ketcher-react 3.9.0-rc.1 → 3.9.0-rc.3

package/dist/cjs/index.js

@@ -44,7 +44,6 @@ var _ = require('lodash');
 var _taggedTemplateLiteral = require('@babel/runtime/helpers/taggedTemplateLiteral');
 var styled = require('@emotion/styled');
 var react = require('@emotion/react');
-var KN = require('w3c-keyname');
 var require$$0$3 = require('util');
 var ReactDOM = require('react-dom');
 var reactRedux = require('react-redux');
@@ -122,7 +121,6 @@ var _toConsumableArray__default = /*#__PURE__*/_interopDefaultLegacy(_toConsumab
 var ___default = /*#__PURE__*/_interopDefaultLegacy(_);
 var _taggedTemplateLiteral__default = /*#__PURE__*/_interopDefaultLegacy(_taggedTemplateLiteral);
 var styled__default = /*#__PURE__*/_interopDefaultLegacy(styled);
-var KN__namespace = /*#__PURE__*/_interopNamespace(KN);
 var require$$0__default = /*#__PURE__*/_interopDefaultLegacy(require$$0$3);
 var ReactDOM__default = /*#__PURE__*/_interopDefaultLegacy(ReactDOM);
 var CFB__namespace = /*#__PURE__*/_interopNamespace(CFB);
@@ -2854,7 +2852,7 @@ var toolActions = (_toolActions = {
     }
   },
   'charge-plus': {
-    shortcut: '+',
+    shortcut: ['Equal', 'Shift+Equal', 'NumpadAdd'],
     title: 'Charge Plus',
     action: {
       tool: 'charge',
@@ -2865,7 +2863,7 @@ var toolActions = (_toolActions = {
     }
   },
   'charge-minus': {
-    shortcut: '-',
+    shortcut: ['Minus', 'NumpadSubtract'],
     title: 'Charge Minus',
     action: {
       tool: 'charge',
@@ -3266,6 +3264,9 @@ var toolActions = (_toolActions = {
   },
   disabled: function disabled(editor) {
     return editor.isMonomerCreationWizardActive || !editor.isMonomerCreationWizardEnabled;
+  },
+  hidden: function hidden(options) {
+    return isHidden(options, ketcherCore.CREATE_MONOMER_TOOL_NAME);
   }
 }), _defineProperty__default["default"](_defineProperty__default["default"](_defineProperty__default["default"](_defineProperty__default["default"](_defineProperty__default["default"](_defineProperty__default["default"](_defineProperty__default["default"](_toolActions, "shapes", {
   disabled: function disabled(editor) {
@@ -3902,7 +3903,7 @@ var zoom = {
     }
   },
   'zoom-out': {
-    shortcut: ['Ctrl+_', 'Ctrl+-'],
+    shortcut: ['Mod+Minus', 'Mod+NumpadSubtract'],
     title: 'Zoom Out',
     enabledInViewOnly: true,
     disabled: function disabled(editor) {
@@ -3924,7 +3925,7 @@ var zoom = {
     }
   },
   'zoom-in': {
-    shortcut: ['Ctrl+=', 'Ctrl++'],
+    shortcut: ['Mod+Equal', 'Mod+NumpadAdd'],
     title: 'Zoom In',
     enabledInViewOnly: true,
     disabled: function disabled(editor) {
@@ -3955,7 +3956,7 @@ var zoom = {
 
 var openHelpLink = function openHelpLink() {
   var _window$open;
-  return (_window$open = window.open("https://github.com/epam/ketcher/blob/".concat("v3.9.0-rc.1\n", "/documentation/help.md#ketcher-overview"))) === null || _window$open === void 0 ? void 0 : _window$open.focus();
+  return (_window$open = window.open("https://github.com/epam/ketcher/blob/".concat("v3.9.0-rc.3\n", "/documentation/help.md#ketcher-overview"))) === null || _window$open === void 0 ? void 0 : _window$open.focus();
 };
 var help = {
   help: {
@@ -8916,7 +8917,7 @@ var Dialog = function Dialog(props) {
     }
   };
   var keyDown = function keyDown(event) {
-    var key = KN__namespace.keyName(event);
+    var key = event.key;
     var active = document.activeElement;
     var activeTextarea = active && active.tagName === 'TEXTAREA';
     if (key === 'Escape' || key === 'Enter' && !activeTextarea) {
@@ -20416,8 +20417,8 @@ function keyHandle(dispatch, getState, hotKeys, event) {
   var hoveredItem = getHoveredItem(render.ctab);
   if (key && key.length === 1 && !hoveredItem) {
     var currentlyPressedKeys = selectAbbreviationLookupValue(state);
-    var isShortcutKey = shortcutKeys.includes(key === null || key === void 0 ? void 0 : key.toLowerCase());
-    var isTheSameKey = key === currentlyPressedKeys;
+    var isShortcutKey = shortcutKeys.includes(key.toLowerCase());
+    var isTheSameKey = key.toLowerCase() === currentlyPressedKeys;
     var isAbbreviationLookupShown = (!isTheSameKey || !isShortcutKey) && currentlyPressedKeys;
     if (isAbbreviationLookupShown) {
       dispatch(showAbbreviationLookup(event.key));
@@ -20435,7 +20436,7 @@ function keyHandle(dispatch, getState, hotKeys, event) {
       dispatch(initAbbreviationLookup(event.key));
     }
   }
-  if (key && key.length === 1 && key.match('/')) {
+  if (key === 'Slash') {
     var hotkeyDialogTypes = {
