「structures」の検索結果

Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG. Parse molecules and reactions from .cdxml/.cdx, write structures with good 2D depiction, and hand-build or modify the parts RDKit cannot write: reaction arrows, plus signs, schemes/steps, and text/labels. Use for reaction schemes, synthesis routes, mechanisms, retrosynthesis, or SI figures. Critical: RDKit writes structures only — round-tripping a reaction through a Mol silently drops arrows and text; this skill shows the XML layer that preserves them. For pure molecular analysis (descriptors, fingerprints, SMARTS) use rdkit-cheminformatics; for multi-format 3D conversion use openbabel.

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Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.

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Generate formal specifications (definitions, predicates, invariants, pre/post-conditions) in Isabelle/HOL or Coq from informal requirements, source code, pseudocode, or mathematical descriptions. Use when users need to: (1) Formalize algorithms or data structures, (2) Create function specifications with contracts, (3) Generate predicates and properties for verification, (4) Translate informal requirements into formal logic, (5) Specify invariants for loops or data structures, or (6) Create formal definitions for mathematical concepts. Supports both Isabelle/HOL and Coq equally.

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Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

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Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

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Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

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Apply before writing logic: choosing core types and data structures, sequencing scaffold-vs-feature work, asking what concurrent actors share. Get the data structures right so downstream code becomes obvious.

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Designing LLM-optimized folder structures: audits and restructures directories for context efficiency, progressive disclosure, and prompt cache performance. Not for general repo structure (Grove).

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Map a current event below the surface into patterns, structures, and mental models. Use when a class or team needs systemic understanding before action.

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Statics, dynamics, stress-strain analysis, materials selection, failure modes, and finite element analysis concepts for engineered structures. Covers free-body diagrams, equilibrium, internal forces (shear and moment), beam deflection, column buckling, material properties, factor of safety, fatigue, fracture mechanics, and FEA workflow. Use when analyzing loads on structures, selecting materials, predicting failure, or interpreting structural behavior.

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Foundations of individual economic decision-making, market structures, and strategic interaction. Covers supply and demand analysis, price elasticity, consumer and producer surplus, market structures (perfect competition, monopoly, oligopoly, monopolistic competition), game theory (Nash equilibrium, dominant strategies, repeated games), and welfare economics. Use when analyzing individual markets, firm behavior, pricing strategies, consumer choice, or strategic interactions between economic agents.

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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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Builds revolving securitization models with replenishment criteria, early amortization triggers, and portfolio composition limits. Use when modeling revolving structures, analyzing credit card ABS, or evaluating asset purchase criteria.

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Builds carry waterfall models with preferred return hurdles, catch-up provisions, and clawback mechanics across deal-by-deal and whole-fund structures. Use when modeling carry economics, comparing waterfall structures, or analyzing GP incentive alignment.

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Evaluates stapled secondary structures combining primary commitment with secondary purchase in coordinated transactions. Use when analyzing stapled deals, structuring combined primary/secondary, or evaluating staple economics.

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Evaluates trade finance structures with letters of credit, supply chain financing, and receivables factoring for cross-border commerce. Use when analyzing trade finance, evaluating LC structures, or assessing supply chain financing.

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Evaluates unitranche structures with first-out/last-out splits, blended pricing, and agreement among lenders provisions. Use when analyzing unitranche options, comparing unitranche vs traditional structures, or modeling blended costs.

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Evaluates management fee designs with commitment-period vs invested-capital bases, step-downs, and offset provisions. Use when analyzing fee structures, comparing fee levels, or modeling fee revenue for GPs.

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Evaluates mezzanine structures with PIK toggle, equity kickers, and intercreditor subordination mechanics. Use when analyzing mezzanine financing, comparing subordinated debt terms, or modeling layered capital structures.

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Evaluates GP-led continuation vehicle structures with existing LP options, pricing methodology, and new investor terms. Use when analyzing continuation vehicles, structuring GP-led transactions, or evaluating tender offers.

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Evaluates CDS, CDX, and bespoke credit derivative structures with spread analysis and credit event mechanics. Use when analyzing credit derivatives, pricing CDS, or evaluating index tranche products.

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"Apply Giddens' structuration theory to analyze the duality of structure — how social structures are both the medium and outcome of the practices they organize. Use this skill when the user needs to bridge agency and structure in organizational or social analysis, explain how routines reproduce or transform institutional patterns, analyze the recursive relationship between action and structure, or when they ask 'do people shape institutions or do institutions shape people', 'how are these routines maintained', or 'where does change come from if structures constrain action'.".

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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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Generalized Partial Global Planning with TAEMS task structures for multi-agent coordination

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