resolutionBits >> 1), 4);
   maxDelta = 0;
   for (i0 = 1; i0 < this.mMol.getAtoms_0(); i0++)
     maxDelta = this.getMaxDelta(this.mGraphAtom[i0], this.mGraphFrom[i0] == -1?-1:this.mGraphAtom[this.mGraphFrom[i0]], maxDelta, coords);
@@ -10838,8 +10828,8 @@ _.encodeCoordinates = function encodeCoordinates(keepPositionAndScale, coords){
     return;
   }
   binCount = 1 << resolutionBits;
-  increment = maxDelta / (binCount / 2 - 1);
-  maxDeltaPlusHalfIncrement = maxDelta + increment / 2;
+  increment = maxDelta / ((binCount >> 1) - 1);
+  maxDeltaPlusHalfIncrement = maxDelta + 0.5 * increment;
   for (i2 = 1; i2 < this.mMol.getAtoms_0(); i2++)
     this.encodeCoords(this.mGraphAtom[i2], this.mGraphFrom[i2] == -1?-1:this.mGraphAtom[this.mGraphFrom[i2]], maxDeltaPlusHalfIncrement, increment, resolutionBits, coords);
   if (includeHydrogenCoordinates) {
@@ -17561,7 +17551,7 @@ _.canonizeCharge_1 = function canonizeCharge_0(allowUnbalancedCharge, doNeutrali
         continue;
       if (this.mAtomicNo[atom1] < 9 && this.getOccupiedValence_0(atom1) > 3 || this.mAtomicNo[atom2] < 9 && this.getOccupiedValence_0(atom2) > 3)
         continue;
-      hasImplicitHydrogen = this.getImplicitHydrogens_0(atom1) != 0;
+      hasImplicitHydrogen = this.getImplicitHydrogens_1(atom1) != 0;
       this.mAtomCharge[atom1] -= 1;
       this.mAtomCharge[atom2] += 1;
       if (!hasImplicitHydrogen) {
@@ -17601,7 +17591,7 @@ _.canonizeCharge_1 = function canonizeCharge_0(allowUnbalancedCharge, doNeutrali
   for (atom3 = 0; atom3 < this.mAllAtoms; atom3++) {
     if (this.mAtomCharge[atom3] > 0) {
       if (!this.hasNegativeNeighbour(atom3) && this.isElectronegative_0(atom3)) {
-        chargeReduction = $wnd.Math.min(this.getImplicitHydrogens_0(atom3), this.mAtomCharge[atom3]);
+        chargeReduction = $wnd.Math.min(this.getImplicitHydrogens_1(atom3), this.mAtomCharge[atom3]);
         if (chargeReduction != 0 && positiveChargeForRemoval >= chargeReduction) {
           overallCharge -= chargeReduction;
           overallChargeChange -= chargeReduction;
@@ -18045,7 +18035,7 @@ _.getAllConnAtomsPlusMetalBonds_0 = function getAllConnAtomsPlusMetalBonds(atom)
 }
 ;
 _.getAllHydrogens_0 = function getAllHydrogens(atom){
-  return this.mAllConnAtoms[atom] - this.getNonHydrogenNeighbourCount_0(atom) + this.getImplicitHydrogens_0(atom);
+  return this.mAllConnAtoms[atom] - this.getNonHydrogenNeighbourCount_0(atom) + this.getImplicitHydrogens_1(atom);
 }
 ;
 _.getAromaticRingCount_0 = function getAromaticRingCount(){
@@ -18427,14 +18417,25 @@ _.getImplicitHigherValence_0 = function getImplicitHigherValence(atom, neglectEx
   return occupiedValence;
 }
 ;
-_.getImplicitHydrogens_0 = function getImplicitHydrogens(atom){
+_.getImplicitHydrogens_0 = function getImplicitHydrogens(){
+  var atom, implicitHydrogens;
+  if (this.mIsFragment)
+    return 0;
+  this.ensureHelperArrays_0(1);
+  implicitHydrogens = 0;
+  for (atom = 0; atom < this.mAtoms; atom++)
+    implicitHydrogens += this.getImplicitHydrogens_1(atom);
+  return implicitHydrogens;
+}
+;
+_.getImplicitHydrogens_1 = function getImplicitHydrogens_0(atom){
   var delocalizedBonds, i, i0, maxValence, occupiedValence, valenceList;
   if (this.mIsFragment && eq_0(and_0(this.mAtomQueryFeatures[atom], 2048), 0))
     return 0;
   if (!this.supportsImplicitHydrogen_0(atom))
     return 0;
-  if (jl.equals_Ljava_lang_Object__Z__devirtual$_2('*', this.getAtomCustomLabel_0(atom)))
-    return 0;
+  if (this.mAtomicNo[atom] == 0 || jl.equals_Ljava_lang_Object__Z__devirtual$_2('*', this.getAtomCustomLabel_0(atom)))
+    return this.mAllConnAtoms[atom] == 0?1:0;
   this.ensureHelperArrays_0(1);
   occupiedValence = 0;
   for (i0 = 0; i0 < this.mAllConnAtoms[atom]; i0++)
@@ -18494,7 +18495,7 @@ _.getMolweight_0 = function getMolweight(){
   molweight = 0;
   for (atom = 0; atom < this.mAllAtoms; atom++) {
     mass = this.mAtomMass[atom] != 0?this.mAtomMass[atom]:(carc2.$clinit_Molecule() , carc2.cRoundedMass)[this.mAtomicNo[atom]];
-    molweight += mass + this.getImplicitHydrogens_0(atom) * (carc2.$clinit_Molecule() , carc2.cRoundedMass)[1];
+    molweight += mass + this.getImplicitHydrogens_1(atom) * (carc2.$clinit_Molecule() , carc2.cRoundedMass)[1];
     if (this.mAtomicNo[atom] >= 171 && this.mAtomicNo[atom] <= 190) {
       connAtoms = this.mAllConnAtoms[atom];
       if (connAtoms > 2)
@@ -18661,7 +18662,7 @@ _.getPathLength_1 = function getPathLength_0(atom1, atom2, maxLength, neglectAto
 }
 ;
 _.getPlainHydrogens = function getPlainHydrogens(atom){
-  return this.getExplicitHydrogens_0(atom) + this.getImplicitHydrogens_0(atom);
