molecule-analysis
Parse and inspect small molecules from SMILES with the local RDKit pipeline.
Skill by phenixace
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Install
Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.
npx agentmarket install skill/phenixace-molecule-analysis
Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.
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About
Use cases: data
Reviews
Write a reviewNo reviews yet. Installed it? Reviews come from verified installers only. How reviews work
Permissions
What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.
- Tools
- No tools found
- Secrets
- None asked for
- Install scripts
- None found
- Runs as
- Python package
Network hosts it talks to 1
codeload.github.com· found in install command
Files it touches
~/.claude/skills/molecule-analysis
What's inside
- Skill name
molecule-analysis- Description
- Parse and inspect small molecules from SMILES with the local RDKit pipeline. Use for molecular graphs, bond orders, rings, formulae, and core drug-like descriptors; do not use it as an experimental ADMET prediction.
- License
- MIT
- Instructions
- 7 lines in SKILL.md · view on GitHub
Before installing
- Ships executable scripts
Files (4)
- SKILL.md
- openai.yaml · agents/
- handler.py · scripts/
- skill.json
SKILL.md (first lines)
# Molecule Analysis Use `chem_analyze_molecule` for concrete SMILES work. Report calculated descriptors as RDKit outputs and keep medicinal-chemistry interpretations separate from computed facts. When suggesting analogues, preserve the stated scaffold and constraints, label every design as a hypothesis, and name the assay or calculation needed to validate it. The returned molecule artifact can be opened in the Molemo structure viewer.
From phenixace/Molemo_WorkBench, MIT.
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hmmer-profile-search
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Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs.
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research-router
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Route broad life-science research questions to the smallest useful set of Molemo skills.
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Create reviewable, researcher-approved plans from Molemo scientific tools.
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Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
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chembl-bioactivity
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Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.554score
clinical-trial-landscape
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Search ClinicalTrials.gov for a bounded trial landscape or review the posted tabular results of one exact NCT record.
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dna-variant-calling
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functional-analysis
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Review a bounded human gene set with Reactome pathway overrepresentation and STRING identifier mapping, enrichment, functional association networks, and PPI…
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geo-dataset-discovery
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Discover public NCBI GEO Series from a biological question with exact GSE-only query provenance, bounded metadata, study-design caveats, and an approved…
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geo-series-matrix-import
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Inspect and import one official NCBI GEO Series Matrix through a researcher-approved, bounded local workflow while preserving sample metadata, values and…
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protein-analysis
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Analyze protein FASTA sequences with local sequence-derived calculations.
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Signals
- Stars
- 2
- Forks
- 0
- Open issues
- 0
- Last commit (this folder)
- Aug 29, 2026 (2 months ago)
From GitHub (fetched Oct 24, 2026).
Details
- License
- MIT
- Repository
- github.com/phenixace/Molemo_WorkBench
- First seen
- Oct 24, 2026
- Last checked
- Oct 24, 2026
- Source
- GitHubgithub-graphql
More from phenixace
- 0.557score
research-router
phenixace
Route broad life-science research questions to the smallest useful set of Molemo skills.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
scientific-visualization
phenixace
Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
hmmer-profile-search
phenixace
Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
protein-structure
phenixace
Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
chembl-bioactivity
phenixace
Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
guided-workflows
phenixace
Create reviewable, researcher-approved plans from Molemo scientific tools.
SkillBFreshness: B★ 2Claude Code +9
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Cite this page
molecule-analysis skill. Agent Mart. https://agentmart.dev/skills/phenixace-molecule-analysis (last updated 2026-10-24)