openchemlib 9.11.1 → 9.12.1

package/dist/openchemlib.d.ts

@@ -3363,6 +3363,47 @@ export declare class SDFileParser {
   getField(name: string): string;
 }
 
+export interface SSSearcherOptions {
+  /**
+   * @default false
+   */
+  matchAtomCharge?: boolean;
+  /**
+   * @default false
+   */
+  matchAtomMass?: boolean;
+  /**
+   * @default false
+   */
+  matchDBondToDelocalized?: boolean;
+  /**
+   * @default true
+   */
+  matchAromDBondToDelocalized?: boolean;
+}
+
+export type SSSearcherCountMode =
+  | 'existence'
+  | 'firstMatch'
+  | 'separated'
+  | 'overlapping'
+  | 'rigorous'
+  | 'unique';
+
+export interface SSSearcherFindFragmentInMoleculeOptions {
+  /**
+   * Count mode.
+   * overlapping: create list not containing multiple matches sharing exactly the same atoms
+   * existence: check only, don't create matchList
+   * firstMatch: create matchList with just one match
+   * separated: create list of all non-overlapping matches / not optimized for maximum match count
+   * rigorous: create list of all possible matches neglecting any symmetries
+   * unique: create list of all distinguishable matches considering symmetries
+   * @default overlapping
+   */
+  countMode: SSSearcherCountMode;
+}
+
 /**
  * Basic substructure searcher.
  */
@@ -3370,7 +3411,7 @@ export declare class SSSearcher {
   /**
    * Creates a new substructure searcher.
    */
-  constructor();
+  constructor(options?: SSSearcherOptions);
 
   /**
    * Set the `fragment` to search.
@@ -3396,6 +3437,30 @@ export declare class SSSearcher {
    * Returns whether the current fragment is in the target molecule.
    */
   isFragmentInMolecule(): boolean;
+
+  /**
+   * Locates all matches of the fragment in the molecule that result in distinguishable
+   * sets of molecule atoms. Multiple matches involving the same atoms, e.g. with a benzene ring,
+   * are counted and listed only once. If count mode is different from 'existence',
+   * then an atom mapping from fragment to molecule is collected and can be retrieved with getMatchList().
+   * @param options
+   * @returns count of sub-structure matches of fragment in molecule
+   */
+  findFragmentInMolecule(
+    options?: SSSearcherFindFragmentInMoleculeOptions,
+  ): number;
+
+  /**
+   * If the match count mode is one of 'firstMatch', 'overlapping',
+   * 'rigorous' then this method returns an array of all counted matches,
+   * i.e. int arrays mapping fragment atoms to molecule atoms. Atoms being part of a
+   * matched bridge bond are naturally not covered by the mapping. Atoms being part of a
+   * matching bridge bond are available with getBridgeBondAtomList().
+   * Note: If some query fragment atoms are marked as exclude group, then the respective
+   * matchlist values are -1.
+   * @returns list of distinct counted matches.
+   */
+  getMatchList(): number[][];
 }
 
 /**

package/dist/openchemlib.debug.js

@@ -1369,7 +1369,8 @@ function extendFromMolfile(Molecule2) {
   Molecule2.fromMolfile = function fromMolfile(molfile, options = {}) {
     const { customLabelPosition } = options;
     const molecule = _fromMolfile.call(this, molfile);
-    const lines = molfile.split("\n");
+    const eol = molfile.includes("\r\n") ? "\r\n" : "\n";
+    const lines = molfile.split(eol);
     if (lines.length < 4 || !lines[3].includes("V2000")) {
       return molecule;
     }
@@ -1426,7 +1427,8 @@ function extendToMolfile(Molecule2) {
     if (!includeCustomAtomLabelsAsALines && !includeCustomAtomLabelsAsVLines && !removeCustomAtomLabels) {
       return molfile;
     }
-    let lines = molfile.split("\n");
+    const eol = molfile.includes("\r\n") ? "\r\n" : "\n";
+    let lines = molfile.split(eol);
     if (removeCustomAtomLabels) {
       lines = lines.filter(
         (line) => !CUSTOM_ATOMS_LABELS_TAGS.some((tag) => line.startsWith(tag))
@@ -1453,7 +1455,7 @@ function extendToMolfile(Molecule2) {
       return molfile;
     }
     lines.splice(mEndIndex, 0, ...newLines);
-    return lines.join("\n");
+    return lines.join(eol);
   };
 }
 
@@ -14710,8 +14712,8 @@ function getExports($wnd) {
   carc2.$clinit_Element$1 = function $clinit_Element$1() {
     carc2.$clinit_Element$1 = emptyMethod;
   };
-  defineClass(817, 1, { 1: 1, 36: 1 });
-  cggl.Lcom_actelion_research_chem_Element$1_2_classLit = createForClass("com.actelion.research.chem", "Element/1", 817, cggl.Ljava_lang_Object_2_classLit);
+  defineClass(811, 1, { 1: 1, 36: 1 });
+  cggl.Lcom_actelion_research_chem_Element$1_2_classLit = createForClass("com.actelion.research.chem", "Element/1", 811, cggl.Ljava_lang_Object_2_classLit);
   carc2.$clinit_ExtendedDepictor = function $clinit_ExtendedDepictor() {
     carc2.$clinit_ExtendedDepictor = emptyMethod;
     jl.$clinit_Object();
@@ -24284,7 +24286,7 @@ function getExports($wnd) {
     }
     return carc2.tbl;
   };
-  defineClass(495, 1, { 1: 1 }, carc2.PeriodicTable);
+  defineClass(494, 1, { 1: 1 }, carc2.PeriodicTable);
   _.$init_41 = function $init_41() {
   };
   _.toString_0 = function toString_10() {
@@ -24305,7 +24307,7 @@ function getExports($wnd) {
   carc2.Silicon = 14;
   carc2.Sulfur = 16;
   carc2.Uranium = 92;
-  cggl.Lcom_actelion_research_chem_PeriodicTable_2_classLit = createForClass("com.actelion.research.chem", "PeriodicTable", 495, cggl.Ljava_lang_Object_2_classLit);
+  cggl.Lcom_actelion_research_chem_PeriodicTable_2_classLit = createForClass("com.actelion.research.chem", "PeriodicTable", 494, cggl.Ljava_lang_Object_2_classLit);
   carc2.$clinit_RingCollection = function $clinit_RingCollection() {
     carc2.$clinit_RingCollection = emptyMethod;
     jl.$clinit_Object();
@@ -25405,10 +25407,10 @@ function getExports($wnd) {
     }
     return true;
   };
-  _.findFragmentInMolecule = function findFragmentInMolecule(countMode, matchMode) {
-    return this.findFragmentInMolecule_0(countMode, matchMode, null);
+  _.findFragmentInMolecule_0 = function findFragmentInMolecule(countMode, matchMode) {
+    return this.findFragmentInMolecule_1(countMode, matchMode, null);
   };
-  _.findFragmentInMolecule_0 = function findFragmentInMolecule_0(countMode, matchMode, atomExcluded) {
+  _.findFragmentInMolecule_1 = function findFragmentInMolecule_0(countMode, matchMode, atomExcluded) {
     var atom, atomUsed, candidate, current, excludeGroup, index_0, isExcludedMatch, maxIndex;
     this.mStop = false;
     this.mMatchList = new ju.ArrayList();
@@ -25687,7 +25689,7 @@ function getExports($wnd) {