+  return this.getExplicitHydrogens_0(atom) + this.getImplicitHydrogens_1(atom);
 }
 ;
 _.getPreferredDoubleBondSide = function getPreferredDoubleBondSide(bond){
@@ -20113,7 +20114,7 @@ _.parse_2 = function parse_2(mol, idcode, coordinates){
 }
 ;
 _.parse_3 = function parse_3(mol, idcode, coordinates, idcodeStart, coordsStart){
-  var EZCount, THCount, abits, allAtoms, allBonds, aromState, aromaticSPBond, atom, atom0, atom1, atom2, atomList, atomicNo, atoms, avbl, avblDefault, avblInt, base, bbits, binCount, bond, bond$array, bond$index, bond$max, bond0, bondOrder, bondType, bondTypes, bridgeData, charge, chargedAtoms, closureBonds, connBits, coords2DAvailable, coordsAre3D, coordsAreAbsolute, count, dataType, dbits, decodeOldCoordinates, dif, dx, dy, dz, e, eNeighbours, f, factor, from, hCount, hint, hydrogen, hydrogenCount, i, i0, i1, i10, i11, i12, i13, i14, i15, i16, i17, i18, i19, i2, i20, i21, i22, i23, i24, i25, i26, i27, i28, i29, i3, i30, i31, i32, i33, i34, i35, i36, i37, i38, i39, i4, i40, i41, i42, i43, i5, i6, i7, i8, i9, index_0, isDelocalizedBond, j, label_0, lbits, mass, neighbours, nitrogens, no, offset, otherAtoms, oxygens, parity, piElectrons, resolutionBits, ringSize, ringState, selectedHydrogenBits, stereoState, targetAVBL, version, xInt, xOffset, yInt, yOffset, zInt, zOffset;
+  var EZCount, THCount, abits, allAtoms, allBonds, aromState, aromaticSPBond, atom, atom0, atom1, atom2, atomList, atomicNo, atoms, avbl, avblDefault, avblInt, base, bbits, binCount, bond, bond$array, bond$index, bond$max, bond0, bondOrder, bondType, bondTypes, bridgeData, charge, chargedAtoms, closureBonds, connBits, coords2DAvailable, coordsAre3D, coordsAreAbsolute, count, dataType, dbits, decodeOldCoordinates, decodedDX, decodedDY, dif, dx, dy, dz, e, eNeighbours, f, factor, from, hCount, hint, hydrogen, hydrogenCount, i, i0, i1, i10, i11, i12, i13, i14, i15, i16, i17, i18, i19, i2, i20, i21, i22, i23, i24, i25, i26, i27, i28, i29, i3, i30, i31, i32, i33, i34, i35, i36, i37, i38, i39, i4, i40, i41, i42, i43, i5, i6, i7, i8, i9, index_0, isDelocalizedBond, j, label_0, lbits, mass, neighbours, nitrogens, no, offset, otherAtoms, oxygens, parity, piElectrons, resolutionBits, ringSize, ringState, selectedHydrogenBits, stereoState, targetAVBL, version, xInt, xOffset, yInt, yOffset, zInt, zOffset;
   mol.clear_0();
   if (jsEquals(idcode, null) || idcodeStart < 0 || idcodeStart >= idcode.length)
     return;
@@ -20652,24 +20653,26 @@ _.parse_3 = function parse_3(mol, idcode, coordinates, idcodeStart, coordsStart)
             from = 0;
             factor = 8;
           }
-          this.mMol.setAtomX_0(atom1, this.mMol.getAtomX_0(from) + factor * (this.decodeBits(resolutionBits) - binCount / 2));
-          this.mMol.setAtomY_0(atom1, this.mMol.getAtomY_0(from) + factor * (this.decodeBits(resolutionBits) - binCount / 2));
+          decodedDX = factor * (this.decodeBits(resolutionBits) + 1 - (binCount >> 1));
+          decodedDY = factor * (this.decodeBits(resolutionBits) + 1 - (binCount >> 1));
+          this.mMol.setAtomX_0(atom1, this.mMol.getAtomX_0(from) + decodedDX);
+          this.mMol.setAtomY_0(atom1, this.mMol.getAtomY_0(from) + decodedDY);
           if (coordsAre3D)
-            this.mMol.setAtomZ_0(atom1, this.mMol.getAtomZ_0(from) + factor * (this.decodeBits(resolutionBits) - binCount / 2));
+            this.mMol.setAtomZ_0(atom1, this.mMol.getAtomZ_0(from) + factor * (this.decodeBits(resolutionBits) + 1 - (binCount >> 1)));
         }
         if (coordinates[coordsStart] == 35) {
           hydrogenCount = 0;
           hCount = initUnidimensionalArray(cggl.I_classLit, {6:1, 4:1, 1:1}, 5, allAtoms, 15, 1);
           for (atom2 = 0; atom2 < allAtoms; atom2++)
-            hydrogenCount += hCount[atom2] = this.mMol.getImplicitHydrogens_0(atom2);
+            hydrogenCount += hCount[atom2] = this.mMol.getImplicitHydrogens_1(atom2);
           for (atom = 0; atom < allAtoms; atom++) {
             for (i = 0; i < hCount[atom]; i++) {
               hydrogen = this.mMol.addAtom_2(1);
               this.mMol.addBond_1(atom, hydrogen, 1);
-              this.mMol.setAtomX_0(hydrogen, this.mMol.getAtomX_0(atom) + (this.decodeBits(resolutionBits) - binCount / 2));
-              this.mMol.setAtomY_0(hydrogen, this.mMol.getAtomY_0(atom) + (this.decodeBits(resolutionBits) - binCount / 2));
+              this.mMol.setAtomX_0(hydrogen, this.mMol.getAtomX_0(atom) + (this.decodeBits(resolutionBits) + 1 - (binCount >> 1)));
+              this.mMol.setAtomY_0(hydrogen, this.mMol.getAtomY_0(atom) + (this.decodeBits(resolutionBits) + 1 - (binCount >> 1)));
               if (coordsAre3D)
