npm - @datagrok-libraries/bio - Versions diffs - 5.40.2 → 5.40.4 - Mend

@datagrok-libraries/bio 5.40.2 → 5.40.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (11) hide show

package/CHANGELOG.md +13 -0
package/package.json +1 -1
package/src/monomer-works/to-atomic-level-utils.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level-utils.js +27 -0
package/src/monomer-works/to-atomic-level-utils.js.map +1 -1
package/src/monomer-works/to-atomic-level.d.ts +4 -2
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +43 -6
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/monomer-works/types.d.ts +1 -0
package/src/monomer-works/types.d.ts.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,18 @@
 # bio changelog
+## 5.40.4 (2024-04-09)
+### Features
+* Modified STEABS block generation when linking monomers (adding not more than 80 symbols per row)
+## 5.40.3 (2024-04-08)
+### Features
+* Ability to link monomers in molV3000 format
+* Adding STEABS block when linking monomers
 ## 5.40.2 (2024-04-07)
 ### Bug fixes

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.40.2",
+  "version": "5.40.4",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.68",

package/src/monomer-works/to-atomic-level-utils.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AACA,OAAO,EACL,QAAQ,EAAC,MAAM,SAAS,CAAC;AAC3B,OAAO,EAC0B,iBAAiB,EACjD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAC,QAAQ,EAAC,MAAM,+BAA+B,CAAC;AACvD,OAAO,EAAC,WAAW,EAAU,MAAM,UAAU,CAAC;AAG9C;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC1E,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAsBlB;AAED;;;;;qCAKqC;AACrC,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,EACzD,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,GACjD,MAAM,~~CA0ER~~;~~AA+ND~~;;;EAGE;AACF,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}
1	+ {"version":3,"file":"to-atomic-level-utils.d.ts","sourceRoot":"","sources":["to-atomic-level-utils.ts"],"names":[],"mappings":"AACA,OAAO,EACL,QAAQ,EAAC,MAAM,SAAS,CAAC;AAC3B,OAAO,EAC0B,iBAAiB,EACjD,MAAM,gBAAgB,CAAC;AACxB,OAAO,EAAC,QAAQ,EAAC,MAAM,+BAA+B,CAAC;AACvD,OAAO,EAAC,WAAW,EAAU,MAAM,UAAU,CAAC;AAG9C;;;;iHAIiH;AACjH,wBAAgB,sBAAsB,CACpC,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC1E,GAAG,CAAC,MAAM,EAAE,GAAG,CAAC,CAsBlB;AAED;;;;;qCAKqC;AACrC,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,EACzD,QAAQ,EAAE,QAAQ,EAAE,WAAW,EAAE,iBAAiB,GACjD,MAAM,CAkFR;AAqPD;;;EAGE;AACF,wBAAgB,aAAa,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAE/C"}

package/src/monomer-works/to-atomic-level-utils.js CHANGED Viewed

@@ -71,9 +71,14 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
         atomCount: atomCount,
         bondCount: bondCount,
     };
+    const steabsCollection = [];
+    let nAtoms = 0;
     for (v.i = 0; v.i < LC.seqLength; ++v.i) {
         const monomer = monomersDict.get(monomerSeq[v.i]);
         addMonomerToMolblock(monomer, molfileAtomBlock, molfileBondBlock, v, LC);
+        //adding stereo atoms to array for further STEABS block generation
+        monomer.stereoAtoms?.forEach((i) => steabsCollection.push(i + nAtoms));
+        nAtoms += monomer.atoms.x.length;
     }
     capResultingMolblock(molfileAtomBlock, molfileBondBlock, v, LC);
     const molfileCountsLine = C.V3K_BEGIN_COUNTS_LINE + atomCount + ' ' + bondCount + C.V3K_COUNTS_LINE_ENDING;
@@ -91,11 +96,33 @@ export function monomerSeqToMolfile(monomerSeq, monomersDict, alphabet, polymerT
     result += C.V3K_BEGIN_BOND_BLOCK;
     result += molfileBondBlock.join('');
     result += C.V3K_END_BOND_BLOCK;
+    if (steabsCollection.length > 0)
+        result += getCollectionBlock(steabsCollection);
     result += C.V3K_END_CTAB_BLOCK;
     result += C.V3K_END;
     // return molfileParts.join('');
     return result;
 }
+function getCollectionBlock(collection) {
+    //one row in STEABS block can be no longer than 80 symbols
+    //maxSymbols = 80 symbols minus ' -\n' (4 symbols)
+    const maxSymbols = 76;
+    const rowsArray = [];
+    let newCollectionRow = `M  V30 MDLV30/STEABS ATOMS=(${collection.length}`;
+    for (let i = 0; i < collection.length; i++) {
+        const updatedRow = `${newCollectionRow} ${collection[i]}`;
+        if (updatedRow.length > maxSymbols) {
+            rowsArray.push(`${newCollectionRow} -\n`);
+            newCollectionRow = `M  V30 ${collection[i]}`;
+        }
+        else
+            newCollectionRow = updatedRow;
+        //in case last atom was added - close the block
+        if (i === collection.length - 1)
+            rowsArray.push(`${newCollectionRow})\n`);
+    }
+    return `M  V30 BEGIN COLLECTION\n${rowsArray.join('')}M  V30 END COLLECTION\n`;
+}
 /** Cap the resulting (after sewing up all the monomers) molfile with 'O'
  * @param {string[]} molfileAtomBlock - Array of lines of the resulting molfile atom block
  * @param {string[]} molfileBondBlock - Array of lines of the resulting molfile bond block

package/src/monomer-works/to-atomic-level-utils.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/to-atomic-level.d.ts CHANGED Viewed

@@ -42,9 +42,11 @@ export declare function parseBondBlock(molfileV3K: string, bondCount: number): B
 /** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
  * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
  * while R3 is the branching attachment point.
- * @param {string} molfileV2K - V2000 molfile
+ * @param {string} molfile - V2000 or V3000 molfile
  * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
-export declare function parseCapGroupIdxMap(molfileV2K: string): Map<number, number>;
+export declare function parseCapGroupIdxMap(molfile: string): Map<number, number>;
+export declare function parseCapGroupIdxMapV2K(molfileV2K: string): Map<number, number>;
+export declare function parseCapGroupIdxMapV3K(molfileV3K: string): Map<number, number>;
 export declare function parseAtomAndBondCounts(molfileV3K: string): {
     atomCount: number;
     bondCount: number;

package/src/monomer-works/to-atomic-level.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"to-atomic-level.d.ts","sourceRoot":"","sources":["to-atomic-level.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAc,iBAAiB,EAAqB,MAAM,gBAAgB,CAAC;AAClF,OAAO,EAAC,QAAQ,EAAW,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,UAAU,CAAC;AAO9C,OAAO,EAAQ,KAAK,EAAe,QAAQ,EAAwC,MAAM,SAAS,CAAC;AAOnG;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,WAAW,GACnE,OAAO,CAAC;IAAE,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAG,CAAA;CAAE,CAAC,CAsDzD;AAED;;4EAE4E;AAC5E,wBAAgB,wBAAwB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,EAAE,EAAE,CAoBnF;AAGD;;;;;;;qFAOqF;AACrF,wBAAsB,sBAAsB,CAC1C,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC7G,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAsChC;~~AAqID~~;;wDAEwD;AACxD,wBAAgB,cAAc,CAAC,aAAa,EAAE,GAAG,EAAE,GAAG,MAAM,EAAE,CAe7D;AAmGD;;;qCAGqC;AACrC,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,GAAG,MAAM,CAMhF;AAED;;;mCAGmC;AACnC,wBAAgB,cAAc,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,KAAK,CA8C3E;AAED;;;;8EAI8E;AAC9E,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,~~CAyC3E~~;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAcnG;AA6cD,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,QAAQ,GAAG,MAAM,CAmEtE;AAED,wBAAsB,2BAA2B,CAAC,eAAe,EAAE,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAAC,~~CA6BlH~~;AAED;;iCAEiC;AACjC,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,~~CAmB1D~~"}
1	+ {"version":3,"file":"to-atomic-level.d.ts","sourceRoot":"","sources":["to-atomic-level.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAMtC,OAAO,EAAc,iBAAiB,EAAqB,MAAM,gBAAgB,CAAC;AAClF,OAAO,EAAC,QAAQ,EAAW,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAC,WAAW,EAAE,OAAO,EAAC,MAAM,UAAU,CAAC;AAO9C,OAAO,EAAQ,KAAK,EAAe,QAAQ,EAAwC,MAAM,SAAS,CAAC;AAOnG;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,WAAW,GACnE,OAAO,CAAC;IAAE,GAAG,EAAE,EAAE,CAAC,MAAM,GAAG,IAAI,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAG,CAAA;CAAE,CAAC,CAsDzD;AAED;;4EAE4E;AAC5E,wBAAgB,wBAAwB,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,EAAE,EAAE,CAoBnF;AAGD;;;;;;;qFAOqF;AACrF,wBAAsB,sBAAsB,CAC1C,qBAAqB,EAAE,MAAM,EAAE,EAAE,EAAE,UAAU,EAAE,WAAW,EAAE,WAAW,EAAE,iBAAiB,EAAE,QAAQ,EAAE,QAAQ,GAC7G,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAsChC;AAwJD;;wDAEwD;AACxD,wBAAgB,cAAc,CAAC,aAAa,EAAE,GAAG,EAAE,GAAG,MAAM,EAAE,CAe7D;AAmGD;;;qCAGqC;AACrC,wBAAgB,mBAAmB,CAAC,UAAU,EAAE,MAAM,EAAE,WAAW,EAAE,GAAG,GAAG,MAAM,CAMhF;AAED;;;mCAGmC;AACnC,wBAAgB,cAAc,CAAC,UAAU,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,KAAK,CA8C3E;AAED;;;;8EAI8E;AAC9E,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAGxE;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAyC9E;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAc9E;AAED,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,MAAM,GAAG;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,SAAS,EAAE,MAAM,CAAA;CAAE,CAcnG;AA6cD,wBAAgB,2BAA2B,CAAC,QAAQ,EAAE,QAAQ,GAAG,MAAM,CAmEtE;AAED,wBAAsB,2BAA2B,CAAC,eAAe,EAAE,GAAG,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAAC,CA8BlH;AAED;;iCAEiC;AACjC,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAoB1D"}

package/src/monomer-works/to-atomic-level.js CHANGED Viewed

@@ -153,12 +153,15 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
         const libObject = formattedMonomerLib.get(monomerSymbol);
         const capGroups = parseCapGroups(libObject["rgroups" /* HELM_FIELDS.RGROUPS */]);
         const capGroupIdxMap = parseCapGroupIdxMap(libObject["molfile" /* HELM_FIELDS.MOLFILE */]);
-        const molfileV3K = convertMolfileToV3K(removeRGroupLines(libObject["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
+        //in case molfile is molV2000 need to convert it to molV3000
+        const molfileV3K = libObject["molfile" /* HELM_FIELDS.MOLFILE */].includes('V3000') ? libObject["molfile" /* HELM_FIELDS.MOLFILE */] :
+            convertMolfileToV3K(removeRGroupLines(libObject["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
         const counts = parseAtomAndBondCounts(molfileV3K);
         const atoms = parseAtomBlock(molfileV3K, counts.atomCount);
         const bonds = parseBondBlock(molfileV3K, counts.bondCount);
         const meta = getMonomerMetadata(atoms, bonds, capGroups, capGroupIdxMap);
-        const monomerGraph = { atoms: atoms, bonds: bonds, meta: meta };
+        const steabs = getAbsStereocenters(molfileV3K);
+        const monomerGraph = { atoms: atoms, bonds: bonds, meta: meta, stereoAtoms: steabs };
         if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */)
             adjustPeptideMonomerGraph(monomerGraph);
         else { // nucleotides
@@ -175,6 +178,20 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
         return monomerGraph;
     }
 }
+function getAbsStereocenters(molfileV3K) {
+    let collection = [];
+    let indexCollection = molfileV3K.indexOf('M  V30 MDLV30/STEABS ATOMS=('); // V3000 index for collections
+    while (indexCollection !== -1) {
+        indexCollection += 28;
+        const collectionEnd = molfileV3K.indexOf(')', indexCollection);
+        //using slice(1) because first digit in brackets is a number of stereo atoms
+        collection = collection.concat(molfileV3K.substring(indexCollection, collectionEnd).split(' ')
+            .slice(1).map((it) => parseInt(it)));
+        indexCollection = collectionEnd;
+        indexCollection = molfileV3K.indexOf('M  V30 MDLV30/STEABS ATOMS=(', indexCollection);
+    }
+    return collection;
+}
 function setShiftsAndTerminalNodes(polymerType, monomerGraph, monomerSymbol) {
     // remove the 'rightmost' chain-extending r-group node in the backbone
     if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
@@ -384,9 +401,13 @@ export function parseBondBlock(molfileV3K, bondCount) {
 /** Constructs mapping of r-group nodes to default capGroups, all numeration starting from 1.
  * According to https://pubs.acs.org/doi/10.1021/ci3001925, R1 and R2 are the chain extending attachment points,
  * while R3 is the branching attachment point.
- * @param {string} molfileV2K - V2000 molfile
+ * @param {string} molfile - V2000 or V3000 molfile
  * @return {Map<number, number>} - Map of r-group nodes to default capGroups*/
-export function parseCapGroupIdxMap(molfileV2K) {
+export function parseCapGroupIdxMap(molfile) {
+    const isMolV3K = molfile.includes('V3000');
+    return isMolV3K ? parseCapGroupIdxMapV3K(molfile) : parseCapGroupIdxMapV2K(molfile);
+}