       queryDefaults |= 4194304;
     return queryDefaults;
   };
-  _.getMatchList = function getMatchList() {
+  _.getMatchList_0 = function getMatchList() {
     return this.mMatchList;
   };
   _.getSortedMatch = function getSortedMatch(match_0) {
@@ -25829,10 +25831,10 @@ function getExports($wnd) {
     return false;
   };
   _.isFragmentInMolecule_0 = function isFragmentInMolecule() {
-    return this.findFragmentInMolecule(1, this.mDefaultMatchMode) > 0;
+    return this.findFragmentInMolecule_0(1, this.mDefaultMatchMode) > 0;
   };
   _.isFragmentInMolecule_1 = function isFragmentInMolecule_0(matchMode) {
-    return this.findFragmentInMolecule(1, matchMode) > 0;
+    return this.findFragmentInMolecule_0(1, matchMode) > 0;
   };
   _.isListMember = function isListMember(atomicNo, list) {
     var i;
@@ -26268,10 +26270,10 @@ function getExports($wnd) {
     }
     return index_0;
   };
-  _.findFragmentInMolecule = function findFragmentInMolecule_1(countMode, matchMode) {
-    return this.findFragmentInMolecule_0(countMode, matchMode, null);
+  _.findFragmentInMolecule_0 = function findFragmentInMolecule_1(countMode, matchMode) {
+    return this.findFragmentInMolecule_1(countMode, matchMode, null);
   };
-  _.findFragmentInMolecule_0 = function findFragmentInMolecule_2(countMode, matchMode, atomExcluded) {
+  _.findFragmentInMolecule_1 = function findFragmentInMolecule_2(countMode, matchMode, atomExcluded) {
     var i;
     if (jsNotEquals(this.mMoleculeIndexLong, null)) {
       for (i = 0; i < this.mMoleculeIndexLong.length; i++)
@@ -26290,7 +26292,7 @@ function getExports($wnd) {
       this.mFragment = new carc2.IDCodeParser(false).getCompactMolecule_1(this.mFragmentIDCode);
     this.mSSSearcher.setMolecule_0(this.mMolecule);
     this.mSSSearcher.setFragment_1(this.mFragment);
-    return this.mSSSearcher.findFragmentInMolecule_0(countMode, matchMode, atomExcluded);
+    return this.mSSSearcher.findFragmentInMolecule_1(countMode, matchMode, atomExcluded);
   };
   _.getGraphMatcher = function getGraphMatcher() {
     return this.mSSSearcher;
@@ -33470,12 +33472,12 @@ function getExports($wnd) {
       templateMol = template.getFragment();
       if (useFFP) {
         searcherWithIndex.setFragment_3(templateMol, template.getFFP());
-        if (searcherWithIndex.findFragmentInMolecule(4, 8) != 0)
-          matchList = searcherWithIndex.getGraphMatcher().getMatchList();
+        if (searcherWithIndex.findFragmentInMolecule_0(4, 8) != 0)
+          matchList = searcherWithIndex.getGraphMatcher().getMatchList_0();
       } else {
         searcher.setFragment_1(templateMol);
-        if (searcher.findFragmentInMolecule(4, 8) != 0)
-          matchList = searcher.getMatchList();
+        if (searcher.findFragmentInMolecule_0(4, 8) != 0)
+          matchList = searcher.getMatchList_0();
       }
       if (isNotNull(matchList)) {
         for (match$iterator = matchList.iterator(); match$iterator.hasNext_0(); ) {
@@ -36804,8 +36806,8 @@ function getExports($wnd) {
     }
     return false;
   };
-  defineClass(816, 1, { 1: 1 });
-  cggl.Lcom_actelion_research_chem_forcefield_mmff_type_Angle_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Angle", 816, cggl.Ljava_lang_Object_2_classLit);
+  defineClass(817, 1, { 1: 1 });
+  cggl.Lcom_actelion_research_chem_forcefield_mmff_type_Angle_2_classLit = createForClass("com.actelion.research.chem.forcefield.mmff.type", "Angle", 817, cggl.Ljava_lang_Object_2_classLit);
   carcfmt2.$clinit_Atom_0 = function $clinit_Atom_0() {
     carcfmt2.$clinit_Atom_0 = emptyMethod;
     jl.$clinit_Object();
