StarDrop Release Notes

StarDrop

Version 7.3.2 release notes (October 2022).

Bug Fixes

macOS​​:
• Fixed an issue where the bundled Python was dependent on system Python libraries
• Fixed an issue where pyodbc was unable to obtain ODBC driver details
• Fixed an issue where StarDrop crashed when working with invalid dates

Servers:
• Fixed an issue where the model server failed to load models when models generated by the Auto-Modeller were present

 

 

StarDrop

Version 7.3.1 release notes (July 2022).

Bug Fixes

Chemical Structure Handling​:
• Fixed an issue where stereochemistry inversions were occurring in the StarDrop Designer and when a structure was added to a dataset
• Fixed an issue around rendering of hydrogens at stereocentres
• Fixed an issue where the Show hydrogen on stereocentres preference was not being maintained
• Fixed an issue related to incorrect behaviour when sketching hydrogen
• Fixed an issue where stereochemistry was not being detected correctly for some structures, resulting in misassignment of Nitrogen
• Fixed an issue where an uncharged Nitrogen could have more than four bonds without showing a valence error
• Fixed an issue where Nova removes relative stereochemistry from result structures and parent IDs in the Chemistry Transformations workflow

Usability:
• Fixed an issue to disambiguate duplicate data in a third-party platform integration
• Fixed an issue where longer running models caused the models server to become unresponsive
• Fixed an issue where creating a custom line on a scatter plot caused StarDrop to crash
• Fixed an issue in Nova where loading some Matched Series Knowledge Bases caused StarDrop to become unresponsive

Changes

Core application:
• EULA updated to reflect date, new products, trademarks, etc. Further, the text formatting in the StarDrop start-up was cleaned up to improve readability

SeeSAR:
• BioSolveIT libraries were upgraded to the most recent version

 

StarDrop

Version 7.3 release notes (May 2022).

Python 2 to Python 3 upgrade

Core application:
• Upgraded StarDrop client to Python 3
• Embedded Python 3 into the StarDrop dmg to ensure continued macOS support
• Python scripts have been ported to Python 3
• StarDrop servers (P450, Model, Auto-Modeller, Pose Generation) have been upgraded to Python 3
• Python scripts directory has been changed to C:\Users\<Username>\AppData\Roaming\StarDrop\py3 on Windows and /Users/<Username>/StarDrop/py3 on macOS. This change is included to ensure that existing Python 2 scripts are not overwritten during the installation process

Cerella Integration

Core application:
• Suggested measurements functionality is disabled if no structure column exists in the data set
• Issue causing unexpected white boxes on Cerella value distribution histograms has been fixed
• An error message is now returned when incorrect credentials are entered
• Query Interface improvements:
– Fixed an issue where query plugin fails to retrieve some columns from PostgreSQL databases
– Fixed an issue where the query plugin makes an unnecessary number of Cerella login requests
– Fixed an issue where query results were not read from a NUMERIC column in PostgreSQL databases
– Fixed an issue where data source configuration for PostgreSQL databases shows no preview columns

 

Interface/Usability

Core application:
• Long path awareness has been added to handle files with long filenames
• Users must now specify a fragment name when sketching fragments in Nova
• Users can now specify a StarDrop model server, but run pKa calculations on a local machine
• Users can now open multiple model (.aim) files at the same time
• A data set refresh button has been added to the right-hand toolbar
• In Card View Design Preferences, users can now resize the width of the panel so that long column names are not truncated
• The initial (default) similarity threshold has been lowered for Matched Molecular Pairs
• Fixed a crash triggered by manipulating cards and stacks of cards in Card View
• Fixed an issue where 3D coordinates were not saved to SD files in cases where rows contained a single conformer
• Fixed an issue where Nova’s Matched Series Analysis misidentified a scaffold versus a substituent
• Fixed an issue where categorical columns were not available in the Select Properties dialogue of MPO Explorer
• Fixed an issue where a persistent “read-only” message remained in the project title bar
• Fixed an issue where the 2D structure (molecular diagram) was not displayed in the data set for results returned from the pose generation interface
• Fixed errors encountered when opening an SD file:
  – Files containing blank cells are now imported correctly
  – V3000 files containing SMILES property values in the data block are now imported correctly
  – Files that contain blank lines between M End and the first property are now imported correctly
• Fixed an issue where the “remove salts” option added rather than removed a hydrogen when neutralising a charge

StarDrop

Version 7.2 release notes (1 March 2022).

New features

Added the Inspyra module
Core application:
• Table View column headers now support text wrapping
• Visualisation pop-ups can be customised and display chemical structures with multiple properties
• Chart axes can now be logged and unlogged via a context-sensitive pop-up menu
• Added a “6 x 4” plate option in the “assign to plate” action
• Added an opt-in logging facility. Current log statements only cover main startup events
• Refreshing now supports data set headers changed by the user
• Hidden columns remain hidden when pasted into a new data set

Nova:
• The Matched molecular pairs results table now has shown transform IDs in all relevant tables. Also additional columns in the matched pairs table now shown compound IDs.

Changes

Core application:
• Changed the import policy for large integers to treat them as text by default (to avoid precision errors and support compound IDs).
• Default charts now use logged axes for properties that represent molar concentration values with unlogged units
• Custom 2D ring templates now have priority over built in templates
• The RingTemplates folder is now automatically generated in the user’s StarDrop folder
• Image columns are now updated when merging or refreshing
• The Glowing Molecule colour swatch has been removed from from designer
• Removed case sensitivity when searching for models
• Mol block parsing was ported from Optibrium to the OEChem implementation

Nova:
• Changed the Nova setup wizard to no longer show results in card view by default
• Nova was updated to use an updated Matsy knowledge base based on ChEMBL 29

Surflex eSim3D:
• ligand import is now restricted to a maximum of 20 compounds when importing from an SD file

SeeSAR:
• Updated to use the latest BioSolveIT library

Derek Nexus:
• Derek Nexus should now be installed with OpenJDK

Servers:
• Minimum RedHat/CentOS version is now 7.4. A version check has been added to the servers installer
• SSL protocol now set to TLS V1.2

Bug fixes

Core application:
• Addressed an issue where r-group enumeration could generate molecules with values errors
• Fixed an issue where fragments sketched in Nova do not always add successfully to the fragment library
• Modified the charts ellipses button to pop up when there is no space to pop down
• Modified the remove salts logic to avoid neutralising C[N+](=C)C to C[NH](=C)C
• Modified the remove salts logic to allow neutralization of aromatic [N+]
• Fixed an issue where an unexpected SMILES was generated when drawing deuterium
• Fixed a scenario where deuterium would not show in Table View
• Added the ability to create a scoring profile radar plot with axes that represent the score contribution for individual properties in the range 0 to 1
• Fixed an issue where the first pose returned by the Pose Generation Interface server would have no score in the pose table pop-up
• Fixed an issue when editing probabilites where ellided category names would show all ellipses and no category name
• Fixed an issue where editing a column name after importing a CSV file leads to non-deterministic behavior
• Fixed an occasional crash triggered when editing a data set name
• Model search no longer ignnores non-alphanumeric characters
• Fixed a crash encountered when refreshing a data set from Python
• Fixed a hang experienced when changing column type whilst importing a text file
• Fixed an issue where sketched bond lengths no longer match diagram bond lengths
• Fixed a crash encountered when right-clicking a text item in Card View
• Fixed a crash encountered when editing a new column by adding category details
• Improved the responsiveness of StarDrop when running models concurrently
• Fixed a crash encountered when copying data set rows where a row contains a null data entry
• Fixed an issue resulting in missing model results when running models concurrently

Nova:
• Fixed ChEMBL links reported in the Nova matched series results table
• The strictness of strict masking in R-group decomposition has been increased. Strict masking now applies a greaterThanOrEqualTo hydrogen count constraint on scaffold atoms adjacent to r-groups
• Resolved an issue where a different number of suggestions were returned for Matched Series Analysis on macOS and Windows
• Fixed an issue where the chemistry transformations ‘show applicable’ option would give an incorrect transformation count
• Fixed an issue where strict masking was not kept when a compound was pasted into the Nova wizard
• Fixed an issue where the chemistry transformations file location would not be saved between sessions
• Fixed a stall caused by StarDrop attempting to read a corrupt transforms.xml file
• Fixed an issue where the Reaction-based Library Enumeration status message can get “stuck” on “<number> structures generated (100%)” progress for a significant time
• Fixed an issue where the property used for selection in Scaffold-based Library Enumeration was not honoured
• 2D diagram ring templates are now honoured within the Nova area and Nova setup wizards
• Fixed an invalid SMIRKS pattern for the “Acetyl to carboxyl” transformation

BIOSTER:
• Added the tautomer form to BIOSTER entry PYR311. There can now be mutiple transformations for a single BIOSTER entry ID code
• BIOSTER transformations are no longer read at startup to improve startup time

SeeSAR:
• Fixed scenarios where SeeSAR flexX generates no poses

Derek Nexus:
• Fixed a crash when running Derek models

Cerella link:
• Fixed an issue where Cerella values were not added to cells with only measured values
• Fixed a crash stopping a Nova run early when using Cerella models
• Fixed a crash when running scoring using a profile that includes Cerella models
• Cerella batch sizes can no longer be set to zero
• Fixed an issue where Cerella access from StarDrop would expire silently after an hour of inactivity
• Fixed the status message displayed when Cerella models fail to return results. The message no longer says ‘model calculations running’
• Fixed a scaling issue when displaying a Cerella value distribution

Servers:
• Fixed a typo in model_server.log
• Fixed an issue where the servers install would not reinstate the full directory structure for custom models
• Addressed an issue where Auto-Modeller models in the cache are lost if there isn’t enough space in the /tmp folder. If the available diskspace in /tmp is insufficient to backup the files, then the user is prompted for another location.
• Fixed an issue where StarDrop models return “No result from server” when a custom model returns “Missing dependency!”

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