openchemlib 9.12.1 → 9.14.0

package/dist/openchemlib.d.ts

@@ -2995,6 +2995,7 @@ export interface DepictorOptions {
   suppressChiralText?: boolean;
   suppressCIPParity?: boolean;
   suppressESR?: boolean;
+  noCarbonLabelWithCustomLabel?: boolean;
 
   showSymmetryAny?: boolean;
   showSymmetrySimple?: boolean;

package/dist/openchemlib.debug.js

@@ -1397,6 +1397,13 @@ function extendFromMolfile(Molecule2) {
           }
         }
       }
+      if (line.startsWith("M  ZZC")) {
+        const atom = Number(line.slice(7, 10).trim());
+        const label = line.slice(10).trim();
+        if (atom && label) {
+          molecule.setAtomCustomLabel(atom - 1, label);
+        }
+      }
     }
     changeMolfileCustomLabelPosition(molecule, customLabelPosition);
     return molecule;
@@ -6797,7 +6804,7 @@ function getExports($wnd) {
     this.setColorCode(this.mStandardForegroundColor);
   };
   _.mpDrawAtom = function mpDrawAtom(atom, esrGroupMemberCount) {
-    var angle, atmStart, atomStr, bestSide, bnd, charge, chax, chay, cipStr, counterHindrance, counterSide, eNegNeighbours, esrInfo, esrStr, hHeight, hNoStr, hNoWidth, hindrance, hydrogenWidth, hydrogens, hydrogensToAdd, i, i0, isoStr, j, labelWidth, largeIsoString, mapStr, minHindrance, neighbours, piElectrons, propStr, queryFeatures, ringBonds, theAngle, theColor, unpairedElectrons, valStr, x_0, xdiff, y_0, ydiff;
+    var angle, atmStart, atomStr, bestSide, bnd, charge, chax, chay, cipStr, counterHindrance, counterSide, eNegNeighbours, esrInfo, esrStr, hHeight, hNoStr, hNoWidth, hindrance, hydrogenWidth, hydrogens, hydrogensToAdd, i, i0, isSmallCustomLabel, isSmallCustomLabelOnly, isoStr, j, labelWidth, mapStr, minHindrance, neighbours, piElectrons, propStr, queryFeatures, ringBonds, theAngle, theColor, unpairedElectrons, valStr, x_0, xdiff, y_0, ydiff;
     if (!this.mIsValidatingView)
       this.onDrawAtom(atom, this.mMol.getAtomLabel_0(atom), this.getAtomX_0(atom), this.getAtomY_0(atom));
     propStr = null;
@@ -7016,12 +7023,14 @@ function getExports($wnd) {
           hydrogensToAdd = this.mMol.getImplicitHydrogens_1(atom);
       }
     }
-    largeIsoString = false;
+    isSmallCustomLabelOnly = false;
+    isSmallCustomLabel = false;
     atomStr = this.mMol.getAtomCustomLabel_0(atom);
     if (jsNotEquals(atomStr, null) && jl.startsWith_Ljava_lang_String__Z__devirtual$(atomStr, "]")) {
+      isSmallCustomLabelOnly = jsEquals(isoStr, null);
+      isSmallCustomLabel = true;
       isoStr = this.append(jl.substring_I_Ljava_lang_String___devirtual$(atomStr, 1), isoStr);
       atomStr = null;
-      largeIsoString = true;
     }
     if (jsNotEquals(atomStr, null)) {
       hydrogensToAdd = 0;
@@ -7036,7 +7045,7 @@ function getExports($wnd) {
       atomStr = "?";
       if (neq(and_0(this.mMol.getAtomQueryFeatures(atom), 2048), 0))
         hydrogensToAdd = -1;
-    } else if (this.mMol.getAtomicNo_0(atom) != 6 || jsNotEquals(propStr, null) || jsNotEquals(isoStr, null) || hydrogensToAdd > 0 || !this.mAtomIsConnected[atom])
+    } else if (this.mMol.getAtomicNo_0(atom) != 6 || jsNotEquals(propStr, null) || jsNotEquals(isoStr, null) && (!isSmallCustomLabelOnly || (this.mDisplayMode & 256) == 0) || hydrogensToAdd > 0 || !this.mAtomIsConnected[atom])
       atomStr = this.mMol.getAtomLabel_0(atom);
     labelWidth = 0;
     if (!this.mMol.isSelectedAtom_0(atom) & this.mMol.isExcludeGroupAtom(atom))
@@ -7057,7 +7066,7 @@ function getExports($wnd) {
     if ((this.mDisplayMode & 2) != 0)
       isoStr = jl.valueOf_18(atom);
     if (jsNotEquals(isoStr, null)) {
-      if (largeIsoString)
+      if (isSmallCustomLabel)
         this.mpSetReducedLabelSize();
       else
         this.mpSetSmallLabelSize();
@@ -8059,6 +8068,7 @@ function getExports($wnd) {
   carc2.cDModeBondNo = 4;
   carc2.cDModeDrawBondsInGray = 16384;
   carc2.cDModeHiliteAllQueryFeatures = 8;
+  carc2.cDModeNoCarbonLabelWithCustomLabel = 256;
   carc2.cDModeNoColorOnESRAndCIP = 4096;
   carc2.cDModeNoImplicitAtomLabelColors = 1024;
   carc2.cDModeNoImplicitHydrogen = 8192;