@@ -38508,8 +38510,8 @@ function getExports($wnd) {
     carcn.$clinit_StructureNameResolver();
     return carcn.sResolver;
   };
-  defineClass(811, 1, { 1: 1 });
-  cggl.Lcom_actelion_research_chem_name_StructureNameResolver_2_classLit = createForClass("com.actelion.research.chem.name", "StructureNameResolver", 811, cggl.Ljava_lang_Object_2_classLit);
+  defineClass(812, 1, { 1: 1 });
+  cggl.Lcom_actelion_research_chem_name_StructureNameResolver_2_classLit = createForClass("com.actelion.research.chem.name", "StructureNameResolver", 812, cggl.Ljava_lang_Object_2_classLit);
   carcp.$clinit_CLogPPredictor = function $clinit_CLogPPredictor() {
     carcp.$clinit_CLogPPredictor = emptyMethod;
     jl.$clinit_Object();
@@ -40847,12 +40849,12 @@ function getExports($wnd) {
     genericReactant = this.mGenericReaction.getReactant_0(no);
     this.mSSSearcher.setMol_0(genericReactant, this.mReactant[no]);
     matchMode = 8 + (this.mAllowChargeCorrections ? 0 : 1);
-    if (this.mSSSearcher.findFragmentInMolecule(5, matchMode) == 0) {
+    if (this.mSSSearcher.findFragmentInMolecule_0(5, matchMode) == 0) {
       setCheck(this.mMatchList, no, new ju.ArrayList());
       this.mReactantMatchCombinationCount = 0;
       return false;
     }
-    setCheck(this.mMatchList, no, this.mSSSearcher.getMatchList());
+    setCheck(this.mMatchList, no, this.mSSSearcher.getMatchList_0());
     for (j = this.mMatchList[no].size() - 1; j >= 0; j--) {
       matchingAtom = castTo(this.mMatchList[no].getAtIndex(j), 6);
       for (k = 0; k < matchingAtom.length; k++) {
@@ -40953,11 +40955,11 @@ function getExports($wnd) {
     this.mTargetMolecule = molecule;
     this.mSSSearcher.setMol_0(this.mReactant, this.mTargetMolecule);
     matchMode = 8;
-    if (this.mSSSearcher.findFragmentInMolecule(countMode, matchMode) == 0) {
+    if (this.mSSSearcher.findFragmentInMolecule_0(countMode, matchMode) == 0) {
       this.mMatchList = null;
       return 0;
     }
-    this.mMatchList = this.mSSSearcher.getMatchList();
+    this.mMatchList = this.mSSSearcher.getMatchList_0();
     for (j = this.mMatchList.size() - 1; j >= 0; j--) {
       matchingAtom = castTo(this.mMatchList.getAtIndex(j), 6);
       for (k = 0; k < matchingAtom.length; k++) {
@@ -41422,12 +41424,12 @@ function getExports($wnd) {
         break;
       reactantSearcher.setFragment_1(rule.getReactant_1());
       reactantSearcher.setFragmentSymmetryConstraints(rule.getReactantAtomSymmetryConstraints());
-      if (0 != reactantSearcher.findFragmentInMolecule(6, 8)) {
+      if (0 != reactantSearcher.findFragmentInMolecule_0(6, 8)) {
         productSearcher.setFragment_1(rule.getProduct_1());
-        if (0 != productSearcher.findFragmentInMolecule(2, 8) && reactantSearcher.getMatchList().size() <= 512) {
+        if (0 != productSearcher.findFragmentInMolecule_0(2, 8) && reactantSearcher.getMatchList_0().size() <= 512) {
           historyScore = -1e4;
-          productMatch = castTo(productSearcher.getMatchList().getAtIndex(0), 6);
-          for (reactantMatch$iterator = reactantSearcher.getMatchList().iterator(); reactantMatch$iterator.hasNext_0(); ) {
+          productMatch = castTo(productSearcher.getMatchList_0().getAtIndex(0), 6);
+          for (reactantMatch$iterator = reactantSearcher.getMatchList_0().iterator(); reactantMatch$iterator.hasNext_0(); ) {
             reactantMatch = castTo(reactantMatch$iterator.next_3(), 6);
             if (ruleApplicationCount++ >= this.mMaxRuleTries)
               break;
@@ -49985,14 +49987,58 @@ function getExports($wnd) {
     cargja.$clinit_JSSSSearcher = emptyMethod;
