「scaffolds」の検索結果

Cheminformatics toolkit for fine-grained molecular control. Parse and write SMILES, SDF, MOL and InChI; compute descriptors (MW, LogP, TPSA, QED, Bertz); build fingerprints (Morgan/ECFP, RDKit, MACCS, atom pair, torsion) and score Tanimoto, Dice or cosine similarity; run SMARTS substructure search and reaction SMARTS; generate 2D depictions and ETKDG 3D conformers; extract Murcko scaffolds and canonical hashes; control sanitization and stereochemistry directly. Also trigger on rdkit, Chem.MolFromSmiles, rdFingerprintGenerator, SDMolSupplier, SMARTS query, ETKDG, or FilterCatalog. For standard workflows with a simpler interface use the datamol skill, which wraps RDKit; use rdkit for advanced control, custom sanitization, and specialized algorithms.

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Pythonic wrapper around RDKit with a simplified interface and sensible defaults. Preferred for standard drug discovery work — SMILES/SELFIES/InChI conversion, molecule standardization and sanitization, descriptors, ECFP and other fingerprints, Tanimoto distance matrices, Butina clustering and diverse subset picking, Bemis-Murcko scaffolds and scaffold splits, BRICS/RECAP fragmentation, 3D conformer generation, SDF/CSV/Excel and cloud I/O, and parallel processing via n_jobs. Returns native rdkit.Chem.Mol objects, so it composes with RDKit throughout. Also trigger on datamol, `import datamol as dm`, dm.to_mol, dm.standardize_mol, dm.cluster_mols, or dm.pick_diverse. For advanced control or custom parameters, use the rdkit skill directly.

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Use when a course needs numbered problem, solution, and explainer scaffolds. Not for a CLI or Next.js project scaffold: use scaffold-nextjs.

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Scaffolds a structured investigation in scratch/ for empirical research and documentation. Use when the user says "start an investigation" or wants to: trace code paths or data flow ("trace from X to Y", "what touches X", "follow the wiring"), document system architecture comprehensively ("document how the system works", "archeology"), investigate bugs ("figure out why X happens"), explore technical feasibility ("can we do X?"), or explore design options ("explore the API", "gather context", "design alternatives"). Creates dated folder with README. NOT for simple code questions or single-file searches.

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Detect drift in .arkhe/roadmap/ context files and regenerate them from the current codebase state. Scaffolds context directory if missing. Use when user runs /roadmap:refresh, mentions "refresh context", "update context", "init roadmap", "stale context", or "scaffold roadmap".

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Install Tilt and scaffold or audit Tiltfile + tilt/ configurations with ecosystem-aware templates. Auto-detects Java/Gradle (Spring Boot), Next.js, Python/uv, and external infrastructure; recommends single-file or modular tilt/*.star + service-config.yaml + environments.yaml patterns based on project complexity. Bakes in production-context safety guards, PVC persistence toggles, JDWP debug ports, and optional Prometheus/Grafana/Traefik scaffolds. Use when user runs /devtools:tilt-setup, mentions "tilt setup", "setup tilt", "scaffold tiltfile", "audit tiltfile", "tilt configure", "tilt project setup", "Tiltfile", "local kubernetes dev", or "kubernetes development environment".

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Use when building C# applications with .NET 8+, ASP.NET Core APIs, or Blazor web apps. Builds REST APIs using minimal or controller-based routing, configures database access with Entity Framework Core, implements async patterns and cancellation, structures applications with CQRS via MediatR, and scaffolds Blazor components with state management. Invoke for C#, .NET, ASP.NET Core, Blazor, Entity Framework, EF Core, Minimal API, MAUI, SignalR.

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Scaffolds Pulumi TypeScript infrastructure-as-code projects, writes IaC code with proper resource configuration, manages Pulumi ESC environments for centralized secrets and configuration, configures OIDC authentication for cloud providers, and builds multi-language component resources. Use when the user asks to create Pulumi TypeScript projects, write Pulumi infrastructure code, set up ESC environments, configure OIDC for Pulumi, implement infrastructure automation with Node.js/TypeScript, create reusable Pulumi components, or work with stack references. Also use when the user mentions Pulumi with TypeScript, AWS/Azure/GCP infrastructure in TypeScript, or PulumiPlugin.yaml for multi-language components.

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Orchestrate the remote rules registry — the shared registry (often connected as a local folder or git repo) that the project's rules are published to and pulled from. Three modes, picked from the user's wording: create scaffolds a new local rules registry ("create a local rules registry", "init a rules registry"); update migrates/promotes local knowledge-base rules from .unikit/memory/ into the remote registry with automatic semver bumps ("migrate local rules to the remote registry", "promote my rules to the registry", "push local rules", "publish local rules", "update the rules registry"); sync pulls registry updates back into memory ("sync the rules registry", "pull registry updates"). Pass "--module <id>" to scope to one knowledge-base module. This skill ONLY orchestrates the CLI (`unikit-ai rules *`) — it never edits .unikit.json or .unikit/memory/ sources directly.

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Expert-level tissue engineering covering scaffold design, cell culture, bioreactors, stem cells, vascularization, and clinical translation of engineered tissues.

