AC molecular-docking
Run and diagnose expert-grade protein-ligand molecular docking through SciMiner using Gnina, AutoDock Vina, PackDock, SurfDock, DiffDock, and fpocket. Use for focused docking, pocket-aware engine selection, multi-seed ensemble sampling, pose-pool construction, energy-gap filtering, RMSD clustering, cross-run recurrence analysis, critical-contact checks, physics sanity checks, confidence grading, and multi-engine comparisons. Do not use a single run or Rank 1 score as the final answer.
As a process C 63/100 · Has gaps — weak spots: result and completion, running it twice, progress reporting
How to improve
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 0
✓ No critical or high findings
Files scanned: 2. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
✓ No remarks against the Agent Skills spec
Process rating: all ten parameters 63/100
- 0Result and completion. Does not say what the result is
- 0Progress reporting. Says nothing while it works
- 30Running it twice. 3 mutating operations with no state check
- 50When it triggers. No condition that starts the skill
- 60Tools and files. Uses tools (bash) that frontmatter does not declare
- 70Failures and branches. 8 branches
- 85Steps. 76 steps, 1 vague phrases
- 100Inputs and preconditions. Inputs and preconditions are listed
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 3862 tokens
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +5Description has no quoted example phrases that should trigger the skill
- +3Output format is not stated: the model decides each time
- +1No license
- +2Single-language instructions
- +4Description says when NOT to use the skill
- +3Description length 489: enough signal without eating the budget
- +4Structure: 25 headings
- +3Step-by-step instructions: 76 items
- +4Has examples (1 code blocks)
Quality base 70; lint remarks subtract, signals add up to 100. Result: 88.