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Use when developing GIMP 3.0+ plugins in Python 3 - procedure registration, image and layer operations, GEGL operations, PDB calls, dialogs and progress bars, file export, or batch processing plugins

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Plans, executes, and validates Google Kubernetes Engine (GKE) cluster upgrades and maintenance operations for both Standard and Autopilot clusters. Produces upgrade plans, pre/post-upgrade checklists, maintenance runbooks with gcloud commands, release channel strategy, and troubleshooting guides. Handles node pool upgrade strategies (surge, blue-green), version compatibility, PDB management, and workload-specific concerns (stateful, GPU, operators). Use this skill whenever the user mentions GKE upgrades, Kubernetes version bumps, node pool maintenance, GKE patching, cluster version management, release channel selection, maintenance windows, surge upgrades, stuck upgrades, or any GKE lifecycle management task — even casual mentions like "we need to upgrade our clusters" or "plan our next GKE maintenance" or "our upgrade is stuck." Don't use for GKE cluster creation, application onboarding, general networking/routing setup, or security policy configurations (use gke-basics or relevant GKE skills instead).

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Generate production-grade Kubernetes manifests — Deployments with probes and security contexts, Services, Ingress with TLS, HPA, PDB, NetworkPolicy, ConfigMaps, Secrets — with optional Helm charts, Kustomize overlays, Istio mesh, and ArgoCD GitOps

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MUST USE for any real runtime debugging across ANY language or binary — crashes, silent failures, wrong responses, stuck processes, memory leaks, async misbehavior, unexplained timing, reverse engineering. Runs a hypothesis-driven loop: form ≥3 hypotheses, investigate in parallel, after 2 failed rounds spawn Oracles from orthogonal angles, confirm root cause, lock with a failing test, fix minimally, QA by actually USING the system, scrub artifacts. The actual HOW lives in `references/` — READ THEM. Triggers: 'debug this', 'why is X not working', 'hanging', 'attach a debugger', 'reverse engineer', 'pwndbg', 'gdb', 'lldb', 'node inspect', 'tsx debug', 'pdb', 'dlv', 'delve', 'rust-gdb', 'set a breakpoint', 'context window exploded', 'why is the response empty', 'attach the debugger', 'debug it', 'why is this happening', 'trace this bug', 'reproduce and fix', 'silent failure', 'HTTP 200 but empty', 'why did it stop', 'inspect the binary', 'reverse engineering', 'playwright'.

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Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

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Debug Python: pdb REPL + debugpy remote (DAP).

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Debug Python: pdb REPL + debugpy remote (DAP).

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Make a WooCommerce plugin HPOS-compatible (High-Performance Order Storage, default-on in WC 10.x) — declare via FeaturesUtil::declare_compatibility on before_woocommerce_init, replace $wpdb->postmeta / WP_Query order code with wc_get_orders + WC_Order::get_meta / update_meta_data, gate runtime branches on OrderUtil::custom_orders_table_usage_is_enabled, build admin hook names dynamically with OrderUtil::get_order_admin_screen (HPOS = woocommerce_page_wc-orders, legacy = shop_order). Use when scaffolding an order-touching plugin, auditing existing code for HPOS readiness, or fixing post-WC-10 silent breakage. Triggers on shop_order, get_post_meta with order context, FeaturesUtil, OrderUtil, custom_order_tables, before_woocommerce_init.

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Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

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Debug Python: pdb REPL + debugpy remote (DAP).

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Debug Python code using tracebacks, pdb, and structured logging.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Analyzes chemical libraries by scaffold using Bemis-Murcko scaffolds, generic frameworks, cyclic skeletons, matched molecular pair (MMP) analysis via mmpdb, R-group decomposition, Free-Wilson analysis, scaffold hopping, and chemotype-aware ML train/test splits. Use when identifying chemotype clusters in a library, deriving SAR transformation rules, decomposing series into R-groups, performing scaffold-balanced QSAR splits, or planning analog campaigns.

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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, MMTF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.

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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.

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Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.

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