JmolK

JmolK is a term used for a proposed extension of the open-source Jmol molecular visualization platform. It is described as a concept aimed at adding kinetic analysis and trajectory exploration capabilities within the Jmol environment, without implying an official, released product.

Overview and purpose

The idea behind JmolK is to augment Jmol with tools for analyzing molecular dynamics trajectories, computing simple kinetic metrics, and integrating these features into the existing visualization workflow. The goal is to provide a unified interface where users can view structures, inspect trajectories, and perform basic kinetic assessments without switching between separate software.

Features (conceptual)

Proposed features for JmolK include improved trajectory handling (support for common MD formats, frame control, and playback), lightweight kinetic analysis tools (rate estimates, reaction coordinates, and progress plotting), and an extensible scripting framework (plugins written in Java or JavaScript) that ties visualization to analysis. It would maintain compatibility with Jmol’s selection language and support multiple representations, annotations, and export options for figures and data. Cross-platform operation and web compatibility via existing JSmol components are often envisioned as part of the concept.

Development status

As a concept, JmolK has appeared in discussions and hypothetical planning but has no official release, maintained fork, or formal documentation. Any practical implementation would depend on community contributions, formal planning, and alignment with the broader Jmol project roadmap.

Reception and scope

The JmolK concept is seen as a potential bridge between visualization and kinetic analysis, offering a streamlined workflow if realized. Its adoption hinges on clear goals, stable releases, and comprehensive documentation.

See also

Jmol, JSmol, molecular dynamics, trajectory visualization.