Recent Releases of 3dmol
3dmol - 2.5.0
What's Changed
- py3dmol supports data argument
- mesh surfaces
- antialiasing improvements
- make upscaling configurable
- better symmetry support for surface objects; can more easily modify symmetries
- improved fog implementation, including configurability
- fix for grids on very large canvases
- more robust selection by model
- text cif files populate lchain property now
- cartoon gap visualization with gapcutoff style option
- improved prmtop parsing
- assorted minor fixes, tweaks, and documentation changes.
This release introduces some minor breaking changes in the GLModel API. Models now keep track of their viewer so any functions (e.g. vibrate) that took a viewer as an argument now don't.
What's Changed (PRs)
- fix docstring CIF location by @cmishra in https://github.com/3dmol/3Dmol.js/pull/814
- Bump cross-spawn from 7.0.3 to 7.0.6 by @dependabot in https://github.com/3dmol/3Dmol.js/pull/815
- Build as both UMD and ES6 modules. by @asford in https://github.com/3dmol/3Dmol.js/pull/831
- Improvements to learning-environments.md by @prajwalkulkarni in https://github.com/3dmol/3Dmol.js/pull/765
New Contributors
- @cmishra made their first contribution in https://github.com/3dmol/3Dmol.js/pull/814
- @asford made their first contribution in https://github.com/3dmol/3Dmol.js/pull/831
Full Changelog: https://github.com/3dmol/3Dmol.js/compare/2.4.2...2.5.0
- Jupyter Notebook
Published by dkoes 9 months ago
3dmol - 2.4.0
Update rendering engine to use a single, shared OffscreenCanvasRenderer (if available). This should eliminate lost WebGL context errors for most cases. Improved antialiasing. Support colorscheme updates on surfaces. Add show/hide methods to labels. Add maxpixels option for outline mode to limit the screen space width of the outline. Improved VASP file parsing.
- Jupyter Notebook
Published by dkoes over 1 year ago
3dmol - 2.3.0
Ambient occlusion view style (enable with setViewStyle or as part of viewer configuration). Better antialiasing. More robust viewer regeneration. A few other tweaks.
This release has fairly significant changes in the rendering pipeline that may cause problems with older devices (but not on any I have access to). Please report any device/browser issues.
- Jupyter Notebook
Published by dkoes over 1 year ago
3dmol - 2.1.0
Dashed bond drawing contributions from @dxdc, code improvements from @prajwalkulkarni, assorted improvements to visualizing CIF files in the unit cell (include ability to wrap individual atoms to cell), more robust handling of lost contexts, assorted other bug fixes.
- Jupyter Notebook
Published by dkoes almost 2 years ago
3dmol - 2.0.0
This is a massive refactoring of the code base that may (unintentionally) break things. * Now written in TypeScript * jquery no longer used or included * new build system (webpack) with better tools (code coverage and testing) * custom linear gradients now supported * improved cartoon quality * hbondCufoff parser option * can now pause animation
Many thanks to @RyanGuild , @angel4576 and @tjakubiec218 for their contributions.
- Jupyter Notebook
Published by dkoes about 3 years ago
3dmol - 2.0.0-rc.1
This is a massive refactoring of the codebase into typescript. This release candidate is to enable broader testings. Use at your own risk (and report issues!).
- Jupyter Notebook
Published by dkoes about 3 years ago
3dmol - 1.8.0
Possibly breaking changes: reordered arguments in py3Dmol.view so you can do py3Dmol.view('1ycr') to easily display your desired molecule. Changed how javascript is assembled to temporarily disable amd for better functionality in amd situations.
Allow style to be set with style strings (e.g., can do 'sphere:colorscheme~greenCarbon' instead of creating a dictionary).
Fix for memory usage from @dumplings
Resolved display issues reported in Issue #548 .
Added support for creating an animated PNG from an animation (apng in py3Dmol).
Assorted fixes.
- Jupyter Notebook
Published by dkoes about 4 years ago
3dmol - 1.7.0
GSoC @jaxmatrix contributed a built-in viewer/style editor that can be enabled in the embedded viewer by specifying data-ui='true'.
Preliminary support for non-ortho boxes with volumetric data. Support for pruning volumetric data by a selection. Added ability to have gradient backgrounds in labels to make colorbars. Add ability to provide coordinates as an array in setCoordinates (makes for nice interface with python generated coordinates in py3Dmol).
Possible fix for memory leak in notebooks, assignBonds parser option, py3Dmol improvements, spectrum option in viewer, fix cartoon quality bug. Contributed bug fixes from @camilacanhete (eye separation), @mindon (vasp parsing), @Luthaf (wheel).
Issues #530 #520 #440 #439 #366
- Jupyter Notebook
Published by dkoes over 4 years ago
3dmol - 1.6.3
Better support for reapplication of vibrate. Lattice parsing for xyz (thanks to @pvstishenko). Speed option for spin (thanks to @BradyAJohnston). backgroundalpha embed option. screenToModelDistance viewer function. Minor code and documentation tweaks.
- Jupyter Notebook
Published by dkoes almost 5 years ago
3dmol - 1.6.2
Implement coloring an isosurface by a different volume data (e.g. isosurface drawn from electron density, colored by electrostatic potential). setCameraParameters from @Luthaf. Several bug fixes, documentation tweaks, and added tests.
- Jupyter Notebook
Published by dkoes about 5 years ago
3dmol - 1.6.0
A number of improvements to handling of crystallographic files. Unit cells have more options for rendering and can be animated (with multi-model cif files). A normalizedSymmetry option will pack things into the cell.
Improved handling of boolean selectors. Improved resize detection. Documentation improvements and minor bug fixes.
Many thanks to Guillaume Fraux and Qiang Zhu for their contributions.
- Jupyter Notebook
Published by dkoes over 5 years ago
3dmol - 1.5.0
With this release we switch to using WebGL 2.0 canvases if available. This enables volumetric rendering and will allow us to implement other sophisticated rendering techniques in the future.
Preliminary volumetric rendering is implemented with support for orthorhombic boxes only (e.g. file formats that do not use a matrix transformation, so unfortunately ccp4 isn't supported yet).
APIs for shared sessions, which enables an "active learning" environment for education are provided.
Clickability for cartoon traces, python integration fixes, improved documentation, better handling of changing device pixel ratios, default to higher resolution rendering, additional tests and bug fixes.
- Jupyter Notebook
Published by dkoes about 6 years ago
3dmol - 1.4.0
Switch to gulp build systems with lots of related code cleanup. V3000 support from Paul Watson. dashed option for CylinderSpec from Michael Silveira. Enhancements to vibrate (bothways option). Animation support for labels and shapes. Improved remove label functionality. Assorted bug fixes.
- Jupyter Notebook
Published by dkoes over 6 years ago
3dmol - 1.3.5
New features: addCurve, improved model selection indexing (especially useful for py3Dmol) Bug fixes: wireframe shapes, cylinder enums, better slabbing on zoomTo, mmtf secondary structure assignment, hide applied to stick style, improved documentation/tests
- Jupyter Notebook
Published by dkoes over 7 years ago
3dmol - Bug fix update
An assortment of bug fixes - orthographic click handling, fixed bounding spheres, fix for translation, addBox, better stereoviewers.
- Jupyter Notebook
Published by dkoes almost 8 years ago
3dmol - 1.2.0
Support for more MD file formats, a new Promises-based api, implementation of a split viewer that supports multiple viewers on a single canvas, initial support for stereo viewers, improved hosted viewer, several bug fixes and feature tweaks.
- Jupyter Notebook
Published by dkoes over 8 years ago
3dmol - 1.0.6
Additional and improved support for volumetric data formats (e.g. ccp4). Preliminary support for mmtf. Implementation of a simple static widget for ipython notebooks. Add support for discrete colormaps in style. Add support for orthographic projection. Minor bug fixes.
- Jupyter Notebook
Published by dkoes almost 10 years ago
3dmol -
Imposter and instanced rendering for spheres and sticks for substantial performance and memory usage improvement. Variety of bug fixes.
- Jupyter Notebook
Published by dkoes almost 10 years ago
3dmol - 1.0.4
Improved cartoon rendering (several more styles available). Improved support for multi-model files and animation. Better support for transparency. Additional crystallography support (e.g. addUnitCell, etc.). Outline viewer style. Numerous bug fixes and minor enhancements.
- Jupyter Notebook
Published by dkoes over 10 years ago
3dmol -
Numerous bug fixes. Improved support for cartoons (e.g. nucleic acids), better support for symmetries.
- Jupyter Notebook
Published by dkoes almost 11 years ago
3dmol - April 11, 2015
SemVer compatible release tag
- Jupyter Notebook
Published by dkoes almost 11 years ago
3dmol - Jan 21, 2015
This release provides support for rendering of trace cartoons (even for CA only files) and improved support for specifying file format options.
The primary reason for the release though is to make sure the automatic updating to the jsDelvr CDN is working.
- Jupyter Notebook
Published by dkoes about 11 years ago