「structural」の検索結果

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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Assess designs, public interfaces, state ownership, readability, and refactor proposals when the task calls for design review or structural simplification; not for unrelated routine edits.

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JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by taxon (human, mouse) or TF family (bHLH, zinc finger). Use for motif enrichment input, TFBS scanning, and regulatory sequence analysis. For ChIP-seq peak motif discovery use homer-motif-analysis; for regulatory variant scoring use regulomedb-database.

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Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural analysis; use OpenMM/GROMACS for running simulations.

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mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.

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Medicinal chemistry filters for compound triage. Drug-likeness rules (Lipinski Ro5, Veber, Oprea, CNS, leadlike, REOS, Golden Triangle, Ro3), structural alerts (PAINS, NIBR, Lilly Demerits), chemical group detectors, complexity metrics, and filter composition query language. Built on RDKit/datamol. For hit-to-lead filtering, library design, ADMET pre-screening. For molecular I/O use rdkit-cheminformatics or datamol.

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Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity. POST with a JSON body for all cross-reference queries; only /sources is GET. No auth required.

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Methodology for exploratory data analysis on scientific files. Decision frameworks by data type (tabular, sequence, image, spectral, structural, omics), quality assessment, report generation, format detection across 200+ formats. Use when given a data file for initial exploration or to pick an analysis before a pipeline.

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Use when writing a complete SEO article. Includes the full anti-AI-slop ruleset (banned vocabulary, banned phrases, banned structural patterns) and voice rules. The agent researches the SERP itself if needed — no keyword data exports required.

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Detect and analyze geometric clashes in BIM models. Identify MEP, structural, and architectural conflicts before construction.

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Refreshes README structure favoring concision (an index, not a manual). Use when the README needs a structural update after significant project changes.

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Assesses architecture decisions, ADR compliance, and coupling. Use when evaluating design changes or validating structural decisions before merging.

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Audits business spreadsheet models (.xlsx, .xlsm, or Google Sheets exported to .xlsx) for structural integrity errors and explains each fix -- budgets, forecasts, pricing models, commission calculators, FP&A packs, ops trackers, not only banking models. A bundled openpyxl script finds hardcoded numbers inside formulas, typed values pasted over formulas, inconsistent formulas across a row or column,

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Use when a pipeline DOT file has passed structural validation but may still have flow inefficiencies, spec fidelity gaps, or information loss in prompts. Use after dotfile-audit or dotfile-from-spec when you want to deeply verify a pipeline captures everything from the original spec. Use when prompts might be missing critical domain rules, data models, or invariants.

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Use GemPy 3.x for CPU-first 3-D implicit geological modeling, structural data preparation, grid evaluation, visualization, persistence, and optional integrations.

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Use code-review-graph for local-first CLI/MCP code knowledge graphs, graph-backed code review, structural search, and repository-analysis integrations.

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This skill should be used when the user asks about "mystery", "fair play", "clue", "red herring", "romance beats", "HEA", "thriller", "ticking clock", "horror", "dread", "MG", "YA", "middle grade", "young adult", "science fiction", "sci-fi", "fantasy", "quest", "chosen one", "historical fiction", "period voice", "anachronism", "comedy", "humour", "humor", "romcom", "farce", "satire", "running gag", "serial", "episodic", "web serial", "genre conventions", or wants genre-specific structural craft for a story project. NOT for a clue check as a revision pass (use revision-continuity).

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This skill should be used when the user asks to "revise a chapter", "continuity check", "find inconsistencies", "audit character state", "check timeline consistency", "developmental edit", "structural revision", "reverse outline", "cut a subplot", "revision passes", "what pass next", "pacing check" as a revision pass, "clue check", "cut to a word count", or "length pass", or to prepare existing story material for the next revision pass. NOT for planning book structure (use plot-structure), scene-level craft (use scene-craft), voice consistency (use voice-style), or reconciling a chapter drafted by discovery (use discovery-drafting).

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Create original relaxed black-pen graphics from concepts or visual references, including sparse illustrations, narrative scenes, animals, objects, abstract relationships, icons, and logo marks. Use when the user wants quick hand-drawn line energy, causal story staging, non-equilibrium proportion, shorthand forms, open contours, structural line drift, misregistered junctions, selective retracing, physical pen texture, or a transferable illustration system that must not collapse into clean vector minimalism or polished period-sketch drawing.

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Performs deep architectural analysis of a specified module, directory, or feature area by examining structural coupling, data flow, concurrency patterns, risk, and SOLID alignment. Use when the user wants to assess, evaluate, or review the architecture, design quality, dependency structure, coupling, cohesion, or technical debt of an existing part of the codebase. Not for investigating specific bugs, runtime errors, or failures — use investigate. Not for test planning — use automated-test-planning. Not for file-level code review — use code-review. Not for researching open-ended options, prior art, or how something works — use research. Not for designing a new interface or contract — use design-an-api. Not for planning the change its findings imply — use plan-a-change. Not for discovering bounded contexts, ubiquitous language, or where code boundaries diverge from domain boundaries — use ddd-analysis. Not for writing documentation or architectural decision records.

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Produce a standalone test plan by analyzing code for test coverage gaps and edge cases. Use when you need to create, generate, or draft a test plan for a branch, need to analyze test coverage, or need to identify what tests to write for specific files or directories. Does not produce a plain-language plan for a person to run tests by hand — use manual-test-planning for that. Does not write test code — use tdd to implement behavior test-first. Does not refine existing plans — use iterative-plan-review. Does not review code quality, security, or style — use code-review for full code review. Does not evaluate architectural testability or structural coupling — use architectural-analysis for architectural assessment.

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Produces a human-readable, progressive-disclosure overview of unfamiliar code or a pull request's changes — why it exists (the real problem it solves or goal it serves for the business or a user), and from there what it does, how it flows, and where to start — so you can get up to speed before working on or reviewing it. Use when you want to understand, get oriented in, make sense of, explain, or get up to speed on a chunk of code, a file, a directory, a symbol, or a PR's changes. Writes the overview to a scratch file and changes no code. Does not review code quality or raise findings — use code-review for auditing changes or post-code-review-to-pr for posting them. Does not produce durable feature or system documentation — use project-documentation. Does not assess architecture or structural risk — use architectural-analysis. Does not diagnose bugs or root-cause failures — use investigate. Does not pace a person through the code one step at a time in conversation — use code-walkthrough.

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Applies Judea Pearl's causal reasoning frameworks to distinguish correlation from causation, evaluate AI capabilities, and make counterfactual decisions. Reach for this skill whenever Claude encounters questions about causal inference, structural causal models, the limitations of deep learning, AGI, experimental design, covariate selection, or personalized decision-making. Trigger this skill for topics involving Bayesian networks, the do-calculus, the Ladder of Causation, or when a user tries to answer 'what if' or 'why' questions using purely observational data. Pearl's principles are essential for moving beyond probability calculus into true causal understanding.

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Use Jacobian’s typed operations when exact computation or structural analysis can help solve a mathematical problem.

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