       atoms: configWithNonViewOnlyActionsDisabled['atom-props'].action,
       bonds: configWithNonViewOnlyActionsDisabled['bond-props'].action
@@ -25641,11 +25642,35 @@ var Editor$3 = function () {
       }
       return false;
     }
+  }, {
+    key: "isMinimalViableStructure",
+    value: function isMinimalViableStructure() {
+      var _this = this;
+      var nonLeavingAtoms = this.struct().atoms.filter(function (atomId) {
+        assert_1(_this.monomerCreationState);
+        return Array.from(_this.monomerCreationState.assignedAttachmentPoints.values()).every(function (atomPair) {
+          return atomPair[1] !== atomId;
+        });
+      });
+      if (nonLeavingAtoms.size < 2) {
+        return false;
+      }
+      var nonLeavingAtomBonds = this.struct().bonds.filter(function (_, bond) {
+        return nonLeavingAtoms.has(bond.begin) && nonLeavingAtoms.has(bond.end);
+      });
+      if (nonLeavingAtomBonds.size < 1) {
+        return false;
+      }
+      var simpleSingleBonds = nonLeavingAtomBonds.filter(function (_, bond) {
+        return bond.type === ketcherCore.Bond.PATTERN.TYPE.SINGLE && bond.stereo === ketcherCore.Bond.PATTERN.STEREO.NONE;
+      });
+      return simpleSingleBonds.size >= 1;
+    }
   }, {
     key: "openMonomerCreationWizard",
     value: function openMonomerCreationWizard() {
       var _selection$atoms2,
-        _this = this;
+        _this2 = this;
       var currentStruct = this.render.ctab.molecule;
       var selection = this.selection();
       assert_1(selection);
@@ -25657,7 +25682,7 @@ var Editor$3 = function () {
         return a - b;
       }).forEach(function (atomId, i) {
         originalToSelectedAtomsIdMap.set(atomId, i);
-        _this.selectedToOriginalAtomsIdMap.set(i, atomId);
+        _this2.selectedToOriginalAtomsIdMap.set(i, atomId);
       });
       var assignedAttachmentPoints = new Map();
       var sideTerminalSGroupAtoms = this.terminalRGroupAtoms.filter(function (_ref) {
@@ -25726,10 +25751,10 @@ var Editor$3 = function () {
           pp: leavingAtom.pp
         });
         var selectedStructLeavingAtomId = selectedStruct.atoms.add(selectedStructLeavingAtom);
-        _this.selectedToOriginalAtomsIdMap.set(selectedStructLeavingAtomId, atomId);
+        _this2.selectedToOriginalAtomsIdMap.set(selectedStructLeavingAtomId, atomId);
         var selectedStructAttachmentAtomId = originalToSelectedAtomsIdMap.get(attachmentAtomId);
         assert_1(selectedStructAttachmentAtomId !== undefined);
-        _this.selectedToOriginalAtomsIdMap.set(selectedStructAttachmentAtomId, attachmentAtomId);
+        _this2.selectedToOriginalAtomsIdMap.set(selectedStructAttachmentAtomId, attachmentAtomId);
         var newBond = new ketcherCore.Bond({
           type: ketcherCore.Bond.PATTERN.TYPE.SINGLE,
           begin: selectedStructAttachmentAtomId,
@@ -25823,7 +25848,7 @@ var Editor$3 = function () {
   }, {
     key: "assignConnectionPointAtom",
     value: function assignConnectionPointAtom(atomId) {
-      var _this2 = this;
+      var _this3 = this;
       assert_1(this.monomerCreationState);
       var potentialLeavingAtoms = this.monomerCreationState.potentialAttachmentPoints.get(atomId);
       var leavingAtomId;
@@ -25832,7 +25857,7 @@ var Editor$3 = function () {
             return a - b;
           }).reduce(function (acc, currentAtomId) {
             var _Elements$get;
-            var atom = _this2.struct().atoms.get(currentAtomId);
+            var atom = _this3.struct().atoms.get(currentAtomId);
             assert_1(atom);
             var atomicNumber = (_Elements$get = ketcherCore.Elements.get(atom.label)) === null || _Elements$get === void 0 ? void 0 : _Elements$get.number;
             if (atomicNumber !== undefined) {
@@ -25888,14 +25913,16 @@ var Editor$3 = function () {
       assert_1(_.isNumber(originalLeavingAtomId));
       var originalLeavingAtom = this.originalStruct.atoms.get(originalLeavingAtomId);
       assert_1(originalLeavingAtom);
-      originalLeavingAtom.rglabel = null;
-      originalLeavingAtom.label = leavingAtom.label;
-      this.originalStruct.calcImplicitHydrogen(originalLeavingAtomId);
+      if (originalLeavingAtom.rglabel !== null) {
+        originalLeavingAtom.rglabel = null;
+        originalLeavingAtom.label = leavingAtom.label;
+        this.originalStruct.calcImplicitHydrogen(originalLeavingAtomId);
+      }
     }
   }, {
     key: "saveNewMonomer",
     value: function saveNewMonomer(data) {
-      var _this3 = this,
+      var _this4 = this,
