# Molclaw Pack Sidechains

> Predicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.

- Skill: `internscience/molclaw-pack-sidechains` (Agent Skill)
- Install (CLI): `npx skillmds@latest add internscience/molclaw-pack-sidechains`
- Raw SKILL.md: https://api.skillmd.com/api/skills/internscience/molclaw-pack-sidechains/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: MIT license
- Author: internscience (https://skillmd.com/u/internscience)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/internscience/molclaw-pack-sidechains

---


# AttnPacker Sidechain Packing

Note: 
- Local files are not directly accessible by the server. Please upload them to the server using `molclaw-file-transfer` before execution. 
- For PDB file inputs, it is recommended to preprocess them using `molclaw-pdbfixer` before execution.
- Please refer to skill `molclaw-scp-server` to complete tool invocation.

## Usage

### 1. Protein Sidechain Packing
The description of tool *pack_sidechains*.

```tex
Predict full-atom sidechain conformations from backbone PDBs for protein structure preparation workflows.
Args:
  input_pdb (str): Input PDB file path, required.
  device (str|None): Compute device such as cuda:0, default None (auto by source script).
  chunk_size (int): Inference chunk size for long proteins, default 500.
  no_post_process (bool): Skip rotamer post-processing for faster runtime, default False.
  max_optim_iters (int): Maximum optimization iterations in post-process, default 250.
  steric_wt (float): Steric clash penalty weight, default 1.0.
  optim_repeats (int): Post-process optimization repeats, default 2.
  dry_run (bool): Create a traceable run directory without running inference, default False.
Return:
  status (str): 'success', 'error', or 'partial_success'.
  msg (str): Human-readable execution message.
  input_pdb (str): Input PDB path used for this run.
  output_dir (str): Unique run directory under tool_result/pack_sidechains_result.
  output_pdb (str): Expected or generated output PDB path.
  device (str|None): Device value used for execution.
  chunk_size (int): Chunk size used.
  no_post_process (bool): Whether post-process was skipped.
  max_optim_iters (int): Max optimization iterations used.
  steric_wt (float): Steric weight used.
  optim_repeats (int): Optimization repeats used.
  dry_run (bool): Whether dry-run mode was used.
  error_type (str, optional): Exception type when status is 'error'.
  traceback (str, optional): Python traceback when status is 'error'.
```

How to use tool *pack_sidechains* :

```python
response = await client.session.call_tool(
    "pack_sidechains",
    arguments={
        "input_pdb": "/path/to/input.pdb",
        "device": "cuda:0",
        "chunk_size": 500,
        "no_post_process": False,
        "max_optim_iters": 250,
        "steric_wt": 1.0,
        "optim_repeats": 2,
        "dry_run": False
    }
)
result = client.parse_result(response)
output_pdb = result["output_pdb"]

```

#### Example parameter sets

```python
# 1) Main mode
{
    "input_pdb": "/path/to/input.pdb",
    "device": "cuda:0",
    "chunk_size": 500,
    "no_post_process": False,
    "max_optim_iters": 250,
    "steric_wt": 1.0,
    "optim_repeats": 2,
    "dry_run": False
}

# 2) Variant mode
{
    "input_pdb": "relative/path/to/test_backbone.pdb",
    "chunk_size": 500,
    "dry_run": True
}
```