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Bio changelog

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.