Bio changelog

v.next

• Manage Monomers: Rebuilt the monomer editor with u2: each R group is a choice of the 15 common cap groups (H, OH, Allyl, Br, Cl, Alkyne, Azide, I, F, NH2, Me, Ac, OMe, SH, Et) read from the library definition however it is written, with what the cap is beside it and its four fields behind a pencil; Save stays at the bottom and its tooltip says why it is disabled; dialogs offer CANCEL
• Manage Monomers: Fixed the copilot's monomer details leaving out the cap SMILES of every library monomer
• Manage Monomers: Fixed Fix All turning every nested meta value (monomer colors included) into text; it now says how many monomers it fixed
• Manage Monomers: The editor fits narrow screens (captions go above inputs), and Save/Add follows the chosen polymer type
• Manage Monomers: The CSV export's Capped Molecule, the monomer details and the natural-analog suggestion close each R group with its actual cap (OMe, Ac, Azide, ...), not its name in brackets, which was no molecule
• Manage Monomers: Switching or creating a library clears the editor, a new library name gets its .json, meta values keep their types on save, the editor shows the colors the grid draws and writes them only when changed, and a closed editor panel comes back with Add or Edit
• public#4226: Menu: Similarity Search, Diversity Search, Composition, Convert Sequence Notation, Compare sequences, MSA, Apply Numbering Scheme, Manage Annotations, Scan Liabilities and Subsequence Search are disabled until the current table has a macromolecule column, and Activity Cliffs, Sequence Space and Extract Region unless the current view is such a table, instead of failing or warning
• Manage Monomers: Fixed an error logged when the monomer table reloads within half a second of a save (the scroll to the saved monomer ran on the replaced table)
• WebLogo: Counts each sequence once per render instead of once per position, and averages, sums, minima and maxima of the value column directly (100,000 sequences: 3.5 s to open and 11.5 s with a value column before)
• Apply Numbering Scheme: Applies results row by row without keeping every row's parsed map and cells, and writes per-row annotations with one change event (100,000 rows crashed the tab); the same single event for Scan Liabilities
• Apply Numbering Scheme, MSA: An engine's description shows its first sentence, the rest in the tooltip
• WebLogo: Fixed the position width becoming infinite when the viewer first renders with no positions (data still loading), which left the slider collapsed at 0 until dragged; a saved infinite or zero width falls back to the default
• MSA: A long engine description wraps instead of widening the dialog
• Apply Numbering Scheme: An engine from another package (e.g. HMM's ANARCI) is the default when installed; the built-in immunum stays available as the fallback
• Apply Numbering Scheme: Fixed an engine with options (HMM's ANARCI) offering only IMGT when the dialog was opened again
• WebLogo: Added the Profile property: draws a sequence profile supplied by another package (functions with meta.role: webLogoProfile, e.g. HMM's profile HMM logos) with the viewer's own layout, scrolling and colors; when the column is aligned to the profile, clicking a letter selects the rows that have it there (in @datagrok-libraries/bio)
• Annotations: Moved the annotation storage helpers (annotation-manager.ts) to @datagrok-libraries/bio so other packages write annotations the same way; Bio re-exports them
• Tests: The BDD features no longer repeat what the package tests cover (project round trips, notation permutations, renderer checks); the MSA dialog's engine switch on a HELM column is claimed again (it contacts no container)
• Demo: Fixed Similarity, Diversity clustering the next demo's table ("Could not resolve column sequence") when that one opened within a second
• GROK-21049: Activity Cliffs: Fixed the "Column already exists" error when run alongside another embedding analysis
• Demo: Fixed Similarity, Diversity returning before its layout was applied, which then landed on whatever view was open next
• Tests: Added package tests for Scan Liabilities (rule hits and positions, the annotation and count columns), Similarity against another row and a shorter or longer reference (GROK-20963), Sequence Space and Activity Cliffs on HELM and MSA, an antibody numbering's project round trip and an MSA column of multi-letter monomers converted to HELM; the BDD features keep the dialogs and leave these numbers to the tests, and the project round-trip tests delete their projects

2.28.4 (2026-09-29)

• MSA header: Numbered positions by the column's position names on the ruler and in the WebLogo tooltip, so a region extracted from a numbered aligned column (Extract Region, or Extract CDR3 from the cell menu) keeps the scheme's numbering, e.g. CDR3 from 105 instead of 1 (in @datagrok-libraries/bio)

• MSA header: Fixed long columns sometimes left without the header: it now repaints once installed, shows on a column wider than the view, and a new column no longer shrinks the shared header height; a scrolled-away header no longer blocks clicks on other columns' headers (in @datagrok-libraries/bio)

• Tests: Added render/msa-header.feature — both chains get the header, and CDR3 extracted either way is ruled from 105; the header reports its tracks, ruler names and positions through the grid's status

• Manage Monomer Libraries: Deleting a library removes its file first, so its row leaves the list as soon as the file is gone instead of after a settings save and a reload of every library

• Similarity scoring: Fixed blank scores for sequences whose length differs from the reference's; the score covers the reference's positions, as identity does (in @datagrok-libraries/bio)

• Tests: BDD suite closed its gaps against the TestTrack cases and the old Playwright specs: HELM and MSA runs of Analyze and Convert, the empty current row (GROK-16111), Molecules to HELM, the FASTA file handler and exporter, project round-trips, monomer library CRUD, BILN rendering; every feature states what it does not translate

• Fixed sequence and monomer context panels staying on the previous cell when a grid cell is clicked within two seconds of expanding a section (core grid fix).

• Tests: Atomic-level conversion selects the standard HELM library so custom monomers on the stand cannot change the fixture's chemistry, and restores the previous selection afterwards.

• Tests: Monomer library uploads support stands with only Files storage as well as stands with multiple storage providers.

• Fixed WebAssembly asset URLs in package workers so sequence-space clustering loads the DBSCAN binary from the published package.

• Tests: Added the package's Gherkin features under bdd/ (analyze, transform, calculate, search, annotate, top menu, service surface, monomer libraries and collections, cell renderers and cell actions) on @datagrok-libraries/bdd

• Tests: Kept the sequence helper in the page in the init step (returned to Node it serialized the RDKit heap, ten seconds per feature) and listed each top-menu group's commands in one walk

• Monomer libraries: Fired the bio-monomer-lib-loaded custom event after every library load and awaited the library update before reporting the load complete

• Monomer Collections: Named the cards for automation and marked the selected ones with aria-selected

• Diversity Search: Fixed the "importScripts failed to load" errors of the distance-matrix workers spawned beyond the job's size and terminated mid-load (in @datagrok-libraries/ml)

• WebLogo, Similarity Search, Diversity Search: Exposed widget status (hit areas and readings), a render-pending flag and a rendered event for automation

• Subsequence Search: Fixed the filter dropping keystrokes typed while a search was applied

• Manage Annotations: Named the annotation list, its rows and the delete icon

• Registered getHelmMonomers under its plain name and gave Match with Monomer Library its dialog title

• Extract Region: Fixed disabled Start/End position selectors for columns without region annotations

• AI: Exposed AI view functions on the monomer-management views — Manage Monomer Libraries (activate/deactivate, delete, merge, resolve duplicates), Manage Monomers (browse, edit-form fill/save, delete, create library), and Monomer Collections (list, create, update, delete).

• To Atomic Level panel: Added scrollable windowed structure view for long linear single-chain sequences — shows a 20-monomer window with a slider and 1-based start/end position indicators

• Flow: Added table-aware twins of the Bio | Transform entries, which mutate the input frame and return void (or hand the same frame back) — unusable on a pipeline canvas, where the node shows a bare pass-through arrow instead of a named result: Extract Sequence Region, To Atomic Level Column, Molecules to HELM Column, and Split to Monomers Columns (which returns the per-position monomer columns as a table of their own). All share the original implementation

• Flow: Added Convert Sequence Notation (table, sequence, targetNotation{fasta,separator,helm}, separator?) -> column, wrapping ISeqHandler.convert(). Notation conversion previously existed only behind a dialog

• Flow: Added Tag as Macromolecule (table, sequence) -> column, which runs sequence detection on a plain string column. Nothing could tag a column built inside a flow, so every semType-dependent bio function silently no-opped on derived data

• Flow: Added Motif Search (table, sequence, motif) -> dataframe, returning the matching rows; reuses linearSubstructureSearch

• Flow: Added Apply Antibody Numbering (table, sequence, scheme{imgt,kabat}), the canonical non-interactive entry point — it applies the annotations and the aligned column to the table. immunumAntibodyNumbering is the ENGINE, and its DataFrame of position maps and annotation JSON is dialog plumbing, not a pipeline result