-                this.mMol.setAtomZ_0(hydrogen, this.mMol.getAtomZ_0(atom) + (this.decodeBits(resolutionBits) - binCount / 2));
+                this.mMol.setAtomZ_0(hydrogen, this.mMol.getAtomZ_0(atom) + (this.decodeBits(resolutionBits) + 1 - (binCount >> 1)));
               if (jsNotEquals(selectedHydrogenBits, null) && (selectedHydrogenBits[atom] & 1 << i) != 0)
                 this.mMol.setAtomSelection_0(hydrogen, true);
             }
@@ -20981,7 +20984,7 @@ _.appendBondOrderSymbol = function appendBondOrderSymbol(bond, parentAtom, build
   if (this.mEZHalfParity[bond] != 0)
     builder.append_4(this.mEZHalfParity[bond] == 1?47:92);
   if (this.mMode == 1) {
-    bondTypes = this.mMol.getBondQueryFeatures_0(31 | 96);
+    bondTypes = this.mMol.getBondQueryFeatures_0(bond) & (31 | 96);
     if (bondTypes != 0) {
       if ((bondTypes & 1) != 0 && this.mEZHalfParity[bond] == 0) {
         builder.append_4(45);
@@ -21367,7 +21370,7 @@ _.getAtomParitySymbol = function getAtomParitySymbol(atom, parent_0){
       neighborAtom[index_0] = parent_0;
       neighborRank[index_0++] = 8 * this.mSmilesIndex[parent_0];
     }
-    if (this.mMol.getImplicitHydrogens_0(atom) != 0) {
+    if (this.mMol.getImplicitHydrogens_1(atom) != 0) {
       neighborAtom[index_0] = 2147483647;
       neighborRank[index_0++] = 8 * this.mSmilesIndex[atom];
     }
@@ -21877,7 +21880,7 @@ carc2.MolecularFormula = function MolecularFormula(mol){
     if (mol.getAtomicNo_0(atom1) >= 171 && mol.getAtomicNo_0(atom1) <= 190)
       atomCount[1] += 2 - mol.getOccupiedValence_0(atom1);
     else {
-      atomCount[1] += mol.getImplicitHydrogens_0(atom1);
+      atomCount[1] += mol.getImplicitHydrogens_1(atom1);
     }
   atomicNoCount = 0;
   for (i0 = 1; i0 <= 190; i0++)
@@ -22136,7 +22139,7 @@ carc2.removeAcidicHydrogens = function removeAcidicHydrogens(mol, maxHydrogens){
         found = false;
         for (i = 0; i < mol.getConnAtoms_0(atom); i++) {
           connAtom = mol.getConnAtom_0(atom, i);
-          if (mol.getAtomCharge_0(connAtom) == 0 && mol.isElectronegative_0(connAtom) && mol.getImplicitHydrogens_0(connAtom) > 0) {
+          if (mol.getAtomCharge_0(connAtom) == 0 && mol.isElectronegative_0(connAtom) && mol.getImplicitHydrogens_1(connAtom) > 0) {
             mol.setAtomCharge_0(connAtom, -1);
             maxHydrogens--;
             if (maxHydrogens == 0)
@@ -22164,7 +22167,7 @@ carc2.removeAcidicHydrogens = function removeAcidicHydrogens(mol, maxHydrogens){
 carc2.removeAcidicHydrogensFromAcid = function removeAcidicHydrogensFromAcid(mol, maxHydrogens, atomicNo, centralAtomicNo){
   var atom, centralAtom, connAtom, deprotonated, deprotonatedFound, i, j, oxoFound;
   for (atom = 0; atom < mol.getAtoms_0(); atom++) {
-    if (mol.getAtomicNo_0(atom) == atomicNo && mol.getAtomCharge_0(atom) == 0 && mol.getImplicitHydrogens_0(atom) > 0) {
+    if (mol.getAtomicNo_0(atom) == atomicNo && mol.getAtomCharge_0(atom) == 0 && mol.getImplicitHydrogens_1(atom) > 0) {
       deprotonated = false;
       for (i = 0; i < mol.getConnAtoms_0(atom); i++) {
         if (mol.getConnBondOrder_0(atom, i) == 1) {
@@ -25046,7 +25049,7 @@ _.areAtomsSimilar = function areAtomsSimilar(moleculeAtom, fragmentAtom){
 }
 ;
 _.areBondsSimilar = function areBondsSimilar(moleculeBond, fragmentBond){
-  var found, frgBondType, frgBondTypes, frgDefaults, i, molBondType, molDefaults, ringSet, ringSize;
+  var found, frgBondType, frgBondTypes, frgDefaults, i, molBondType, molDefaults, moleculeRingSize, ringSet, ringSize;
   molDefaults = this.mMoleculeBondFeatures[moleculeBond];
   frgDefaults = this.mFragmentBondFeatures[fragmentBond];
   if ((this.mFragment.getBondQueryFeatures_0(fragmentBond) & 8388608) != 0) {
@@ -25064,6 +25067,13 @@ _.areBondsSimilar = function areBondsSimilar(moleculeBond, fragmentBond){
   if (ringSize != 0) {
     if (this.mMolecule.isFragment_0() && ringSize == (this.mMolecule.getBondQueryFeatures_0(fragmentBond) & 917504) >> 17)
       return true;
+    if (ringSize <= 2) {
+      moleculeRingSize = this.mMolecule.getBondRingSize_0(moleculeBond);
+      if (ringSize == 1)
+        return moleculeRingSize >= 8 && moleculeRingSize <= 12;
+      else 
+        return moleculeRingSize >= 12;
+    }
     found = false;
     ringSet = this.mMolecule.getRingSet_0();
     for (i = 0; i < ringSet.getSize_0(); i++) {
@@ -27386,7 +27396,7 @@ _.visitMolAtom = function visitMolAtom(molAtom, molBond){
     this.mSmiAtomStr[currentSmiAtom] += '' + jl.toString_49(atomIsotope);
   this.mSmiAtomStr[currentSmiAtom] += '' + atomLabel;
   if (addBracket == true) {
-    if (0 < (implicitHs = this.mMol.getImplicitHydrogens_0(molAtom))) {
