Siyoung,
I did make a bundle that can parse and save SDF files, but I probably won't be uploading it to the toolshed any time soon. I don't really have the time to support it or develop it much further, but hopefully it can help as an intermediate solution. This bundle was just for helping with the Ess/Fleming groups' ORA (organic reaction animation) project. The trajectories shown on the website (
https://webora.chem.byu.edu/) or iPhone app (iORA) are stored as SDF files, and we found that automated ways to set the bond order often struggled because of the vibrations during the trajectory. This bundle was really just for making sure we can set the correct bond order in these trajectories, rather than viewing bond order data in ChimeraX. I pretty much just work with small molecule stuff, so I can't promise it will work well for larger biomolecules.
Different bond orders are represented using different pseudobond groups. There's some mouse modes for setting the bond orders, where you just click on one atom and then another. There's also a 'guessBondOrders' command that will replace all bonds with pseudobonds based on the distance between atoms.
The code for the bundle is here:
https://github.com/ajs99778/ChimeraX_ora_stuff . You will have to compile and install the bundle manually. That process is basically just running "devel install /path/to/ChimeraX_ora_stuff" and restarting ChimeraX.
Best,
Tony