@datagrok/peptides 1.16.0 → 1.17.1

package/.eslintrc.json

@@ -10,12 +10,15 @@
   "parserOptions": {
     "ecmaVersion": 12,
     "sourceType": "module",
-    "project": ["tsconfig.json"]
+    "project": [
+      "tsconfig.json"
+    ]
   },
   "plugins": [
     "@typescript-eslint"
   ],
   "rules": {
+    "require-jsdoc": "off",
     "indent": [
       "error",
       2
@@ -25,9 +28,13 @@
       120
     ],
     "no-unused-vars": "off",
-    "@typescript-eslint/no-unused-vars": ["warn", { "varsIgnorePattern": "^_", "argsIgnorePattern": "^_" }],
-    "require-jsdoc": "off",
-    "valid-jsdoc": "off",
+    "@typescript-eslint/no-unused-vars": [
+      "warn",
+      {
+        "varsIgnorePattern": "^_",
+        "argsIgnorePattern": "^_"
+      }
+    ],
     "spaced-comment": "off",
     "linebreak-style": "off",
     "curly": [
@@ -37,10 +44,14 @@
     "brace-style": [
       "error",
       "1tbs",
-      { "allowSingleLine": true }
+      {
+        "allowSingleLine": true
+      }
     ],
     "block-spacing": 2,
-    "@typescript-eslint/explicit-function-return-type": ["error"],
+    "@typescript-eslint/explicit-function-return-type": [
+      "error"
+    ],
     "@typescript-eslint/no-unsafe-return": "error"
   }
 }

package/CHANGELOG.md

@@ -1,17 +1,42 @@
 # Peptides changelog
 
+## 1.17.0 (2023-11-29)
+
+### Features
+
+* Renamed activity column to _Activity_ (previously: _Scaled activity_).
+* Improved input tooltip in the Mutation Cliffs pairs panel.
+* Autosize grids in the Mutation Cliffs pairs panel.
+* Hid sequence space embedding columns and axes selectors.
+* Saving context panels state.
+* Selected cells now have an orange thick border.
+* Distribution panel now shows distribution for (1) all activity values, (2) selected rows, (3) peptides selection from
+  viewers if mismatched with the total selection.
+* Sequence space viewer now uses the Needleman-Wunsch algorithm to compute distances.
+* Linearization of helm format macromolecules before sequence space computation.
+* Improved rendering speed of invariant map (no lags).
+* Improved rendering speed upon selection/filtering.
+
+### Bug Fixes
+
+* Fixed accordion wouldn't update after selection in table view.
+* Filtering dataframe causing most potent residues viewer and context panel to crash.
+* Filtering dataframe causing major lags.
+* Most potent residues viewer crashing on some data.
+* Weblogo viewer crashing or causing major lag on selection/filtering.
+
 ## 1.16.0 (2023-11-05)
 
 ### Features
 
-* Added Select All and Desect All functionality to all viewers.
+* Added Select All and Deselect All functionality to all viewers.
 * Added Mean activity column for the Most Potent Residues viewer.
 * Added Mean activity to tooltips.
-* Added WebLogo to Selection table.
+* Added WebLogo to the Selection table.
 
 ### Bug Fixes
 
-* Fixed Logo Summary Table tooltip wouldn't show if analysis table doesn't contain column names 'Cluster'.
+* Fixed Logo Summary Table tooltip wouldn't show if the analysis table doesn't contain column name 'Cluster'.
 * Fixed tooltips would show irrelevant info.
 
 ## 1.15.3 (2023-10-26)
@@ -36,23 +61,23 @@
 
 ### Bug Fixes
 
-* Fixed Invariant Map color coding wouldn't change when changing color column.
+* Fixed Invariant Map color coding wouldn't change when changing the color column.
 
 ## 1.15.0 (2023-10-12)
 
 ### Features
 
 * Added Sequence Space viewer.
-* Selection panel columns now inherti width from main table.
-* Invarian Map cell values now rendered with contrast color relative to background.
+* Selection panel columns now inherit width from the main table.
+* Invariant Map cell values are now rendered with contrast color relative to the background.
 
 ### Bug Fixes
 
 * Fixed WebLogo in header margin width.
 * Widgets in Context panel will now fill all the available width.
-* Fixed LST rows not resizable.
+* Fixed LST rows are not resizable.
 * Fixed selection inconsistency.
-* Fixed Most Potent Residues keyboar navigation.
+* Fixed Most Potent Residues keyboard navigation.
 * Fixed analysis not starting when there are columns of the same name.
 
 ## 1.14.1 (2023-09-28)

package/README.md

@@ -1,19 +1,23 @@
 # Peptides
 
-Provides advanced tools for analyzing collections of peptides.
-
-Status: Beta
-Owner: Leonid
+Provides sequence-activity relationship analysis for peptides.
 
 ## Detection and usage
 
-Once a dataframe is opened with Datagrok, the column(s) containing peptides are detected automatically. Each amino acid is rendered with a different color, which helps to visually identify patterns. Clicking on the column header brings up the options to launch peptide-specific tools, such as [SAR](#sar) and [Peptide space](#peptides-space).
+Once a dataframe is opened with Datagrok, the column(s) containing peptides are detected automatically. 
+Each amino acid is rendered with a different color, which helps to visually identify patterns. 
+Clicking on the column header brings up the options to launch peptide-specific tools, such as [SAR](#sar) 
+and [Peptide space](#peptides-space).
 
 ## Sar
 
-Wiki: _Structure-Activity Relationship (SAR) is an approach designed to find relationships between chemical structure (or structural-related properties) and biological activity (or target property) of studied compounds._
+Wiki: _Structure-Activity Relationship (SAR) is an approach designed to find relationships between chemical structure
+(or structural-related properties) and biological activity (or target property) of studied compounds._
 
-Peptides SAR is an interactive analysis tool to help identify point mutations that cause large change in activity. Given a `peptide` column with aligned sequences (max length N, number of unique amino acids A) and `activity` column, it produces an N*A dataframe where (n, a) element contains a measure of the change of activity caused by mutating the amino acid at position n to a.
+Peptides SAR is an interactive analysis tool to help identify point mutations that cause large change in
+activity. Given a `peptide` column with aligned sequences (max length N, number of unique amino acids A)
+and `activity` column, it produces an N*A dataframe where (n, a) element contains a measure of the change 
+of activity caused by mutating the amino acid at position n to a.
 
 [Issue tracker](https://github.com/datagrok-ai/public/issues/93)
 
@@ -22,3 +26,4 @@ Peptides SAR is an interactive analysis tool to help identify point mutations th
 Visualizes a collection of peptides in 2-dimensional space, using [t-SNE](https://en.wikipedia.org/wiki/T-distributed_stochastic_neighbor_embedding) with the [edit distance](https://en.wikipedia.org/wiki/Edit_distance) function.
 
 [Issue tracker](https://github.com/datagrok-ai/public/issues/93)
+[Datagrok community: Macromolecules](https://community.datagrok.ai/t/macromolecules-updates/661/1)