Agent skill

Molecular Descriptors Calculation

Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.

MITAuto-check passedResearch & Science

Install Molecular Descriptors Calculation

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/molecular-descriptors-calculation .claude/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .claude/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/molecular-descriptors-calculation .agents/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .agents/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/molecular-descriptors-calculation .cursor/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .cursor/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/InternScience/scp.git --path skills/molecular-descriptors-calculation

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/molecular-descriptors-calculation .gemini/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .gemini/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/molecular-descriptors-calculation .github/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .github/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add InternScience/scp --skill molecular-descriptors-calculation -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install InternScience/scp molecular-descriptors-calculation --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/InternScience/scp.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/molecular-descriptors-calculation .opencode/skills/molecular-descriptors-calculation && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "molecular-descriptors-calculation" agent skill from https://github.com/InternScience/scp/tree/main/skills/molecular-descriptors-calculation into .opencode/skills/molecular-descriptors-calculation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "molecular-descriptors-calculation", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: molecular-descriptors-calculation
GitHub stars: 169
Used in: 1 other repo
Token cost: ~1.7k tokens
SKILL.md length: 374 words
Files: 1
Skills in repo: 73
Repo updated: Jun 3, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.

Works in 2 steps: MCP Server Definition → Molecular Descriptors Calculation Workflow
Tasks that involve Drug discovery and cheminformatics
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Molecular Descriptors Calculation is an agent skill from InternScience/scp. Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.

Its SKILL.md is about 1.7k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Drug discovery and cheminformatics. The licence is MIT.

When your agent uses it

Tasks that involve Drug discovery and cheminformatics

Example prompts

“/molecular-descriptors-calculation”

Requirements

Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

MCP Server Definition
Molecular Descriptors Calculation Workflow

What it can do on your machine

Read from SKILL.md and the folder at commit cea5398. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Molecular Descriptors Calculation loads about 1.7k tokens when it runs. Until then it costs about 44 tokens; SKILL.md has 374 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~44
When it runs · the whole SKILL.md, loaded when a task matches: ~1.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from InternScience/scp at commit cea5398, republished under its MIT licence (© InternScience). 374 words, ~1,665 tokens.

Download SKILL.mdSave it as .claude/skills/molecular-descriptors-calculation/SKILL.md (or your agent's skills folder).

name: molecular-descriptors-calculation
description: Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.
license: MIT license
metadata.skill-author: PJLab

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:

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

Implementation:

python

## 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()

Tool Descriptions

SciToolAgent-Chem Server:

Shape Descriptors:

GetKappa1, GetKappa2, GetKappa3: Kappa shape indices (molecular shape)

Connectivity Indices:

GetChi0n, GetChi0v: Zero-order chi indices
GetChi1n, GetChi1v: First-order chi indices
GetChi2n, GetChi2v: Second-order chi indices
GetChi3n, GetChi3v, GetChi4n, GetChi4v: Higher-order chi indices

Structural Features:

GetRotatableBondsNum: Count rotatable bonds (flexibility)
GetHBDNum/GetHBANum: Hydrogen bond donors/acceptors
GetRingsNum: Total ring count
GetAromaticRingsNum: Aromatic ring count
GetAliphaticRingsNum: Aliphatic ring count

Physicochemical Descriptors:

GetCrippenDescriptors: LogP (lipophilicity) and molar refractivity
CalculateTPSA: Topological polar surface area
GetFractionCSP3: Fraction of sp³ hybridized carbons
GetLabuteASA: Labute accessible surface area

Input/Output

Input:

smiles: Molecule in SMILES format

Output:

Kappa Indices: Molecular shape descriptors (1, 2, 3)
Chi Indices: Topological connectivity indices
Structural Counts: Rings, bonds, functional groups
LogP: Lipophilicity (partition coefficient)
TPSA: Topological polar surface area (Ų)
Fraction sp³: Proportion of sp³ carbons (0-1)

Show full SKILL.md (180 more words)Show less

Descriptor Applications

Kappa Shape Indices

κ₁, κ₂, κ₃: Describe molecular shape from linear to spherical
Used in: QSAR models, molecular shape comparison

Chi Connectivity Indices

Encode information about branching and cyclicity
Used in: Property prediction, similarity searching

Structural Features

Rotatable bonds: Molecular flexibility, bioavailability
H-bond donors/acceptors: Solubility, permeability
Rings: Rigidity, drug-likeness

Physicochemical Descriptors

LogP: Lipophilicity, membrane permeability
TPSA: Oral bioavailability, BBB penetration
Fraction sp³: Molecular complexity, drug-likeness

Drug-Likeness Rules

Lipinski's Rule of Five:

MW ≤ 500 Da
LogP ≤ 5
HBD ≤ 5
HBA ≤ 10

Veber's Rules (Oral Bioavailability):

Rotatable bonds ≤ 10
TPSA ≤ 140 Ų

CNS Drug-Likeness:

TPSA < 90 Ų (for blood-brain barrier penetration)

Use Cases

QSAR model development
Virtual screening and compound prioritization
Drug-likeness assessment
Molecular similarity calculations
Pharmacokinetic property prediction
Lead optimization
Chemical space exploration

Additional Descriptor Tools

The SciToolAgent-Chem server provides 160+ tools including:

GetBCUT: BCUT descriptors
GetAutocorrelation2D/GetAutocorrelation3D: Autocorrelation descriptors
GetWHIM: WHIM descriptors
GetGETAWAY: GETAWAY descriptors
GetMORSE: MORSE descriptors
GetRDF: Radial distribution function
GetUSR/GetUSRCAT: Ultrafast shape recognition descriptors

Performance Notes

Most descriptor calculations are very fast (<1 second)
Can batch process multiple molecules
Descriptors are deterministic (same molecule → same descriptors)

Files

Just SKILL.md in skills/molecular-descriptors-calculation of InternScience/scp.

Open the folder on GitHubat commit cea5398

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in InternScience/scp, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Molecular Descriptors Calculation next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Molecular Descriptors Calculation compared with similar skills
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Molecular Descriptors Calculation this skillInternScience/scp	169	1 repos	~1.7k	Automated safety check: Pass	MIT	4 mo ago
MolecodeAtomFlow-AI/MoleCode	306	—	~1.9k	Automated safety check: Pass	MIT	4 mo ago
Drug DiscoveryTommy-yw/RunbookHermes	546	1 repos	~2.3k	Automated safety check: Pass	MIT	4 mo ago
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills	48k	1 repos	~3k	Automated safety check: Notes	MIT	3 days ago
Biomedical Analysis Dispatchxjtulyc/MedgeClaw	617	1 repos	~2k	Automated safety check: Pass	None	7 mo ago
Edu Chem Reactionwy51ai/edulab	1.4k	—	~1.2k	Automated safety check: Pass	Apache-2.0	10 days ago

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Questions about Molecular Descriptors Calculation

What does Molecular Descriptors Calculation do?

Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery. Molecular Descriptors Calculation is an agent skill from InternScience/scp. Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.

When should I use Molecular Descriptors Calculation?

Molecular Descriptors Calculation fits situations like: tasks that involve Drug discovery and cheminformatics.

How do I install Molecular Descriptors Calculation in Claude Code?

Run `npx skills add InternScience/scp --skill molecular-descriptors-calculation -a claude-code`. Or copy the skill folder (skills/molecular-descriptors-calculation in InternScience/scp) into .claude/skills/molecular-descriptors-calculation in your project. Claude Code loads it when a task matches its description.

How do I install Molecular Descriptors Calculation in Codex?

Run `npx skills add InternScience/scp --skill molecular-descriptors-calculation -a codex`. Or copy the skill folder (skills/molecular-descriptors-calculation in InternScience/scp) into .agents/skills/molecular-descriptors-calculation in your project. Codex loads it when a task matches its description.

Can I use Molecular Descriptors Calculation in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add InternScience/scp --skill molecular-descriptors-calculation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/molecular-descriptors-calculation, .gemini/skills/molecular-descriptors-calculation, .github/skills/molecular-descriptors-calculation and .opencode/skills/molecular-descriptors-calculation in your project.

What does Molecular Descriptors Calculation need to run?

SKILL.md names no scripts, command-line tools or credentials: Molecular Descriptors Calculation is instructions for the agent only. Our summary lists: Python 3.

Does Molecular Descriptors Calculation access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Molecular Descriptors Calculation safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Molecular Descriptors Calculation use?

Molecular Descriptors Calculation is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Molecular Descriptors Calculation use?

About 1.7k tokens (SKILL.md is roughly 6.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Molecular Descriptors Calculation?

Skills that share tags, products or a category with Molecular Descriptors Calculation: Molecode (AtomFlow-AI/MoleCode, 306 stars), Drug Discovery (Tommy-yw/RunbookHermes, 546 stars), DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars) and Biomedical Analysis Dispatch (xjtulyc/MedgeClaw, 617 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Molecular Descriptors Calculation?

InternScience (a GitHub organization) maintains it in InternScience/scp, which has 169 GitHub stars. The repository holds 73 skills in this directory. The repository was last updated on June 3, 2026.

Source: InternScience/scp on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Molecular Descriptors Calculation

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Molecular Descriptors Calculation

Usage

1. MCP Server Definition

2. Molecular Descriptors Calculation Workflow

Tool Descriptions

Input/Output

Descriptor Applications

Drug-Likeness Rules

Use Cases

Additional Descriptor Tools

Performance Notes

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from InternScience/scp

Related

Questions about Molecular Descriptors Calculation