TrajMapQuick: Towards Fast Molecular Dynamics Trajectory Map Analysis and Visualization

Trajectory map visualization has redefined our approach to handling conformational dynamics of proteins and post-molecular dynamics (MD) analyses. Beyond the classical RMSF plots, trajectory maps allow us to visualize the temporal sequence of fluctuations across the residues of the whole protein. In the TrajMap.py tool, Kožić and Bertoša (2024) showed that specific regions of proteins (e.g., loops) can be extracted from the trajectory map, and a time series residual shift constructed. Despite these astonishing results, TrajMap.py tool is not well-suited to realize the full potential of this utility. Slow parsing of multi-model PDB files, mandatory manual editing of files, low throughput, and a lack of a well-defined command-line interface (CLI) for end users are key limitations. Herein, we present TrajMapQuick, a lightweight Python tool designed to overcome the above limitations. It operates via a global command (tmq), passed to subcommands on the CLI, to control the whole pipeline from trajectory loading to visualization of plots. Using four subcommands (shift, hotspot, diff, and average), the user has more control over the full analysis pipeline. Additionally, the hotspot subcommand allows the user to detect regions of peak fluctuations in their proteins in an automated way. It also offers the user an interactive interface for analysis via its Python API. We demonstrate a >5x improvement in speed, usability, and throughput of TrajMapQuick compared to TrajMap.py. We believe that TrajMapQuick will assist scientists in the rapid analysis and visualization of trajectory maps in their MD workflows. TrajMapQuick is available under MIT license here https://github.com/SHEDOOMTC/TrajMapQuick.git.