@datagrok/peptides 1.27.8 → 1.27.10

package/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Peptides changelog
 
+## 1.27.10 (2026-07-08)
+
+### Features
+
+* Peptide Generation: New viewer that designs new candidate peptides from monomer-position statistics using an additive positional model, ranked by predicted activity (High/Low target) with per-peptide statistical support and novelty flags. Reuses the SAR viewers'/model's cached statistics when available, reacts to the dataframe filter, applies empirical-Bayes shrinkage to damp low-support noise, and carries an info icon explaining the model and its caveats. Appends per-position "basis" columns that render each chosen monomer (colored from the monomer library, width-fitted) with an effect circle (size = per-row-normalized effect magnitude, color = direction × significance: red raises, blue lowers, pale ≈ weak, grey = untestable) and the signed contribution value, with Most-Potent-Residues-style activity-distribution tooltips that explain the encoding. A header "+" button opens the generated peptides as a standalone table view, flattening the basis columns to "monomer, contribution, p-value" text. Not added to SAR analysis by default — add it manually from the viewers menu.
+
+* Moved the Peptides Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright
 ## 1.27.4 - 1.27.7 (2026-03-20)
 
 ### Features

package/CLAUDE.md

@@ -80,6 +80,7 @@ Key types:
 | `mutation-cliffs-viewer.ts` | `MutationCliffsViewer` | Line chart of mutation cliffs at a selected position. Splits by series column, syncs selection with main dataframe |
 | `cluster-max-activity-viewer.ts` | `ClusterMaxActivityViewer` | Scatter plot: cluster size vs max activity per cluster. Draws threshold lines, supports auto-selection of top quadrants |
 | `position-statistics-viewer.ts` | `SequencePositionStatsViewer` | Box/violin plot of numerical values grouped by monomers at a selected position. Configurable motif overhang |
+| `peptide-generation-viewer.ts` | `PeptideGenerationViewer` | **Optional, not added by default.** De novo peptide generator. Reuses `calculateMonomerPositionStatistics` (sharing the SAR viewers'/model's cached stats when they match) and an additive positional (Free-Wilson-style) model with empirical-Bayes shrinkage to synthesize new candidate peptides via bounded beam search, ranked by predicted activity (High/Low). Each row reports predicted activity, confidence, min support, mean p-value, significant positions and novelty. Appends per-position **basis columns** custom-rendered via `onCellRender` (library-colored width-fitted monomer + effect circle whose size = per-row-normalized effect magnitude and color = direction × significance (red raises / blue lowers, pale = weak, grey = untestable) + signed contribution number) with `showTooltip` activity-distribution tooltips that explain the encoding, mirroring Most Potent Residues. Builds sequences with `seqHandler.joiner` + `StringListSeqSplitted` + `getNewColumnFromList` |
 
 ### Export Features (context menu on Sequence Variability Map / Most Potent Residues)
 

package/CREDITS.md

@@ -0,0 +1,74 @@
+# Peptides — Third-Party Libraries
+
+The `@datagrok/peptides` package is distributed under the MIT license that
+covers the rest of the `public/` repository (see
+[`../../LICENSE.md`](../../LICENSE.md)). It incorporates the open-source
+components listed below; this file reproduces the attribution and notices
+required by their respective licenses.
+
+All runtime dependencies bundled into the published artifact are under
+permissive licenses (MIT). No copyleft (GPL/LGPL/MPL) component is bundled
+into the published Peptides plugin.
+
+---
+
+## 1. Bundled in the published artifact (`dist/`)
+
+### uuid (10.x)
+
+RFC-compliant UUID generation, used to assign stable identifiers to
+clusters / mutation-cliff records and to namespace viewer settings.
+
+- Upstream: https://github.com/uuidjs/uuid
+- License: **MIT**
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2010-2020 Robert Kieffer and other contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+```
+
+---
+
+## 2. Linked at runtime via the Datagrok platform (webpack externals)
+
+These libraries are not bundled into Peptides' `dist/` — they are provided
+once by the platform host and shared across all packages.
+
+| Component | Version | License | Upstream                                |
+|-----------|---------|---------|-----------------------------------------|
+| cash-dom  | 8.x     | MIT     | https://github.com/fabiospampinato/cash |
+| RxJS      | 6.x     | Apache-2.0 | https://github.com/ReactiveX/rxjs    |
+| wu.js     | 2.x     | MIT     | https://github.com/fitzgen/wu.js        |
+
+---
+
+## 3. Fetched at runtime from third-party CDNs (not bundled)
+
+None.
+
+---
+
+## 4. Docker container images (`dockerfiles/`)
+
+None.
+
+---
+
+## 5. Development-only dependencies
+
+Tools used during the build/test cycle (not in the runtime tree, not bundled):
+the `datagrok-tools` CLI, the TypeScript / webpack toolchain, and `file-loader`
+(MIT, *Copyright JS Foundation and other contributors*) used by webpack at
+build time only. The peer/devDependencies on other Datagrok plugins
+(`@datagrok/bio`, `@datagrok/chem`, `@datagrok/dendrogram`, `@datagrok/eda`,
+`@datagrok/helm`) and on `@datagrok-libraries/helm-web-editor` /
+`@datagrok-libraries/js-draw-lite` are MIT — covered by the repo-wide
+`LICENSE.md`. These are **not** redistributed as part of the published
+Peptides plugin and impose no obligation on users of the plugin.