openchemlib 9.22.0 → 9.22.1

package/dist/openchemlib.debug.js

@@ -7124,14 +7124,12 @@ function getExports($wnd) {
       atomStr = atmStart + ("" + this.mMol.getAtomListString_0(atom)) + "]";
       if (length__I__devirtual$_0(atomStr) > 5)
         atomStr = atmStart + this.mMol.getAtomList_0(atom).length + "]";
-      if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 2048), 0))
-        hydrogensToAdd = -1;
     } else if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 1), 0)) {
       atomStr = "?";
-      if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 2048), 0))
-        hydrogensToAdd = -1;
     } else if (this.mMol.getAtomicNo_0(atom) != 6 || jsNotEquals(propStr, null) || jsNotEquals(isoStr, null) && (!isSmallCustomLabelOnly || (this.mDisplayMode & 32768) == 0) || hydrogensToAdd > 0 || !this.mAtomIsConnected[atom])
       atomStr = this.mMol.getAtomLabel_0(atom);
+    if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 2048), 0) && hydrogensToAdd == 0)
+      isoStr = this.append(isoStr, "!s");
     labelWidth = 0;
     if (!this.mMol.isSelectedAtom_0(atom) & this.mMol.isExcludeGroupAtom(atom))
       this.setColorCode(-8);
@@ -7236,11 +7234,7 @@ function getExports($wnd) {
       hydrogenWidth = this.getStringWidth("H");
       hNoWidth = 0;
       hHeight = this.getTextSize();
-      if (hydrogensToAdd == -1) {
-        hNoStr = "n";
-        this.mpSetSmallLabelSize();
-        hNoWidth = this.getStringWidth(hNoStr);
-      } else if (hydrogensToAdd > 1) {
+      if (hydrogensToAdd > 1) {
         hNoStr = valueOf_18(hydrogensToAdd);
         this.mpSetSmallLabelSize();
         hNoWidth = this.getStringWidth(hNoStr);
@@ -15710,33 +15704,32 @@ function getExports($wnd) {
     return -$wnd.Math.atan2(v2.getLength() * v1.dot(n2), n1.dot(n2));
   };
   _.changeAtom_0 = function changeAtom(atom, atomicNo, mass, abnormalValence, radical) {
-    var changed;
+    var isAtomicNoChange;
     if ((atomicNo == 1 || atomicNo == 151 || atomicNo == 152) && this.getOccupiedValence_0(atom) > 1)
       return false;
-    changed = this.mIsFragment && neq(and_0(this.mAtomQueryFeatures[atom], not_0(1)), 0);
-    this.mAtomQueryFeatures[atom] = and_0(this.mAtomQueryFeatures[atom], not_0(1));
-    if (jsNotEquals(this.mAtomList, null) && jsNotEquals(this.mAtomList[atom], null)) {
-      this.mAtomList[atom] = null;
-      changed = true;
-    }
-    if (jsNotEquals(this.mAtomCustomLabel, null) && jsNotEquals(this.mAtomCustomLabel[atom], null)) {
-      this.mAtomCustomLabel[atom] = null;
-      changed = true;
-    }
-    if (atomicNo == this.mAtomicNo[atom] && mass == this.mAtomMass[atom] && abnormalValence == this.getAtomAbnormalValence_0(atom) && radical == this.getAtomRadical_0(atom))
-      return changed;
     if (atomicNo == 151 || atomicNo == 152) {
       mass = atomicNo - 149;
       atomicNo = 1;
     }
-    this.mAtomFlags[atom] &= 448 | 512;
-    this.mAtomicNo[atom] = atomicNo;
+    isAtomicNoChange = atomicNo != this.mAtomicNo[atom] && (!this.mIsFragment || eq(and_0(this.mAtomQueryFeatures[atom], 1), 0) && (jsEquals(this.mAtomList, null) || jsEquals(this.mAtomList[atom], null)));
+    if (isAtomicNoChange) {
+      this.mAtomQueryFeatures[atom] = 0;
+      if (jsNotEquals(this.mAtomList, null) && jsNotEquals(this.mAtomList[atom], null))
+        this.mAtomList[atom] = null;
+      if (jsNotEquals(this.mAtomCustomLabel, null) && jsNotEquals(this.mAtomCustomLabel[atom], null))
+        this.mAtomCustomLabel[atom] = null;
+    } else if (mass == this.mAtomMass[atom] && abnormalValence == this.getAtomAbnormalValence_0(atom) && radical == this.getAtomRadical_0(atom)) {
+      return false;
+    }
+    if (isAtomicNoChange) {
+      this.mAtomicNo[atom] = atomicNo;
+      this.mAtomFlags[atom] &= 448 | 512;
+      this.mAtomCharge[atom] = 0;
+      this.removeMappingNo(this.mAtomMapNo[atom]);
+    }
     this.mAtomMass[atom] = mass;
-    this.mAtomCharge[atom] = 0;
