molclaw-peptide-sampling

name	molclaw-peptide-sampling
description	Generate peptide molecules using PepInvent, supporting template-based generation, custom peptide sequence modification, and info queries for available templates and amino acids.
license	MIT license
metadata	{"skill-author":"PJLab"}

Peptide Molecule Generation (PepInvent)

When to Use This Tool

Use PepInvent when you need to generate peptide or peptide-like molecules. This includes exploring peptide scaffolds with masked positions, generating analogs of a known peptide sequence, and building peptide libraries.

Do NOT use when: designing peptides that must bind a specific protein target (use L2 Skill 09 which combines PepInvent with EvoBind and validation); generating small molecules (use other REINVENT4 tools).

Overview — Three Tools

1. get_pepinvent_info — Query available templates and supported amino acids (call first if unsure)
2. pepinvent_peptide_sampling_by_template — Generate peptides from predefined structural templates
3. pepinvent_peptide_sampling_by_peptide — Generate variants of a user-provided peptide sequence

Recommended Workflow

Step 1: Call get_pepinvent_info('templates') → see available templates
Step 2: Call get_pepinvent_info('amino_acids') → see supported amino acids
Step 3: Choose the appropriate generation tool

---

Tool 1: get_pepinvent_info

Retrieve information about PepInvent's available templates or supported amino acids.
Args:
    mode (str): 'templates' or 'amino_acids'
Return:
    status (str): 'success' or 'error'
    msg (str): Descriptive message
    content (str): The requested information as text

response = await client.session.call_tool("get_pepinvent_info", arguments={"mode": "templates"})
templates = client.parse_result(response)["content"]

Tool 2: pepinvent_peptide_sampling_by_template

Generate peptide molecules from a predefined structural template.
Args:
    template (str): Template name. Options:
        - 'tripeptide_mask_middle', 'tripeptide_mask_ends'
        - 'tetrapeptide_mask_ends', 'tetrapeptide_mask_middle'
        - 'pentapeptide_mask_partial', 'pentapeptide_mask_all'
        - 'hexapeptide_mask_partial', 'hexapeptide_alternating'
        - 'cyclic_scaffold', 'stapled_peptide'
    n (int): Number of peptides to sample
    filter_preset (str): Options: 'none', 'minimal', 'default', 'strict'. Default 'default'.
    mw_min (float): Minimum MW filter. 0 = no constraint. Default 0.
    mw_max (float): Maximum MW filter. 0 = no constraint. Default 0.
Return:
    status, msg, save_smiles_file, output_smiles_list

response = await client.session.call_tool(
    "pepinvent_peptide_sampling_by_template",
    arguments={"template": "tetrapeptide_mask_middle", "n": 50, "filter_preset": "default", "mw_min": 400, "mw_max": 800}
)

Tool 3: pepinvent_peptide_sampling_by_peptide

Generate peptide variants by modifying a user-provided peptide sequence.
Args:
    peptide (str): Peptide as SMILES with residues separated by '|?|'. Example: 'N[C@@H](CCCCN)C(=O)|?|N[C@@H](CC(C)C)C(=O)|?|N[C@@H](CCCNC(=N)N)C(=O)'
    n (int): Number of peptides to sample
    filter_preset (str): Default 'default'
    mw_min (float): 0 = no constraint. Default 0.
    mw_max (float): 0 = no constraint. Default 0.
Return:
    status, msg, save_smiles_file, output_smiles_list

response = await client.session.call_tool(
    "pepinvent_peptide_sampling_by_peptide",
    arguments={"peptide": "N[C@@H](CCCCN)C(=O)|?|N[C@@H](CC(C)C)C(=O)|?|N[C@@H](CCCNC(=N)N)C(=O)", "n": 50, "filter_preset": "default", "mw_min": 300, "mw_max": 800}
)

Template Selection Guide

Need	Template	Rationale
Vary middle residue	tripeptide_mask_middle	Fixed anchors, explore core
Diversify terminals	tripeptide_mask_ends / tetrapeptide_mask_ends	N/C-terminal diversity
Maximum diversity	pentapeptide_mask_all	All positions open
Cyclic peptide	cyclic_scaffold	Constrained ring topology
Stapled peptide	stapled_peptide	Enhanced metabolic stability

MW Guide

Length	Typical MW	Suggested mw_min-mw_max
Tripeptide	300-500	250-600
Tetrapeptide	400-650	350-750
Pentapeptide	500-800	400-900
Hexapeptide	600-1000	500-1100

Important Notes

1. Lipinski does NOT apply to peptides. Peptides inherently violate RO5.
2. mw_min=0 and mw_max=0 mean "no constraint", not "MW must be 0."
3. Call get_pepinvent_info first when unfamiliar with available options.

---

⚠ Mandatory Generation Count Verification (L3 Principle 11)

actual_count = len(result["output_smiles_list"])

If actual count < 70% of requested: Retry with filter_preset='none', wider MW range, or increased n.