         _this$originalSelecti;
       if (!this.monomerCreationState) {
         throw new Error('Monomer creation wizard is not active, cannot save new monomer');
@@ -25952,25 +25979,25 @@ var Editor$3 = function () {
       this.monomerCreationState.assignedAttachmentPoints.forEach(function (_ref11) {
         var _ref12 = _slicedToArray__default["default"](_ref11, 2),
           leavingAtomId = _ref12[1];
-        return _this3.cleanupAttachmentPoint(leavingAtomId);
+        return _this4.cleanupAttachmentPoint(leavingAtomId);
       });
       this.monomerCreationState.potentialAttachmentPoints.forEach(function (leavingAtomIds) {
         return Array.from(leavingAtomIds.values()).forEach(function (leavingAtomId) {
-          return _this3.cleanupAttachmentPoint(leavingAtomId);
+          return _this4.cleanupAttachmentPoint(leavingAtomId);
         });
       });
       this.closeMonomerCreationWizard();
       (_this$originalSelecti = this.originalSelection.atoms) === null || _this$originalSelecti === void 0 || _this$originalSelecti.forEach(function (atomId) {
-        var atom = _this3.render.ctab.molecule.atoms.get(atomId);
+        var atom = _this4.render.ctab.molecule.atoms.get(atomId);
         if (atom) {
           atom.fragment = -1;
         }
       });
       var sGroupAttachmentPoints = ketcherCore.MacromoleculesConverter.convertMonomerAttachmentPointsToSGroupAttachmentPoints(monomer, this.selectedToOriginalAtomsIdMap);
       sGroupAttachmentPoints.forEach(function (ap) {
-        _this3.render.ctab.molecule.bonds.forEach(function (bond) {
-          var _this3$originalSelect, _this3$originalSelect2;
-          if ((bond.begin === ap.atomId || bond.end === ap.atomId) && (!((_this3$originalSelect = _this3.originalSelection.atoms) !== null && _this3$originalSelect !== void 0 && _this3$originalSelect.includes(bond.begin)) || !((_this3$originalSelect2 = _this3.originalSelection.atoms) !== null && _this3$originalSelect2 !== void 0 && _this3$originalSelect2.includes(bond.end)))) {
+        _this4.render.ctab.molecule.bonds.forEach(function (bond) {
+          var _this4$originalSelect, _this4$originalSelect2;
+          if ((bond.begin === ap.atomId || bond.end === ap.atomId) && (!((_this4$originalSelect = _this4.originalSelection.atoms) !== null && _this4$originalSelect !== void 0 && _this4$originalSelect.includes(bond.begin)) || !((_this4$originalSelect2 = _this4.originalSelection.atoms) !== null && _this4$originalSelect2 !== void 0 && _this4$originalSelect2.includes(bond.end)))) {
             bond.beginSuperatomAttachmentPointNumber = ap.attachmentPointNumber;
           }
         });
@@ -26039,6 +26066,7 @@ var Editor$3 = function () {
   }, {
     key: "removeAttachmentPoint",
     value: function removeAttachmentPoint(name) {
+      var _this5 = this;
       assert_1(this.monomerCreationState);
       var atomPair = this.monomerCreationState.assignedAttachmentPoints.get(name);
       assert_1(atomPair);
@@ -26055,8 +26083,18 @@ var Editor$3 = function () {
           var action = ketcherCore.fromOneBondDeletion(this.render.ctab, preservedBondId).mergeWith(ketcherCore.fromOneAtomDeletion(this.render.ctab, preservedLeavingAtomId));
           this.update(action, true);
         }
+        this.preservedConnectionPointData["delete"](attachmentAtomId);
+      } else {
+        var leavingAtoms = this.findPotentialLeavingAtoms(attachmentAtomId);
+        var leavingAtomIdsSet = new Set();
+        leavingAtoms.forEach(function (atom) {
+          var atomId = _this5.struct().atoms.keyOf(atom);
+          if (atomId !== null) {
+            leavingAtomIdsSet.add(atomId);
+          }
+        });
+        this.monomerCreationState.potentialAttachmentPoints.set(attachmentAtomId, leavingAtomIdsSet);
       }
-      this.preservedConnectionPointData["delete"](attachmentAtomId);
       this.monomerCreationState.assignedAttachmentPoints["delete"](name);
       this.monomerCreationState = Object.assign({}, this.monomerCreationState);
       this.render.update(true);
@@ -26105,7 +26143,7 @@ var Editor$3 = function () {
   }, {
     key: "findPotentialLeavingAtoms",
     value: function findPotentialLeavingAtoms(attachmentAtomId) {
-      var _this4 = this;
+      var _this6 = this;
       var bondsToOutside = this.struct().bonds.filter(function (_, bond) {
         return attachmentAtomId === bond.begin && attachmentAtomId !== bond.end || attachmentAtomId === bond.end && attachmentAtomId !== bond.begin;
       });
@@ -26115,7 +26153,7 @@ var Editor$3 = function () {