+    if (0 < (implicitHs = this.mMol.getImplicitHydrogens_1(molAtom))) {
       this.mSmiAtomStr[currentSmiAtom] += 'H';
       if (1 < implicitHs)
         this.mSmiAtomStr[currentSmiAtom] += implicitHs;
@@ -27811,7 +27821,7 @@ _.locateAromaticDoubleBonds = function locateAromaticDoubleBonds(allowSmartsFeat
   }
    else {
     for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
-      if (this.mMol.isMarkedAtom_0(atom) && this.mMol.getImplicitHydrogens_0(atom) != 0) {
+      if (this.mMol.isMarkedAtom_0(atom) && this.mMol.getImplicitHydrogens_1(atom) != 0) {
         this.mMol.setAtomMarker_0(atom, false);
         this.mMol.setAtomRadical_0(atom, 32);
         this.mAromaticAtoms--;
@@ -32254,7 +32264,7 @@ carcc2.isCsp3 = function isCsp3(mol, atomID){
     return false;
   if (mol.getAtomCharge_0(atomID) != 0)
     return false;
-  if (mol.getImplicitHydrogens_0(atomID) + mol.getConnAtoms_0(atomID) != 4)
+  if (mol.getImplicitHydrogens_1(atomID) + mol.getConnAtoms_0(atomID) != 4)
     return false;
   return true;
 }
@@ -32295,7 +32305,7 @@ carcc2.addImplicitHydrogens_0 = function addImplicitHydrogens_0(molecule, iAtom)
   carcc2.$clinit_HydrogenHandler();
   var angle1, angle2, angle3, atom, atomicNo, averageLength, bond, currentDistance, distance, dx, dx1, dx2, dy, dy1, dy2, i, i0, iHydrogen, iNew, length_0, length1, length2, nHydrogens, nNeighbours, nNeighbours0, normal, stereoAtom1, stereoAtom2, stereoBond, x_0, y_0;
   atomicNo = 1;
-  nHydrogens = molecule.getImplicitHydrogens_0(iAtom);
+  nHydrogens = molecule.getImplicitHydrogens_1(iAtom);
   x_0 = molecule.getAtomX_0(iAtom);
   y_0 = molecule.getAtomY_0(iAtom);
   switch (nHydrogens) {
@@ -34923,7 +34933,7 @@ carcf.AbstractForceField = function AbstractForceField(mol){
   this.$init_79();
   implicitHydrogens = 0;
   for (at = 0; at < mol.getAtoms_0(); at++) {
-    implicitHydrogens += mol.getImplicitHydrogens_0(at);
+    implicitHydrogens += mol.getImplicitHydrogens_1(at);
   }
   if (implicitHydrogens > 0) {
     throw toJs(new jl.IllegalArgumentException_0('molecule needs explicit hydrogen atoms for force field calculations'));
@@ -37530,7 +37540,7 @@ carcfmt2.$clinit_Atom_0 = function $clinit_Atom_0(){
 }
 ;
 carcfmt2.degree = function degree(mol, atom){
-  return mol.getAllConnAtoms_0(atom) + mol.getImplicitHydrogens_0(atom);
+  return mol.getAllConnAtoms_0(atom) + mol.getImplicitHydrogens_1(atom);
 }
 ;
 carcfmt2.getHeavyType = function getHeavyType(mol, atom){
@@ -37730,7 +37740,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
         nbr = mol.getConnAtom_0(atom, i1);
         if (mol.getAtomicNo_0(nbr) == 8 && carcfmt2.degree(mol, nbr) == 1)
           nTermOtoN++;
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) >= 3 && (mol.getAtomicNo_0(nbr) == 15 || mol.getAtomicNo_0(nbr) == 16)) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) >= 3 && (mol.getAtomicNo_0(nbr) == 15 || mol.getAtomicNo_0(nbr) == 16)) {
           nOtoSP = 0;
           for (j = 0; j < mol.getAllConnAtoms_0(nbr); j++) {
             nbr2 = mol.getConnAtom_0(nbr, j);
@@ -37749,7 +37759,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
       }
 
       if (carcfmt2.degree(mol, atom) == 3) {
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) >= 4) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) >= 4) {
           doubleCN = false;
           for (i = 0; i < mol.getAllConnAtoms_0(atom); i++) {
             nbr = mol.getConnAtom_0(atom, i);
@@ -37772,7 +37782,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
           if (doubleCN)
             return 54;
         }
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) >= 3) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) >= 3) {
           isNCOorNCS = false;
           isNCNplus = false;
           isNGDplus = false;
@@ -37881,7 +37891,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
       }
 
       if (carcfmt2.degree(mol, atom) == 2) {
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) == 4) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) == 4) {
           isIsonitrile = false;
           for (i = 0; !isIsonitrile && i < mol.getAllConnAtoms_0(atom); i++) {
             nbr = mol.getConnAtom_0(atom, i);
@@ -37891,7 +37901,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
             return 61;
           return 53;
         }
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) == 3) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) == 3) {
           isNitroso = false;
           isImineOrAzo = false;
           for (i = 0; i < mol.getAllConnAtoms_0(atom); i++) {
@@ -37906,7 +37916,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
           if (isImineOrAzo)
