CHANGELOG.md

Bio changelog

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.md 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.