“molecules”的搜索结果

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.

中文简介正在准备中。当前显示原文说明。

Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking. Property (MW/logP) filtering is done locally with RDKit. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.

中文简介正在准备中。当前显示原文说明。

PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet), social/knowledge graphs, 3D point clouds. For non-graph DL use PyTorch; for classical graph algorithms use NetworkX.

中文简介正在准备中。当前显示原文说明。

Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.

中文简介正在准备中。当前显示原文说明。

Validate any Lattice SKILL.md against all tier conventions — atoms, molecules, and refiners. Catches structural errors, broken cross-references, and convention violations before they reach the repo. If you just wrote or modified a Lattice skill file and haven't run this yet, run it now — manual review consistently misses the same categories of errors this skill is specifically designed to catch. Use when the user says 'validate this skill', 'check this skill', 'does this follow conventions', 'review this skill file', 'check my SKILL.md', or 'skill validate'. Reports PASS/FAIL with specific file-and-section findings and actionable fixes. Standalone — does not call other skills.

中文简介正在准备中。当前显示原文说明。

Apply clean code principles when generating or modifying implementation code. Enforces function focus, naming clarity, complexity management, error handling, and self-documenting style. Use when the user mentions 'clean code', 'code quality', 'coding guidelines', or 'implementation quality'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the craft of writing individual code units -- not architecture (see architecture), not security posture (see secure-coding), not test structure (see test-quality), and not refactoring workflows (see refactor-safely).

中文简介正在准备中。当前显示原文说明。

Apply test quality principles when generating or reviewing test code. Enforces Arrange-Act-Assert structure, one behavior per test, assertion quality, test isolation, meaningful naming, and test data management. Use when writing tests, reviewing test code, or when the user mentions 'write tests', 'test this', 'test quality', 'test review', 'improve tests', or 'test structure'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the craft of writing individual test cases -- not what to test (that is driven by the code being implemented) but how to write tests that are reliable, readable, and maintainable.

中文简介正在准备中。当前显示原文说明。

Protocol for handling ambiguous decisions and missing/conflicting knowledge during code generation, design, and review. Ensures AI surfaces genuine judgment calls with structured options and stops on hallucination risk instead of silently assuming. Use when a decision has multiple valid approaches, when facts are missing or contradictory, when the user asks 'what should we do here?', 'is this a judgment call?', 'should I ask about this?', 'am I guessing here?', 'what are the tradeoffs?', or when deciding between two reasonable architectural or design options. Also composed by molecules to define how judgment calls and clarification requests are surfaced and resolved.

中文简介正在准备中。当前显示原文说明。

Apply security-conscious thinking when generating or modifying code. Enforces trust boundary awareness, input validation, injection prevention, secrets management, and defense-in-depth authorization. Use when generating code that handles user input, authentication, authorization, database queries, external APIs, or file operations, or when the user mentions 'security review', 'secure this', 'check for vulnerabilities', 'trust boundary', 'input validation', or 'OWASP'. Loaded automatically by the code-generating molecules (code-forge, refactor-safely, bug-fix). This skill governs the security posture of generated code -- not architecture (see architecture) and not code craft (see clean-code).

中文简介正在准备中。当前显示原文说明。

All-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz.

中文简介正在准备中。当前显示原文说明。

Ligand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.

中文简介正在准备中。当前显示原文说明。

Use when adding or reusing Flutter UI - organize widgets as atoms, molecules, and organisms in a shared library and never hand-roll a component that already exists

中文简介正在准备中。当前显示原文说明。

Used to invoke the PXMeter tool for rigorous quality assessment of biomolecular structure prediction models (e.g., proteins, nucleic acids, small molecules). This skill covers single-sample CIF evaluations and large-scale dataset benchmarks, providing rich result parsing support. Trigger this skill when the user asks to "run PXMeter", "compare PDB/CIF evaluation results of different tools", "check benchmark scores", or asks "how accurate is the structure generated by the model".

中文简介正在准备中。当前显示原文说明。

Craft CMS 5 front-end Twig development — atomic design, template architecture, components, Vite buildchain. Covers atoms/molecules/organisms, props/extends/block patterns, layout chains, view routing, content builders, image presets, Tailwind named-key collections, multi-brand CSS tokens, JavaScript boundaries (Alpine/DataStar/Vue, tabs, accordions), Vite asset loading, and front-end auth (login, registration, password reset, profiles).

中文简介正在准备中。当前显示原文说明。

Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

中文简介正在准备中。当前显示原文说明。

Generate and optimise novel small molecules with REINVENT 4 — de novo sampling from a chemical language model, scaffold decoration with LibInvent, fragment linking with LinkInvent, and similarity-constrained analogue generation with Mol2Mol. Use this skill to set up reinforcement-learning or curriculum runs, compose a multi-parameter scoring function from docking scores, predictive models, and physicochemical desirability, and read the resulting sampled sets. Also trigger on REINVENT, LibInvent, LinkInvent, Mol2Mol, scaffold hopping, R-group replacement, linker design, chemical language model, or reinforcement-learning molecule optimisation.

中文简介正在准备中。当前显示原文说明。

Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

中文简介正在准备中。当前显示原文说明。

Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. Distinguishes de novo CALLING (scanning a panel for unknown variants, bounded by per-locus error and multiple testing) from tumor-informed DETECTION (tracking a pre-specified variant set, where panel integration reaches single-ppm). Covers VarDict and Mutect2 for de novo calling, UMI-aware callers, and a pysam-based known-variant VAF tracker, with matched-WBC subtraction as the mandatory defense against clonal hematopoiesis (the dominant false positive). Use when calling or tracking tumor mutations from plasma cfDNA, setting a VAF threshold, or deciding whether a low-VAF call is tumor versus CHIP.

中文简介正在准备中。当前显示原文说明。

Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

中文简介正在准备中。当前显示原文说明。

Build an Atomic Design system from Figma style guides - extract tokens, create atoms/molecules/organisms/templates/pages as reusable component libraries. Use when building or extending a design system or component library.

中文简介正在准备中。当前显示原文说明。

Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.

中文简介正在准备中。当前显示原文说明。

Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.

中文简介正在准备中。当前显示原文说明。

Compound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug repurposing, and identifying molecules with desired multi-target profile.

中文简介正在准备中。当前显示原文说明。

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

中文简介正在准备中。当前显示原文说明。