This PR intends to build a converter that will take in NERDSS trajectory data and build a .simularium file. The data is represented as a bunch of PDB files, each representing a different timestep, and the timestep is reflected in the file name.
For preliminary data to use and details, see this document.
The jupyter notebook file (examples/Tutorial_nerdss.ipynb) contains an example usage of the converter with the 3 test files I pulled in from the above google doc.
Work Still To Do
At this time, the PDB data is translated and can be rendered as expected. However, we would also like to show intermolecular bonds and intramolecular bonds between specific bond sites based on their locations relative to each other and the distance thresholds specified in the above linked file. These can be represented as fiber agents with 2 sets of XYZ coordinates, representing each of the relevant bond sites. The work to read the inputted bonds and distance thresholds, and then determine what bonds should be drawn and where, still needs to be completed. The basic data structures have been build and a potential plan of action is outlined in TODOs in comments.
TLDR:
[ ] try reading input inter- / intra-molecular bond data
[ ] during conversion, compare distances between relevant agents and determine if a bond should be drawn
[ ] draw fibers to represent the bonds. each fiber will have two XYZ coordinate positions, represented in the subpoint data, one for each of the bond sites
Details
This PR intends to build a converter that will take in NERDSS trajectory data and build a .simularium file. The data is represented as a bunch of PDB files, each representing a different timestep, and the timestep is reflected in the file name.
For preliminary data to use and details, see this document.
The jupyter notebook file (examples/Tutorial_nerdss.ipynb) contains an example usage of the converter with the 3 test files I pulled in from the above google doc.
Work Still To Do
At this time, the PDB data is translated and can be rendered as expected. However, we would also like to show intermolecular bonds and intramolecular bonds between specific bond sites based on their locations relative to each other and the distance thresholds specified in the above linked file. These can be represented as fiber agents with 2 sets of XYZ coordinates, representing each of the relevant bond sites. The work to read the inputted bonds and distance thresholds, and then determine what bonds should be drawn and where, still needs to be completed. The basic data structures have been build and a potential plan of action is outlined in TODOs in comments.
TLDR: