CHANGELOG.md

Bio changelog

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.