     jl.$clinit_Object();
   };
-  cargja.JSSSSearcher = function JSSSSearcher() {
+  cargja.JSSSSearcher = function JSSSSearcher(options) {
     cargja.$clinit_JSSSSearcher();
+    var matchMode;
     Object_0.call(this);
     this.$init_182();
+    matchMode = this.getMatchMode(options);
+    this.mMatchMode = matchMode;
+    this.searcher = new carc2.SSSearcher_0(matchMode);
   };
   defineClass(586, 1, { 1: 1 }, cargja.JSSSSearcher);
   _.$init_182 = function $init_182() {
-    this.searcher = new carc2.SSSearcher();
+  };
+  _.findFragmentInMolecule = function findFragmentInMolecule_3(options) {
+    var countMode;
+    countMode = this.getCountMode(options);
+    return this.searcher.findFragmentInMolecule_0(countMode, this.mMatchMode);
+  };
+  _.getCountMode = function getCountMode(options) {
+    options = options || {};
+    var countMode = options.countMode || "overlapping";
+    switch (countMode) {
+      case "overlapping":
+        return 4;
+      case "existence":
+        return 1;
+      case "firstMatch":
+        return 2;
+      case "separated":
+        return 3;
+      case "rigorous":
+        return 5;
+      case "unique":
+        return 6;
+      default:
+        throw new Error("invalid count mode: " + countMode);
+    }
+  };
+  _.getMatchList = function getMatchList_0() {
+    return cargju.convertIntArrayArrayList(this.searcher.getMatchList_0());
+  };
+  _.getMatchMode = function getMatchMode(options) {
+    options = options || {};
+    var matchMode = 0;
+    if (options.matchAtomCharge === true)
+      matchMode |= 1;
+    if (options.matchAtomMass === true)
+      matchMode |= 2;
+    if (options.matchDBondToDelocalized === true)
+      matchMode |= 4;
+    if (options.matchAromDBondToDelocalized === true || options.matchAromDBondToDelocalized === void 0)
+      matchMode |= 8;
+    return matchMode;
   };
   _.isFragmentInMolecule = function isFragmentInMolecule_2() {
     return this.searcher.isFragmentInMolecule_0();
@@ -50007,6 +50053,7 @@ function getExports($wnd) {
   _.setMolecule = function setMolecule_4(molecule) {
     this.searcher.setMolecule_0(molecule.getStereoMolecule());
   };
+  _.mMatchMode = 0;
   cggl.Lcom_actelion_research_gwt_js_api_JSSSSearcher_2_classLit = createForClass("com.actelion.research.gwt.js.api", "JSSSSearcher", 586, cggl.Ljava_lang_Object_2_classLit);
   cargja.$clinit_JSSSSearcherWithIndex = function $clinit_JSSSSearcherWithIndex() {
     cargja.$clinit_JSSSSearcherWithIndex = emptyMethod;
@@ -51218,6 +51265,19 @@ function getExports($wnd) {
     cargju.$clinit_Util = emptyMethod;
     jl.$clinit_Object();
   };
+  cargju.convertIntArray = function convertIntArray(source) {
+    return Array.from(source);
+  };
+  cargju.convertIntArrayArrayList = function convertIntArrayArrayList(list) {
+    cargju.$clinit_Util();
+    var array, i, size_0;
+    size_0 = list.size();
+    array = cargju.newJsArray(size_0);
+    for (i = 0; i < size_0; i++) {
+      cggcc.$set(array, i, cargju.convertIntArray(castTo(list.getAtIndex(i), 6)));
+    }
+    return array;
+  };
   cargju.convertParameterizedStringList = function convertParameterizedStringList(list) {
     cargju.$clinit_Util();
     var array, i, size_0;
@@ -51894,7 +51954,7 @@ function getExports($wnd) {
   cggcc.uncheckedConversion = function uncheckedConversion(elapsed) {
     return elapsed;
   };
-  defineClass(494, 1, { 1: 1 }, cggcc.Duration);
+  defineClass(495, 1, { 1: 1 }, cggcc.Duration);
   _.$init_212 = function $init_212() {
     this.start_0 = cggcc.currentTimeMillis();
   };
@@ -51902,7 +51962,7 @@ function getExports($wnd) {
