v1.5.3

This release fixes a few issues that were identified during beta testing and makes some stability improvements under the hood.

Specifically, the bug with --cycle-snapshots was fixed and all the flag handling was made more stable by the use of the tclap library. Furthermore, a --one-slot flag was introduced that tells the viewer to only display the first non-core-17 slot from a FAHClient instance, rather than all available slots. Once FAHClient can read FahCore_17 slots, I will add a --slot flag, which will be used in conjunction with this flag to show that particular slot. Note that --slot=id is passed to FAHViewer by FAHControl, so this flag will bring Folding Atomata closer to becoming fully compatible with FAHViewer.

v1.4.1

This is a major release. It introduces a large number of features, bug fixes, and major efficiency improvements under the hood. It adds a skybox, textured with a soft square-point gradient. It adds the capability to show all proteins from all non-FahCore_17 slots from a single instance of FAHClient, which it does by default. It also introduces a small light-green wiremesh that bounds each protein, and a few other visual tweaks.

Atomata will now use minimalistic resources when idle, and only renders when necessary, which is either when the camera moves or when animation happens. You can now use a flag to slow the animation down, and if the camera is still, almost no computational resources will be used. Alternatively, increase the fineness of the animation and the resolution of the atoms for a very clean rendering of the protein. With the significant efficiency improvements, enjoy flying around the model at a high FPS!

v0.6.8

A few changes from 0.6.7, this release offers the following:

1. Slight reduction in camera control acceleration.
2. Atoms are drawn in proportion to their electron shell count.
3. Fixed camera not being centered on protein at startup.

These are small changes, but the visual difference is very apparent. Try it out and see for yourself!

v0.6.7

This release completes many of the issues in the 0.7 milestone. This release introduces the following:

1. Stick rendering mode, wherein only the bonds are drawn. Active using --mode 3 or -m 3.
2. A detailed demo protein with 18 snapshots, used as a backup when the connection to FAHClient fails.
3. Reduction in dependencies: glm and png++ are now included, though libpng is still needed.
4. The resolution of the atom spheres can be increased with the --slices and --stacks flags.
5. Behind-the-scenes changes to the data structures for atoms, bonds, and snapshots.
6. Split proteins (a simply visual glitch with FAHViewer) can now be identified in milliseconds. This is preparation for a future fix where all the identified pieces will be unified back together.
7. Attempts to improve efficiency and decrease CPU while rendering.

v0.6

This release implements key command-line flags and allows connections to remote FAHClients using a password. The easiest way to see this is to replace FAHViewer with FoldingAtomata in the Preferences tab in FAHControl.

Commands:

--help, -h	Show usage and flag options.
--connect, -c	Address and port to use to connect to FAHClient.
--license	Prints license information.
--password, -p	Password for accessing the remote FAHClient.
--version, -v	Print version information.

Examples:

• FoldingAtomata
• FoldingAtomata --connect=203.0.113.0:36330 --password=example

v0.5.1

Bug fixes identified during the first round of alpha testing on IRC.

• Fixed segfault that occurred if slot 0 was unavailable. (#33)
• Improvements to the install-from-source script. (#34)
• Easier compilation if GCC or Clang are compiled from source. (#35)

Big thanks to TheFlipside and jimerickson for their feedback.

v0.5.0.1

First public release! I published this stable edition my Launchpad PPA; ppa:jvictors/gitstable
For installation instructions, please see the README.

This fixes a minor dependency error that was present in the main v0.5 release.

v0.5

This completes the v0.5 milestone! The ball-and-stick model of trajectory 0 is now animated using all available snapshots. Camera movement is more fluid and smooth as it uses acceleration. I also added a little spot of light to each atom to make them look more 3D. Atomata handles dual-monitors better now as well.

v0.4.9-alpha

This completes almost all of the v0.5 milestone. Atomata creates a ball-and-stick model from snapshot 0 of trajectory 0, through which the user can fly through and look around. The atoms are color-coded in accordance with the CPK coloring scheme, and bonds are drawn between them. This release also offers improved camera controls and better handling of a window resize event. Furthermore, Debian files, folders, and shell scripts are set up to fully install the program on the filesystem, and there's a manpage. More importantly, there's now support for pushing to Launchpad, where code is compiled and built remotely, and the binaries can be distributed through a PPA and automatically updated via apt-get. All the code is now sharable under the GPLv3 license.

Here's an example of v0.4.9 rendering a protein that my CPU is working on:

v0.3-alpha

This release looks visually identical to v0.2-alpha, but there's been some important behind-the-scenes changes. I've organized the code that communicates with FAHClient and handles its PyON-formatted output. The SlotViewer class is now ready to generate and position the 3D models that will represent a snapshot from each protein trajectory. Mniip helped me develop the command to concurrently compile the code, which helps development.