Chem changelog

v.next

• Generate Conformers: Fixed the run failing with AttributeError: Cannot set unknown attribute 'maxAttempts' — ETKDGv3 takes maxIterations
• Chem | Calculate | IUPAC Name: Added a Python script that names molecules with openclatura
• GROK-20753: Added moleculeFilterOperators (meta.role: filterOperators) — substructure, superstructure, exact, stereo-agnostic and similarity operators for the u2 filter builder
• GROK-20808: MMP: Fixed a crash when no table was selected in the dialog
• GROK-20829: Guard isBitsetStale against the valueless root tree group
• GROK-20824: MPO: Fixed the profile description picking up the title's text styling when styled text was pasted into it
• GROK-20821: MPO: Fixed the dataset list ignoring newly opened tables
• GROK-20823: MPO: Fixed Edit opening duplicate editor tabs and leaving a stale profile preview in the context panel
• GROK-20832: MPO: Fixed Save being disabled on a freshly cloned profile — the copy could not be kept
• GROK-20831: MPO: Fixed truncated profile descriptions not expanding on click after saving a profile
• GROK-20830: MPO: Fixed data-driven Save not using the name and description typed on the tab
• GROK-20805: Chem: Butina cluster doesn't work in a project with datasync

1.17.15 (2026-09-02)

• Added SAR Matrix, rendered in a virtualized grid, with SAR Transfer to the grid
• SAR Matrix: Fixed the SAR Transfer tab rebuilding the whole panel (grid flicker, list scroll jumping to the top) on expanding/collapsing a series or selecting a transfer — the list now toggles and swaps in place like the SAR Matrix navigator
• Fixed the package build failing on TS2610 — name is an accessor on the u2 Component base, so the viewer overrides it with its own accessor instead of redeclaring it as a property
• Fixed Gasteiger Partial Charges panel on current RDKit — GetSimilarityMapFromWeights now requires an explicit MolDraw2DCairo drawer (passed by keyword, so pre-2023.09 RDKit still works)

1.17.14 (2026-08-13)

• Reaction Enumerator: Added package settings (category "Enumeration") letting admins set per-group default file paths for reaction templates, building blocks and reagents; missing files show a warning balloon and fall back to the bundled ones
• Substructure filter: Added a 'Filter as you draw' checkbox to the sketcher dialog — when unchecked, filtering is deferred until OK is clicked instead of running on every sketch edit
• Added Filter by Substructure, Similarity To and Diverse Subset — table-aware twins of searchSubstructure, getSimilarities and getDiversities, which take a bare column. They declare (table, column {semType: Molecule}, …) and return rows or a column added to the table, so a caller has something to carry on with instead of a detached frame or a boxed BitSet
• Added Apply Reaction — the non-interactive twin of the Transformation dialog, applying a one-component reaction SMARTS to a molecule column
• Added To SDF, which serializes a table to SDF text; the only SDF write path was a zero-argument file exporter reading the current table
• Added Chemical Space Columns — Chem Space with typed, enumerated parameters that never plots and returns the X, Y, cluster and cluster-MCS columns it added
• MPO Score by Profile: Refuses to run when a scored property has no column, naming the ones it couldn't resolve — the underlying computeMpo only warns and scores over the rest, which returns a plausible number computed from fewer properties than requested
• Added MPO Score by Profile, getMpoProfileNames and getMpoProfileProperties: mpoCalculate scores columns that already carry desirability tags and mpoTransformFunction wants those tags as a JSON blob, so neither could be driven from a profile name. The new function also takes a property→column mapping, so a profile can score a table whose columns are named differently
• Parameters with a default now declare initialValue — the metadata generator reads that, not the TypeScript default, so aggregation = 'Average' and friends were registering with no declared default at all
• Chemical Similarity Search: Added choices and defaults for metric, fingerprint, max hits and min similarity, and tagged the query molecule semType: Molecule
• Substructure Search: Tagged the query semType: Molecule and defaulted the molblock fallback
• Curate: Flipped normalization, reionization, neutralization and main-fragment on by default — with every flag off the function ran and changed nothing
• Fixed display names that were declared via //friendlyName:, which the metadata parser ignores: Remove Water and Salts, Run Reaction, Two-Component Reaction
• Remove Water and Salts: Its molecules parameter never carried semType: Molecule — the decorator options were nested one level too shallow, so it accepted any string column
• Marked genuinely-required parameters non-nullable across the reaction, clustering, scaffold and R-group functions (Two Component Reaction's second table/column, Cluster MCS's cluster column, FindMCS, FindRGroupsWithCore, Murcko, Butina, Curate)
• Docker (chem/chemprop): Cleared reported CVEs — pinned Flask/Werkzeug/gunicorn to fixed releases, upgraded pip/setuptools/wheel (build + runtime tooling), pinned urllib3/idna in chemprop, and added apt upgrade to patch base-image OS packages
• Docker (chem/chemprop): Raised security floors (VEX) — torch/torchvision/torchaudio to 2.6.0+cu118 via PyPI wheels (CVE-2025-32434) and removed padelpy's bundled PaDEL-Descriptor jars (log4j 1.2.15, guava 17.0)
• Moved the Chem Playwright E2E suite into the package (playwright/); helpers from @datagrok-libraries/test/src/playwright
• GROK-20239: Chem: OCL renderer: Structures do not appear in labels in some visualisations
• Scaffold Tree: Colors/labels columns are now named <molColumn> colors/labels (<id>) using a persisted per-viewer id instead of the editable title, avoiding column-name collisions when viewers share a title
• GROK-20505: Chem: Some descriptors return string values instead of numeric
• InChI / InChI Keys: Moved the conversion to the parallel RDKit service (web workers) instead of the single-threaded module — To InchI, To InchI Keys, getInchis and getInchiKeys are now async
• GROK-20486: Fixed a crash in _demoMMPA when the viewer didn't load in time

