Changelog

This update focuses on UI refinement and workflow optimization, while resolving several inconsistencies.

• Added a column to the atom list to display Wyckoff positions.
• Added a visual indicator to signal when the bond list is filtered by bond type.
• Added LaTeX export functionality for the atom list.
• Added tooltips for atoms and bonds within the atom list, bond list, and Navigator window.
• Atom tooltips now display anisotropic displacement parameter (ADP) data, where available.
• Bond tooltips now display the assigned bond type.
• Integrated missing keyboard shortcuts into the main menu.
• Introduced a Set View Direction dialog for camera orientation.
• Tooltips for atoms and bonds in the atom list, bond list, and the Navigator window.

• Disabled camera adjustment during Expand Atoms when holding Ctrl to ensure consistency.
• Improved the formatting of atom and bond tooltips for better readability.
• Optimized the layout of the View context menu in the structure view.
• Set the default reference axes to display crystal coordinates.
• Updated the atom list to display non-normalized coordinates for the asymmetric unit.

• Corrected the sorting logic for the asymmetric unit and unit cell within the atom list.
• Fixed a bug where the selection box would incorrectly select the first entity in the structure (typically the reference axes).
• Fixed a rendering issue where labels and other objects failed to update after undo/redo operations.
• Resolved a conflict where redundant atom definitions in CIFs led to inconsistent structure growth.
• Resolved an issue where expanding a structure from an initial structure produced displaced atoms in specific scenarios.

This update improves the general workflow with chemical structures and fixes some inconsistencies.

• Added a Remove All → Weak Interactions command to specifically delete hydrogen bonds, van der Waals, and metallophilic interactions.
• Added an Apply button to the bond determination dialog; internal molecule definitions can now be updated too.
• Added descriptive tooltips and implemented previously missing shortcuts for mouse actions.
• Atom, bond, and bond angle lists now support both sorting and multi-selection.
• Bond determination parameters are now saved within shapeXT files, ensuring consistent settings across sessions.
• Electron density calculations can now be performed while excluding specific atoms.
• Introduced shortcut C to complete a structure.
• Surface calculations can be targeted to specific selected atoms or configured to exclude selected atoms.
• Users can now select or delete entire molecules by holding Ctrl while clicking on an individual atom or bond via the Select Objects and Delete Objects actions.

• Adjusted default settings: Unit cell visualizers (box, arrows, and labels) are no longer created by default.
• Increased the default minimum bond length to 0.6 Å.
• Optimized GPU utilization in certain situations when managing multiple open structures.
• Updated the P shortcut to toggle the on-screen drawing tool (double-tap P to clear).

• Fixed a regression introduced in v2026.07.1 that caused the over-detection of hydrogen bonds.
• Fixed an issue where atoms were displaced due to internal coordinate snapping while growing periodic structures.
• Resolved an issue where dative bonds were incorrectly categorized as “custom” bonds in the bond list.

• Enhanced the Build → Determine Bonds… workflow by introducing a dedicated settings dialog.
• Implemented a Fill Asymmetric Unit command, allowing users to generate only the asymmetric unit.

• Refined the handling of initial asymmetric units; coordinate shifts to the [0; 1) range are no longer applied automatically, ensuring better data consistency.
• Set Asymmetric Unit + Complete Fragments as the new default for initial structures (CIF/SHELX).
• The view no longer auto-adjusts when completing a single fragment via an atom's context menu.

• Corrected a bug where valid hydrogen bonds were being removed due to angle checks.
• Ensured that minimum and maximum bond length constraints are strictly enforced.
• Fixed an issue in the Calculate Electron Density dialog that prevented changing the calculation mode while atoms were selected.
• Resolved an issue where the CShM algorithm could hang on specific edge-case geometries.

This update introduces automated molecule detection and enhances the initial view configuration when loading new structures.

• Implemented automated molecule detection.
• Molecules can now be selected or toggled (hidden/shown) via the Navigator window.
• Molecules/fragments can now be completed via Build → Complete Fragments.
• Specific molecules/fragments can now be completed via Complete Fragment (right click on an atom).
• Specific molecules/fragments can now be completed via the Expand Atoms mouse action by clicking on an atom while holding the Ctrl key.
• Added customization for initial structure visualization via Settings → Default View.
• Added support for selecting a fractional coordinate origin for periodic surface calculations.
• Added support for VASP file formats (POSCAR/CONTCAR).

• Update notifications can now be dismissed using the Esc or Enter keys.

• Corrected aspect ratio scaling for structure preview renderings.
• Custom settings for bond detection have not always been applied.
• Fixed parsing of FVAR-based SOF (occupancy) values within the SHELX file format.
• Resolved an issue parsing floating-point values with leading '+' signs in input files (Linux).

This release addresses a stability issue affecting Intel integrated graphics on Windows that caused shapeXT to crash on startup for these users.

• Preferences are now preserved across updates. The settings will no longer reset after launching a new version.
• When using “Select Molecule” (Ctrl+M) with nothing currently selected, the app will now automatically select the last focused molecule.

• Fixed a crash issue for users with Intel integrated GPUs on Windows.
• Fixed an error where chemical bonds appeared incorrectly on Intel integrated GPUs.

• Added customizable atom and bond visual styles.
• Added support for dative (coordinate) bonds.
• Bond list now supports filtering by bond type.
• Bond angle measurements can now be copied to the clipboard for easy export.
• Bond Valence Sum (BVS) calculations with user-defined reference parameters.
• New settings dialog with a “Default View” configuration option.
• New dialog for adding atom vectors.
• Automatic calculation of estimated standard uncertainties (ESD) for unit cell volume.
• Support for reading estimated standard deviations (e.s.d.) of cell parameters from CIF, SHELX, and DSF files.
• Windows: Structure files can now be associated with shapeXT for seamless integration.

• Dark mode is now the default UI theme.
• Updated and reorganized example structure files.
• Enhanced SSAO (ambient occlusion) rendering for smoother molecular surface shading.
• Improved built-in updater.
• Removed visual transitions during image sequence rendering for more accurate frame-by-frame output.
• Background settings are now view-specific, allowing different backgrounds for each saved view.
• Updated to Dear ImGui v1.92.8, ImPlot v1.1 WIP, and Qt 6.11.1.
• macOS builds are now code-signed and notarized.
• Refined layout and usability of the Hierarchy and Navigator panels.
• Graphics initialization now properly synchronizes with the main window to prevent startup crashes.

• Bond angle list now updates in real time when structures change.
• Fixed preview rendering to no longer display unwanted object outlines.
• Resolved SSAO rendering artifacts (bright halos and incorrect dark shading).
• Fixed loading of PNG files containing embedded molecular/crystal data.
• Improved handling of non-periodic (finite) structures in COSMOS (.coo) files.
• Fixed on-screen label rendering caused by depth buffer inversion.
• Resolved transparency rendering issues on Intel Arc GPUs.
• macOS builds now include MoltenVK to ensure reliable Vulkan support.
• Fixed library path resolution (RPATH) for Linux distributions.