• Scripts: Renamed the sequence generator function to Generate Sequences. Its previous name camelized to SequenceGenerator, colliding with the sibling sequence_generator (a script with no #name: falls back to its filename), so the real generator was pushed to a server-assigned SequenceGenerator_1 while the parameterless doc entity held the name callers reach for — including the generated package-api.ts

2.28.3 (2026-07-12)

• Docker: Cleared reported CVEs — added apt upgrade for base-image OS packages (also inherits the patched datagrok/python base)
• GROK-18695: PepSeA Docker: raised security floors for the web stack (fastapi/starlette/h11/uvicorn/gunicorn/ujson/certifi/urllib3/requests/idna/pydantic/numpy) over the pinned PepSeA requirements (VEX)
• Moved the Bio Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright
• GROK-19794: MSA dialog: Fixed misaligned Alignment Parameters gap inputs (now share the dialog form's label alignment and width)

2.28.2 (2026-06-22)

• Migrated to the standalone HELM Web Editor (@datagrok-libraries/hwe), replacing the legacy helm-web-editor / js-draw-lite dependencies; fixed HELM substructure filter editor sizing.
• Fixed monomer library not fully resetting on reload — stale SMILES-to-monomer cache is now cleared so updated libraries take effect immediately.
• To Atomic Level widget: molecule size is now configurable via column tags, with a clearer message when the monomer limit is exceeded.

2.27.15 (2026-06-10)

• Support complex entities in linear translation workflow, like, multiple linkers, conjugates, multi-phosphates, etc.

2.27.11 (2026-05-15)

• Sequence Space / Sequence Activity Cliffs editors: bail with a clear error when no current table or Macromolecule column is available (prevents NullError in DimReductionBaseEditor)
• HELMCore monomer library: assigned chemistry-keyed colors to RNA sugars, linkers, and conjugates.

2.27.4 (2026-04-29)

• Support for non canonical RNA and correct splitting in helm

2.27.0 (2026-04-09)

• Engine based MSA

2.26.5 (2026-04-01)

Features

• Added monomer canonicalization support

Bug Fixes

• GROK-19928: Sequence space and Activity cliffs now correctly save and restore in datasync projects

2.26.4 (2026-03-20)

Features

• Liabilities: Added separator support
• Sequence Difference Renderer: Added support for custom notations
• Added draggable sequence column header
• Improved explicit notation conversion and detection
• Added sequence column input with region cutting

Bug Fixes

• VD Regions viewer no longer shows errors
• Custom difference columns are now correctly restored
• Tag pickup for datasync projects now works correctly

2.26.0 (2026-03-04)

• Antibodies support: Numbering schemes, highlighting, allignment, liabilities detection, extracting regions, and more.

2.25.15 (2026-02-26)

• Monomer collections
• Handling edge cases of r groups in monomer libraries
• Fixing some issues with custom notation provider

2.25.12 (2026-02-20)

• Isotope support in monomers
• More R group validation and auto fixing
• Support for custom notation provider from-helm converter

2.25.11 (2026-02-18)

• Support for complex R-groups in monomer libraries, like allyls and others

2.25.10 (2026-02-17)

• Softer detectors for provider specific notations
• HELM workflow for custom providers

2.25.9 (2025-12-02)

• Fix Substructure filter for datasync

2.25.2 (2025-11-03)

• Update Bio Lib API
• Sequence header: Enable for shorter and non-MSA sequences
• Monomer manager: Chech both capped and uncapped monomers when matching mols with libraries, provide multiple sources for matching
• Mol-To-Helm converter: Add initial version of Molecules to sequence converter

2.25.1 (2025-10-30)

• Rework User lib settings storage to accomodate shortened duplicate preferences
• Detectors: Improve BILN with SMILES/CHEMS detection
• Support BILN with SMILES/CHEMS rendering, conversion and Helm converter
• Monomer libraries: Fix dialogs for adding/removing libraries

2.25.0 (2025-10-29)

• CHEMS and SMILES support in HELM

2.24.0 (2025-10-28)

• Monomer library management rework: Transition to library providers, instead of single file based monomer libraries. Support multiple library providers.
• NB! BREAKING CHANGE to the monomer library management API. Update your code accordingly.

2.23.2 (2025-10-17)

• Fix Helm converter to support multi type polymers

2.23.1 (2025-10-16)

• Monomer Cell: Support polymer type source
• Support multy polymer type helm
• Speedup Monomer lib loading

2.23.0 (2025-10-03)

• Full BILN support: conversion to/from HELM/separator/fasta/molecular form, parsing, rendering, monomer library handling.

2.22.12 (2025-09-30)

• Match with Monomer Library tool
• Fix monomer lib loading for tests
• Converter improvements

2.22.2 (2025-06-11)

• Harmonized options for Similarity/Diversity viewers
• Force detection of macromolecules for arbitrary columns

2.22.0 (2025-06-03)

• MSA header tracks (Conseration and WebLogo)
• Tooltips for WebLogo header
• Speedup calculations for conservation and weblogo, corrected limits

2.21.11 (2025-05-29)

• Add faster methods for getting monomers at given positions

2.21.10 (2025-05-22)

• Fix all monomers script
• Optional Sequence scrolling header for short sequences

2.21.9 (2025-05-15)

• Correct scrolling header alignment with sequences.
• Correct detection of max length sequence
• Better display of current position
• Fix keyboard navigation for sequence position scroller

2.21.7 (2025-05-14)

• Enable Header scrolling for non-MSA

2.21.6 (2025-05-14)

• Sequence position scrolling header

2.21.5 (2025-05-12)

• Shifted sequence rendering support

2.21.4 (2025-05-12)

• Support monomer renderer in viewers

2.21.3 (2025-05-01)

• Similarity search viewer: Fix for clearing selection
• Substructure filter: Corrected even management for setting separator

2.21.2 (2025-04-28)

Monomer Manager:

• Style fixes
• Calculations of missing monomer properties when saving/loading monomer libraries
• Date column fixes
• Null meta fixes

2.21.1 (2025-04-22)

• Weblogo: Fix behavior, correct fitting, reaction to slider, property harmonization
• Better formatting of source monomer lib name
• Support of sequence space for custom notation

2.21.0 (2025-04-14)

• Move separator refinement to seq-handler stage
• Add support for custom notation macromolecule difference rendering

2.20.5 (2025-04-14)

• Non blocking behavior of OCL mol converter

2.20.4 (2025-04-08)

• Fix linearization, wrong rgroups and notation problems for toAtomicLevel

2.20.2 (2025-03-31)

• Detectors: more sensitive for very likely column names
• Add to atomic level panel widget

2.20.1 (2025-03-29)

• Improve Activity cliffs demo
• Fix Sim/Div viewers

2.19.0 (2025-02-20)

• Correct conversion and highlighting of toAtomicLevel
• Added context actions

2.18.4 (2025-02-17)

• ToAtomicLevel support for DNA/RNA
• Monomer manager: Fix correcting R-group lines

2.18.3 (2025-02-10)

Correct molblock conversion in monomer library extraction

2.18.2 (2025-01-22)

Improve grid cell renderer

2.18.1 (2024-12-30)

• Removed dependency from Helm package
• Moved substructure filter types to bio library
• Updated tests

2.17.6 (2024-12-11)

• Add monomer manager app view with library dashboards
• Improve detectors

2.17.5 (2024-12-09)

Monomer manager: Correct loading.

2.17.3 (2024-11-27)

Monomer managers as apps

2.17.2 (2024-11-19)

• Support Sequence renderer resizing

2.17.1 (2024-11-15)

• Fix Tests
• Fix Fix monomer manager styles
• Fix Monomer manager incorrect loading
• Add R-groups validations

2.17.0 (2024-11-06)

Cell renderer: Harmonize macromolecule renderers

2.16.9 (2024-11-01)

Correct package initialization

2.16.8 (2024-10-31)

Bug fixes

• Fix SeqHandler check for custom notation
• Fix SeqHandler adding splitter, getHelm, isCustom

2.16.7 (2024-10-30)

Bug fixes

• Fix splitterAsHelm for multiple simple polymers, add test

2.16.6 (2024-10-22)

Bug fixes

• Fix toAtomicLevel using pseudo molfile with removed gaps
• Fix toAtomicLevel Helm parser to clean symbols square brackets
• Fix toAtomicLevel using column's overridden monomer lib
• Fix OverriddenMonomerLibrary for added monomers as not missed
• Fix SeqHandler getValue of type MacromoleculeValueBase
• Fix monomerLibraries override test

2.16.5 (2024-10-18)

Bug fixes

• WebLogo: fix compatibility with column types and fix aggregations
• Monomer manager: Fix validations

Features

Monomer manager: Add new empty monomer

2.16.4 (2024-10-16)

Bug fixes

• Fix helm parser for separate simple polymers, add tests
• Fix adding MonomerPlacer lengths tests
• Fix monomer lib getTooltip for gaps

2.16.3 (2024-10-15)

Bug fixes

• Fix weblogo slider not visible

2.16.2 (2024-10-11)

Bug fixes

• Fix moving setUnits methods to SeqHelper

2.16.1 (2024-10-11)

Bug fixes

• GROK-16782: Fix bio-substructure-filters tests

2.16.0 (2024-10-10)

New features

• Add SeqHandler factory to SeqHelper

Bug fixes

• Fix monomer lib loading timout
• Fix natural nucleotides' colors
• Fix SeqHandler.getHelm to return SemanticValue
• Fix moving harmonized sequence notation provider to Helm

2.15.13 (2024-10-08)

Monomer manager: Fix Molv2k Rgroup line generation

2.15.12 (2024-10-07)

Fix weblogo colors

2.15.11 (2024-10-04)

Monomer renderer: Choose correct colors for background

2.15.10 (2024-10-04)

Monomer manager: Better discoverabilty of errors.

2.15.9 (2024-10-03)

New features

• Add monomer lib getMonomerTextColor

Bug fixes

• Fix sample monomer Aca colors
• Fix Difference, Monomer renderers to use getMonomerTextColor
• Fix MacromoleculeCustomCellRenderer console error on onMouseLeave

2.15.8 (2024-10-02)

New features

• Add use monomer lib colors for Monomer Difference Macromolecule
• Add use monomer lib colors fpr WebLogoViewer

Bug fixes

• Fix test splitters.splitToMonomers for default monomer lib
• Fix monomer lib colors for natural monomers
• Fix monomer colors for empty monomer lib

2.15.7 (2024-10-02)

Adjust monomer colors for very 'white' colors.

2.15.6 (2024-09-27)

Bug fixes

• Fix detectMacromolecule forbidding monomers '2,...', add test
• Fix using IMonomerLibHelper.loadMonomerLibForTests
• Fix cell renderer to reset reference sequence on reset current row
• GROK-16699: Fix PepSeA container return meaningful error messages, unskip test
• Fix test data monomers add aG, azG
• Fix unskip toAtomicLevel tests depending on HelmHelper
• Fix detectMacromolecule for harmonized sequences, add test

2.15.5 (2024-09-25)

New features

• Add custom notation, fix tests
• Add overriding monomer library for toAtomicLevel

Bug fixes

• Fix skipping tests depending on new Helm

2.15.4 (2024-09-24)

New features

• Add monomer hover handling for substruct
• Add highlight param for toAtomicLevel
• Add HelmHelper parse and removeGaps methods
• Add naturalMonomerColors for monomers of MonomerLib
• Add MonomerLib.getWebEditorMonomer (for color)
• Add function Identity for Add new Column

Bug fixes

• Fix toAtomicLevel for sequences with gaps
• Fix ISeqSplitted remove .canonicals and .originals
• Fix toAtomicLevel tests for linear with gaps

2.15.3 (2024-09-22)

Add monomer background coloring

2.15.2 (2024-09-18)

Add monomer coloring for fasta/separator from monomer library

2.15.1 (2024-09-10)

Bug fixes

• Fix benchmark tests to sync calls
• Bump dependencies versions

2.15.0 (2024-09-04)

Monomer manager

Features

• Add getHelm for Cyclized notation provider
• Add detector for Dimerized notation provider
• Add Monomer library manager view with duplicate preferences
• Add Monomer manager for editing/adding/removing monomers
• Add monomer lib for PolyTool rules

Bug fixes

• Fix tests benchmark
• Fix typo Needleman-Wunsch
• Fix test flapping benchmark separatorDnaShorts50Few50
• Fix toAtomicLevel workers error DG is not defined
• Fix biosubstructure filter
• Fix SeqHandler.getHelm lost cycles, add tests
• Fix SeqlHelper.helmToAtomicLevel to work without table

2.14.3 (2024-08-27)

Bug fixes

• Order Top menu
• Fix to Atomic Level hide highlight column
• Fix to Atomic Level for column
• Bump dependencies version, fix tests

2.14.2 (2024-08-23)

Features

• Add highlighting monomer at atomic level

Bug fixes

• Add tests for toAtomicLevel UI
• Fix demo Helm, MSA, Sequence Space viewer adding

2.14.1 (2024-08-14)

Fix monomer substitution matrix calculation

2.14.0 (2024-08-06)

Features

• Add loading monomer sets from .json files

Bug fixes

• Fix cell renderer dirty flag and reset

2.13.8 (2024-08-08)

• Downgrade API version

2.13.7 (2024-08-08)

• Adjust monomer max lengths for monomer renderer

2.13.6 (2024-07-29)

• SequenceChemSimilarity: warning in case reference monomer not found in monomer library

2.13.5 (2024-07-23)

Bug fixes

• Fix tests for Helm package init wait
• Add detectMacromolecule tests for fasta single char unknown alphabet
• Fix detectMacromolecule checkBadMultichar wo RegExp and fail early
• Fix use allowUnionTypes to allow union types in JSON schema
• GROK-15793: Fix Calculate Identity, Similarity error Index out of bounds
• Add progress indicator for loading monomer libraries
• Fix detectMacromolecule to reject FASTA with numeric monomer

2.13.4 (2024-07-02)

Bug fixes

• GROK-15798: Fix To Atomic Level for units FASTA, UN alphabet
• Fix detectMacromolecule to check for bad monomers on separator
• Fix for review camelCase properties

2.13.3 (2024-06-28)

Bug fixes

• Fix MaxMonomerLength package setting, and column setting
• Fix loading monomer libs for explicit stuck from tests

2.13.2 (2024-06-26)

Features

• Add package settings for MonomerWidthMode

Bug fixes

• Fix cell renderer for long mode
• Fix Cell Renderer column widget for MonomerWidthMode
• Enable package settings editor widget

2.13.1 (2024-06-25)

Bump dependencies versions JSDraw.Lite and HELMWebEditor

2.13.0 (2024-06-24)

Bug fixes

• PolyTool: files moved to SequenceTranslator
• GROK-15994: Bio: Color missing monomers
• Use types from js-draw-lite, helm-web-editor
• Fix error on access to MaxMonomerLength package settings
• Fix getMonomer for PolymerType unspecified as any
• Fix monomer lib validation
• GROK-15995: Colors for libraries monomers
• Fix error on open Manage Monomer Libraries
• Fix WebLogo in a column header tooltip

2.12.23 (2024-05-30)

Bug fixes

• to Atomic level: fix the issue with isotopes

2.12.22 (2024-05-28)

Bug fixes

• GROK-15525: MSA: Add check unsuitable data to avoid running MSA with them
• GROK-15796: Bio: Fix cell renderer for convert to Helm
• GROK-15798: Bio: Fix To Atomic Level for units FASTA and alphabet UN
• Fix converter MSA to fasta invalid tags, fix tests

2.12.21 (2024-05-20)

Fix cell renderer for column width changed

2.12.20 (2024-05-16)

Bug fixes

• Fix monomer tooltip layout
• Fix monomer name for gaps and any monomer

2.12.19 (2024-05-16)

Bug fixes

• Fix tests cell renderer monomer placer for default monomer lib
• Add tests for monomer placer hitBounds
• Fix cell renderer to limit for visible monomers
• Fix MacromoleculeColumnWidget to limit WebLogo for visible
• Fix WebLogo to limit seq splitting on end position specified
• GROK-15678: Bio: Fix bio-substructure-filter tests on Helm
• GROK-15293: Fix MSA Dialog error while picking empty value in Sequence

2.12.18 (2024-05-13)

Bug fixes

Bio: Fix MonomerLibManager composition with files and events Bio: Unveil cell renderer errors for tests

2.12.17 (2024-05-01)

Features

• Add MonomerLib.getSummary
• Use Pistoia typization

Bug fixes

• Fix rendering on grid and without (row tooltip, scatter plot)

2.12.16 (2024-04-25)

Bio: Fix crushing substructure filter.

2.12.15 (2024-04-19)

Bio: Some optimization in Polytool

2.12.14 (2024-04-18)

Bio: Fixed stereochemistry in Polytool

2.12.13 (2024-04-15)

Bio: Fix cell renderer for scatter plot, add test

2.12.12 (2024-04-15)

Features

• Polytool: working with molV3000

2.12.11 (2024-04-12)

Features

• Add displaying a monomer's origin lib

Bug fixes

• Fix the cell-renderer tooltip not showing a hovered monomer

2.12.10 (2024-04-11)

Bug fixes

• Bio: Fix detector for non-fasta seqs of the same length

2.12.9 (2024-04-10)

Bug fixes

• Fix SDF to JSON for Biovia lib

2.12.8 (2024-04-09)

Features

• To atomic level: STEABS block contains less than 80 symbols per row

2.12.7 (2024-04-08)

Features

• Ability to link monomers in molV3000 format

2.12.6 (2024-04-07)

Bug fixes

• Fix detectMacromolecule to invalidate on custom notation

2.12.5 (2024-04-05)

Features

• Add KNN computation on webGPU for UMAP (sequence space).

2.12.4 (2024-04-05)

Features

• Add support for custom notations, splitters
• Add notation provider, splitter for cyclized macromolecules

Bug fixes

• Fix cell renderer for original and tooltip with canonical
• Fix WebLogo for positions out of seq length

2.12.3 (2024-04-03)

Updated version of openchemlib in dependencies

2.12.2 (2024-04-03)

Harmonized MM distance function with monomer similarity matrices.

2.12.1 (2024-04-02)

Bug fixes

• Fix bioSubstructureFilter with two columns
• Fix bioSubstructureFilter error on filters reopen
• GROK-15292: Fix bioSubstructureFilter for reset

2.12.0 (2024-03-30)

Features

• #2707: Add original and canonical to monomer

2.11.42 (2024-03-27)

Bug fixes

• Fix MacromoleculeColumnWidget error with WebLogo disabled
• Fix WebLogo for GAP_SYMBOL
• Fix CompositionAnalysisWidget for gaps

2.11.41 (2024-03-26)

Features

• Polytool: ability to use special engine to create molV3000 with CFG flags in the atoms block

2.11.40 (2024-03-22)

Features

• Polytool rules file handling

2.11.39 (2024-03-11)

Bug fixes

• GROK-15150: Fix display hidden/showed inputs

2.11.38 (2024-03-08)

Bug fixes

• GROK-14910: PepSeA verbose output
• MSA ensures docker container for PepSeA
• Sample files harmonized

2.11.37 (2024-03-08)

Bug fixes

• Check Bio publishing, PepSeA docker

2.11.36 (2024-02-28)

Bug fixes

• GROK-15086: Fix GetRegion, Notation: result column does not render

2.11.35 (2024-02-26)

Features

• #2706: Polytool: init rule based generation

2.11.34 (2024-02-20)

Bug fixes

• Downgrade datagrok-api dependency version to 1.17.4

2.11.32 (2024-02-20)

Bug fixes

• GROK-11982: Bio: Fix duplicates WebLogo on layout, test
• GROK-11983: Bio: Fix duplicates WebLogo on project, test

2.11.31 (2024-02-19)

Features

• GROK-14230: Bio: Add basic UI for monomer lib files adding / validation

2.11.30 (2024-02-15)

Features

• GROK-14598: Bio: Substructure filter sync between cloned views, tests

Bug fixes

• GROK-14916: Bio: Fix biosubstructure filter for sequences of Helm
• GROK-14913: Bio: Fix To Atomic Level for sequences with gaps, tests

2.11.28 (2024-02-07)

Features

Bug fixes

• Fix detectMacromolecule allowing double quoted sequences and gaps.
• Fix for min seq length 10, tests.
• Fix user library settings for tests
• Fix test substructureFilter/helm
• Fix README images, GIFs size

2.11.0 (2023-10-25)

Features

• Add VdRegionsViewer filterSource property.
• Add ToAtomicLevel for non-linear HELM structures.
• Add WebLogo aggregation function.
• Add WebLogo position tooltip with composition table (for count).
• Add PolyTool with Helm2Molfile support

Bug fixes

• Fix GetRegion to detect semantic type and renderer for created column.
• Fix GetRegion dialog column name field for default value.
• Fix WebLogo viewer for gaps with Helm.
• Fix cell renderer for empty values MSA.
• Fix detectMacromolecule to ignore empty seqs.
• Add property fitWidth for VdRegionsViewer.
• Fix VdRegionsViewer fit width accounting position margin of WebLogo.
• Fix similarity/diversity viewer tests.
• Fix reset filters for Substructure Search filter.
• Fix Macromolecule cell renderer width limit for devicePixelRatio less than 1.
• Fix VdRegionsViewer positionHeight transmit to enclosed WebLogo.
• Fix added by Split to monomers columns to be not used as a filter.
• Fix WebLogo with filterSource of Selection to work from project.
• Fix WebLogo with filterSource of Selection display all in case of empty selection.
• Fix VdRegionsViewer for initial filterSource.
• Fix Macromolecule cell render to skip on closed grid.
• Fix WebLogoViewer for empty column (annotated).
• Fix WebLogoViewer and VdRegionsViewer deadlock.
• Fix Activity Cliffs error on Helm dataset
• Fix Macromolecule tooltip, context widget for detach
• Fix WebLogo optimize with postponed update positions
• Fix error in bioSubstructureFilter for Helm

2.10.0 (2023-09-06)

Features

• GetRegion for Macromolecule:
  • Added dialog Top menu Bio | Convert | GetRegion.
  • Added maintaining .positionNames tag for GetRegion derived column.
  • Added using .regions tag annotation for GetRegion dialog.

Bug fixes

• Fixed UnitsHandler.posList length.
• Fixed mistyping top menu path for Identity scoring.
• Fixed Get Region missed in short top menu.
• Fixed tests detectMacromoleculeBenchmark to specify test failed.

2.9.0 (2023-08-30)

Features

• WebLogo: add property showPositionLabels.
• WebLogo: optimized with splitterAsFastaSimple.
• WebLogo: disable userEditable for fixWidth.
• VdRegionsViewer: optimized preventing rebuild on positionWidth changed and resize.
• VdRegionsViewer: to fit WebLogo enclosed on positionWidth of value 0.
• Introduced sequence identity and similarity scoring.

Bug fixes

• Fix vdRegionsViewer viewer package function name consistency.
• GROK-13310: Bio | Tools: Fix Split to monomers for multiple runs.
• GROK-12675: Bio | Tools: Fix the Composition dialog error on the selection column.
• Allow characters '(', ')', ',', '-', '_' in monomer names for fasta splitter.
• WebLogo: Fix horizontal alignment to the left while `fixWidth``.
• WebLogo: Fix layout for fixWidth, fitArea, and normal modes.
• VdRegionsViewer: Fix postponed rendering for tests.
• MacromoleculeDifferenceCellRenderer: Fix to not use UnitsHandler.

2.8.2 (2023-08-01)

This release focuses on improving the monomer cell renderer.

Dependency: datagrok-api >= 1.13.3

Features

• Added sample datasets for natural and synthetic peptide sequences.
• Added sample dataset for cyclic sequences with HELM notation.

Bug fixes

• GROK-13659: Bio | Tools: Fix MaxMonomerLength for Macromolecule cell renderer.

2.8.1 (2023-07-24)

This release focuses on improving the monomer cell renderer.

Dependency: datagrok-api >= 1.13.3

Features

• Monomer cell renderer now defaults to 6 characters per monomer.

2.8.0 (2023-07-21)

This release focuses on improving feature stability and usability.

Dependency: datgarok-api >= 1.13.3

Features

• Add Copy group to Macromolecule cell context menu.
• Add DefaultSeparator package property settings.

Bug Fixes

• Fix VdRegionsViewer filter source checkbox tooltip, workaround.

2.7.2 (2023-07-21)

This release focuses on improvements and bug fixes.

Dependency: datagarok-api >= 1.13.3

Features

• Set default values in all dialogs where appropriate.
• Detected Helm monomer type for separator data and made it usable for MSA.
• Added alignment options to Kalign.
• Added separator support for Sequence Space and Activity Cliffs.
• Tooltip: shows monomer atomic structure for macromolecules.
• For macromolecule cells, added the ability to show composition ratios in the property panel.
• Top menu: organized the items into groups SAR, Structure, Atomic level, and Search.

Bug Fixes

• GROK-13048: Activity cliffs identification for macromolecules.