New commands enable agentic setup of simulation#30
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March 30, 2026 10:23
This commit introduces new validation commands to check the completeness of hydrogens and the parameterization of residues in ISOLDE models. The `isolde_validate_hydrogens` function assesses hydrogen presence and ratios, while `isolde_validate_parameters` checks for unparameterised residues without starting a simulation. These enhancements are meant to make it easier for agents to use ISOLDE.
tristanic
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May 11, 2026
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These make sense... but (and yes, I know I do this already in the GUI) I'm a little jumpy about conflating the two different definitions of "validate" (the MD-specific "is the model ready for simulation?" and the more classic "does this model make sense in terms of geometry and fit to data?"). To avoid future confusion, how about putting these under something like "isolde preflight" instead?
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Completely agree - latest commit makes this change. Note that I elected to keep these new "isolde preflight" commands still in |
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This PR adds four new commands:
This has allowed me to get my agent to setup an isolde simulation from scratch via the ChimeraX MCP bridge.