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Sequence Translator changelog

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  • PolyTool: Enumerate: Fixed Highlight monomers applying unseen: the box was hidden for macromolecules, where its value (restored from the dialog's history) was used, and ignored for templates, where it showed; it now shows whenever To atomic level is on and applies to both
  • PolyTool: Convert, Convert Notation and Enumerate: Removed the Chirality engine option, which no longer did anything (stereo is always absolute). polyToolConvert2 no longer declares chiralityEngine: a caller that passes it is not refused
  • PolyTool: Convert and Enumerate: Added tooltips to the column, Highlight monomers, Keep original, To atomic level, Get HELM, Trivial name and Append to table inputs; Linearize's tooltip says what it does now
  • PolyTool: Convert and Enumerate convert on Chem's macromolecule assembler through Bio, and the cyclized column's hover maps come from the assembler per row (they came from the linear builder even for molecules the non-linear converter built, so they could highlight the wrong atoms); Highlight monomers now takes effect; Convert, Enumerate and the rule previews no longer load RDKit for the conversion
  • PolyTool: parseHelm on Bio's hwe splitter: fixed HELM ending in $$$ failing, a connection resolving its chain by the number of its polymer id (PEPTIDE1 and CHEM1 were the same chain), polymer types other than PEPTIDE, and a } inside brackets cutting the chain

## 1.11.6 (2026-10-30)​

  • Markush Enumerator: Fixed every molecule failing for a core whose R-labels carry a bond, such as a stereo alkene [*:1]/C([*:2])=C(\[*:3])[*:4], and hydrogen R-groups (the template's [H][*:1] or a drawn [H]) joining with the wrong double-bond geometry

  • Markush Enumerator: Fixed R-groups that start with their label ([*:1][C@@H](C)N) coming out as the other enantiomer, and a stereo R-group on a stereo double bond losing or flipping one of the two geometries

  • core#1146: Enumerate: the placeholders validator no longer schedules a second warnings update 100 ms later; Chem enumeration settings fix their popup overflow once attached; the oligo demo fills its inputs as soon as they exist instead of after 500 ms each

  • Markush Enumerator: Edit and Duplicate on a core or an R-group open it in the sketcher (with Crux as the sketcher they opened it empty)

  • Markush Enumerator: Fixed Chem | Transform | Markush Enumeration... failing with a TypeError when the table has no current column yet, as right after it opens

  • core#886: Oligo Translator: Fixed Get SDF failing for HELM input and Copy SMILES copying an invalid value when the sequence has no structure

  • Tests: Added package tests for the Translator (bulk translation, the app's Axolabs sample, a plain RNA HELM, unreadable codes, GROK-20958), Combine Sequences and the oligo converters

  • public#4226: PolyTool: Convert is disabled until the current table has a macromolecule column and Combine Sequences until an open table has one; fixed Enumerate HELM failing when the current view is not a table view

  • GROK-21149: Pattern: Fixed bulk Convert failing with "Column already exists" when run again on the same table

  • GROK-20959: Warn on Save SDF when a strand cannot be converted instead of linking an empty sense molfile

  • GROK-20958: Handle MonomerNotFoundError in Oligo Translator getMolfile so unknown-monomer input refreshes the view instead of throwing

  • GROK-20806: Uniquify Bulk Convert output column name via columns.getUnusedName

  • AI: Exposed AI functions and briefings on the HELM Enumerator dialog and the Markush Enumerator dialog/app — state introspection, macromolecule/placeholder/core/R-group editing, options, and running the enumeration.

  • GROK-16674: Delete the pattern selected in the Load block's Pattern combobox instead of the live editor name

  • Oligo Pattern, Oligo Translator: Named the captionless inputs (Delete pattern, Edit strands modifications, translation examples, the single-sequence format) for test automation

1.11.5 (2026-07-12)​

  • Moved the SequenceTranslator Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright

1.11.4 (2026-07-03)​

  • Markush enumerator redesign
  • Function name harmonization

1.11.3 (2026-06-23)​

  • Markush enumeration: R-group templates picker backed by a built-in catalogue of common substituents (alkyl, aryl, heteroaryl, halogens, amines, protecting groups); copy R-groups between positions, append/replace with de-duplication, and export R-groups to CSV.
  • Markush enumeration: added "Remove duplicates" option (dedupe results by canonical SMILES) and a custom result table name.
  • Added MarkushDefaults package setting and settings editor — admin-configured defaults (cores, R-groups, mode and output options) seed the Markush Enumerator, distributed per user group.
  • HELM Web Editor migration: PolyTool HELM enumeration now operates directly on HELM strings, dropping the JSDraw2 globals while preserving input formatting.

1.10.26 (2026-06-10)​

  • OligoNucleotide renderer: standalone backbone linkers (p, [sp], or any monomer whose natural analog is p) — whether a 5'/3' cap, mid-strand, or a consecutive run — now render as linkage arcs (no chip), instead of being mistaken for conjugate pills. Recognized from the monomer library.
  • OligoNucleotide renderer: alignment now accounts for standalone linkers. A run of linkers on one strand that the other lacks opens a gap (bases stay aligned / paired), and the partner strand draws a single wider arc across it.
  • Demo data (files/samples/sirna-demo.csv): added a phosphate-capped single strand with mid-strand linkers and a duplex with a sense-only linker bulge.

1.10.25 (2026-06-09)​

  • OligoNucleotide renderer: strand alignment is now driven by the HELM when present — strandtype annotations decide the sense/antisense roles (chains are swapped accordingly) and $connections$ pair entries fix the base-pair register.
  • OligoNucleotide renderer: when no explicit info is present, sense/antisense are auto-aligned by sliding the antisense to the column shift with the most complementary base pairs (natural-analog aware), with terminal overhangs on either end rendered true.
  • Oligo context panel: shows the resolved duplex register (blunt vs overhangs, and whether it came from explicit HELM pairs or auto-alignment).
  • Oligo Structures panel: order the Sense / Antisense panes by the parsed strand roles (honoring strandtype swaps) rather than raw chain order, so a flipped HELM (sense = RNA2) no longer mislabels the strands.
  • Demo data (files/samples/sirna-demo.csv): added rows with 3' overhangs and rows carrying explicit HELM pair / strandtype info.

1.10.24 (2026-05-19)​

  • Removed redundant demos

1.10.23 (2026-05-15)​

  • OligoNucleotide renderer: adaptive chip sizing (no hard max cap), 10px vertical breathing room, base-pair indicators (G-C 3 lines, A-U/A-T 2 lines, mismatches dashed), size-proportional chip corners.
  • OligoNucleotide cell: double-click opens a full-screen canvas viewer with hover tooltips; HELM editing moved to a separate "Edit HELM" action alongside "Copy as HELM" and "Copy as Image".
  • WK lines between matching bases.

1.10.22 (2026-05-15)​

  • OligoNucleotide renderer: strand-oriented redesign — sugar stripes on the outside edge of each strand, linkages as rounded apex arches; all colors sourced from the Bio monomer library.
  • OligoNucleotide renderer: fixed reversed-antisense linkage placement (was shifted by one gap and dropping the leftmost-data linkage).
  • Speedup canonicalization of Markush enumeration results.

1.10.21 (2026-05-14)​

  • Markush enumeration UI redesign, history and bug fixes

1.10.18 (2026-05-11)​

  • OligoNucleotide cell renderer: Fixed bracketed monomer base parsing (e.g. [5Br-dC] inside (...)) so renderer/resolver pick up modification colors and structures correctly.
  • OligoNucleotide: Added double-click HELM Web Editor for OligoNucleotide cells; OK saves the edited HELM back to the cell

1.10.14 (2026-04-21)​

  • Chem Enumeration
  • Helm enumeration improvements, paralel mode
  • Polytool: support for custom notation back-conversion, fix for reversed rule order

1.10.5 (2025-12-11)​

  • PT-Synthetic: Fix missing molfile handler errors

1.10.3 (2025-11-03)​

  • Fix synthetic rule application for multiple instances when r group numbering is reversed

1.10.2 (2025-11-03)​

  • Update Bio Lib API
  • Fix synthetic rule errors for missing monomers
  • Fix incosistent R group conneections for reversed rule orders

1.9.5 (2025-05-02)​

  • Fix changing bond numbers when fixing molblocks

1.9.4 (2025-04-08)​

  • Linearization fix for polytool convert.

1.9.1 (2025-03-31)​

  • Combination of sequence sets dialog.

1.8.0 (2025-02-20)​

  • Support for enumeration in all notations
  • fallback for polytool convert
  • Corrected highlighting

1.6.5 (2024-12-01)​

New features​

  • PolyTool: highlight in mol based on given notation
  • PolyTool: Rule manager enhancements

Bug fixes​

  • PolyTool fix R3, R4 and elder groups capping

1.6.4 (2024-11-27)​

  • PolyTool: linearization of single sequence molecules
  • Enumerator: Added whole library enumeration

1.6.3 (2024-11-22)​

Moved Context menu items to detector

1.6.2 (2024-11-17)​

New features​

  • PolyTool rule manager enhancement
  • Sequence renderer font resizing

1.6.1 (2024-11-15)​

Bug fixes​

  • PolyTool fix default options
  • PolyTool fix explicit carbon cut

1.6.0 (2024-11-14)​

New features​

  • Add PolyTool work with sinthetic monomers

1.5.3 (2024-11-06)​

Bug fixes​

  • PolyTool fix rules empty specification (all monomers undergo)

1.5.2 (2024-11-06)​

Bug fixes​

  • PolyTool rules several instances bug fix

1.5.1 (2024-11-06)​

Bug fixes​

  • PolyTool rules fixes rule management
  • PolyTool rules fixes crash if monomer is absent

1.5.0 (2024-11-04)​

New features​

  • Add PolyTool interface for rule management

1.4.10 (2024-11-01)​

Bug fixes​

  • Fix build

1.4.9 (2024-10-31)​

Bug fixes​

  • Fix package initializing helmHelper
  • Fix Chain using HelmAtom.bio of type PtBio
  • Fix PT Enumerate dialog for harmonized sequences
  • Fix PT Enumerate for monomer hovering
  • Fix PT Enumerate for historical values
  • Fix PT Enumerate adding buildCyclizedMonomerHoverLink, WIP
  • Fix adding CyclizedGridCellRenderBack

1.4.8 (2024-10-25)​

Bug fixes​

  • PolyTool ambigous R groups handling bug

1.4.7 (2024-10-25)​

Bug fixes​

  • PolyTool ambigous R groups handling bug

1.4.6 (2024-10-25)​

New features​

  • Add PolyTool Enumerate for harmonized sequences
  • PolyTool ambigous R groups handling

Bug fixes​

  • Fix PolyTool chain, add check consistency, add tests
  • Fix PolyTool Convert tests
  • Fix the package init

1.4.5 (2024-10-11)​

Bug fixes​

  • Fix for grok.userSettings
  • Fix moving support custom notation harmonized sequence
  • Fix PT Convert for monomer highlighting
  • Fix PT Convert reaction monomer colors
  • Fix PT detectors adding tests
  • Bump dependencies versions

1.4.4 (2024-09-30)​

New features​

  • Add convert with reaction rules

Bug fixes​

  • Fix sample reaction rule and monomer order
  • Fix isolate PolyTool convert error on row
  • Fix adding test for Chain .fromNotation
  • Fix adding test toAtomicLevel getNewMonomer

1.4.3 (2024-09-27)​

Features​

  • Add PolyTool convert reverse

Bug fixes​

  • Add sample reaction rule aG + azG = GGaz, test data
  • Fix using MonomerLibHelper.loadMonomerLibForTests
  • Add test toAtomicLevel with overridden monomer lib
  • Fix PolyTool Enumerate for zero-based monomer position
  • Fix Chain.getHelm square brackets for multi char symbols

1.4.2 (2024-09-24)​

New features​

  • Add PolyTool breadth enumerator

1.4.1 (2024-09-12)​

Bug fixes​

  • Input style fixes

1.4.0 (2024-09-10)​

Features​

  • Add PolyTool Enumerator Chem dialog to context menu for Molecule

Bug fixes​

  • Fixes for PolyTool Enumerator Helm dialog
    • Trivial Name input Behavior
    • Enable for any Macromolecule cell
    • Example with monomers existing in default monomer lib
  • Fixes for datagrok-api changes
  • Add sample cyclized.csv for rules_examples.json
  • Fix PolyTool Convert, add tests cyclized
  • Fix PolyTool enumerate add progress indicator
  • Fixes for api changes
  • Fix PT dialogs destroy on build fail
  • Fix rules_examples for NH2-D with R3 and syclized sample
  • Fix polyToolConvert to work without table
  • Add tests for polyToolConvert, ui

1.3.14 (2024-09-02)​

Fix remove CyclizedNotationProvider

1.3.13 (2024-08-19)​

Features​

  • Improve PolyTool Enumerate Dialog
    • Add check and warning for substituting missed monomers
    • Add flag to keep the original molecule in the result
    • Add choice to select a molecule id and generate derivative

Bug fixes​

  • Fix PolyTool Enumerate dialog hanging on monomer click
  • Fix user settings for publish

1.3.12 (2024-08-16)​

PolyTool Enumerator Single and Matrix, dialog, tests

Bug fixes​

  • PolyTool Enumerator dialog grid input for placeholders, to atomic level option
  • PolyTool Enumerator dialog mouse interactivity, to atomic level, dialog size
  • PolyTool Enumerator dialog size and fit molecule input

1.3.11 (2024-07-31)​

Features​

  • Added chemical based enumerator

1.3.10 (2024-07-29)​

Features​

  • Add 'Create/Modified' date metadata to patterns

Bug fixes​

  • Load new patterns upon saving / overwriting

1.3.9 (2024-07-23)​

  • Dependency: datgarok-api >= 1.20.0

1.3.8 (2024-07-09)​

Features​

  • Add PolyTool-enumerate context menu for macromolecule cell

Bug fixes​

  • Use HelmInput from Helm
  • Bump dependencies versions

1.3.7 (2024-07-01)​

Bug fixes​

  • Fix style for colored text input

1.3.6 (2024-06-26)​

Bug fixes​

  • Fix bulk input in Pattern app

1.3.5 (2024-06-13)​

Features​

  • PolyTool Enumeration: cell with helm is added to the input

1.3.4 (2024-06-12)​

Bug fixes​

  • Fix terminal modification SVG rendering

1.3.3 (2024-06-12)​

Bug fixes​

  • Fix terminal modification SVG rendering

1.3.2 (2024-06-10)​

Features​

  • Add package MonomersPath package settings fallback to monomers-sample
  • Add README for monomers-sample
  • Add sample for bulk translation in Translator app

Bug fixes​

  • Fix tests for MonomersPath package settings

1.3.1 (2024-06-05)​

Bug fixes​

  • PolyTool: example data added to project

1.3.0 (2024-03-30)​

Features​

  • PolyTool: algorithm of conversion facilitated, json files are used as rules
  • PolyTool: enumeration feature (demo) added

1.2.9 (2024-03-30)​

Features​

  • #2707: Add original and canonical to monomer

1.2.7 (2024-01-29)​

Features​

  • Bulk translation for formats

1.2.6 (2024-01-29)​

Bug fixes​

  • Fixed column input in Pattern
  • Fixed whitespaces in molfiles

1.2.0 (2023-10-27)​

Features​

  • Tabs implemented as separate apps
  • Clear buttons added to sequence inputs

1.1.4 (2023-09-07)​

Bug fixes​

  • Fixed molfile direction for AS and AS2 on SDF tab

1.1.3 (2023-09-07)​

Bug fixes​

  • Fixed Direction of AS and AS2 for SDF tab

1.1.2 (2023-08-16)​

Bug fixes​

  • Fixed HELM generation for modifications

1.1.1 (2023-08-10)​

Features​

  • Updated dependencies

1.1.0 (2023-07-26)​

  • Dependency: datgarok-api >= 1.15.2

Features​

  • Option to add extra formats for translation in addition to Axolabs, BioSpring and MerMade12
  • Generation of HELM strings
  • Improved SMILES generation
  • UI/UX adjustments