     return cggcc.uncheckedConversion(cggcc.currentTimeMillis() - this.start_0);
   };
   _.start_0 = 0;
-  cggl.Lcom_google_gwt_core_client_Duration_2_classLit = createForClass("com.google.gwt.core.client", "Duration", 494, cggl.Ljava_lang_Object_2_classLit);
+  cggl.Lcom_google_gwt_core_client_Duration_2_classLit = createForClass("com.google.gwt.core.client", "Duration", 495, cggl.Ljava_lang_Object_2_classLit);
   cggcc.$clinit_Scheduler$ScheduledCommand = function $clinit_Scheduler$ScheduledCommand() {
     cggcc.$clinit_Scheduler$ScheduledCommand = emptyMethod;
   };
@@ -54886,11 +54946,11 @@ function getExports($wnd) {
   ji.$clinit_BufferedWriter = function $clinit_BufferedWriter() {
     ji.$clinit_BufferedWriter = emptyMethod;
   };
-  defineClass(813, 442, { 1: 1 });
+  defineClass(814, 442, { 1: 1 });
   _.newLine = function newLine() {
     ocu.throwUnimplemented();
   };
-  cggl.Ljava_io_BufferedWriter_2_classLit = createForClass("java.io", "BufferedWriter", 813, cggl.Ljava_io_Writer_2_classLit);
+  cggl.Ljava_io_BufferedWriter_2_classLit = createForClass("java.io", "BufferedWriter", 814, cggl.Ljava_io_Writer_2_classLit);
   ji.$clinit_File = function $clinit_File() {
     ji.$clinit_File = emptyMethod;
   };
@@ -58716,9 +58776,9 @@ function getExports($wnd) {
     jm.$clinit_Multiplication();
     return add_20(add_20(mul_0(and_0(fromInt_0(a), 4294967295), and_0(fromInt_0(b), 4294967295)), and_0(fromInt_0(c), 4294967295)), and_0(fromInt_0(d), 4294967295));
   };
-  defineClass(812, 1, { 1: 1 });
+  defineClass(813, 1, { 1: 1 });
   jm.whenUseKaratsuba = 63;
-  cggl.Ljava_math_Multiplication_2_classLit = createForClass("java.math", "Multiplication", 812, cggl.Ljava_lang_Object_2_classLit);
+  cggl.Ljava_math_Multiplication_2_classLit = createForClass("java.math", "Multiplication", 813, cggl.Ljava_lang_Object_2_classLit);
   jm.$clinit_RoundingMode = function $clinit_RoundingMode() {
     jm.$clinit_RoundingMode = emptyMethod;
     jl.$clinit_Enum();
@@ -61921,8 +61981,8 @@ function getExports($wnd) {
     ju.$clinit_InternalJsMapFactory();
     return new ju.jsMapCtor();
   };
-  defineClass(815, 1, { 1: 1 });
-  cggl.Ljava_util_InternalJsMapFactory_2_classLit = createForClass("java.util", "InternalJsMapFactory", 815, cggl.Ljava_lang_Object_2_classLit);
+  defineClass(816, 1, { 1: 1 });
+  cggl.Ljava_util_InternalJsMapFactory_2_classLit = createForClass("java.util", "InternalJsMapFactory", 816, cggl.Ljava_lang_Object_2_classLit);
   ju.$clinit_InternalStringMap = function $clinit_InternalStringMap() {
     ju.$clinit_InternalStringMap = emptyMethod;
     jl.$clinit_Object();
@@ -65750,8 +65810,8 @@ function getExports($wnd) {
     ocu.$clinit_JSException();
     ocu.throwError_0("unimplemented");
   };
-  defineClass(814, 1, { 1: 1 });
-  cggl.Lorg_cheminfo_utils_JSException_2_classLit = createForClass("org.cheminfo.utils", "JSException", 814, cggl.Ljava_lang_Object_2_classLit);
+  defineClass(815, 1, { 1: 1 });
+  cggl.Lorg_cheminfo_utils_JSException_2_classLit = createForClass("org.cheminfo.utils", "JSException", 815, cggl.Ljava_lang_Object_2_classLit);
   ocu.$clinit_PlainJSObject = function $clinit_PlainJSObject() {
     ocu.$clinit_PlainJSObject = emptyMethod;
     cggcc.$clinit_JavaScriptObject();
@@ -71192,7 +71252,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.11.1";
+  toReturn.version = "9.12.1";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -71336,8 +71396,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.11.1
- * @date 2025-10-14T12:21:23.561Z
+ * @version v9.12.1
+ * @date 2025-10-22T07:23:31.337Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */