chemical-structure-analysis
Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.
Best use case
chemical-structure-analysis is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.
Teams using chemical-structure-analysis should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/chemical-structure-analysis/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How chemical-structure-analysis Compares
| Feature / Agent | chemical-structure-analysis | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# Chemical Structure Analysis
## Usage
### 1. MCP Server Definition
```python
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession
class InternAgentClient:
"""InternAgent MCP Client"""
def __init__(self, server_url: str, api_key: str):
self.server_url = server_url
self.api_key = api_key
self.session = None
async def connect(self):
try:
self.transport = streamablehttp_client(
url=self.server_url,
headers={"SCP-HUB-API-KEY": self.api_key}
)
self.read, self.write, self.get_session_id = await self.transport.__aenter__()
self.session_ctx = ClientSession(self.read, self.write)
self.session = await self.session_ctx.__aenter__()
await self.session.initialize()
return True
except Exception as e:
print(f"✗ connect failure: {e}")
return False
async def disconnect(self):
try:
if self.session:
await self.session_ctx.__aexit__(None, None, None)
if hasattr(self, 'transport'):
await self.transport.__aexit__(None, None, None)
except Exception as e:
print(f"✗ disconnect error: {e}")
def parse_result(self, result):
try:
if hasattr(result, 'content') and result.content:
content = result.content[0]
if hasattr(content, 'text'):
return json.loads(content.text)
return str(result)
except Exception as e:
return {"error": f"parse error: {e}", "raw": str(result)}
```
### 2. Chemical Structure Analysis Workflow
Analyze chemical structures from compound names.
**Implementation:**
```python
## Initialize client
client = InternAgentClient(
"https://scp.intern-ai.org.cn/api/v1/mcp/28/InternAgent",
"<your-api-key>"
)
if not await client.connect():
print("connection failed")
exit()
## Input: Compound name
compound_name = "aspirin"
## Analyze chemical structure
result = await client.session.call_tool(
"ChemicalStructureAnalyzer",
arguments={
"compound_name": compound_name
}
)
data = client.parse_result(result)
print(f"Compound: {compound_name}")
print(f"SMILES: {data.get('smiles', 'N/A')}")
print(f"Molecular Formula: {data.get('molecular_formula', 'N/A')}")
print(f"Molecular Weight: {data.get('molecular_weight', 'N/A')}")
print(f"LogP: {data.get('logP', 'N/A')}")
await client.disconnect()
```
### Tool Descriptions
**InternAgent Server:**
- `ChemicalStructureAnalyzer`: Analyze chemical structure from compound name
- Args:
- `compound_name` (str): Chemical compound name
- Returns:
- `smiles` (str): SMILES notation
- `molecular_formula` (str): Chemical formula
- `molecular_weight` (float): Molecular weight (g/mol)
- `logP` (float): Partition coefficient
### Use Cases
- Chemical property lookup
- Drug-likeness assessment
- Compound identification
- Chemical database searchesRelated Skills
uniprot_deep_analysis
UniProt Deep Protein Analysis - Deep UniProt analysis: entry data, UniRef clusters, UniParc cross-references, and gene-centric view. Use this skill for protein science tasks involving get uniprotkb entry by accession get uniref cluster by id get uniparc entry by upi get gene centric by accession. Combines 4 tools from 1 SCP server(s).
proteome_analysis
Proteome-Level Analysis - Analyze at proteome level: get proteome from UniProt, gene-centric view, functional annotation from STRING. Use this skill for proteomics tasks involving get proteome by id get gene centric by proteome get functional annotation. Combines 3 tools from 2 SCP server(s).
protein_structure_analysis
Protein Structure Comprehensive Analysis - Comprehensive structure analysis: download PDB, extract chains, calculate geometry, quality metrics, and composition. Use this skill for structural biology tasks involving retrieve protein data by pdbcode extract pdb chains calculate pdb structural geometry calculate pdb quality metrics calculate pdb composition info. Combines 5 tools from 1 SCP server(s).
protein_complex_analysis
Protein Complex Visualization & Analysis - Analyze protein complex: download structure, visualize complex, extract chains, and calculate quality metrics. Use this skill for structural biology tasks involving retrieve protein data by pdbcode visualize complex extract pdb chains calculate pdb basic info. Combines 4 tools from 1 SCP server(s).
protein_classification_analysis
Protein Classification Analysis - Classify protein: ChEMBL protein classification, UniProt entry, InterPro domains, and Ensembl biotypes. Use this skill for protein science tasks involving search protein classification get uniprotkb entry by accession query interpro get info biotypes. Combines 4 tools from 4 SCP server(s).
mutation_impact_analysis
Mutation Impact Analysis - Analyze mutation impact: predict structure, predict mutations from sequence and structure, and check variant effects with Ensembl VEP. Use this skill for molecular biology tasks involving pred protein structure esmfold zero shot sequence prediction predict zero shot structure get vep hgvs. Combines 4 tools from 3 SCP server(s).
full_protein_analysis
Full Protein Characterization - Complete protein characterization: validate sequence, compute all properties, predict structure, and analyze pockets. Use this skill for protein biochemistry tasks involving is valid protein sequence analyze protein ComputeProtPara pred protein structure esmfold run fpocket. Combines 5 tools from 4 SCP server(s).
code_execution_analysis
Computational Analysis via Code Execution - Execute custom computational analysis code, analyze software, and search for reference implementations. Use this skill for computational science tasks involving exec code software analysis search dataset search literature. Combines 4 tools from 2 SCP server(s).
blast_protein_analysis
BLAST & Protein Analysis Pipeline - BLAST search followed by comprehensive protein analysis: BLAST, then structure prediction, properties, and function. Use this skill for sequence bioinformatics tasks involving blast search pred protein structure esmfold calculate protein sequence properties predict protein function. Combines 4 tools from 4 SCP server(s).
antibody_target_analysis
Antibody-Target Analysis - Analyze an antibody target: UniProt protein info, InterPro domains, protein properties, and biotherapeutic data from ChEMBL. Use this skill for immunology tasks involving get uniprotkb entry by accession query interpro ComputeProtPara get biotherapeutic by name. Combines 4 tools from 4 SCP server(s).
alphafold_structure_pipeline
AlphaFold Structure Analysis Pipeline - AlphaFold pipeline: download predicted structure, predict pockets, extract sequence, and compute properties. Use this skill for computational biology tasks involving download alphafold structure run fpocket extract pdb sequence calculate pdb basic info. Combines 4 tools from 3 SCP server(s).
thermal_analysis
Thermal & Heat Transfer Analysis - Analyze thermal system: calculate heat released, convert energy units, compute potential energy, and dynamic viscosity. Use this skill for thermal engineering tasks involving calculate heat released convert energy MeV to J calculate potential energy calculate dynamic viscosity. Combines 4 tools from 1 SCP server(s).