1.17.13 (2026-06-08)

• Chem: MPO: Optimized score calculation for large datasets
• GROK-18818: Chem: MMP: do not allow to choose empty column in dialog
• GROK-15991: Invalid argument(s): Array lengths differ
• Chem: Fixed waitFor clearing the wrong timer handle, leaving the polling interval running after the condition was met
• OCL worker: Added missing break statements so a drug-likeness or molfile-to-V3K request no longer also runs and posts later cases' results
• OCL worker: Fixed an off-by-one atom loop that could miscalculate molecule charge
• RDKit worker: Fixed the R-group analysis handler posting a stray undefined result due to a shadowed variable
• Identifiers: Fixed the UniChem home-page link mapped to the base-ID URL instead of src_url
• Map Identifiers: Fixed column ids.key does not exist when converting from InChIKey or via the ChEMBL bridge — _chemMapViaQuery now renames a cloned input column to key to match the converter SQL parameter name
• Chem search: Replaced a floating promise with proper if/.catch() so substructure-search sub-task rejections are handled
• RDKit service: Worker terminate() now rejects in-flight calls instead of leaving callers hung forever; guarded the cluster-MCS timeout path accordingly
• BitBIRCH clustering: Guaranteed the clustering worker is terminated even if the request fails synchronously
• Highlight widget: Unsubscribe ItemsGrid event subscriptions when the grid is rebuilt or the widget is detached

1.17.12 (2026-06-05)

• GROK-20193: SDF import: Preserve molecule name and comment fields
• MPO: Fixed disabled OK button with no explanation when creating a new profile
• #3811: Chem: Added "Export as SVG" action for molecule cells
• Scaffold tree: Improved project loading performance for large datasets and trees — child-node substructure searches are now narrowed to the parent scaffold's matching rows (structure→superstructure relationship), avoiding redundant full-column searches

1.17.10 (2026-05-28)

• Chem: Record all generated reaction results in the enumerator

1.17.9 (2026-05-26)

• Scaffold tree: Remove the lingering … colors fragments column when the last color-coded node is deleted one-by-one (previously only cleaned up on viewer detach or "Drop all trees")
• Chem Space: Guard editor entry against null current dataFrame / missing Molecule column to prevent NullError: method not found: 'dart' on null from setColumnInputTable
• Chem: Toxicity Risks: Avoid 'Column already exists' crash on repeat invocation by using getUnusedName before adding risk columns
• GROK-20108: Docker API: Throw a clear error when the chem-chem container is not available, instead of Cannot read properties of undefined (reading 'id')
• Scaffold tree: Fixed severe load/scroll slowdown on large dataframes — molecule rendering and substructure searches now run only for on-screen nodes (IntersectionObserver rooted at the actual scroll container) instead of the entire tree
• Scaffold tree: Deduplicated per-node bitset computation (reuses in-flight and completed searches) and added a one-time shared fingerprint warm-up, eliminating redundant full-column searches on load
• Scaffold tree: Debounced scroll-driven substructure searches so fast scrolling no longer spawns a search for every node scrolled past

1.17.8 (2026-05-12)

• Scaffold tree: Migrated drop handler to the new doDrop(args) signature in ui.makeDroppable
• Chem: Scaffold Tree: Fixed Array.from(undefined) crash in getPeerViewers when the active view is not a TableView
• Reaction enumerator: Reworked UI — replaced the preview with side-by-side reaction templates and building blocks grids that subset the enumeration via row selection; renamed inputs and the full-config button for clarity
• Reaction enumerator: Right pane is now a tabbed view (Reaction templates, Building blocks, Reagents, Preview); preview tab re-runs lazily on activation
• Reaction enumerator: Added reagents-mode enumeration — when a reagents file/column are provided, each step uses exactly one BB or earlier-round product plus reagents in every remaining slot (produces derivatives of each BB across rounds)
• Reaction enumerator: Added a plain-English mode summary under the config buttons describing how the current selections drive the run
• Reaction enumerator: Added test coverage for reagents-mode enumeration (round 1 / multi-round step-pool invariants, empty-reagents fallback, BB-BB combo isolation)

1.17.5 (2026-04-15)

Features:

• Chem: Stereo agnostic search
• Chem: Pharmacophore feature highlighting

Bug fixes

• GROK-19962: Fixed crash in checkCurrentView when table is opened in Files preview without a registered TableView
• GROK-19994: MMP: Fixed crash when navigating away from MMP view while tab content is lazily rendered
• GROK-19921: Bio, Chem: Make table view active when adding scatter plot for chemical/sequence space and activity cliffs (in case it was switched during function execution)
• GROK-19862: Radar: Viewer type naming issue
• GROK-14952: Chem: Filter Panel and Hamburger menu molecular filters are not sync
• GROK-18530: Chem: Substructure Filter: incorrect filtering in the cloned view when using the "Similar" option
• Chem: Scaffold Tree: Fix double vertical scrollbar
• Chem: MPO: Add EDA package guard and deduplicate profile loading
• Chem: MPO: Preserve profile name and description on dataset change
• Chem: MPO: Fix profile naming and cancel behavior

1.17.4 (2026-03-30)

• #3708: Chem: Chemical space: Add tags on columns with embeddings

1.17.3 (2026-03-26)

• Improved reaction renderer supporting smiles reactions.

1.17.2 (2026-03-23)

RDKit render: Render without fixed scaling if rendered outside the global context (for single values like in custom tooltips).

1.17.1 (2026-03-17)

• GROK-19867: Chem: Alignment setting (Scaffold column) is not saved to the data-sync project

1.17.0 (2026-03-13)

• Chem: MPO: Fix desirability label positioning and rename templates to profiles
• Chem: MPO: Use name derived from the profile
• Chem: MPO: Use mapped columns in calculation
• #3497: Chem: MPO: Implement profile management
• Chem: MMP: Fixed broken pairs grid filtration (by current molecule) after switching from Transfromations tab in demo
• GROK-19543: Chem: MMP: Cliffs: broken color icon location
• Chem: MPO: Use line min/max as defaults when not defined in profile
• GROK-19575: Chem | Descriptors: Broken count for selection
• GROK-19569: Chem | MPO: "Add as column" is stuck in updating
• #3645: Chem: MPO: Improvements
• GROK-19576: Chem | Descriptors: Disable modification of selected descriptors when added as a column from the panel
• #3650: Chem: MPO: Improvements
• GROK-19623: Chem: MPO: Profiles list: Truncate long descriptions
• Chem: Move Generate Conformers to Calculate
• GROK-19620: Chem: MPO: Saving cloned profile replaces parent profile
• GROK-19621: MPO: 'Edit MPO profile' tab including profile`s name
• GROK-19624: Chem | MPO: Deleting a profile should update browse tree without manual refresh
• Chem: MPO: Ensure the OK button only applies changes (not saving to file)
• Chem: MPO: Highlight matching profiles in the profiles input to give users a quick overview of suitable options
• Chem: MPO: Disable OK button when profile is incompatible or mapping is missing
• Chem: MPO: Avoid showing balloons when previewing results
• GROK-19629: Chem: MPO: Enable actions on Browse view
• GROK-19632: Chem: MPO: error on saving profile
• GROK-19627: Chem: MPO: Multiple times cloned profile case
• GROK-19641: Chem: MPO: Close opened/previewed profiles after their deleting from the browse
• Chem: Add pMPO-generated profile to the Chem folder for demo usage
• Chem: MPO: Display warning in dialog footer
• Chem: MPO: Use ObjectHandler for context menu actions and profile preview in the context panel
• Chem: Explicit smiles setting for sketchers
• Chem: MPO: Align option values in the profiles input
• Chem: Add BitBIRCH clustering for O(N) incremental molecule clustering
• Chem: Bitbirch worker
• Chem: Removing explicit Hs for morgan FPS
• Chem: Smiles length limit
• #3658: Chem: Scaffold Tree: Add support for custom labels
• Chem: MPO: Fix description column showing clickable cursor without expand behaviour
• Chem: MPO: Fix issue where clicking a profile in the list does not open it in the context panel
• Chem: MPO: Update match emoji and fix best/worst score interactivity
• Chem: Synthon search
• Chem: Scaffold Tree: Support for custom labels (fixes)
• Chem: MPO: Fix issue with Desirability profile detection
• Chem: MPO: Align ui between pMPO and MPO dialogs
• Chem: MPO: Add fallback color section to settings dialog
• Chem: MPO: Prevent context panel from switching the current object when clicks originate from histogram or scores viewers
• Chem: MPO: Add UI hints
• GROK-18490: Chem: MMP: molecule pairs: improve data rendering in context panel
• Chem: Get mol details
• Chem: MPO: Display profile names in the dialog instead of filenames to avoid confusion (in the app we use profile names)
• Chem: Reaction toolkit: Initial UI
• GROK-19715: Chem: MMP: Fragments: correspond empty trellis plot with molecule pairs list
• Chem: Improved reactions editor and app views
• Chem: MPO: Make aggregation to be part of the profile
• Chem: MPO: Remove hints and add descriptive text in front of the input
• Chem: MPO: Fix issues with routing
• Chem: MPO: Fix recalculation and data sync issues
• Chem: Chemprop: Fix docker container discovery
• #3681: Chem: MPO: Improvements to the “Create Profile” view
• Chem: MPO: Improve profile creation flow in the dialog
• Chem: MPO: Fix crash when selecting a profile with no matching columns
• GROK-19837: Chem: MMP Demo: clicking on "/\ hERG_pIC50" in Fragments causes errors
• GROK-19838: Chem: Scaffold Tree: Folder style overlaps
• Chem: MPO: Vertical form layout with descriptions under labels
• Chem: MPO: Prevent default override when saving from the MPO dialog
• Chem: MPO: Add profile import and export
• Chem: MPO: Add breadcrumbs for navigation
• Chem: MPO: Move Save button to ribbon and fix dialog opening in design mode by default
• Chem: MPO: Rename “probabilistic” to “data-driven” and rearrange the viewers
• Chem: MPO: Add checkbox for adding the radar plot to the grid
• Chem: MPO: Add reset button and fix onChanged not firing for gaussian and sigmoid on change

1.16.14 (2026-01-05)

• Chem: Rendering: Introduce an option to disable post–R-group analysis highlighting

1.16.13 (2025-12-23)

• Butina clustering: Expose Python implementation to top-menu

1.16.12 (2025-12-22)

• GROK-18406: Chem | Scaffold Tree: Disallow multiple filters on the same column
• Chem: Detector: Extend valid smiles characters to support additional symbols

1.16.11 (2025-12-09)

• Add kekulize option to molecule notation conversion functions

1.16.10 (2025-12-08)

• R Group analysis: fixed ability to perform analyziz only for certain positions

1.16.9 (2025-11-19)

• Validated deprotection feature with more precise reactions.

1.16.8 (2025-11-11)

• Support datasync for biochemical functions

1.16.7 (2025-10-22)

• Fix compatibility issues with platform version 1.25.3

1.16.6 (2025-10-16)

Bug fixes

• GROK-19062 Similarity Search viewer: incorrect coloring after sorting a dataset
• GROK-18817: Chem | Scaffold tree: Add explanation tooltip why the tree can't be generated
• GROK-18901: Chem | Scaffold tree: Error when loading the layout
• Chem: Fix Distance functions
• GROK-18916: Chem: Remove hint on viewer close
• GROK-18931: Chem | Properties: Molecule charge is NaN
• GROK-18944: Chemprop: train model: 'Creating interactive model preview' step takes too long
• GROK-18945: Chem | Scaffold Tree: Color column not restored when reapplying saved layout
• GROK-18815, GROK-18816, GROK-18820: Top Menu: UI/UX improvements: Fixed names, captions
• #3497: Chem: MPO: Update to work correctly with data sync

Features

• Chem: Mixtures widget in context panel: show components names where available
• Chem: calculate context panel descriptors via docker
• Ability to run Descriptors, Properties, Toxicity risks, Structural alerts using Add new column dialog

1.16.5 (2025-09-15)

• Add layout persistant tag for scaffold alignment

1.16.4 (2025-09-05)

• Fixed issues with tableview getting for cloned views in functions.

1.16.3 (2025-08-26)

Features

• Removed on demand from docker containers

1.16.2 (2025-08-07)

Bug fixes

• GROK-18622: Implement logic to check and switch TableView if needed
• #3445 Structure filter does not realign when coordinates change but structure does not

1.16.1 (2025-08-04)

Bug fixes

• GROK-18609: MMP: Demo throws errors: Cannot read properties of null (reading 'toList')

1.16.0 (2025-07-28)

Features

• Chem: MMP: Added hints
• Chem: Similarity/Diversity: Show error in case no molecule column was found
• Chem: MMP: Collaborative filtering with parent table
• Chem: MMP: Ability to filter fragments/pairs
• Chem: MMP: View results on PC plot, select activity difference function with scaling, in cell pc plots for activities, show trellis filters in popup, added trellis legend
• Chem: Added description to scatter plot for chemical space and activity cliffs
• Chem: Mixtures renderer, mixtures widgets and semantic type
• #3426 CPC: Moved to chem, factored into a separate widget file

Bug fixes

• Chem: Scaffold Tree: Fix bitset not updating on structure change
• Chem: Scaffold Tree: Check if viewer is detached
• GROK-18069: Chem | Scaffold tree: Error when closing
• GROK-18074 Chem: Context Panel: Content tab: df flickers when filtering by Scaffold Tree and Activity Cliffs simultaneously
• Chem: Deprotect: Column already exists
• GROK-18103: Chem | Scaffold Tree: Skip processing if column is empty
• Chem: Correct most diverse structures logic
• GROK-18066: Chem: Context Panel: Structural Alerts: calculate for whole dataset doesn't work for some data
• GROK-18061: Chem: Prevent from running functions which add viewers not on the active table view
• Chem: Scaffold Tree: Exclude fragment column from Select columns dialog
• GROK-18283: Chem | Scaffold Tree: Error when changing scaffold size
• GROK-18284: Chem | Scaffold Tree: Resetting Description > Title creates duplicates
• GROK-18305: Chem | Scaffold tree: Error when uploading tree for non-molecular dataset
• GROK-18269: Chem: Scaffold Tree: Viewer is empty when opening a project
• Chem: MMP: Do not interpret missing values as zero
• GROK-18290 : Substructure filter: multiple identical filters issue
• #3346: Export as SDF: Fixed none values are written as numbers ant not as empty strings
• GROK-18388: Chem | Scaffold tree filter: Error after Close All
• #3399: Do not allow to modify Scaffold colors from Scatterplot or other viewers
• Chem: do not allow multiple substructure filters
• GROK-18391: Chem: the project opens with different filtering results before and after clearing the cache
• GROK-18409: Chem: R-group analysis: column prefix in dialog not working
• GROK-18405: Chem | Scaffold tree: Incorrect filtering after layout application
• GROK-18417: Chem: Fix column parent in structural alerts
• GROK-18419: Chem: MMP: activity list is empty
• GROK-18495: Chem: Fix errors on current row unselection
• GROK-18477: Chem: MMP: Update legend when changing activities on tp
• GROK-18491: Chem: MMP: Fragments: "Full screen" trellis plot icon is not working
• GROK-18479: Chem: MMP: Generation: should be no empty values
• GROK-18493: Chem: MMP: Fragments: trellis legend optimization in case of big amount of legend items
• GROK-18494: Chem: MMP: Properties: changing Molecules name cause no effect and triggers "reading 'toList'" errors in console
• GROK-18570: Chem | Structural Alerts: Broken styles
• GROK-18530 Chem: Substructure Filter: incorrect filtering in the cloned view when using the "Similar" option
• GROK-18567: Chem | Chemprop: Cross validation fails for mol1k.csv

1.15.1 (2025-04-23)

Features

• #3302: Multiple scaffold trees: Naming/coloring should be saved in projects

Bug fixes

• GROK-17929: Chem: Similarity sorting checks
• GROK-17958: Chem: some demos overwrite Datagrok tab name

1.15.0 (2025-03-29)

Features

• #3273: Scaffold tree: add the ability to apply Scaffold tree colors to Scatterplot or other viewers
• GROK-17731: Chem | Scaffold Tree: Remember previous hide/show state
• GROK-17867: Chem: Demo improvements
• Add caching to Gasteiger charges
• #3302: Multiple scaffold trees: add the ability to apply Scaffold tree colors to Scatterplot
• MMP: Open scatter plot context menu when right click on cliffs sp, separate generations scatter plots for each activity, cliffs tab scatter plot improvements, trellis filters improvements, use column descriptions instead of custom tooltips for non molecule columns, added help url
• Chem: Cluster MCL Implementation
• #3314: Chem: Scaffold Tree: Demo improvements
• Chem: Parallel beautification

Bug fixes

• GROK-17761: Chem: Demo: Chem: Activity cliffs: Viewer initialization function failed
• GROK-17791: Chem: Scaffold tree: Coloring the scaffold tree element triggers the grid scroll to the end
• Chem: Similarity/DIversity search: some progress bar related fixes
• GROK-17892: Chem | Scaffold tree: Errors on closing viewer
• GROK-17867: Chem: Demo: Added setTimeout for showing help

1.14.0 (2025-02-24)

Features

• New improved MMP implementation
• Integration with Reinvent
• Copy molecule as image
• Context actions for chemical columns

Bug fixes

• GROK-17483: Chem: Structure filter is not reset on reseting the filtering in some cases
• GROK-17461: Scaffold tree: Error when uploading the saved tree
• GROK-17511: Chem | ChemProp: Error when training a model
• GROK-17555: Filter Panel: Reset filter causes errors in some cases
• GROK-17471: Chem: Incorrect filter UI when adding filter via 'Use as filter' or 'Add filter'
• GROK-17597: Chem: Wrong filtering when opening the project

1.13.1 (2025-01-06)

Bug fixes

• Fix RDKit cell renderer isolating MonomerHoverData.getSubstruct
• Fix RDKit cell renderer isolating ISubstructProvider.getSubstruct

1.13.0 (2024-10-25)

Bug Fixes

• #3055: Page is freezing after applying layout with multiple scaffold trees with large number of structures

1.12.4 (2024-10-18)

Bug fixes

• Fix rdkit cell renderer for viewers tooltip, enable test
• Invalidate fingerprints column only in case column data (not metadata) has been changed

1.12.3 (2024-10-01)

Bug fixes

• GROK-16730: Demo: Activity cliffs: Cannot read properties of null

1.12.2 (2024-09-25)

Bug fixes

• Fix rdkit cell renderer error in scatter plot tooltip, add test

1.12.1 (2024-09-25)

Bug fixes

• Expect GPU to be unavailable on some browsers
• Fix MMPa crushing without errors

1.11.6 (2024-09-20)

Bug Fixes

• #3055: Page is freezing after applying layout with multiple scaffold trees with large number of structures

1.11.5 (2024-08-27)

Bug fixes

• Add tableView to runChemSpace for reduce dimensionality ui options
• #3004: Chem: Scaffold tree is based on wrong table by default in some cases
• GROK-15938: Chem | Scaffold Tree: Array length differ
• Chem: MMPA: Fix demo

1.11.4 (2024-08-23)

Features

• Chem: MMPA: filter fragments by significance
• Chem: MMPA: project and layout saving
• Chem: MMPA: demo loaded not calculated
• Chem: Removed r-groups settings download from init

Bug Fixes

• Chem: MMPA: Fixed property panel on cliff line click
• #2983: Chem: fix tooltip styles for structure columns
• GROK-16493: MMPA: Fixed Summary viewer doesn't show the values

1.11.3 (2024-08-12)

Features

• Chem: MMPA: Work with multucomponent entities

1.11.2 (2024-08-12)

Features

• Chem: Chemprop: Remove redundant calls in the core and move it fully to package
• Chem: MMPA: Add meaningfull dataset for demo
• Chem: MMPA: Restrictions and CPU fallback
• Chem: MMPA: Compensate filtering by cutoff
• Chem: MMPA: Add reflection for selection
• Chem: MMPA: Add pairs filter, expose filters object so it can be used in any tab, minor improvements
• Chem: Update demos in order to be shown in the Browse

Bug Fixes

• Chem: MMPA: Fixes for cliffs tab and lines improvements
• #2964: Scaffold Tree: 'Selection to filter' reset immediately for some data if scaffold tree is present

1.11.1 (2024-07-25)

Bug Fixes

• Removed unnecessary code

1.11.0 (2024-07-24)

Dependency: datagarok-api >= 1.20.0

Bug Fixes

• GROK-16328: Chem: R-Group analysis: Broken styles
• GROK-16329: Chem: R-Group analysis: Error when none R groups were found
• GROK-16338: Chem: Chemical space: Reseting marker type to circles
• Chem: Scaffold Tree: Fix representation when the viewers are stacked
• Chem: Chemprop: Fix applying the model to different datasets
• Chem: Fix substructure filter style
• Chem: Do not render molecules with invisible width

1.10.0 (2024-06-12)

Features

• Webgpu acceleration for chem space, activity cliffs, molecule generations
• GROK-15299: Chem: Ability to save results of Chem functions to projects with and without data sync
• GROK-15454: Chem: Similarity/Diversity search viewers: Row source property
• GROK-15508: Chem: MMP: Generated - show what cases are actually generated
• GROK-15501: Chem: MMPA: UI/UX improvements
• GROK-15502: Chem: MMPA: Ability to swith activity on/off
• GROK-15507: Chem: MMP: Control of fragments size
• Chem: Integrate with Chemprop
• Chem: Chemprop upgrade from version "1.6.7" to version "2.0" (reduced memory usage, improved performance)

Bug Fixes

• GROK-15285: Chem: MMP: Error on re-run
• GROK-15321: Chem: MMP: Error while running Close All after running MMP

1.9.2 (2024-04-12)

Features

• R Group analysis improvements: ability to select 'Only match at R groups', saving R group user settings, small UI improvements

1.9.1 (2024-04-12)

Features

• R Group analysis: in browser R group analysis using RDKit JS, highlight of r groups, ability to define enumerated R groups in core
• Similarity/Diversity search: ability to recalculate results on filtering

1.9.0 (2024-03-21)

Features

• #2495: Chem: MMP - initial vesrion
• #2540: Chem | Substructure search: Add an option to toggle the realignment of molecules by molecular filter
• #2525: Chem | Scaffold Tree: Remove the intermediate dialog before the color picker
• #2504: Filter panel: The question mark hovering doesn’t show the filtering of the scaffold tree viewer

Bug Fixes

• GROK-15147: Chem | Scaffold Tree: Highlighting disappears in some cases
• GROK-15240: Chem | RGroups: Handling malformed data
• GROK-15213: Chem | RGroups: Undo latest analysis doesn't work when run on multiple dataframes
• GROK-15187: Chem | RGroups: Fixed memory consumption
• GROK-15171: Chem: Substructure filter doesn't apply correctly after removing rows and disable

1.8.13 (2024-02-29)

Bug Fixes

• Warm up substructure search web workers only once when first filter is created on column

1.8.12 (2024-02-15)

Bug Fixes

• Fixed multiple substructure search calls with the same structure (in case multiple layouts are applied to cloned views at once)

1.8.11 (2024-02-08)

Bug Fixes

• #2642: Filtering done using viewers is unexpectedly reset on applying other filters in some cases
• #2639: Structure in filter is unexpectedly changed when there are two views in some cases
• #2646: Structure highlighting is not removed when filters panel is closed

1.8.10 (2024-01-19)

Features

• Molecule labels on scatter plot zoom in Chemical Space and Activity Cliffs

Bug Fixes

• #2626: Unexpected warning on adding child node to the scaffold tree if parent contains 'H' atom
• #2628: Structure filter is not applied in some cases when there are two views opened
• #2629: Structure filter filters out all molecules in the presence of filter-by-zoom scatterplot and multiple views
• GROK-14542: Filter Panel | Structure filter: incorrect behavior on deleting a filter in a cloned view

1.8.9 (2024-01-09)

Features

• Update MinimalLib to 1.2.15 featuring support for RGroups (support for R-group decomposition)
• Chem: Add ability to specify fingerprint types and cluster embeddings for chemical space

Bug Fixes

• GROK-14383: Chem | Scaffold Tree: The selection doesn't change on folder node click
• GROK-14411: Demo: Exception while closing Scaffold Tree
• GROK-14409: Chem | R-Group Analysis: Error with prefix
• GROK-14375: Chem | Activity cliffs: Implement scatter plot lines renderer
• #2612: Chem | Scaffold tree: Structure part containing H atom is replaced with '?' in some cases

1.8.8 (2023-12-07)

Bug Fixes

• Chem: Fix demos for scaffold tree, chemical databases and similarity/diversity search.

1.8.7 (2023-12-05)

Features

• #2550: Chem: Scaffold Tree: Counter is not updated when applying the filters
• #2525: Chem: Scaffold Tree: Highlighting improvements:
  • More specific fragments should be drawn on top
  • New icons for different coloring states

Bug Fixes

• #2536: Chem: Substructure Filter: Not terminated on fiter reset
• #2553: Chem | Scaffold tree: Realignment issue when the scaffold color is set
• GROK-14305: Chem | Scaffold Tree: Error when deleting rows in grid

1.8.6 (2023-11-17)

Bug Fixes

• #2525: Chem: Scaffold tree: Highlighting improvements:
  • Add a tooltip for the checkbox
  • Add a tooltip for NOT
• #2526: Chem: Molecules realignment improvements:
  • Scaffold tree shouldn't reorient molecules in the grid
• #2533: RdKitService stays unresponsive as terminateFlag is not reset after substructure search has completed

1.8.5 (2023-11-14)

Features

• #2459: Chem: Scaffold Tree: Improvements:
  • Add resetting the scaffold tree viewer (on the reset filter click)
  • Add a tooltip for removing orphans

Bug Fixes

• #2511: Scaffold tree: highlighting is not updated when structure is edited
• #2512: Filtering options (contains, exact, included in etc.) are not synchronised for structure filters on different tabs in some cases

1.8.4 (2023-11-07)

Features

• #2459: Chem: Scaffold Tree: Improvements:
  • The “trash can” icon is red and stands out from the general style; make a blue one from the same collection
  • Add Expand All/Collapse All icons for easy navigation
  • Save the state of the tree (what was selected, what was expanded) when saving
• #2420: Chem | Scaffold tree coloring:
  • use the trash iscon instead of '-'

Bug Fixes

• #2474: Chem | Scaffold tree: Colour is not inherited by child node properly
• #2476: Chem | Scaffold tree: Rows are shown as filtered for a while after applying structure even if checkbox is not selected
• #2448: Some structures are displayed incorrectly when highlighted if they are in SMILES format
• #2473: Structure filter: 'current value > use as filter' breaks filtering in some cases

1.8.3 (2023-10-26)

Features

• #2421: Chem | Molecular Search options:
  • Add some hint to explain the new options to users
  • Fix the ability to collapse the controls after switching from Similarity to Contains
  • Make the icon more noticeable
• #2420: Chem | Scaffold Tree coloring:
  • The custom coloring should override the default one
  • Coloring for child structures - it's very inconvenient that you can't click the icon again to return to the custom color
  • Add the icon for removing the specific node of the scaffold tree

Bug Fixes

• #2399: Scaffold tree viewer: coloring can't be saved to the Layout
• #2450: Scaffold tree imported from file is not restored on applying saved layout
• #2448: Some structures are displayed incorrectly when highlighted if they are in SMILES format

1.8.2 (2023-10-22)

Bug Fixes

• GROK-14149: Add progress indicator to sequence/chem space and remove jumping points

1.8.1 (2023-10-16)

Bug Fixes

• #2399: Scaffold Tree: Coloring can't be saved to the Layout
• #2400: Molecular search: Three dots infinite loading

1.8.0 (2023-08-09)

Features

• GROK-13817: Highlighting multiple substructures with different colors inside one molecule structure
• #2355: Integrate Scaffold Tree with color-coded fragments
• GROK-13993: Fast Chemical space on large datasets (> 20k) using sparse matrix
• GROK-13994: Implemented filter by superstructure, exact structure, similarity score
• GROK-13966: Exposed fingerprints options for similarity, diversity search

1.7.2 (2023-09-05)

Bug Fixes

• Chem: Scaffold Tree: Checkbox shouldn't be set, when group is expanded
• Chem: Scaffold Tree: Fix the behaviour of allowGenerate property

1.7.1 (2023-08-31)

Features

• GROK-13571: Chem | Ability to terminate substructure search if substructure has been changed

Bug Fixes

• GROK-13327: Chem | Substructure Search: two identical panels open on the Filter Panel
• GROK-13791: Chem | Chemical space (using t-SNE) fails on smiles dataset
• #2135:
  • The structure rendering is too small.
• #2322: Properties panel is unexpectedly reset on changing viewer properties if there is a scaffold tree filter in filters panel
• GROK-13848: Chem: Substructure search results flickering

1.7.0 (2023-08-09)

Features

• GROK-13172: Chem | implement substructure search using preliminary filtration by pattern fingerprints

1.6.22 (2023-08-07)

Bug Fixes

• GROK-13713: Chem | Incorrect molecule rendering

1.6.21 (2023-08-02)

Dependency: datagarok-api >= 1.16.0

Features

• Calculate drug likeness, toxicity and alerts for whole table from widgets
• Color Coding for toxicity
• Scaffold Tree improvements:
  • #2154: Scaffold Tree: harmonization.

Bug Fixes

• GROK-13586: _chemFindSimilar fails with 'Cannot read properties of null (reading 'rows')'
• #2135:
  • The counts and controls are partially hidden
  • When change the drawing of a scaffold, then selection (checkbox) of all other scaffolds gets reset (to unchecked)
• #2139: Scaffold tree stops working after adding an invalid structure

1.6.20 (2023-07-21)

This release focuses on improvements and bug fixes.

Dependency: datagarok-api >= 1.14.0

Features

• Set default values in all dialogs where appropriate.
• Unified the layout of the search panel results.
• Work with DBs APIs: Added links to sources, similarity search viewer style, reproduce for ChemicalSpace, Enamine.
• Elemental Analysis: the resulting column name now includes the specific column for which calculations were conducted.
• R-Groups Analysis: a new option to choose between searching for MCS exact atoms or MCS exact bonds.
• Similarity Search: a new Follow Current Row setting prevent recalculation when the current row is changed.
• For proper handling of properties and rendering, we now check for smarts and molecular fragments separately.
• Ability to copy data from the Descriptors and Properties tabs on the Context Pane.
• Moved Descriptors and Fingerprints from the Context Pane to the Top Menu ( Chem > **Calculate **).
• Added Substructure Search to the Top Menu ( Chem > Search)
• Modified the tooltip for dialog and drag-n-drop to prevent it from overlapping with the data.
• Implemented RDKit rendering for Chembl, ChemblAPI, PubChem, and DrugBank databases if OCL is used currently.
• UI polishing: harmonized input field names, repositioned elements in dialogs, added tooltips, and organized the top menu items into groups: Calculate, ADME/Tox, Search, Analyze, and Transform.
• Scaffold Tree improvements:
  • #1730: Implemented Scaffold Tree integration to the Filters Panel.
  • #1998: Now a scaffold tree shows a confirmation dialog before dropping all trees on the Clear icon click.
  • Added the Allow Generate property for the viewer in order to control autogeneration.

Bug Fixes

• GROK-13105: Substructure search doesn't work after similarity search.
• GROK-13118: Activity cliffs selects non-numeric column as activity.
• GROK-13123: Substructure Search: error when the Filter Panel is opened with substructure filtering.
• #1492: Elemental analysis: malformed data handling.
• GROK-11898: Orientation for smiles in Structural Alerts.
• GROK-12115: Hamburger menu closing while switching a sketcher.
• GROK-12905: Sketcher is not opening from the Filter Panel.
• GROK-12929: Scripts don't work if called from the package.
• GROK-12933: Drug likeness: set score precision.
• GROK-12961: Elemental Analysis: Unsupported operation: NaN.round() error on some data.
• GROK-12962: Similarity Search: doesn't work on malformed data.