-    this.mAtomQueryFeatures[atom] = 0;
     this.setAtomAbnormalValence_0(atom, abnormalValence);
     this.setAtomRadical_0(atom, radical);
-    this.removeMappingNo(this.mAtomMapNo[atom]);
     this.mValidHelperArrays = 0;
     return true;
   };
@@ -18385,17 +18378,27 @@ function getExports($wnd) {
     return implicitHydrogens;
   };
   _.getImplicitHydrogens_1 = function getImplicitHydrogens_0(atom) {
-    var delocalizedBonds, i, i0, maxValence, occupiedValence, valenceList;
+    var delocalizedBonds, i, i0, i1, maxValence, occupiedValence, valenceList;
     if (this.mIsFragment && eq(and_0(this.mAtomQueryFeatures[atom], 2048), 0))
       return 0;
     if (!this.supportsImplicitHydrogen_0(atom))
       return 0;
+    this.ensureHelperArrays_0(1);
+    if (this.mIsFragment) {
+      if (neq(and_0(this.mAtomQueryFeatures[atom], 1), 0))
+        return 0;
+      if (jsNotEquals(this.mAtomList, null) && jsNotEquals(this.mAtomList[atom], null) && this.mAtomList[atom].length > 1)
+        return 0;
+      for (i0 = 0; i0 < this.mAllConnAtoms[atom]; i0++)
+        if (bitCount_1(this.mBondQueryFeatures[this.mConnBond[atom][i0]] & 127) > 1)
+          return 0;
+    }
     if (this.mAtomicNo[atom] == 0 || equals_Ljava_lang_Object__Z__devirtual$_2("*", this.getAtomCustomLabel_0(atom)))
       return this.mAllConnAtoms[atom] == 0 ? 1 : 0;
-    this.ensureHelperArrays_0(1);
     occupiedValence = 0;
-    for (i0 = 0; i0 < this.mAllConnAtoms[atom]; i0++)
-      occupiedValence += this.mConnBondOrder[atom][i0];
+    for (i1 = 0; i1 < this.mAllConnAtoms[atom]; i1++)
+      if (!this.mIsFragment || eq(and_0(this.mAtomQueryFeatures[this.mConnAtom[atom][i1]], 536870912), 0))
+        occupiedValence += this.mConnBondOrder[atom][i1];
     if (this.mIsFragment) {
       delocalizedBonds = 1;
       for (i = 0; i < this.mConnAtoms[atom]; i++)
@@ -28160,7 +28163,7 @@ function getExports($wnd) {
   _.mSingleDotSeparator = false;
   _.mSmartsFeatureFound = false;
   _.mSmartsMode = 0;
-  var BRACKET_LEVELS = 32, HYDROGEN_IMPLICIT_ZERO = 9, INITIAL_CONNECTIONS = 16, MAX_AROMATIC_RING_SIZE = 15, MAX_CONNECTIONS = 100, MODE_CREATE_SMARTS_WARNING = 64, MODE_ENUMERATE_SMARTS = 128, MODE_MAKE_HYDROGEN_EXPLICIT = 8, MODE_NO_CACTUS_SYNTAX = 16, MODE_SINGLE_DOT_SEPARATOR = 32, MODE_SKIP_COORDINATE_TEMPLATES = 4, SMARTS_MODE_GUESS = 1, SMARTS_MODE_IS_SMARTS = 2, SMARTS_MODE_IS_SMILES = 0, SMARTS_MODE_MASK = 3;
+  var BRACKET_LEVELS = 32, HYDROGEN_IMPLICIT_ZERO = 9, INITIAL_CONNECTIONS = 16, MAX_AROMATIC_RING_SIZE = 15, MAX_CONNECTIONS = 100, MODE_CREATE_SMARTS_WARNING = 64, MODE_ENUMERATE_SMARTS = 128, MODE_MAKE_HYDROGEN_EXPLICIT = 8, MODE_NO_CACTUS_SYNTAX = 16, MODE_NO_STACKTRACES = 256, MODE_SINGLE_DOT_SEPARATOR = 32, MODE_SKIP_COORDINATE_TEMPLATES = 4, SMARTS_MODE_GUESS = 1, SMARTS_MODE_IS_SMARTS = 2, SMARTS_MODE_IS_SMILES = 0, SMARTS_MODE_MASK = 3;
   var Lcom_actelion_research_chem_SmilesParser_2_classLit = createForClass("com.actelion.research.chem", "SmilesParser", 159, Ljava_lang_Object_2_classLit);
   function $clinit_SmilesParser$EnumerationPosition() {
     $clinit_SmilesParser$EnumerationPosition = emptyMethod;
@@ -43482,7 +43485,7 @@ function getExports($wnd) {
         break;
       case 12:
         if (realNeighbours <= 1)
-          queryFeatures = or_0(queryFeatures, or_0(or_0(131072, 1099511627776), 2097152));
+          queryFeatures = or_0(queryFeatures, or_0(or_0(131072, 262144), 2097152));
         else if (realNeighbours <= 3)
           queryFeatures = or_0(queryFeatures, 2097152);
         break;
@@ -71072,7 +71075,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.22.0";
+  toReturn.version = "9.22.1";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -71217,8 +71220,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.22.0
- * @date 2026-03-26T09:27:41.846Z
+ * @version v9.22.1
+ * @date 2026-05-02T08:37:42.417Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */