inst/visu/lib/bio-pv/README.md

In jwist/visualizeR: visualize metabolomics data interactively

pv - WebGL protein viewer

pv is a WebGL-based protein viewer whose goal is to once-for-all end the reign of Java applets on websites that require visualisation of protein structures. It's not you Java, it's all the annoying security popups and slow loading times. pv implements all major render modes that you would expect, and supports custom color schemes.

Because there is nothing worse than a unresponsive website, pv has been implemented with maximum performane in mind. Even very large macromolecules can be visualised at interactive framerates.

Trying it out

You can try the online demo or run it locally on your computer.

Clone this repository

git clone https://github.com/biasmv/pv.git

Change to the pv directory and serve the files using the serve script in the source directory. This will start a simple static-file server using Python's SimpleHTTPServer module.

cd pv
./serve 

Open a WebGL-enabled web browser and visit http://localhost:8000

Want to use PV on your website?

I would love you to! Most features you would expect from a protein viewer are already present and working. One considerations is important though:

• WebGL is only supported in a subset of browsers. If you can afford to lose users of IE and older versions of browsers, pv is a good solution for protein visualisation.

Citing PV?

I'm planning on writing a small application note, but in the mean time, use the following DOI for citing PV in your work.

Contributing

Contributions of any kind (bugfixes, documentation, new features etc) are more than welcome. Just file bugs or file bug requests. Before submitting pull requests, please make sure to follow these guide-lines.

Acknowledgements

PV uses the amazing gl-matrix JavaScript library for matrix and vector operations.

Thanks to @Traksewt, @kozmad, @greenify for their contributions

Documentation

Documentation for pv is available here.

Changelog

New in Version 1.5.0

• Added Viewer.spin command to spin the camera around an axis
• Relax some limits on number of elements that could be rendered at full connectivity level. Now it would theoretically be possible to render 2^24 atoms, even though the amount of geometry is likely to take down the browser.
• Fix rendering for very long RNA molecules that broke some assumptions in the cartoon rendering code (1J5E, for example see issue #82).
• Improve heuristics to determine whether two residues belong to the same trace by not introducing trace breaks in case the residues are connected by a bond. This allows users to manually set bonds in case they have other means of knowing that two residues are to part of the same trace (#83).

New in Version 1.4.0

• Basic support RNA/DNA rendering for all render modes
• Multi-touch support for iOS and Android (with contributions by @kozmad, @lordvlad)
• improved visual clarity of text labels
• use correct line width when manual anti-aliasing is enabled.
• text labels can now be styled (color, font-family, font-weight, size)
• reduced file size of minified JavaScript file by a little more than 10%
• ability to add geometric shapes to the 3D scene through customMesh
• ability to specify custom color palettes (@andreasprlic)
• viewerReady event (@andreasprlic)
• PV can optionally be used as an AMD module without polluting the global namespace
• added more unit and functional tests. The tests reach a coverage of 80% of the total number of exectuable lines of code.
• support for loading small molecules from SDF files

New in Version 1.3.1

• fix bug in strand smoothing which would cause residues at the beginning of the trace to get collapsed.
• rendering: check for null slab object to allow drawing to work when no objects are visible.

New in Version 1.3

• publish it as an npm module
• PDB IO: parse insertion codes
• add method to retrieve current color of atom. This is useful for highlighting purposes, where the color of certain atoms is temporarily changed and then reverted back to the original.
• smoothing of strands when rendering as helix, strand, coil cartoon
• implement proper strand "arrows"
• improved auto-slabbing when the rendered objects are off-center

New in Version 1.2

• add transparancy support to mesh and line geoms (@kozmad)
• substantial speed improvements through implementation of buffer pool for typed arrays.
• method to assign secondary structure based on carbon-alpha positions
• improved documentation
• improve dictionary selection
• support for adding text labels to the 3D scene
• autoZoom to fit structure into viewport
• work around uint16 buffer limit of WebGL by automatically splitting the geometry of large molecules into multiple buffers
• support for different color notations, e.g. hex, color names.
• support for displaying molecular assemblies, including support for picking of symmetry-related copies
• implement different slab-modes
• rudimentary support for rendering MSMS surfaces in the browser. Requires conversion to binary format first.
• adding customisable animation time (@Traksewt)
• add customizable atom picking events (double and single click) (@Traksewt)
• improved animation support (@Traksewt)
• customizable background color (@Traksewt)

jwist/visualizeR documentation built on Dec. 1, 2019, 5:11 p.m.