           return;
         }
         var atomIdToUse = attachmentAtomId === bond.begin ? bond.end : bond.begin;
-        var atom = _this4.struct().atoms.get(atomIdToUse);
+        var atom = _this6.struct().atoms.get(atomIdToUse);
         assert_1(atom);
         if (atom.neighbors.length === 1) {
           potentialLeavingAtoms.push(atom);
@@ -26126,15 +26164,15 @@ var Editor$3 = function () {
   }, {
     key: "subscribeToChangeEventInMonomerCreationWizard",
     value: function subscribeToChangeEventInMonomerCreationWizard() {
-      var _this5 = this;
+      var _this7 = this;
       if (this.changeEventSubscriber) {
         return;
       }
       var handleChangeEvent = function handleChangeEvent(data) {
-        if (!_this5.isMonomerCreationWizardActive || data.length === 0) {
+        if (!_this7.isMonomerCreationWizardActive || data.length === 0) {
           return;
         }
-        _this5.collectChangesForMonomerCreationStateInvalidation(data);
+        _this7.collectChangesForMonomerCreationStateInvalidation(data);
       };
       this.changeEventSubscriber = this.subscribe('change', handleChangeEvent);
     }
@@ -26177,7 +26215,7 @@ var Editor$3 = function () {
   }, {
     key: "invalidateMonomerCreationWizardState",
     value: function invalidateMonomerCreationWizardState(changesMap) {
-      var _this6 = this;
+      var _this8 = this;
       if (!this.monomerCreationState) {
         return;
       }
@@ -26191,7 +26229,7 @@ var Editor$3 = function () {
           switch (operation) {
             case ketcherCore.OperationType.ATOM_DELETE:
               {
-                var attachmentPointsToInvalidate = Array.from(_this6.monomerCreationState.assignedAttachmentPoints.entries()).filter(function (_ref13) {
+                var attachmentPointsToInvalidate = Array.from(_this8.monomerCreationState.assignedAttachmentPoints.entries()).filter(function (_ref13) {
                   var _ref14 = _slicedToArray__default["default"](_ref13, 2),
                     atomPair = _ref14[1];
                   return ids.has(atomPair[0]) || ids.has(atomPair[1]);
@@ -26207,18 +26245,39 @@ var Editor$3 = function () {
                     attachmentAtomId = _atomPair4[0],
                     leavingAtomId = _atomPair4[1];
                   if (ids.has(attachmentAtomId)) {
-                    var _this6$monomerCreatio;
-                    (_this6$monomerCreatio = _this6.monomerCreationState) === null || _this6$monomerCreatio === void 0 || _this6$monomerCreatio.assignedAttachmentPoints["delete"](attachmentPointName);
+                    var _this8$monomerCreatio;
+                    (_this8$monomerCreatio = _this8.monomerCreationState) === null || _this8$monomerCreatio === void 0 || _this8$monomerCreatio.assignedAttachmentPoints["delete"](attachmentPointName);
                   } else if (ids.has(leavingAtomId)) {
-                    var potentialLeavingAtoms = _this6.findPotentialLeavingAtoms(attachmentAtomId);
+                    var potentialLeavingAtoms = _this8.findPotentialLeavingAtoms(attachmentAtomId);
                     if (potentialLeavingAtoms.length === 0) {
-                      var _this6$monomerCreatio2;
-                      (_this6$monomerCreatio2 = _this6.monomerCreationState) === null || _this6$monomerCreatio2 === void 0 || _this6$monomerCreatio2.assignedAttachmentPoints["delete"](attachmentPointName);
+                      var _this8$monomerCreatio2;
+                      (_this8$monomerCreatio2 = _this8.monomerCreationState) === null || _this8$monomerCreatio2 === void 0 || _this8$monomerCreatio2.assignedAttachmentPoints["delete"](attachmentPointName);
                     } else {
-                      var _this6$monomerCreatio3;
-                      var newLeavingAtomId = _this6.struct().atoms.keyOf(potentialLeavingAtoms[0]);
+                      var _this8$monomerCreatio3;
+                      var newLeavingAtomId = _this8.struct().atoms.keyOf(potentialLeavingAtoms[0]);
                       assert_1(newLeavingAtomId !== null);
-                      (_this6$monomerCreatio3 = _this6.monomerCreationState) === null || _this6$monomerCreatio3 === void 0 || _this6$monomerCreatio3.assignedAttachmentPoints.set(attachmentPointName, [attachmentAtomId, newLeavingAtomId]);
+                      (_this8$monomerCreatio3 = _this8.monomerCreationState) === null || _this8$monomerCreatio3 === void 0 || _this8$monomerCreatio3.assignedAttachmentPoints.set(attachmentPointName, [attachmentAtomId, newLeavingAtomId]);