             return 9;
         }
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) >= 2) {
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) >= 2) {
           isNSO = false;
           for (i = 0; i < mol.getAllConnAtoms_0(atom); i++) {
             nbr = mol.getConnAtom_0(atom, i);
@@ -37953,7 +37963,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
       if (carcfmt2.degree(mol, atom) == 3)
         return 49;
       if (carcfmt2.degree(mol, atom) == 2) {
-        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_0(atom) == 3)
+        if (mol.getOccupiedValence_0(atom) + mol.getImplicitHydrogens_1(atom) == 3)
           return 51;
         nHtoO = 0;
         for (i = 0; i < mol.getAllConnAtoms_0(atom); i++) {
@@ -37961,7 +37971,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
           if (mol.getAtomicNo_0(nbr) == 1)
             nHtoO++;
         }
-        if (nHtoO + mol.getImplicitHydrogens_0(atom) == 2)
+        if (nHtoO + mol.getImplicitHydrogens_1(atom) == 2)
           return 70;
         return 6;
       }
@@ -37970,7 +37980,7 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
         nNtoS = 0;
         nOtoS = 0;
         nStoS = 0;
-        isOxideOtoH = mol.getAllConnAtoms_0(atom) - mol.getConnAtoms_0(atom) + mol.getImplicitHydrogens_0(atom) > 0?true:false;
+        isOxideOtoH = mol.getAllConnAtoms_0(atom) - mol.getConnAtoms_0(atom) + mol.getImplicitHydrogens_1(atom) > 0?true:false;
         isCarboxylateO = false;
         isCarbonylO = false;
         isOxideOtoC = false;
@@ -38028,8 +38038,8 @@ carcfmt2.getHeavyType = function getHeavyType(mol, atom){
           if (mol.getAtomicNo_0(nbr) == 7) {
             isNitrosoO = mol.getBondOrder_0(mol.getBond_0(atom, nbr)) == 2;
             if (mol.getBondOrder_0(mol.getBond_0(atom, nbr)) == 1 && nOtoS == 1) {
-              isOxideOtoN = carcfmt2.degree(mol, nbr) == 2 || mol.getOccupiedValence_0(nbr) + mol.getImplicitHydrogens_0(nbr) == 3;
-              isNOxideO = mol.getOccupiedValence_0(nbr) + mol.getImplicitHydrogens_0(nbr) == 4;
+              isOxideOtoN = carcfmt2.degree(mol, nbr) == 2 || mol.getOccupiedValence_0(nbr) + mol.getImplicitHydrogens_1(nbr) == 3;
+              isNOxideO = mol.getOccupiedValence_0(nbr) + mol.getImplicitHydrogens_1(nbr) == 4;
             }
             isNitroO = nOtoS >= 2;
           }
@@ -38343,7 +38353,7 @@ carcfmt2.ringIsMMFFAromatic_0 = function ringIsMMFFAromatic_0(mol, r){
   if (rings.getRingSize_0(r) == 6) {
     for (a$array = rings.getRingAtoms_0(r) , a$index = 0 , a$max = a$array.length; a$index < a$max; ++a$index) {
       a = a$array[a$index];
-      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_0(a) != carcfmt2.degree(mol, a) + 1)
+      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_1(a) != carcfmt2.degree(mol, a) + 1)
         return carcfm.$clinit_RingBoolean() , carcfm.FALSE;
     }
     for (b$array = rings.getRingBonds_0(r) , b$index = 0 , b$max = b$array.length; b$index < b$max; ++b$index) {
@@ -38375,11 +38385,11 @@ carcfmt2.ringIsMMFFAromatic_0 = function ringIsMMFFAromatic_0(mol, r){
     passes = 1;
     for (a$array = rings.getRingAtoms_0(r) , a$index = 0 , a$max = a$array.length; a$index < a$max; ++a$index) {
       a = a$array[a$index];
-      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_0(a) == carcfmt2.degree(mol, a) && passes > 0) {
+      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_1(a) == carcfmt2.degree(mol, a) && passes > 0) {
         passes--;
         continue;
       }
-      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_0(a) != carcfmt2.degree(mol, a) + 1) {
+      if (mol.getOccupiedValence_0(a) + mol.getImplicitHydrogens_1(a) != carcfmt2.degree(mol, a) + 1) {
         return carcfm.$clinit_RingBoolean() , carcfm.FALSE;
       }
     }
@@ -38427,7 +38437,7 @@ carcfmt2.$clinit_Charge_0 = function $clinit_Charge_0(){
 }
 ;
 carcfmt2.degree_0 = function degree_0(mol, atom){
-  return mol.getAllConnAtoms_0(atom) + mol.getImplicitHydrogens_0(atom);
+  return mol.getAllConnAtoms_0(atom) + mol.getImplicitHydrogens_1(atom);
 }
 ;
 carcfmt2.getCharges = function getCharges(table, mol){
@@ -43621,6 +43631,8 @@ _.build_0 = function build_0(mol, bond){
   this.mComboBoxRingSize.addItem_0('is in 5-membered ring');
   this.mComboBoxRingSize.addItem_0('is in 6-membered ring');
   this.mComboBoxRingSize.addItem_0('is in 7-membered ring');
+  this.mComboBoxRingSize.addItem_0('smallest ring 8 to 11');
+  this.mComboBoxRingSize.addItem_0('smallest ring >= 12');
   this.mDialog.add_9(this.mComboBoxRingSize, 1, 13, 3, 13);
   this.mCBMatchFormalOrder = this.mDialog.createCheckBox_0('Match formal bond order');
   this.mCBMatchFormalOrder.setSelected_0((mol.getBondQueryFeatures_0(bond) & 8388608) != 0);
@@ -43746,7 +43758,7 @@ _.setInitialStates_0 = function setInitialStates_0(){
    else 
     this.mComboBoxRing.setSelectedIndex_0(0);
   ringSize = (queryFeatures & 917504) >> 17;
-  this.mComboBoxRingSize.setSelectedIndex_0(ringSize == 0?0:ringSize - 2);
+  this.mComboBoxRingSize.setSelectedIndex_0(ringSize == 0?0:ringSize <= 2?ringSize + 5:ringSize - 2);
   if ((queryFeatures & 130560) != 0) {
     this.mCBIsBridge.setSelected_0(true);
     minAtoms = (queryFeatures & 7680) >> 9;
@@ -43846,9 +43858,12 @@ _.setQueryFeatures_2 = function setQueryFeatures_2(bond){
     }
     if (this.mComboBoxRingSize.getSelectedIndex_0() != 0) {
       ringSize = this.mComboBoxRingSize.getSelectedIndex_0() + 2;
+      if (ringSize > 7)
+        ringSize -= 7;
       implicitSize = this.mMol.getBondRingSize_0(bond);
-      if (ringSize != implicitSize)
+      if (ringSize <= 2 || ringSize != implicitSize) {
         queryFeatures |= ringSize << 17;
+      }
     }
   }
   this.mMol.setBondQueryFeature_0(bond, 16777215, false);
@@ -44989,7 +45004,7 @@ _.eventHappened_2 = function eventHappened_7(e){
 }
 ;
 _.eventHappened_3 = function eventHappened_8(e){
-  var angleChange, atom, avbl, drawingObject, drawingObject$iterator, dx, dy, i, i0, i1, isSelected, lastX, lastY, magnification, object, repaintNeeded, s0, s1, s2, selectedAtomsFound, selectedObjectsFound, selectedOnly, selectedShape, x_0, y_0;
+  var angleChange, atom, drawingObject, drawingObject$iterator, i, i0, i1, isSelected, magnification, object, repaintNeeded, selectedAtomsFound, selectedObjectsFound, selectedOnly, selectedShape, x_0, y_0;
   if (e.getWhat() == 1) {
     if (this.mCurrentHiliteAtom != -1 && this.mAtomKeyStrokeBuffer.length_0() != 0)
       this.expandAtomKeyStrokes(this.mAtomKeyStrokeBuffer.toString_0());
@@ -45046,79 +45061,8 @@ _.eventHappened_3 = function eventHappened_8(e){
     repaintNeeded = this.trackHiliting(this.mX2, this.mY2, true);
     switch (this.mPendingRequest) {
       case 2:
-        if (this.mChainAtoms > 0) {
-          lastX = this.mChainAtomX[this.mChainAtoms - 1];
-          lastY = this.mChainAtomY[this.mChainAtoms - 1];
-        }
-         else {
-          lastX = 0;
-          lastY = 0;
-        }
-
-        avbl = this.getScaledAVBL();
-        s0 = round_int(avbl);
-        s1 = round_int(0.866 * avbl);
-        s2 = round_int(0.5 * avbl);
-        dx = this.mX2 - this.mX1;
-        dy = this.mY2 - this.mY1;
-        if ($wnd.Math.abs(dy) > $wnd.Math.abs(dx)) {
-          this.mChainAtoms = round_int(2 * $wnd.Math.abs(dy) / (s0 + s2));
-          if ($wnd.Math.abs(dy) % (s0 + s2) > s0) {
-            this.mChainAtoms++;
-          }
-          this.mChainAtomX = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
-          this.mChainAtomY = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
-          if (this.mX2 < this.mX1) {
-            s1 = -s1;
-          }
-          if (this.mY2 < this.mY1) {
-            s0 = -s0;
-            s2 = -s2;
-          }
-          for (i0 = 0; i0 < this.mChainAtoms; i0++) {
-            this.mChainAtomX[i0] = this.mX1 + 0.5 * (i0 + 1) * s1;
-            this.mChainAtomY[i0] = this.mY1 + 0.5 * (i0 + 1) * (s0 + s2);
-            if ((i0 & 1) == 0) {
-              this.mChainAtomY[i0] += s0;
-            }
-          }
-        }
-         else {
-          this.mChainAtoms = round_int($wnd.Math.abs(dx) / s1);
-          this.mChainAtomX = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
-          this.mChainAtomY = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
-          if (this.mX2 < this.mX1) {
-            s1 = -s1;
-          }
-          if (this.mY2 < this.mY1) {
-            s2 = -s2;
-          }
-          for (i0 = 0; i0 < this.mChainAtoms; i0++) {
-            this.mChainAtomX[i0] = this.mX1 + (i0 + 1) * s1;
-            this.mChainAtomY[i0] = this.mY1;
-            if ((i0 & 1) == 0) {
-              this.mChainAtomY[i0] += s2;
-            }
-          }
-        }
-
-        if (this.mChainAtoms > 0) {
-          this.mChainAtom = initUnidimensionalArray(cggl.I_classLit, {6:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
-          for (i0 = 0; i0 < this.mChainAtoms; i0++) {
-            this.mChainAtom[i0] = this.mMol.findAtom_0(this.mChainAtomX[i0], this.mChainAtomY[i0]);
-            if (this.mChainAtom[i0] != -1) {
-              this.mChainAtomX[i0] = this.mMol.getAtomX_0(this.mChainAtom[i0]);
-              this.mChainAtomY[i0] = this.mMol.getAtomY_0(this.mChainAtom[i0]);
-            }
-          }
-          if (this.mChainAtomX[this.mChainAtoms - 1] != lastX || this.mChainAtomY[this.mChainAtoms - 1] != lastY) {
-            repaintNeeded = true;
-          }
-        }
-         else if (lastX != 0 || lastY != 0) {
+        if (this.suggestNewChain())
           repaintNeeded = true;
-        }
-
         break;
       case 1:
         if ((this.mX2 - this.mX1) * (this.mX2 - this.mX1) + (this.mY2 - this.mY1) * (this.mY2 - this.mY1) < 100) {
@@ -45150,10 +45094,10 @@ _.eventHappened_3 = function eventHappened_8(e){
           }
         }
 
-        for (i1 = 0; i1 < this.mMol.getAllAtoms_0(); i1++) {
-          if (this.mMol.isSelectedAtom_0(i1)) {
-            this.mMol.setAtomX_0(i1, this.mX[i1] + this.mX2 - this.mX1);
-            this.mMol.setAtomY_0(i1, this.mY[i1] + this.mY2 - this.mY1);
+        for (i0 = 0; i0 < this.mMol.getAllAtoms_0(); i0++) {
+          if (this.mMol.isSelectedAtom_0(i0)) {
+            this.mMol.setAtomX_0(i0, this.mX[i0] + this.mX2 - this.mX1);
+            this.mMol.setAtomY_0(i0, this.mY[i0] + this.mY2 - this.mY1);
           }
         }
 
@@ -45174,8 +45118,8 @@ _.eventHappened_3 = function eventHappened_8(e){
 
         selectedObjectsFound = false;
         if (isNotNull(this.mDrawingObjectList)) {
-          for (i0 = 0; i0 < this.mDrawingObjectList.size() && !selectedObjectsFound; i0++) {
-            selectedObjectsFound = castTo(this.mDrawingObjectList.getAtIndex(i0), 47).isSelected_0();
+          for (i1 = 0; i1 < this.mDrawingObjectList.size() && !selectedObjectsFound; i1++) {
+            selectedObjectsFound = castTo(this.mDrawingObjectList.getAtIndex(i1), 47).isSelected_0();
           }
         }
 
@@ -45183,9 +45127,9 @@ _.eventHappened_3 = function eventHappened_8(e){
         angleChange = $wnd.Math.abs(this.mX2 - this.mX1) < 20?0:(this.mX2 - this.mX1) / 50;
         selectedOnly = selectedAtomsFound || selectedObjectsFound;
         if (isNotNull(this.mDrawingObjectList) && (!selectedOnly || selectedObjectsFound)) {
-          for (i0 = 0; i0 < this.mDrawingObjectList.size(); i0++) {
-            if (!selectedOnly || castTo(this.mDrawingObjectList.getAtIndex(i0), 47).isSelected_0()) {
-              castTo(this.mDrawingObjectList.getAtIndex(i0), 47).zoomAndRotate_0(magnification, angleChange);
+          for (i1 = 0; i1 < this.mDrawingObjectList.size(); i1++) {
+            if (!selectedOnly || castTo(this.mDrawingObjectList.getAtIndex(i1), 47).isSelected_0()) {
+              castTo(this.mDrawingObjectList.getAtIndex(i1), 47).zoomAndRotate_0(magnification, angleChange);
             }
           }
           this.update(2);
@@ -45213,10 +45157,10 @@ _.eventHappened_3 = function eventHappened_8(e){
         }
 
         if (isNotNull(this.mDrawingObjectList)) {
-          for (i0 = 0; i0 < this.mDrawingObjectList.size(); i0++) {
-            object = castTo(this.mDrawingObjectList.getAtIndex(i0), 47);
+          for (i1 = 0; i1 < this.mDrawingObjectList.size(); i1++) {
+            object = castTo(this.mDrawingObjectList.getAtIndex(i1), 47);
             isSelected = object.isSurroundedBy(selectedShape);
-            if ((!this.mIsAddingToSelection || !this.mIsSelectedObject[i0]) && isSelected != object.isSelected_0()) {
+            if ((!this.mIsAddingToSelection || !this.mIsSelectedObject[i1]) && isSelected != object.isSelected_0()) {
               object.setSelected_0(isSelected);
               this.mUpdateMode = $wnd.Math.max(this.mUpdateMode, 1);
             }
@@ -46720,6 +46664,81 @@ _.storeState = function storeState(){
   this.mUndoDrawingObjectList = isNull(this.mDrawingObjectList)?null:new carc2.DrawingObjectList_0(this.mDrawingObjectList);
 }
 ;
+_.suggestNewChain = function suggestNewChain(){
+  var avbl, bondAngle, candidate1, candidate2, connAngle, dx, dy, exitAngle, i, i0, lastChainAtoms, lastX1, lastX2, lastY1, lastY2, leftAngle, mdx, mdy, mouseAngle, nextAngle;
+  mouseAngle = carc2.getAngle_0(this.mX1, this.mY1, this.mX2, this.mY2);
+  mdx = this.mX2 - this.mX1;
+  mdy = this.mY2 - this.mY1;
+  lastChainAtoms = this.mChainAtoms;
+  lastX1 = 0;
+  lastY1 = 0;
+  lastX2 = 0;
+  lastY2 = 0;
+  if (lastChainAtoms > 0) {
+    lastX1 = toInt_0(jl.round_1(this.mChainAtomX[0]));
+    lastY1 = toInt_0(jl.round_1(this.mChainAtomY[0]));
+  }
+  if (lastChainAtoms > 1) {
+    lastX2 = toInt_0(jl.round_1(this.mChainAtomX[1]));
+    lastY2 = toInt_0(jl.round_1(this.mChainAtomY[1]));
+  }
+  exitAngle = 0;
+  if (this.mAtom1 == -1 || this.mMol.getAllConnAtomsPlusMetalBonds_0(this.mAtom1) == 0) {
+    exitAngle = 3.141592653589793 / 3 * toDouble_0(jl.round_1(mouseAngle * 3 / 3.141592653589793));
+  }
+   else if (this.mMol.getAllConnAtomsPlusMetalBonds_0(this.mAtom1) == 1) {
+    bondAngle = this.mMol.getBondAngle_0(this.mMol.getConnAtom_0(this.mAtom1, 0), this.mAtom1);
+    candidate1 = bondAngle - 3.141592653589793 / 3;
+    candidate2 = bondAngle + 3.141592653589793 / 3;
+    exitAngle = $wnd.Math.abs(carc2.getAngleDif(mouseAngle, candidate1)) < $wnd.Math.abs(carc2.getAngleDif(mouseAngle, candidate2))?candidate1:candidate2;
+  }
+   else {
+    connAngle = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mMol.getAllConnAtomsPlusMetalBonds_0(this.mAtom1), 15, 1);
+    for (i0 = 0; i0 < this.mMol.getAllConnAtomsPlusMetalBonds_0(this.mAtom1); i0++)
+      connAngle[i0] = this.mMol.getBondAngle_0(this.mAtom1, this.mMol.getConnAtom_0(this.mAtom1, i0));
+    ju.sort_2(connAngle);
+    for (i = 0; i < connAngle.length; i++) {
+      leftAngle = i == 0?connAngle[connAngle.length - 1] - 2 * 3.141592653589793:connAngle[i - 1];
+      if (leftAngle < mouseAngle && mouseAngle < connAngle[i]) {
+        exitAngle = (connAngle[i] + leftAngle) / 2;
+        break;
+      }
+      if (leftAngle < mouseAngle - 2 * 3.141592653589793 && mouseAngle - 2 * 3.141592653589793 < connAngle[i]) {
+        exitAngle = (connAngle[i] + leftAngle) / 2;
+        break;
+      }
+    }
+  }
+  avbl = this.getScaledAVBL();
+  this.mChainAtoms = $wnd.Math.abs(carc2.getAngleDif(mouseAngle, exitAngle)) > 3.141592653589793 / 3?0:round_int($wnd.Math.sqrt(mdx * mdx + mdy * mdy) / avbl);
+  if (this.mChainAtoms > 0) {
+    if (jsEquals(this.mChainAtomX, null) || this.mChainAtomX.length < this.mChainAtoms) {
+      this.mChainAtomX = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
+      this.mChainAtomY = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
+    }
+    dx = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, 2, 15, 1);
+    dy = initUnidimensionalArray(cggl.D_classLit, {12:1, 4:1, 1:1}, 5, 2, 15, 1);
+    nextAngle = carc2.getAngleDif(mouseAngle, exitAngle) < 0?exitAngle - 3.141592653589793 / 3:exitAngle + 3.141592653589793 / 3;
+    dx[0] = avbl * $wnd.Math.sin(exitAngle);
+    dy[0] = avbl * $wnd.Math.cos(exitAngle);
+    dx[1] = avbl * $wnd.Math.sin(nextAngle);
+    dy[1] = avbl * $wnd.Math.cos(nextAngle);
+    for (i0 = 0; i0 < this.mChainAtoms; i0++) {
+      this.mChainAtomX[i0] = (i0 == 0?this.mX1:this.mChainAtomX[i0 - 1]) + dx[i0 & 1];
+      this.mChainAtomY[i0] = (i0 == 0?this.mY1:this.mChainAtomY[i0 - 1]) + dy[i0 & 1];
+    }
+    this.mChainAtom = initUnidimensionalArray(cggl.I_classLit, {6:1, 4:1, 1:1}, 5, this.mChainAtoms, 15, 1);
+    for (i = 0; i < this.mChainAtoms; i++) {
+      this.mChainAtom[i] = this.mMol.findAtom_0(this.mChainAtomX[i], this.mChainAtomY[i]);
+      if (this.mChainAtom[i] != -1) {
+        this.mChainAtomX[i] = this.mMol.getAtomX_0(this.mChainAtom[i]);
+        this.mChainAtomY[i] = this.mMol.getAtomY_0(this.mChainAtom[i]);
+      }
+    }
+  }
+  return lastChainAtoms != this.mChainAtoms || this.mChainAtoms != 0 && (lastX1 != toInt_0(jl.round_1(this.mChainAtomX[0])) || lastY1 != toInt_0(jl.round_1(this.mChainAtomY[0]))) || this.mChainAtoms > 1 && (lastX2 != toInt_0(jl.round_1(this.mChainAtomX[1])) || lastY2 != toInt_0(jl.round_1(this.mChainAtomY[1])));
+}
+;
 _.suggestNewX2AndY2 = function suggestNewX2AndY2(atom){
   var angle, angleDiff, avbl, i, i0, i1, j, largestDiff, largestNo, newAngle, temp;
   newAngle = 3.141592653589793 * 2 / 3;
@@ -59616,8 +59635,8 @@ _.getImplicitHigherValence = function getImplicitHigherValence_0(atom, neglectEx
   return this.oclMolecule.getImplicitHigherValence_0(atom, neglectExplicitHydrogen);
 }
 ;
-_.getImplicitHydrogens = function getImplicitHydrogens_0(atom){
-  return this.oclMolecule.getImplicitHydrogens_0(atom);
+_.getImplicitHydrogens = function getImplicitHydrogens_1(atom){
+  return this.oclMolecule.getImplicitHydrogens_1(atom);
 }
 ;
 _.getIndex = function getIndex(){
@@ -94375,7 +94394,7 @@ ooccg.addHydrogenAtoms = function addHydrogenAtoms(mol){
   mol.ensureHelperArrays_0(1);
   implicitHydrogen = initUnidimensionalArray(cggl.I_classLit, {6:1, 4:1, 1:1}, 5, mol.getAtoms_0(), 15, 1);
   for (atom0 = 0; atom0 < mol.getAtoms_0(); atom0++)
-    implicitHydrogen[atom0] = mol.getImplicitHydrogens_0(atom0);
+    implicitHydrogen[atom0] = mol.getImplicitHydrogens_1(atom0);
   hydrogenBondLength = 0.8 * mol.getAverageBondLength_0();
   for (atom1 = 0; atom1 < implicitHydrogen.length; atom1++)
     if (implicitHydrogen[atom1] != 0)
@@ -99723,7 +99742,7 @@ $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps
 
     var toReturn = $wnd["OCL"];
 
-    toReturn.version = '8.16.0';
+    toReturn.version = '8.17.0';
 
     return toReturn;
   }