「structures」の検索結果

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

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Define database models with clear naming, appropriate data types, constraints, relationships, and validation at multiple layers. Use this skill when creating or modifying database model files, ORM classes, schema definitions, or data model relationships. Apply when working with model files (e.g., models.py, models/, ActiveRecord classes, Prisma schema, Sequelize models), defining table structures, setting up foreign keys and relationships, configuring cascade behaviors, implementing model validations, adding timestamps, or working with database constraints (NOT NULL, UNIQUE, foreign keys). Use for any task involving data integrity enforcement, relationship definitions, or model-level data validation.

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Create exercise directory structures with sections, problems, solutions, and explainers that pass linting. Use when user wants to scaffold exercises, create exercise stubs, or set up a new course section.

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Query UCSC Genome Browser REST API for DNA sequences, tracks, gene models, and conservation across 100+ assemblies. Retrieve sequence by region, list/fetch BED/bigWig tracks, chromosome sizes, RefSeq/GENCODE gene structures, PhyloP/PhastCons scores. Use for UCSC annotations; Ensembl REST API for Ensembl gene IDs and VEP variant annotation.

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Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key. For trials use clinicaltrials-database-search; for structures use drugbank-database-access or chembl-database-bioactivity.

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Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth. Always resolve targets via geneSymbol/accession; most metadata lives in sub-resources (/databaseLinks, /structure, /synonyms).

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Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.

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Python Materials Genomics library for structure analysis, thermodynamics, and electronic properties. Parse/create crystal structures (CIF, POSCAR), query Materials Project for DFT-computed properties, analyze phase and Pourbaix diagrams, compute XRD patterns, generate DFT inputs for VASP, Quantum ESPRESSO, CP2K. Alternatives: ASE (MD/geometry), AFLOW (high-throughput), OVITO (visualization).

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Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.

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3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.

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Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam. Use uniprot-protein-database for sequences; pdb-database for 3D structures.

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Provides patterns for unit testing `@ConfigurationProperties` classes with `@ConfigurationPropertiesTest`. Validates property binding, tests validation constraints, verifies default values, checks type conversions, and mocks property sources for Spring Boot configuration properties. Use when testing application configuration binding, validating YAML or application.properties files, verifying environment-specific settings, or testing nested property structures.

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Add or revise source-level Rustdoc for Shift Rust APIs. Use before writing or editing documentation comments in `.rs` files, especially for public or crate-visible APIs, domain structures, compiler adapters, persistence boundaries, trait implementations, unsafe code, or any API where ownership, units, coordinate spaces, mutation, I/O, sparse behavior, failure modes, panics, or concurrency are easy to misunderstand.

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Add or revise source-level JSDoc for Shift APIs. Use this skill before writing or editing documentation comments for exported classes, methods, constructors, domain data structures, render frames, reactive state, or any API where caller intent, side effects, lifetime, ownership, or nullability are easy to misunderstand.

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Design data models for construction projects. Create entity-relationship diagrams, define schemas, and generate database structures.

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Designs memory palace structures with spatial layouts and domain organization. Use when creating a new palace or planning knowledge architecture by hand.

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Manages digital garden notes, link structures, and health metrics. Use when curating a knowledge base, pruning stale notes, or tracking content maturity.

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Writes and restructures technical documentation - READMEs, tutorials, how-to guides, user guides, architecture docs, onboarding guides, runbooks and SOPs, troubleshooting guides, release notes, and knowledge base articles - grounded in the actual code or product, with commands and examples verified where possible. Use when the user asks to document a project, feature, system, or process, write or fix a README, explain a codebase to new developers, turn notes into a guide, or make existing docs clearer. For endpoint-by-endpoint API reference or OpenAPI specs, use api-documentation-writer; for CLAUDE.md or AGENTS.md files, use claude-md-writer.

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Use when drafting a grant or challenge proposal for a radiology or medical AI project, including a Korean government industry-academia plan. Structures significance, innovation, approach, aims, milestones and consortium roles, keeping claims evidence-based and executable.

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Use CausalNex to learn causal structures, fit Bayesian networks, discretize features, generate synthetic graph data, and run inference, evaluation, and latent-variable workflows.

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Use the Folding@home coronavirus repository conventions to curate molecular structures, prepare bounded OpenMM systems, and preserve target, publication, and provenance notes.

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Route Biopython computational biology workflows across sequence objects, file formats, alignments, structures, web databases, BioSQL, motifs, restriction enzymes, and specialized modules.

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Intelligently organizes your files and folders across your computer by understanding context, finding duplicates, suggesting better structures, and automating cleanup tasks. Reduces cognitive load and keeps your digital workspace tidy without manual effort.

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Structures risk mitigation planning and residual risk tracking for Data Protection Impact Assessments under GDPR Article 35(7)(d). Covers mitigation measure identification, implementation tracking, residual risk acceptance, and Art. 36 prior consultation triggers. Keywords: DPIA mitigation, risk treatment, residual risk, Art. 35(7)(d), safeguards, mitigation tracking, prior consultation.

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