+                    }
+                  }
+                });
+                var potentialAttachmentPointsToInvalidate = Array.from(_this8.monomerCreationState.potentialAttachmentPoints.entries());
+                potentialAttachmentPointsToInvalidate.forEach(function (_ref17) {
+                  var _ref18 = _slicedToArray__default["default"](_ref17, 2),
+                    attachmentAtomId = _ref18[0],
+                    leavingAtomIds = _ref18[1];
+                  if (ids.has(attachmentAtomId)) {
+                    var _this8$monomerCreatio4;
+                    (_this8$monomerCreatio4 = _this8.monomerCreationState) === null || _this8$monomerCreatio4 === void 0 || _this8$monomerCreatio4.potentialAttachmentPoints["delete"](attachmentAtomId);
+                  } else {
+                    var updatedLeavingAtomIds = new Set(Array.from(leavingAtomIds).filter(function (id) {
+                      return !ids.has(id);
+                    }));
+                    if (updatedLeavingAtomIds.size === 0) {
+                      var _this8$monomerCreatio5;
+                      (_this8$monomerCreatio5 = _this8.monomerCreationState) === null || _this8$monomerCreatio5 === void 0 || _this8$monomerCreatio5.potentialAttachmentPoints["delete"](attachmentAtomId);
+                    } else {
+                      var _this8$monomerCreatio6;
+                      (_this8$monomerCreatio6 = _this8.monomerCreationState) === null || _this8$monomerCreatio6 === void 0 || _this8$monomerCreatio6.potentialAttachmentPoints.set(attachmentAtomId, updatedLeavingAtomIds);
                     }
                   }
                 });
@@ -26231,24 +26290,40 @@ var Editor$3 = function () {
                 try {
                   var _loop2 = function _loop2() {
                     var id = _step3.value;
-                    var bond = _this6.struct().bonds.get(id);
+                    var bond = _this8.struct().bonds.get(id);
                     assert_1(bond);
-                    var attachmentPointWithBond = Array.from(_this6.monomerCreationState.assignedAttachmentPoints.entries()).find(function (_ref17) {
-                      var _ref18 = _slicedToArray__default["default"](_ref17, 2),
-                        atomPair = _ref18[1];
+                    var attachmentPointWithBond = Array.from(_this8.monomerCreationState.assignedAttachmentPoints.entries()).find(function (_ref19) {
+                      var _ref20 = _slicedToArray__default["default"](_ref19, 2),
+                        atomPair = _ref20[1];
                       return bond.begin === atomPair[0] && bond.end === atomPair[1] || bond.begin === atomPair[1] && bond.end === atomPair[0];
                     });
-                    if (!attachmentPointWithBond) {
-                      return 1;
+                    if (attachmentPointWithBond) {
+                      if (bond.type !== ketcherCore.Bond.PATTERN.TYPE.SINGLE || bond.stereo !== ketcherCore.Bond.PATTERN.STEREO.NONE) {
+                        _this8.monomerCreationState.problematicAttachmentPoints.add(attachmentPointWithBond[0]);
+                      } else {
+                        _this8.monomerCreationState.problematicAttachmentPoints["delete"](attachmentPointWithBond[0]);
+                      }
                     }
                     if (bond.type !== ketcherCore.Bond.PATTERN.TYPE.SINGLE || bond.stereo !== ketcherCore.Bond.PATTERN.STEREO.NONE) {
-                      _this6.monomerCreationState.problematicAttachmentPoints.add(attachmentPointWithBond[0]);
-                    } else {
-                      _this6.monomerCreationState.problematicAttachmentPoints["delete"](attachmentPointWithBond[0]);
+                      _this8.monomerCreationState.potentialAttachmentPoints.forEach(function (leavingAtomIds, attachmentAtomId) {
+                        var updatedLeavingAtomIds = new Set(leavingAtomIds);
+                        var bondFromAttachmentAtom = bond.begin === attachmentAtomId && leavingAtomIds.has(bond.end);
+                        var bondToAttachmentAtom = bond.end === attachmentAtomId && leavingAtomIds.has(bond.begin);
+                        if (bondFromAttachmentAtom || bondToAttachmentAtom) {
+                          updatedLeavingAtomIds["delete"](bondFromAttachmentAtom ? bond.end : bond.begin);
+                        }
+                        if (updatedLeavingAtomIds.size === 0) {
+                          var _this8$monomerCreatio7;
+                          (_this8$monomerCreatio7 = _this8.monomerCreationState) === null || _this8$monomerCreatio7 === void 0 || _this8$monomerCreatio7.potentialAttachmentPoints["delete"](attachmentAtomId);
+                        } else {
+                          var _this8$monomerCreatio8;
+                          (_this8$monomerCreatio8 = _this8.monomerCreationState) === null || _this8$monomerCreatio8 === void 0 || _this8$monomerCreatio8.potentialAttachmentPoints.set(attachmentAtomId, updatedLeavingAtomIds);
+                        }
+                      });
                     }
                   };
                   for (_iterator3.s(); !(_step3 = _iterator3.n()).done;) {
-                    if (_loop2()) continue;
+                    _loop2();
                   }
                 } catch (err) {
                   _iterator3.e(err);
@@ -26264,23 +26339,44 @@ var Editor$3 = function () {
                 try {
                   var _loop3 = function _loop3() {
                     var id = _step4.value;
-                    var bond = _this6.struct().bonds.get(id);
+                    var bond = _this8.struct().bonds.get(id);
                     assert_1(bond);
-                    var attachmentPointWithBondToLeavingAtom = Array.from(_this6.monomerCreationState.assignedAttachmentPoints.entries()).find(function (_ref19) {
-                      var _ref20 = _slicedToArray__default["default"](_ref19, 2),
-                        _ref20$ = _slicedToArray__default["default"](_ref20[1], 2),
-                        leavingAtomId = _ref20$[1];
+                    var attachmentPointWithBondToLeavingAtom = Array.from(_this8.monomerCreationState.assignedAttachmentPoints.entries()).find(function (_ref21) {
+                      var _ref22 = _slicedToArray__default["default"](_ref21, 2),
+                        _ref22$ = _slicedToArray__default["default"](_ref22[1], 2),
+                        leavingAtomId = _ref22$[1];
                       return bond.begin === leavingAtomId || bond.end === leavingAtomId;
                     });
-                    if (!attachmentPointWithBondToLeavingAtom) {
-                      return 1;
+                    if (attachmentPointWithBondToLeavingAtom) {
+                      var _attachmentPointWithB = _slicedToArray__default["default"](attachmentPointWithBondToLeavingAtom, 1),
+                        attachmentPointName = _attachmentPointWithB[0];
+                      _this8.monomerCreationState.assignedAttachmentPoints["delete"](attachmentPointName);
+                    }
+                    if (bond.type === ketcherCore.Bond.PATTERN.TYPE.SINGLE && bond.stereo === ketcherCore.Bond.PATTERN.STEREO.NONE) {
+                      if (_this8.monomerCreationState.potentialAttachmentPoints.has(bond.begin)) {
+                        var leavingAtomIds = _this8.monomerCreationState.potentialAttachmentPoints.get(bond.begin);
+                        assert_1(leavingAtomIds);
+                        var endAtom = _this8.struct().atoms.get(bond.end);
+                        if (endAtom && endAtom.neighbors.length === 1) {
+                          var updatedLeavingAtomIds = new Set(leavingAtomIds);
+                          updatedLeavingAtomIds.add(bond.end);
+                          _this8.monomerCreationState.potentialAttachmentPoints.set(bond.begin, updatedLeavingAtomIds);
+                        }
+                      }
+                      if (_this8.monomerCreationState.potentialAttachmentPoints.has(bond.end)) {
+                        var _leavingAtomIds = _this8.monomerCreationState.potentialAttachmentPoints.get(bond.end);
+                        assert_1(_leavingAtomIds);
+                        var beginAtom = _this8.struct().atoms.get(bond.begin);
+                        if (beginAtom && beginAtom.neighbors.length === 1) {
+                          var _updatedLeavingAtomIds = new Set(_leavingAtomIds);
+                          _updatedLeavingAtomIds.add(bond.begin);
+                          _this8.monomerCreationState.potentialAttachmentPoints.set(bond.end, _updatedLeavingAtomIds);
+                        }
+                      }
                     }
-                    var _attachmentPointWithB = _slicedToArray__default["default"](attachmentPointWithBondToLeavingAtom, 1),
-                      attachmentPointName = _attachmentPointWithB[0];
-                    _this6.monomerCreationState.assignedAttachmentPoints["delete"](attachmentPointName);
                   };
                   for (_iterator4.s(); !(_step4 = _iterator4.n()).done;) {
-                    if (_loop3()) continue;
+                    _loop3();
                   }
                 } catch (err) {
                   _iterator4.e(err);
@@ -26655,6 +26751,17 @@ var Editor$3 = function () {
       }
       return visited.size === atomIds.length;
     }
+  }, {
+    key: "isStructureImpure",
+    value: function isStructureImpure(struct) {
+      var atoms = struct.atoms,
+        sgroups = struct.sgroups,
+        rgroups = struct.rgroups,
+        functionalGroups = struct.functionalGroups;
+      return sgroups.size > 0 || rgroups.size > 0 || functionalGroups.size > 0 || Array.from(atoms.values()).some(function (atom) {
+        return ketcherCore.genericsList.includes(atom.label);
+      });
+    }
   }]);
   return Editor;
 }();
@@ -26730,10 +26837,10 @@ function domEventSetup(editor, clientArea) {
     eventName: 'mouseover',
     toolEventHandler: 'mouseover'
   }];
-  trackedDomEvents.forEach(function (_ref21) {
-    var target = _ref21.target,
-      eventName = _ref21.eventName,
-      toolEventHandler = _ref21.toolEventHandler;
+  trackedDomEvents.forEach(function (_ref23) {
+    var target = _ref23.target,
+      eventName = _ref23.eventName,
+      toolEventHandler = _ref23.toolEventHandler;
     editor.event[eventName] = new subscription.DOMSubscription();
     var subs = editor.event[eventName];
     target.addEventListener(eventName, function () {
@@ -27895,6 +28002,10 @@ var useCreateMonomer = function useCreateMonomer() {
   return [handler, disabled];
 };
 
+var optionsSelector = function optionsSelector(state) {
+  return state.options;
+};
+
 function ownKeys$O(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread$O(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys$O(Object(t), !0).forEach(function (r) { _defineProperty__default["default"](e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys$O(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 var bondNames = getBondNames(tools);
@@ -27935,6 +28046,7 @@ var SelectionMenuItems = function SelectionMenuItems(props) {
       color: color === '' ? 'transparent' : color
     });
   };
+  var options = reactRedux.useSelector(optionsSelector);
   return jsxRuntime.jsxs(jsxRuntime.Fragment, {
     children: [jsxRuntime.jsx(reactContexify.Item, _objectSpread$O(_objectSpread$O({}, props), {}, {
       "data-testid": "Edit selected bonds...-option",
@@ -27964,7 +28076,7 @@ var SelectionMenuItems = function SelectionMenuItems(props) {
           })]
         }, name);
       })
-    })), jsxRuntime.jsx(reactContexify.Item, _objectSpread$O(_objectSpread$O({}, props), {}, {
+    })), !isHidden(options, ketcherCore.CREATE_MONOMER_TOOL_NAME) && jsxRuntime.jsx(reactContexify.Item, _objectSpread$O(_objectSpread$O({}, props), {}, {
       "data-testid": "Create a monomer-option",
       onClick: handleCreateMonomer,
       disabled: createMonomerDisabled,
@@ -29439,9 +29551,11 @@ var useAttachmentPointSelectsData = function useAttachmentPointSelectsData(edito
     leavingAtomId = _atomPair[1];
   var attachmentAtom = editor.struct().atoms.get(attachmentAtomId);
   assert_1(attachmentAtom);
-  var attachmentPointNameOptionsLength = Math.max.apply(Math, _toConsumableArray__default["default"](Array.from(assignedAttachmentPoints.keys()).map(function (name) {
+  var usedNumbers = Array.from(assignedAttachmentPoints.keys()).map(function (name) {
     return ketcherCore.getAttachmentPointNumberFromLabel(name);
-  })));
+  });
+  var maxUsedNumber = Math.max.apply(Math, _toConsumableArray__default["default"](usedNumbers));
+  var attachmentPointNameOptionsLength = maxUsedNumber <= 3 ? 3 : Math.min(maxUsedNumber, 8);
   var nameOptions = Array.from({
     length: attachmentPointNameOptionsLength
   }).map(function (_, i) {
@@ -29601,7 +29715,9 @@ var NotificationMessages = {
   noAttachmentPoints: 'The monomer must have at least one attachment point.',
   incorrectAttachmentPointsOrder: 'Attachment point numbers must be in order, but R1 and R2 may be skipped.',
   creationSuccessful: 'The monomer was successfully added to the library.',
-  incontinuousStructure: 'All monomers must have a continuous structure.'
+  incontinuousStructure: 'All monomers must have a continuous structure.',
+  notMinimalViableStructure: 'Minimal monomer structure is two atoms connected via a single bond.',
+  impureStructure: 'Monomer structure cannot contain S-groups, R-groups, special atoms, or any other query properties.'
 };
 var NotificationTypes = {
   defaultAttachmentPoints: 'info',
@@ -29612,7 +29728,9 @@ var NotificationTypes = {
   noAttachmentPoints: 'error',
   incorrectAttachmentPointsOrder: 'error',
   creationSuccessful: 'info',
-  incontinuousStructure: 'error'
+  incontinuousStructure: 'error',
+  notMinimalViableStructure: 'error',
+  impureStructure: 'error'
 };
 var MonomerCreationExternalNotificationAction = 'MonomerCreationExternalNotification';
 
@@ -29867,6 +29985,21 @@ var validateAttachmentPoints = function validateAttachmentPoints(attachmentPoint
 };
 var validateStructure = function validateStructure(editor) {
   var notifications = new Map();
+  var isStructureImpure = Editor$3.isStructureImpure(editor.struct());
+  if (isStructureImpure) {
+    notifications.set('impureStructure', {
+      type: 'error',
+      message: NotificationMessages.impureStructure
+    });
+  }
+  var isMinimalViableStructure = editor.isMinimalViableStructure();
+  if (!isMinimalViableStructure) {
+    notifications.set('notMinimalViableStructure', {
+      type: 'error',
+      message: NotificationMessages.notMinimalViableStructure
+    });
+    return notifications;
+  }
   var isStructureContinuous = Editor$3.isStructureContinuous(editor.struct());
   if (!isStructureContinuous) {
     notifications.set('incontinuousStructure', {
@@ -36704,6 +36837,11 @@ var TemplateDialog = function TemplateDialog(props) {
       onTabChange(initialTab);
     }
   }, [initialTab, onTabChange]);
+  React.useEffect(function () {
+    if (isMonomerCreationWizardActive && tab === TemplateTabs.FunctionalGroupLibrary) {
+      onTabChange(TemplateTabs.TemplateLibrary);
+    }
+  }, [isMonomerCreationWizardActive, tab, onTabChange]);
   var handleAccordionChange = function handleAccordionChange(accordion) {
     return function (_, isExpanded) {
       setExpandedAccordions(isExpanded ? [].concat(_toConsumableArray__default["default"](expandedAccordions), [accordion]) : _toConsumableArray__default["default"](expandedAccordions).filter(function (expandedAccordion) {
@@ -37911,12 +38049,12 @@ var AbbreviationLookup = function AbbreviationLookup(_ref) {
         });
       },
       renderOption: function renderOption(props, option) {
-        return jsxRuntime.jsx("li", _objectSpread$2(_objectSpread$2({}, props), {}, {
+        return React.createElement("li", _objectSpread$2(_objectSpread$2({}, props), {}, {
           title: option.label,
-          children: jsxRuntime.jsx("div", {
-            className: classes.optionItemContent,
-            children: highlightOptionLabel(option, loweredLookupValue)
-          })
+          key: option.label
+        }), jsxRuntime.jsx("div", {
+          className: classes.optionItemContent,
+          children: highlightOptionLabel(option, loweredLookupValue)
         }));
       },
       "data-testid": ABBREVIATION_LOOKUP_TEST_ID
@@ -38194,8 +38332,8 @@ var KetcherBuilder = function () {
                 cleanup = initApp(prevKetcherId, ketcherId, element, appRoot, staticResourcesUrl, {
                   buttons: buttons || {},
                   errorHandler: errorHandler || null,
-                  version: "3.9.0-rc.1" ,
-                  buildDate: "2025-10-02T16:45:46" ,
+                  version: "3.9.0-rc.3" ,
+                  buildDate: "2025-10-22T18:27:52" ,
                   buildNumber: '',
                   customButtons: customButtons || []
                 }, structService, resolve, togglerComponent);
@@ -38490,7 +38628,7 @@ var ModeControl = function ModeControl(_ref3) {
 function ownKeys(e, r) { var t = Object.keys(e); if (Object.getOwnPropertySymbols) { var o = Object.getOwnPropertySymbols(e); r && (o = o.filter(function (r) { return Object.getOwnPropertyDescriptor(e, r).enumerable; })), t.push.apply(t, o); } return t; }
 function _objectSpread(e) { for (var r = 1; r < arguments.length; r++) { var t = null != arguments[r] ? arguments[r] : {}; r % 2 ? ownKeys(Object(t), !0).forEach(function (r) { _defineProperty__default["default"](e, r, t[r]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(e, Object.getOwnPropertyDescriptors(t)) : ownKeys(Object(t)).forEach(function (r) { Object.defineProperty(e, r, Object.getOwnPropertyDescriptor(t, r)); }); } return e; }
 var MacromoleculesEditorComponent = React.lazy(function () {
-  return Promise.resolve().then(function () { return require('./index.modern-798ecc56.js'); });
+  return Promise.resolve().then(function () { return require('./index.modern-1f472704.js'); });
 });
 var Editor = function Editor(props) {
   var _useState = React.useState(false),