rdeditor

Updating the edit with the drag event. Simplifying the number of actions. More info in the updates README, but most notably, clicking on an atom changes the atom, click-drag on an atom, adds a new atom. dragging between two atoms creates a bond.

rdEditor now has support for showing and editing dummy atoms (i.e. R-groups) thanks to a contribution from @jacktday

A new atomtype "R" with atomnumber 0 has been added, and the number can be changed via the "A#" action which can set the atomMapNumber of atoms. The R-groups support save to molfile, and in SMILES they are supported as * atoms. The "A#" can also be used to edit the atommapnumbers of regular atoms.

Also, some icons missing from the previous release has been added.

rdEditor Release Notes
Bug Fixes and Technical Improvements
Major Bug Fix: Conjugated Aromatic Double Bonds

Fixed an issue where conjugated aromatic double bonds could "shift" incorrectly
This fix necessitated a redesign of the molecule handling and drawing stack
The visualization now more accurately reflects the status of the molecular graph

Stereochemistry Visualization

• Improved drawing code and visualization of R/S and E/Z stereochemistry
• Added distinction between undefined E/Z (visualized as trans) and defined E (visualized as Trans and annotated with (E))

Template Addition Improvements

• Redesigned template addition code for better expandability
• New templates can now be added via definition of SMILES and reaction SMARTS, rather than custom code

Configurable Molecule Handling

• Sanitization and kekulization of molecular objects are now configurable, can be consciously applied to clean up chemistry at any point in the drawing process
• Kekulization is optional, allowing work with aromatic bonds and representations

PySide Upgrade

• Upgraded from PySide2 to PySide6 for improved compatibility and easier installation

Additional Notes:

Various minor bugfixes and performance improvements

We encourage users to test these improvements and report any issues. Your feedback is crucial for the continued development of rdEditor.

v. 0.4.0.1 Bugfix, now stereoinfo is updated when molecule is edited, even outside the stereogenic center.

Fixing a bug that prevented launching for new installations due to an import of a unneeded module.

Updates to PySide6 and minor bug-fixes and improvements.

Last pyside2 release was
https://github.com/EBjerrum/rdeditor/releases/tag/0.2.0.1

Last release for pyside2

Extended features has been added, view widget can now be customized to have different selection colours and unsanitizable responsive background.

Moreover, the edit widget now supports addition of rings, benzene and cyclohexane. This necessitated a new editing paradigm, where either a bond, an atom or a ring is chosen as the chemEntity to draw with, either via that property, or via setAtom, setBond and setRing. It is thus not possible to have a custom atom (e.g. N) and a custom bond (e.g. double), selected at the same time, which anyway could lead to unintuitive and unwanted behaviour when adding new atoms or bonds.

Fixes a bug, where the exit-dialogue failed with python 3.11 and pyside 5.13.2

Fixed an issue, where newer versions of Python install an older version of PySide2, that didn't work with the | comparison as previously used.

Dark mode and persistent setting, including icons

Deploying tagged version to pypi via github actions.