skills/43-wentorai-research-plugins/skills/domains/chemistry/SKILL.md
9 chemistry skills. Trigger: chemical structure analysis, reaction prediction, molecular modeling. Design: computational chemistry tools and cheminformatics workflows.
npx skillsauth add brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research chemistry-skillsInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Select the skill matching the user's need, then read its SKILL.md.
| Skill | Description | |-------|-------------| | cactus-cheminformatics-guide | PNNL cheminformatics LLM agent for molecular analysis | | catalysis-hub-api | Query computational catalysis reaction data via Catalysis Hub GraphQL | | chemeagle-guide | Multi-agent system for chemical literature information extraction | | chemgraph-agent-guide | Automate molecular simulations with the ChemGraph agentic framework | | computational-chemistry-guide | DFT, molecular simulation, and reaction prediction tools for chemists | | molecular-dynamics-guide | Molecular dynamics simulation setup, execution, and trajectory analysis | | pubchem-api-guide | Search PubChem for chemical compounds, structures, and bioassay data | | retrosynthesis-guide | Retrosynthetic analysis and computational reaction prediction | | spectroscopy-analysis-guide | Spectral data analysis for NMR, IR, mass spectrometry, and UV-Vis |
development
Conduct rigorous thematic analysis (TA) of qualitative data following Braun and Clarke's (2006) six-phase framework. Use whenever the user mentions 'thematic analysis', 'TA', 'Braun and Clarke', 'qualitative coding', 'identifying themes', or asks for help analysing interviews, focus groups, open-ended survey responses, or transcripts to identify patterns. Also trigger for questions about inductive vs theoretical coding, semantic vs latent themes, essentialist vs constructionist epistemology, building a thematic map, or writing up a qualitative findings section. Covers all six phases, the four upfront analytic decisions, the 15-point quality checklist, and the five common pitfalls. Produces a Word document write-up and an annotated thematic map. Does NOT cover IPA, grounded theory, discourse analysis, conversation analysis, or narrative analysis — use a different method for those.
development
Guide users through writing a systematic literature review (SLR) following the PRISMA 2020 framework. Use this skill whenever the user mentions 'systematic review', 'systematic literature review', 'SLR', 'PRISMA', 'PRISMA 2020', 'PRISMA flow diagram', 'PRISMA checklist', or asks for help writing, structuring, or auditing a literature review that follows reporting guidelines. Also trigger when the user asks about inclusion/exclusion criteria for a review, search strategies for databases like Scopus/WoS/PubMed, study selection processes, risk of bias assessment, or narrative synthesis for a review paper. This skill covers the full PRISMA 2020 checklist (27 items), produces a Word document manuscript in strict journal article format, generates an annotated PRISMA flow diagram, and enforces APA 7th Edition referencing throughout. It does NOT cover meta-analysis or statistical pooling. By Chuah Kee Man.
testing
Performs placebo-in-time sensitivity analysis with hierarchical null model and optional Bayesian assurance. Use when checking model robustness, verifying lack of pre-intervention effects, or estimating study power.
data-ai
Fit, summarize, plot, and interpret a chosen CausalPy experiment. Use after the causal method has been selected, including when configuring PyMC/sklearn models and scale-aware custom priors.