Molecular Descriptors Calculation

Usage

1. MCP Server Definition

Use the same ChemicalToolsClient class as defined in the molecular-properties-calculation skill.

2. Molecular Descriptors Calculation Workflow

This workflow calculates advanced molecular descriptors used in QSAR modeling, drug discovery, and computational chemistry.

Workflow Steps:

1. Calculate Kappa Shape Indices - Molecular shape descriptors
2. Calculate Connectivity Indices - Topological descriptors
3. Calculate Structural Features - Rings, bonds, and functional groups

Implementation:

## Initialize client
HEADERS = {"SCP-HUB-API-KEY": "<your-api-key>"}

client = ChemicalToolsClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/31/SciToolAgent-Chem",
    HEADERS
)

if not await client.connect():
    print("connection failed")
    exit()

## Input: SMILES string to analyze
smiles = "CCO"  # Ethanol
print(f"=== Molecular Descriptors for {smiles} ===\n")

## Step 1: Calculate Kappa shape indices
print("Step 1: Kappa Shape Indices")
for tool in ["GetKappa1", "GetKappa2", "GetKappa3"]:
    result = await client.client.call_tool(
        tool,
        arguments={"smiles": smiles}
    )
    result_data = client.parse_result(result)
    print(f"{tool}: {result_data}")
print()

## Step 2: Calculate Chi connectivity indices
print("Step 2: Chi Connectivity Indices")
for tool in ["GetChi0n", "GetChi0v", "GetChi1n", "GetChi1v"]:
    result = await client.client.call_tool(
        tool,
        arguments={"smiles": smiles}
    )
    result_data = client.parse_result(result)
    print(f"{tool}: {result_data}")
print()

## Step 3: Calculate structural features
print("Step 3: Structural Features")

# Rotatable bonds
result = await client.client.call_tool(
    "GetRotatableBondsNum",
    arguments={"smiles": smiles}
)
print(f"Rotatable bonds: {client.parse_result(result)}")

# Hydrogen bond donors and acceptors
result = await client.client.call_tool(
    "GetHBDNum",
    arguments={"smiles": smiles}
)
print(f"H-bond donors: {client.parse_result(result)}")

result = await client.client.call_tool(
    "GetHBANum",
    arguments={"smiles": smiles}
)
print(f"H-bond acceptors: {client.parse_result(result)}")

# Ring counts
result = await client.client.call_tool(
    "GetRingsNum",
    arguments={"smiles": smiles}
)
print(f"Number of rings: {client.parse_result(result)}")

result = await client.client.call_tool(
    "GetAromaticRingsNum",
    arguments={"smiles": smiles}
)
print(f"Aromatic rings: {client.parse_result(result)}")
print()

## Step 4: Calculate physicochemical descriptors
print("Step 4: Physicochemical Descriptors")

# LogP and molar refractivity (Crippen descriptors)
result = await client.client.call_tool(
    "GetCrippenDescriptors",
    arguments={"smiles": smiles}
)
print(f"Crippen descriptors (LogP, MR): {client.parse_result(result)}")

# Topological polar surface area
result = await client.client.call_tool(
    "CalculateTPSA",
    arguments={"smiles": smiles}
)
print(f"TPSA: {client.parse_result(result)}")

# Fraction of sp3 carbons
result = await client.client.call_tool(
    "GetFractionCSP3",
    arguments={"smiles": smiles}
)
print(f"Fraction sp3 carbons: {client.parse_result(result)}")
print()

await client.disconnect()