+export function parseCapGroupIdxMapV2K(molfileV2K) {
     const capGroupIdxMap = new Map();
     // parse A-lines (RNA)
     let begin = molfileV2K.indexOf(C.V2K_A_LINE, 0);
@@ -424,6 +445,20 @@ export function parseCapGroupIdxMap(molfileV2K) {
     }
     return capGroupIdxMap;
 }
+export function parseCapGroupIdxMapV3K(molfileV3K) {
+    const capGroupIdxMap = new Map();
+    const regex = /M  V30 (\d+) R#.+RGROUPS=\((\d+) (\d+)\).*/gm;
+    let res;
+    while ((res = regex.exec(molfileV3K)) !== null) {
+        // This is necessary to avoid infinite loops with zero-width matches
+        if (res.index === regex.lastIndex) {
+            regex.lastIndex++;
+        }
+        // index 1 matches array is the atom number, index 3 is R group number
+        capGroupIdxMap.set(parseInt(res[1]), parseInt(res[3]));
+    }
+    return capGroupIdxMap;
+}
 export function parseAtomAndBondCounts(molfileV3K) {
     molfileV3K = molfileV3K.replaceAll('\r', ''); // to handle old and new sdf standards
     // parse atom count
@@ -898,7 +933,8 @@ export async function getSymbolToCappedMolfileMap(monomersLibList) {
         const monomerSymbol = monomerLibObject["symbol" /* HELM_FIELDS.SYMBOL */];
         const capGroups = parseCapGroups(monomerLibObject["rgroups" /* HELM_FIELDS.RGROUPS */]);
         const capGroupIdxMap = parseCapGroupIdxMap(monomerLibObject["molfile" /* HELM_FIELDS.MOLFILE */]);
-        const molfileV3K = convertMolfileToV3K(removeRGroupLines(monomerLibObject["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
+        const molfileV3K = monomerLibObject["molfile" /* HELM_FIELDS.MOLFILE */].includes('V3000') ? monomerLibObject["molfile" /* HELM_FIELDS.MOLFILE */] :
+            convertMolfileToV3K(removeRGroupLines(monomerLibObject["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
         const counts = parseAtomAndBondCounts(molfileV3K);
         const atoms = parseAtomBlock(molfileV3K, counts.atomCount);
         const bonds = parseBondBlock(molfileV3K, counts.bondCount);
@@ -918,7 +954,8 @@ export function capPeptideMonomer(monomer) {
     const moduleRdkit = funcList[0].apply();
     const capGroups = parseCapGroups(monomer["rgroups" /* HELM_FIELDS.RGROUPS */]);
     const capGroupIdxMap = parseCapGroupIdxMap(monomer["molfile" /* HELM_FIELDS.MOLFILE */]);
-    const molfileV3K = convertMolfileToV3K(removeRGroupLines(monomer["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
+    const molfileV3K = monomer["molfile" /* HELM_FIELDS.MOLFILE */].includes('V3000') ? monomer["molfile" /* HELM_FIELDS.MOLFILE */] :
+        convertMolfileToV3K(removeRGroupLines(monomer["molfile" /* HELM_FIELDS.MOLFILE */]), moduleRdkit);
     const counts = parseAtomAndBondCounts(molfileV3K);
     const atoms = parseAtomBlock(molfileV3K, counts.atomCount);
     const bonds = parseBondBlock(molfileV3K, counts.bondCount);

package/src/monomer-works/to-atomic-level.js.map CHANGED Viewed

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package/src/monomer-works/types.d.ts CHANGED Viewed

@@ -45,6 +45,7 @@ export type MolGraph = {
     atoms: Atoms;
     bonds: Bonds;
     meta: MonomerMetadata;
+    stereoAtoms?: number[];
 };
 export type Point = {
     x: number;

package/src/monomer-works/types.d.ts.map CHANGED Viewed

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