@@ -27683,7 +27693,7 @@ function getExports($wnd) {
     this.parse_8(mol, smiles, position, endIndex, true, true);
   };
   _.parse_8 = function parse_9(mol, smiles, position, endIndex, createCoordinates, readStereoFeatures) {
-    var a1, a2, allowSmarts, atom, atom0, atomMass, atomParser, baseAtom, bond, bondQueryFeatures, bondType, bondTypePosition, bracketLevel, compatibleValenceFound, ep, excludedBonds, explicitHydrogen, fromAtom, handleHydrogenAtomMap, hasBondType, hasLeadingBracket, hydrogenCount, i, i0, inventor, isDoubleDigit, newSize, number, oldSize, parity, parity$iterator, parityMap, rca, rca$array, rca$index, rca$max, ringClosureAtom, ringClosureBondQueryFeatures, ringClosureBondType, ringClosurePosition, squareBracketOpen, theChar, usedValence, valence, valence$array, valence$index, valence$max, valences;
+    var a1, a2, allowSmarts, atom, atom0, atomMass, atomParser, baseAtom, bond, bondQueryFeatures, bondType, bondTypePosition, bracketLevel, compatibleValenceFound, ep, excludedBonds, explicitHydrogen, fromAtom, handleHydrogenAtomMap, hasBondType, hasLeadingBracket, hydrogenCount, i, i0, i1, i2, inventor, isDoubleDigit, newSize, number, oldSize, parity, parity$iterator, parityMap, ringClosureAtom, ringClosureBondQueryFeatures, ringClosureBondType, ringClosurePosition, squareBracketOpen, theChar, usedValence, valence, valence$array, valence$index, valence$max, valences;
     this.smiles = smiles;
     this.mMol = mol;
     this.mMol.clear_0();
@@ -27892,8 +27902,8 @@ function getExports($wnd) {
             ringClosurePosition = ju.copyOf_9(ringClosurePosition, newSize);
             ringClosureBondType = ju.copyOf_9(ringClosureBondType, newSize);
             ringClosureBondQueryFeatures = ju.copyOf_9(ringClosureBondQueryFeatures, newSize);
-            for (i = oldSize; i < newSize; i++)
-              ringClosureAtom[i] = -1;
+            for (i1 = oldSize; i1 < newSize; i1++)
+              ringClosureAtom[i1] = -1;
           }
           if (ringClosureAtom[number] == -1) {
             ringClosureAtom[number] = baseAtom[bracketLevel];
@@ -27973,12 +27983,10 @@ function getExports($wnd) {
       throw toJs(new jl.Exception_1("SmilesParser: unexpected character outside brackets: '" + charToString(theChar) + "' position:" + (position - 1)));
     }
     if (bondType != 1)
-      throw toJs(new jl.Exception_1("SmilesParser: dangling open bond"));
-    for (rca$array = ringClosureAtom, rca$index = 0, rca$max = rca$array.length; rca$index < rca$max; ++rca$index) {
-      rca = rca$array[rca$index];
-      if (rca != -1)
-        throw toJs(new jl.Exception_1("SmilesParser: dangling ring closure."));
-    }
+      throw toJs(new jl.Exception_1("SmilesParser: dangling open bond; position:" + position));
+    for (i2 = 0; i2 < ringClosureAtom.length; i2++)
+      if (ringClosureAtom[i2] != -1)
+        throw toJs(new jl.Exception_1("SmilesParser: dangling ring closure: " + i2 + "; position:" + position));
     handleHydrogenAtomMap = this.mMol.getHandleHydrogenMap_0();
     this.mMol.setHydrogenProtection_0(true);
     this.mMol.ensureHelperArrays_0(1);
@@ -28083,7 +28091,7 @@ function getExports($wnd) {
     return jsEquals(smiles, null) ? null : this.parseReaction_1(jl.getBytes_Ljava_nio_charset_Charset___B__devirtual$(smiles, (jnc.$clinit_StandardCharsets(), jnc.UTF_8)));
   };
   _.parseReaction_1 = function parseReaction_0(smiles) {
-    var closingGroupBracketIndex, end, i, index_0, index1, index2, level, mol, molend, part, rxn;
+    var i, index_0, index1, index2, level, mol, molEnd, molStart, part, rxn;
     index1 = caru.indexOf_2(smiles, narrow_byte(62));
     while (index1 > 0 && smiles[index1 - 1] == narrow_byte(45))
       index1 = caru.indexOf_3(smiles, narrow_byte(62), index1 + 1);
@@ -28097,37 +28105,36 @@ function getExports($wnd) {
     rxn = new carcr.Reaction();
     part = 0;
     index_0 = 0;
-    closingGroupBracketIndex = -1;
     while (index_0 < smiles.length) {
       while (index_0 < smiles.length && smiles[index_0] == 46)
         index_0++;
-      if (smiles[index_0] == 40) {
-        if (closingGroupBracketIndex != -1)
-          throw toJs(new jl.Exception_1("Second open group bracket found before closing first one."));
-        index_0++;
-        level = 0;
-        for (i = index_0; i < smiles.length; i++) {
-          if (smiles[i] == 40) {
-            level++;
-          } else if (smiles[i] == 41) {
-            if (level-- == 0) {
-              closingGroupBracketIndex = i;
-              break;
-            }
+      if (index_0 == smiles.length)
+        break;
+      molStart = index_0;
+      molEnd = -1;
+      level = 0;
+      for (i = index_0; i < smiles.length; i++) {
+        if (smiles[i] == 40) {
+          level++;
+          continue;
+        }
+        if (smiles[i] == 41) {
+          if (--level < 0)
+            throw toJs(new jl.Exception_1("Found closing bracket without matching opening one."));
+          continue;
+        }
+        if (level == 0) {
+          if (smiles[i] == 46 && (this.mSingleDotSeparator || i + 1 < smiles.length && smiles[i + 1] == 46) || smiles[i] == 62 && (i == 0 || smiles[i - 1] != 45)) {
+            molEnd = i;
+            break;
           }
         }
       }
-      end = index_0;
-      while (end < smiles.length && smiles[end] != 62 && !(smiles[end] == 46 && (this.mSingleDotSeparator && closingGroupBracketIndex == -1 || closingGroupBracketIndex == end - 1 || end + 1 == smiles.length || smiles[end + 1] == 46)))
-        end++;
-      molend = end;
-      if (closingGroupBracketIndex == end - 1) {
-        molend--;
-        closingGroupBracketIndex = -1;
-      }
-      if (index_0 != molend) {
+      if (molEnd == -1)
+        molEnd = smiles.length;
+      if (molStart < molEnd) {
         mol = new carc2.StereoMolecule();
-        this.parse_7(mol, smiles, index_0, molend);
+        this.parse_7(mol, smiles, molStart, molEnd);
         if (this.mSmartsMode == 1 && this.mSmartsFeatureFound)
           return new carc2.SmilesParser_0(this.mMode | 2).parseReaction_1(smiles);
         if (part == 0)
@@ -28137,7 +28144,7 @@ function getExports($wnd) {
         else
           rxn.addProduct_0(mol);
       }
-      index_0 = end;
+      index_0 = molEnd;
       while (index_0 < smiles.length && smiles[index_0] == 62) {
         index_0++;
         part++;
@@ -30294,6 +30301,7 @@ function getExports($wnd) {
     var atom;
     if (isNull(mol))
       mol = this.mMol.getCompactCopy_0();
+    mol.invalidateHelperArrays_0(248);
     for (atom = 0; atom < mol.getAllAtoms_0(); atom++)
       mol.getAtomCoordinates_0(atom).set_1(this.mCoordinates[atom]);
     if (jsNotEquals(this.mName, null))
@@ -39721,7 +39729,7 @@ function getExports($wnd) {
         mapNo0 = reactant.getAtomMapNo_0(j);
         if (mapNo0 != 0) {
           if (mapNoInReactant[mapNo0])
-            throw toJs(new jl.Exception_1("Duplicate mapping no in reactants"));
+            throw toJs(new jl.Exception_1("Duplicate mapping no in reactants: " + mapNo0));
           mapNoInReactant[mapNo0] = true;
         }
       }
@@ -39733,7 +39741,7 @@ function getExports($wnd) {
         mapNo0 = product.getAtomMapNo_0(j);
         if (mapNo0 != 0) {
           if (mapNoInProduct[mapNo0])
-            throw toJs(new jl.Exception_1("Duplicate mapping no in products"));
+            throw toJs(new jl.Exception_1("Duplicate mapping no in products: " + mapNo0));
           mapNoInProduct[mapNo0] = true;
         }
       }
@@ -51328,6 +51336,8 @@ function getExports($wnd) {
       displayMode |= 64;
     if (options.suppressESR)
       displayMode |= 128;
+    if (options.noCarbonLabelWithCustomLabel)
+      displayMode |= 256;
     if (options.showSymmetryAny)
       displayMode |= 768;
     if (options.showSymmetrySimple)
@@ -71252,7 +71262,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.12.1";
+  toReturn.version = "9.14.0";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -71396,8 +71406,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.12.1
- * @date 2025-10-22T07:23:31.337Z
+ * @version v9.14.0
+ * @date 2025-10-29T09:34:22.062Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */