openchemlib 9.6.0 → 9.7.0

package/dist/openchemlib.debug.js

@@ -8258,7 +8258,6 @@ function getExports($wnd) {
   _.connectSeparatedSingletons = function connectSeparatedSingletons() {
     var atom, bond, candidate, current, currentAtom, found, graphAtom, graphLevel, highest, i, isCompatibleBond, j, parent_0, parentAtom;
     for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
-      this.mMol.ensureHelperArrays_0(1);
       if (this.mIsDelocalizedAtom[atom]) {
         found = false;
         graphAtom = initUnidimensionalArray(cggl.I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mMol.getAtoms_0(), 15, 1);
@@ -8368,6 +8367,18 @@ function getExports($wnd) {
     }
     this.mPiElectronsAdded = 0;
   };
+  _.isAmineOxid = function isAmineOxid(atom, mayChangeAtomCharges) {
+    var connAtom, i;
+    for (i = 0; i < this.mMol.getConnAtoms_0(atom); i++) {
+      connAtom = this.mMol.getConnAtom_0(atom, i);
+      if (this.mMol.getAtomicNo_0(connAtom) == 8 && this.mMol.getConnAtoms_0(connAtom) == 1) {
+        if (mayChangeAtomCharges && this.mMol.getAtomCharge_0(connAtom) == 0)
+          this.mMol.setAtomCharge_0(connAtom, -1);
+        return true;
+      }
+    }
+    return false;
+  };
   _.locateDelocalizedDoubleBonds = function locateDelocalizedDoubleBonds(isAromaticBond) {
     return this.locateDelocalizedDoubleBonds_0(isAromaticBond, false, false);
   };
@@ -8393,7 +8404,7 @@ function getExports($wnd) {
     this.promoteObviousBonds();
     while (this.promoteOuterShellDelocalizedRingSystems(ringSet, mayChangeAtomCharges))
       this.promoteObviousBonds();
-    if (this.promoteSixMemberedAromaticRings(ringSet, mayChangeAtomCharges))
+    while (this.promoteSixMemberedAromaticRings(ringSet, mayChangeAtomCharges))
       this.promoteObviousBonds();
     while (this.promoteOneDelocalizationLeak(ringSet, mayChangeAtomCharges))
       this.promoteObviousBonds();
@@ -8406,7 +8417,7 @@ function getExports($wnd) {
       }
     }
     if (mayChangeAtomCharges)
-      this.unchargeImmoniumNHChains();
+      this.unchargeImmoniumNHChains(mayChangeAtomCharges);
     if (this.mDelocalizedAtoms - this.mPiElectronsAdded >= 2)
       this.connectSeparatedSingletons();
     for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
@@ -8533,14 +8544,14 @@ function getExports($wnd) {
           ringAtom = ringSet.getRingAtoms_0(ring);
           for (i = 0; i < ringAtom.length; i++) {
             atom = ringAtom[i];
+            bondLengthSum = jsEquals(this.mBondLength, null) ? 0 : this.mBondLength[ringBond[i]] + this.mBondLength[ringBond[(i == 0 ? ringAtom.length : i) - 1]];
             priority = this.mIsDelocalizedFiveRingMember[atom] ? this.checkAtomTypeLeak5(atom, false) : this.checkAtomTypeLeak7(atom, false);
             if (bestDelocalizationLeakPriority < priority) {
               bestDelocalizationLeakPriority = priority;
               bestDelocalizationLeakIndex = i;
               if (jsNotEquals(this.mBondLength, null))
-                bestBondLengthSum = this.mBondLength[(i == 0 ? ringAtom.length : i) - 1] + this.mBondLength[i];
+                bestBondLengthSum = bondLengthSum;
             } else if (bestDelocalizationLeakPriority == priority && jsNotEquals(this.mBondLength, null)) {
-              bondLengthSum = this.mBondLength[(i == 0 ? ringAtom.length : i) - 1] + this.mBondLength[i];
               if (bestBondLengthSum < bondLengthSum) {
                 bestDelocalizationLeakIndex = i;
                 bestBondLengthSum = bondLengthSum;
@@ -8801,11 +8812,11 @@ function getExports($wnd) {
       }
     }
   };
-  _.unchargeImmoniumNHChains = function unchargeImmoniumNHChains() {
+  _.unchargeImmoniumNHChains = function unchargeImmoniumNHChains(mayChangeAtomCharges) {
     var atom, bond, candidate, current, currentAtom, found, graphAtom, graphLevel, highest, i, isCompatibleBond, j, parent_0, parentAtom;
     for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
       this.mMol.ensureHelperArrays_0(1);
-      if (this.mMol.getAtomicNo_0(atom) == 7 && this.mMol.getAtomCharge_0(atom) == 1 && this.mMol.getAtomPi_0(atom) == 1) {
+      if (this.mMol.getAtomicNo_0(atom) == 7 && this.mMol.getAtomCharge_0(atom) == 1 && this.mMol.getAtomPi_0(atom) == 1 && !this.isAmineOxid(atom, mayChangeAtomCharges)) {
         found = false;
         graphAtom = initUnidimensionalArray(cggl.I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mMol.getAtoms_0(), 15, 1);
         parentAtom = initUnidimensionalArray(cggl.I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, this.mMol.getAtoms_0(), 15, 1);
@@ -17509,7 +17520,7 @@ function getExports($wnd) {
             newStereoBond = this.preferredTHStereoBond(stereoCenter, false);
             if (this.mBondAtom[0][newStereoBond] != stereoCenter) {
               this.mBondAtom[1][newStereoBond] = this.mBondAtom[0][newStereoBond];
-              this.mBondAtom[1][newStereoBond] = stereoCenter;
+              this.mBondAtom[0][newStereoBond] = stereoCenter;
             }
           }
         }
@@ -24544,19 +24555,21 @@ function getExports($wnd) {
     return (this.mBondRingFeatures[bond] & 65536) != 0;
   };
   _.isAtomMember_0 = function isAtomMember(ringNo, atom) {
-    var i, ringAtom;
-    ringAtom = castTo(this.mRingAtomSet.getAtIndex(ringNo), 6);
-    for (i = 0; i < ringAtom.length; i++)
-      if (atom == ringAtom[i])
+    var ringAtom, ringAtom$array, ringAtom$index, ringAtom$max;
+    for (ringAtom$array = castTo(this.mRingAtomSet.getAtIndex(ringNo), 6), ringAtom$index = 0, ringAtom$max = ringAtom$array.length; ringAtom$index < ringAtom$max; ++ringAtom$index) {
+      ringAtom = ringAtom$array[ringAtom$index];
+      if (atom == ringAtom)
         return true;
+    }
     return false;
   };
   _.isBondMember_0 = function isBondMember(ringNo, bond) {
-    var i, ringBond;
-    ringBond = castTo(this.mRingBondSet.getAtIndex(ringNo), 6);
-    for (i = 0; i < ringBond.length; i++)
-      if (bond == ringBond[i])
+    var ringBond, ringBond$array, ringBond$index, ringBond$max;
+    for (ringBond$array = castTo(this.mRingBondSet.getAtIndex(ringNo), 6), ringBond$index = 0, ringBond$max = ringBond$array.length; ringBond$index < ringBond$max; ++ringBond$index) {
+      ringBond = ringBond$array[ringBond$index];
+      if (bond == ringBond)
         return true;
+    }
     return false;
   };
   _.isDelocalized_0 = function isDelocalized_0(ringNo) {
@@ -24667,20 +24680,22 @@ function getExports($wnd) {
     }
   };
   _.updateRingSize = function updateRingSize(ringAtom, ringBond) {
-    var currentSize, i, i0, ringSize;
+    var atom, atom$array, atom$index, atom$max, bond, bond$array, bond$index, bond$max, currentSize, ringSize;
     ringSize = ringAtom.length;
-    for (i0 = 0; i0 < ringSize; i0++) {
-      currentSize = this.mAtomRingFeatures[ringAtom[i0]] & 65535;
+    for (atom$array = ringAtom, atom$index = 0, atom$max = atom$array.length; atom$index < atom$max; ++atom$index) {
+      atom = atom$array[atom$index];
+      currentSize = this.mAtomRingFeatures[atom] & 65535;
       if (currentSize == 0 || currentSize > ringSize) {
-        this.mAtomRingFeatures[ringAtom[i0]] &= ~65535;
-        this.mAtomRingFeatures[ringAtom[i0]] |= ringSize;
+        this.mAtomRingFeatures[atom] &= ~65535;
+        this.mAtomRingFeatures[atom] |= ringSize;
       }
     }
-    for (i = 0; i < ringSize; i++) {
-      currentSize = this.mBondRingFeatures[ringBond[i]] & 65535;
+    for (bond$array = ringBond, bond$index = 0, bond$max = bond$array.length; bond$index < bond$max; ++bond$index) {
+      bond = bond$array[bond$index];
+      currentSize = this.mBondRingFeatures[bond] & 65535;
       if (currentSize == 0 || currentSize > ringSize) {
-        this.mBondRingFeatures[ringBond[i]] &= ~65535;
-        this.mBondRingFeatures[ringBond[i]] |= ringSize;
+        this.mBondRingFeatures[bond] &= ~65535;
+        this.mBondRingFeatures[bond] |= ringSize;
       }
     }
   };
@@ -43968,6 +43983,10 @@ function getExports($wnd) {
           queryFeatures |= ringSize << 17;
         }
       }
+      if (this.mCBMatchFormalOrder.isSelected_0())
+        queryFeatures |= 8388608;
+      if (this.mCBMatchStereo.isSelected_0())
+        queryFeatures |= 1048576;
     }
     this.mMol.setBondQueryFeature_0(bond, 16777215, false);
     this.mMol.setBondQueryFeature_0(bond, queryFeatures, true);
@@ -71023,7 +71042,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.6.0";
+  toReturn.version = "9.7.0";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -71167,8 +71186,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.6.0
- * @date 2025-07-14T13:46:09.420Z
+ * @version v9.7.0
+ * @date 2025-08-13T10:05:12.842Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */