npm - @datagrok-libraries/bio - Versions diffs - 5.42.5-master → 5.42.6 - Mend

@datagrok-libraries/bio 5.42.5-master → 5.42.6

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 (5) hide show

package/CHANGELOG.md +7 -1
package/package.json +2 -2
package/src/monomer-works/monomer-utils.d.ts.map +1 -1
package/src/monomer-works/monomer-utils.js +11 -7
package/src/monomer-works/monomer-utils.js.map +1 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,6 +1,12 @@
 # bio changelog
-## 5.42.5 (WIP)
+## 5.42.6 (2024-07-29)
+### Features
+* sequenceChemSimilarity: warning in case reference monomer not found in monomer library
+## 5.42.5 (2024-07-23)
 ### Features

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.5-master",
+  "version": "5.42.6",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -16,7 +16,7 @@
     "@datagrok-libraries/utils": "^4.2.11",
     "@deck.gl/core": "8.8.12",
     "cash-dom": "latest",
-    "datagrok-api": "^1.20.0-master",
+    "datagrok-api": "^1.20.0",
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",

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

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package/src/monomer-works/monomer-utils.js CHANGED Viewed

@@ -146,6 +146,8 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
         const referenceMonomerCanonical = position < referenceSequence.length ?
             referenceSequence.getCanonical(position) : GAP_SYMBOL;
         const referenceMol = monomerLib.getMonomer('PEPTIDE', referenceMonomerCanonical)?.smiles ?? '';
+        if (!referenceMol)
+            grok.shell.warning(`Reference monomer ${referenceMonomerCanonical} not found in monomer library`);
         const monomerCol = positionColumns[position];
         const monomerColData = monomerCol.getRawData();
         const monomerColCategories = monomerCol.categories;
@@ -158,14 +160,16 @@ export async function sequenceChemSimilarity(positionColumns, referenceSequence)
         const _df = DG.DataFrame.fromColumns([molCol]); // getSimilarities expects that column is in dataframe
         const similarityCol = (await grok.chem.getSimilarities(molCol, referenceMol));
         const similarityColData = similarityCol ? similarityCol.getRawData() : null;
-        for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
-            const monomerCategoryIdx = monomerColData[rowIdx];
-            if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
-                totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
+        if (similarityColData) {
+            for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
+                const monomerCategoryIdx = monomerColData[rowIdx];
+                if (referenceMonomerCanonical !== GAP_SYMBOL && monomerCategoryIdx !== emptyCategoryIdx) {
+                    totalSimilarity[rowIdx] += similarityColData[monomerCategoryIdx];
+                }
+                else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
+                    totalSimilarity[rowIdx] += 1;
+                } // Do not increase similarity on mismatch score/penalty equals 0;
             }
-            else if (referenceMonomerCanonical === GAP_SYMBOL && monomerCategoryIdx === emptyCategoryIdx) {
-                totalSimilarity[rowIdx] += 1;
-            } // Do not increase similarity on mismatch score/penalty equals 0;
         }
     }
     for (let similarityIndex = 0; similarityIndex < totalSimilarity.length; ++similarityIndex) {

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

	@@ -1 +1 @@
1	- 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