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pymol-mcp

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    Deploy Server
    One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

    TDQS

    B3.4/5.0

    Scored across 32 tools

    Disambiguation4/5

    Most tools are clearly distinct (camera, selection, representation, measurement, loading). A few pairs like load_trajectory/load_trajectory_mda and hbond_network/chill_plus show some overlap, but their descriptions provide enough clarification.

    Naming Consistency4/5

    Tool names predominantly follow a verb_noun pattern (reset_session, render_image, measure_distance). Deviations exist among analysis tools (order_parameter, hbond_network, chill_plus) which use noun-style names, but the overall convention remains consistent and readable.

    Tool Count2/5

    With 32 tools, the server is overstuffed. Several tools could be merged (e.g., measure_distance/angle/dihedral, load_trajectory variants, run_pml/run_python), and the specialized clathrate tools add bulk beyond a general-purpose PyMOL interface.

    Completeness3/5

    Core workflows like loading, selecting, visualizing, measuring, and rendering are covered, but basic operations such as deleting objects, listing selections, or editing structures are missing. The specialized clathrate analysis is thorough, but general PyMOL coverage has notable gaps.

    Maintenance

    ActivityMaintained
    ResponsivenessNo issues

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