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Current UnityMol changelog
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UnityMol_ChangeLog.md

UnityMol Changelog

[1.1.3] - 2021-02-10

  • [Feature] Add orthographic camera mode
  • [Feature] Serialization: export the current UnityMol state to a JSON file (selections, representations, annotations) !
  • [VR|Feature] LeapMotion support re-added
  • [Feature] Tour feature: long click on a selection to add it to the tour animation
  • [Feature] Call python functions each frame of a trajectory: last().NewFrameDeleg += myPythonfunc
  • [Feature] Energy plots for IMD
  • [Feature] Each line of the console can be clicked to copy to clipboard
  • [Feature] LeftAlt + click to display information about atom (like double right click)
  • [Feature] Add color by resid and resnum + Update UI
  • [Feature] Outline color can be changed
  • [Feature] Limited view for cartoon
  • [Feature] Center on selection now has a customizable time to zoom
  • [Feature|Experimental] Grid view (pymol like)
  • [Feature] Remote command from python using ZMQ module (call activateExternalCommands() to enable)
  • [Feature] UnityMolMain.iversion returns 113 for 1.1.3
  • [Feature] Export Ambient Occlusion when exporting FBX and OBJ files
  • [Feature] Follow a selection during a trajectory (desktop only), getManipulationManager().followSelection = "selName"
  • [VR|Feature] New VR scenes added
  • [VR|Fix] Performance issues caused by rendering at 2 times the resolution
  • [Fix] Improve cartoon normals
  • [Fix] Autocompletion works for larger paths
  • [Fix] Annotations, sphere annotation size + world annotation warnings
  • [Fix] Adding hydrogens with Reduce or Haad caused incorrect atom ids
  • [Fix] MDDriver disconnect fixes
  • [Fix] Double click to zoom should behave better
  • [Fix] Empty lines are ignored when loading python scripts
  • [Fix] Line representation trajectory + updating selection caused errors
  • [Fix] Trajectory performance issue at the end of the file
  • [Fix] Unloading dx map
  • [Fix] Simplify AO computation
  • Disable surface threads for large molecules (>50k)
  • Depth of Field effect now follows the selected atom during the trajectory

[1.1.2] - 2020-10-14

  • [⚠️] Change the default selection "all(1kx2)" to "all_1kx2"
  • [Feature] Average trajectory with a sliding window
  • [Feature] Add python standard modules (random/urllib/zlib...) still no numpy :(
  • [Feature] Measurements in desktop mode by pressing "M" and cliking on atoms
  • [Feature] Double click selection name to center the view
  • [Feature] UI for annotations
  • [Feature] Set bounding box line size
  • [Feature] Use MDDriver instead of Artemis for IMD
  • [Feature] Add a function to set trajectory frame: setTrajFrame()
  • [Fix] centerOnStructure now fills the screen with the selection
  • [Fix] Reduce / Haad did not work when UnityMol was in a folder with spaces
  • [Fix] Inverted IMD coordinates !
  • [Fix] Transparent surfaces are now using a dither shader
  • [Fix] UI now shows if all representations of a molecule are shown/hidden
  • [Fix] Saving/restoring the history of commands at launch/quit
  • [Docking] Fix parsing forcefield
  • UI now uses various events to be updated
  • Improve manipulation behaviour when stopping an animation

[1.1.1] - 2020-09-09

  • [Feature] Biological assembly can now be fetched by doing fetch("1BTA", bioAssembly= True)
  • [Feature] Native notifications: NativeNotifications.Notify("Message") / NativeNotifications.AskYesNo("Question") / NativeNotifications.AskContinue("Question")
  • [Feature] Add 2D text annotation: annotate2DText(Vector2(0.5, 0.5), scale= 1.0, "Text", Color.white)
  • [Feature] Cubic interpolation for trajectory
  • [Feature] Add a function to unhide selection representations
  • [Feature] Hyperball parameter switch with interpolation: setHyperBallMetaphore("licorice", lerp= True)
  • [Feature] Get current parent positions/rotations with loadedMolParentToString(addToHistory= True)
  • [Feature] API functions to pause/unpause a video recording
  • [VR] Drop obsolete VRTK plugin, we now move to VIU (https://github.com/ViveSoftware/ViveInputUtility-Unity)
  • [VR] Range selection with long press
  • [VR] Vibrations when hovering UI buttons
  • [Docking] Enable/disable custom colliders based on atom names
  • [Docking] Fix recording docking state to PDB
  • [Fix] exporting hyperball without cubes
  • [Fix] updating empty selections during trajectory when a UnityMolSelection has updateContentWithTraj = True
  • [Fix] mouse interaction when dragging from UI to scene
  • [Parser] Improve atom type recognition
  • [Parser] Fix a GRO parser bug for atom serial
  • [Parser] Fix a PDB parser bug for negative residue ids
  • [Parser] Fix a PDB parser bug when using modelAsTraj and alternative positions
  • [Parser] Fix PDB/PSF/TOP/XML parsers when more than 27 bonds per atom
  • [IMD] Artemis plugin is now compiled without spamming the log file
  • [IMD] Fix distance pull with mouse
  • Various improvements when recording videos/screenshot (antialiasing + post-process effects)
  • Outline now affects transparent surfaces
  • Improved logo: https://drive.google.com/file/d/1XEGGiQK20CN1WwIm02lX9TTrabeAcWDi/preview
  • Faster line update during trajectory reading/IMD
  • Use SharpZipLib to avoid .Net gzip issues
  • .ent extension added to file browser
  • Fix AO for surfaces when UnityMolMain.disableSurfaceThread = True
  • Text annotation orientation fix
  • Stop camera movements when interacting with the scene before the animation is done
  • Various other bug fixes

[1.1.0] - 2020-06-29

  • Wireframe shader for all platforms

  • Transparent cartoon

  • Improve line representations visual

  • Add a PLY mesh exporter

  • Export hyperballs to meshes (WIP)

  • Read/Write large PDB/mmCIF/GRO files

  • Add a way to translate or rotate only the clicked molecule in desktop mode

  • Parse Tuffery rotamer library

  • Set light parameters from API

  • Add function to play a sonar sound at world position

  • Add functions to wait for N frames or N seconds from scripts (yield waitSeconds / yield waitFrames)

  • Autocomplete paths

  • XTC trajectory reader for WebGL

  • Add functions to change cartoon tube size / draw as tube + bfactor

  • Add function to select inside a box

  • Add functions to get and set chi torsion angles

  • Add option to not record every action to console

  • Add input fields to sliders

  • Disable AO for VDW by default + Add a button to compute AO

  • Fix trajectory UI for VR scene

  • Improve PDB/mmCIF/GRO parsers -> faster + less memory

  • UnityMolBonds now uses integers instead of UnityMolAtom -> faster + less memory

  • Fix UI scaling + allocate way less memory per selection + faster creation

  • Fix a lot of memory leaks (Unity meshes and materials)

  • Improve PDB parser: resnum is used instead of the parsed residue id + use hybrid36 parsing norm

  • Fix precision hyperboloid shrink factor precision

[1.0.39] - 2020-04-27

  • Read PSF or TOP files to import a topology (only bonding info is read)
  • Change default selections & representations
  • Fix parenthesis in selection language
  • Import multi-line python script fix
  • Fix PDB writer sometimes causing issues with EDTSurf/Reduce/haad
  • Change UnityMolStructure.uniqueName to UnityMolStructure.name
  • A lot of "quality of life" improvements, shortcuts, UI...
  • Add shortcuts to show/hide the console and the UI: CTRL+Space / CTRL+Backspace
  • Add power saving mode (can cause black screen on Mac)
  • Add customUnityMolColors.txt file in StreamingAssets/ folder to easily add new atom colors/radius
  • Add UI for post-processing effects (DepthOfField/Outline/DepthCueing)
  • Remove + and - operators for selections
  • Can now recompute secondary structure information during a trajectory (structure.updateSSWithTraj)
  • Export OBJ files with exportRepresentationsToOBJFile function
  • Depth cueing works for all the representations/shaders
  • Improve atom type recognition
  • Improve autocompletion
  • Improve automatic selection query content
  • Renamed centerOfGravity to centroid

[1.0.37] - 2020-04-07

  • Trajectory picker
  • Support for non-orthogonal DX maps
  • Partial support for MARTINI files
  • Support for large XTC trajectories, not fully loaded in memory
  • Limited view for iso-surfaces (enableLimitedView/setLimitedViewCenter/setLimitedViewRadius functions)
  • Load bonds from XML file (loadBondsXML function)
  • Add bond order representation based on hyperballs
  • New representations (Point/HireRNA ellipsoids/Alpha trace/Sheherasade/bond order)
  • PDB/GRO/mmCIF multi-model files are read as a trajectory by default
  • Save representation state when changing models or selection content
  • Drag&Drop support for molecular and history script files
  • Pymol sessions to UnityMol commands script [here][https://github.com/LBT-CNRS/PymolToUnityMol]
  • A LOT of bug fixes and performance improvements

[1.0.34] - 2019-10-14

  • Separated threads to compute molecular surfaces at load time
  • Ultra-fast cartoon representation
  • Ambient Occlusion for hyperballs in Van der Waals representation
  • Add a new representation "Sheherasade"
  • Parse mmCIF connectivity
  • Fix some UI + sound issues
  • Performance improvements (fieldlines/trajectory smoother/raycast/center of gravity -> compiled with Burst)
  • Command line arguments (example 'UnityMol.exe -i 1kx2 pdbs/1crn.pdb')
  • Fix recording videos in VR
  • IMD should work on Mac and Linux now
  • Fix PDB writer when residue name is too large
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