# Chem changelog

## 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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/pull/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/pull/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2495): Chem: MMP - initial vesrion
* [#2540](https://github.com/datagrok-ai/public/issues/2540): Chem | Substructure search: Add an option to toggle the
  realignment of molecules by molecular filter
* [#2525](https://github.com/datagrok-ai/public/issues/2525): Chem | Scaffold Tree: Remove the intermediate dialog
  before the color picker
* [#2504](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2642): Filtering done using viewers is unexpectedly reset on
  applying other filters in some cases
* [#2639](https://github.com/datagrok-ai/public/issues/2639): Structure in filter is unexpectedly changed when there are
  two views in some cases
* [#2646](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2626): Unexpected warning on adding child node to the scaffold
  tree if parent contains 'H' atom
* [#2628](https://github.com/datagrok-ai/public/issues/2628): Structure filter is not applied in some cases when there
  are two views opened
* [#2629](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2550): Chem: Scaffold Tree: Counter is not updated when applying
  the filters
* [#2525](https://github.com/datagrok-ai/public/issues/2525): Chem: Scaffold Tree: Highlighting improvements:
  * More specific fragments should be drawn on top
  * New icons for different coloring states

### Bug Fixes

* [#2536](https://github.com/datagrok-ai/public/issues/2536): Chem: Substructure Filter: Not terminated on fiter reset
* [#2553](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2525): Chem: Scaffold tree: Highlighting improvements:
  * Add a tooltip for the checkbox
  * Add a tooltip for NOT
* [#2526](https://github.com/datagrok-ai/public/issues/2526): Chem: Molecules realignment improvements:
  * Scaffold tree shouldn't reorient molecules in the grid
* [#2533](https://github.com/datagrok-ai/public/issues/2533): RdKitService stays unresponsive as terminateFlag is not
  reset after substructure search has completed

## 1.8.5 (2023-11-14)

### Features

* [#2459](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2511): Scaffold tree: highlighting is not updated when structure
  is edited
* [#2512](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2420): Chem | Scaffold tree coloring:
  * use the trash iscon instead of '-'

### Bug Fixes

* [#2474](https://github.com/datagrok-ai/public/issues/2474): Chem | Scaffold tree: Colour is not inherited by child
  node properly
* [#2476](https://github.com/datagrok-ai/public/issues/2476): Chem | Scaffold tree: Rows are shown as filtered for a
  while after applying structure even if checkbox is not selected
* [#2448](https://github.com/datagrok-ai/public/issues/2448): Some structures are displayed incorrectly when highlighted
  if they are in SMILES format
* [#2473](https://github.com/datagrok-ai/public/issues/2473): Structure filter: 'current value > use as filter' breaks
  filtering in some cases

## 1.8.3 (2023-10-26)

### Features

* [#2421](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2399): Scaffold tree viewer: coloring can't be saved to the
  Layout
* [#2450](https://github.com/datagrok-ai/public/issues/2450): Scaffold tree imported from file is not restored on
  applying saved layout
* [#2448](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2399): Scaffold Tree: Coloring can't be saved to the Layout
* [#2400](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2135):
  * The structure rendering is too small.
* [#2322](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/2154): Scaffold Tree: harmonization.

### Bug Fixes

* GROK-13586: _chemFindSimilar fails with 'Cannot read properties of null (reading 'rows')'
* [#2135](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/1730): Implemented Scaffold Tree integration to the **Filters
    Panel**.
  * [#1998](https://github.com/datagrok-ai/public/issues/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](https://github.com/datagrok-ai/public/issues/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.