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Use when invoked as $new-project or when creating a brand-new repository or project from scratch — scaffolds mise-pinned tools, a just task surface, the standard repo files, and CI for Python (uv), TypeScript (bun), Rust (cargo), or Go.

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Apply the local C++ coding conventions of the EMULATORS framework. Use when Codex adds, edits, reviews, or scaffolds C++ code in this repository, especially new classes, headers, cpp files, CORE/COMMODORE module code, emulator components, registers, chips, memory, sound, IO, commands, or InfoClass-derived objects.

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End-to-end orchestrator: from a business idea, app idea, or existing app to running Azure deployment with cost estimates and pre-deploy approval. Analyzes your app, auto-detects the right Azure services, scaffolds infrastructure code, and deploys — tailored to your app, not a template.

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Embedded firmware setup: STM32, ESP32, AVR, RP2040, Nordic nRF, Zephyr/RTOS, vendor SDKs, CMake/CMakePresets, VS Code/clangd, cross toolchains, flash/debug, Docker/CI. Use for MCU scaffolds, existing firmware modernization, BSPs, linker/startup files, SDK package selection, and embedded CI; prefer cpp-project-setup for host-side C++.

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Scaffolds and reviews the main entry-point PHP file of a WordPress plugin — header (with Requires Plugins for WP 6.5+), ABSPATH guard, file/path/url/version constants, Composer + PSR-4 with manual spl_autoload_register fallback, register_activation_hook requirements check, Plugin class instantiation on plugins_loaded, and the WP 6.7+ rule that translation functions must not trigger before after_setup_theme. Use when scaffolding a new plugin or reviewing its main file. Triggers on Plugin Name headers, register_activation_hook, Requires Plugins, spl_autoload_register, plugins_loaded, or composer.json at the plugin root.

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Scaffolds and reviews custom WordPress REST API endpoints registered via register_rest_route on rest_api_init — namespace and version slug, permission_callback authorization (NEVER __return_true on state-changing routes, which is the most common plugin-side vulnerability on wp.org), args schema with validate_callback / sanitize_callback / type / enum, object-level capability checks via current_user_can with object ID, responses with WP_REST_Response and WP_Error carrying an HTTP status, no raw DB rows / sensitive columns in responses, cookie auth via X-WP-Nonce, REST vs admin-ajax decision. Recommends the better-route library when the plugin grows past a few endpoints. Use when scaffolding or reviewing a REST endpoint, or migrating from admin-ajax. Triggers on register_rest_route, rest_api_init, permission_callback, WP_REST_Request, WP_REST_Response, WP_Error, X-WP-Nonce, rest_ensure_response, register_rest_field, or any file path containing /rest/ or /api/ in a WP plugin or theme.

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Scaffolds new agent skills for the dotnet/skills repository. Use when creating a new skill, generating SKILL.md files, or setting up skill directory structures. Handles frontmatter generation, section templates, and validation guidance.

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Scaffolds eval.yaml test files for agent skills in the dotnet/skills repository. Use when creating skill tests, writing evaluation scenarios, defining assertions and rubrics, or setting up test fixture files. Handles eval.yaml generation, fixture organization, and overfitting avoidance. Do not use for running or debugging existing tests nor for skills authoring.

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Create data-driven presentation slides using React, Vite, and Recharts with Sentry branding. Use when asked to "create a presentation", "build slides", "make a deck", "create a data presentation", "build a Sentry presentation". Scaffolds a complete slide-based app with charts, animations, and single-file HTML output.

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Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it. Profiles the genome first (k-mer spectrum -> size, heterozygosity, ploidy), QCs reads, chooses an assembly path by data type (SPAdes for Illumina, Flye for noisy long reads, hifiasm for HiFi, metaFlye for communities), polishes only when needed, decontaminates, scaffolds with Hi-C, and finishes with three-axis QC (contiguity + completeness + correctness). Use when assembling a genome from raw reads and deciding which assembler, whether to polish, and how to prove the result is good.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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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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Scaffolds a complete .NET solution following Clean Architecture principles with proper layer separation (API, Application, Domain, Infrastructure). Creates project structure, dependency injection setup, and cross-cutting concerns configuration.

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Orders and orients assembled contigs into chromosome-scale scaffolds from long-range linking data, inserting N-gap spacers (adds no sequence). Covers Hi-C/Omni-C scaffolding (YaHS, SALSA2, 3D-DNA/Juicer), Hi-C read-mapping prerequisites (map each end separately, no mate rescue, dedup, enzyme-aware), reading the contact map for misjoins/inversions/false-duplications, manual curation in Juicebox/PretextView (the VGP/DToL standard), reference-guided scaffolding (RagTag) and its karyotype-erasure hazard, genetic-map (ALLMAPS) and Bionano optical-map integration, chimera-breaking before scaffolding, gap-filling, and telomere/contig-vs-scaffold-N50 QC (tidk). Use when turning contigs into chromosomes with Hi-C, integrating a linkage map or optical map, choosing a scaffolder by available linking data, or judging whether a chromosome-scale assembly is trustworthy.

日本語の概要は準備中です。原文の説明を表示しています。