README.md

---
pretty_name: SwissSidechain Residues
license: other
tags:
- biology
- chemistry
- protein
- amino-acids
- sidechains
- molecular-dynamics
- smiles
- pdb
- mol2
- parquet
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*.parquet
  - split: test
    path: data/test-*.parquet
---

# SwissSidechain Residues

SwissSideChain is a molecular and structural database of non-natural amino-acid sidechains, including structures, rotamers, and molecular mechanics parameters.

This dataset contains a viewer-friendly Parquet table derived from the SwissSidechain archives in this repository. Each row is one unique residue entry from the L or D SMI archives, with parsed availability and summary fields for PDB, MOL2, CHARMM topology, GROMACS RTP/HDB, bundle files, and rotamer libraries.
The original ZIP archives remain in the repository. The default `datasets` configuration uses the normalized Parquet files under `data/` so that the Hugging Face Dataset Viewer and `load_dataset()` can read the residue table directly.
The source library comments state that the SwissSidechain entries are copyright of the Swiss Institute of Bioinformatics, with non-profit use allowed when the content is not modified and the copyright statement is retained. Commercial use requires a license agreement. Check the original SwissSidechain terms before commercial use.

## Splits

The split is deterministic by entry identifier: `sha256(entry_id) % 10`. Bucket `0` is `test`; buckets `1` through `9` are `train`.

| Split | Rows |
|---|---:|
| train | 400 |
| test | 59 |
| total | 459 |

## Dataset Statistics

| Field | Value |
|---|---:|
| Unique residue entries | 459 |
| L entries | 230 |
| D entries | 229 |
| Entries with PDB | 459 |
| Entries with MOL2 | 459 |
| Entries with CHARMM topologies | 437 |
| Entries with GROMACS RTP/HDB | 437 |
| Entries with source bundles | 459 |
| Entries with backbone-dependent rotamers | 454 |
| Entries with backbone-independent rotamers | 453 |
| Backbone-dependent rotamer rows | 15,256,136 |
| Backbone-independent rotamer rows | 11,144 |

## Usage

Install the Hugging Face Datasets library:

```bash
pip install datasets
```

Load all splits:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/SwissSidechain")
print(ds)

row = ds["train"][0]
print(row["entry_id"], row["residue_code"], row["smiles"])
```

Load one split:

```python
from datasets import load_dataset

train = load_dataset("LiteFold/SwissSidechain", split="train")
test = load_dataset("LiteFold/SwissSidechain", split="test")
```

Stream rows without downloading the full table first:

```python
from datasets import load_dataset

stream = load_dataset("LiteFold/SwissSidechain", split="train", streaming=True)
for row in stream.take(5):
    print(row["entry_id"], row["stereochemistry"], row["pdb_atom_count"])
```

Filter D residues with complete topology files:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/SwissSidechain", split="train")
d_topologies = ds.filter(
    lambda row: row["stereochemistry"] == "D"
    and row["has_top"]
    and row["has_rtp"]
    and row["has_hdb"]
)
print(d_topologies[0])
```

Find entries with rotamer data:

```python
from datasets import load_dataset

ds = load_dataset("LiteFold/SwissSidechain", split="train")
with_rotamers = ds.filter(lambda row: row["bbdep_rotamer_rows"] > 0)
print(with_rotamers[0]["entry_id"], with_rotamers[0]["bbdep_rotamer_rows"])
```

Load metadata tables directly:

```python
import pandas as pd
from huggingface_hub import hf_hub_download

rotamer_path = hf_hub_download(
    repo_id="LiteFold/SwissSidechain",
    repo_type="dataset",
    filename="metadata/rotamer_library_counts.parquet",
)
rotamers = pd.read_parquet(rotamer_path)
print(rotamers.head())

manifest_path = hf_hub_download(
    repo_id="LiteFold/SwissSidechain",
    repo_type="dataset",
    filename="metadata/archive_manifest.parquet",
)
manifest = pd.read_parquet(manifest_path)
print(manifest)
```

## Columns

| Column | Description |
|---|---|
| `entry_id` | Stable table ID in the form `L:<code>` or `D:<code>`. |
| `residue_code` | Residue code from the source file names. |
| `stereochemistry` | Source stereochemistry group: `L` or `D`. |
| `smiles` | SMILES string from the SMI archive. |
| `smiles_reference_file` | Filename referenced inside the SMI row. |
| `source_*_path` | Source archive path used for each parsed format. |
| `has_smi` | Whether an SMI file exists. |
| `has_pdb` | Whether a PDB file exists. |
| `has_mol2` | Whether a MOL2 file exists. |
| `has_top` | Whether a CHARMM `.top` file exists. |
| `has_rtp` | Whether a GROMACS `.rtp` file exists. |
| `has_hdb` | Whether a GROMACS `.hdb` file exists. |
| `has_bundle` | Whether the entry appears in `L_sidechain.zip` or `D_residues.zip`. |
| `has_png` | Whether the source bundle contains a PNG image. |
| `has_bundle_bbdep_lib` | Whether the source bundle contains a per-entry backbone-dependent rotamer ZIP. |
| `has_bundle_bbind_lib` | Whether the source bundle contains a per-entry backbone-independent rotamer ZIP. |
| `bundle_file_extensions` | File extensions found in the source bundle. |
| `pdb_residue_names` | Residue names parsed from PDB records. |
| `pdb_atom_names` | Atom names parsed from PDB records. |
| `pdb_elements` | Element symbols parsed from PDB records. |
| `pdb_atom_count` | Number of PDB atoms. |
| `pdb_heavy_atom_count` | Number of non-hydrogen PDB atoms. |
| `pdb_hydrogen_atom_count` | Number of hydrogen PDB atoms. |
| `mol2_molecule_name` | Molecule name from the MOL2 file. |
| `mol2_molecule_type` | MOL2 molecule type. |
| `mol2_charge_type` | MOL2 charge type. |
| `mol2_atom_names` | Atom names parsed from MOL2. |
| `mol2_atom_types` | Atom types parsed from MOL2. |
| `mol2_atom_charges` | Partial charges parsed from MOL2. |
| `mol2_atom_count` | Number of MOL2 atoms. |
| `mol2_bond_count` | Number of MOL2 bonds. |
| `mol2_total_partial_charge` | Sum of MOL2 partial charges. |
| `charmm_residue_name` | Residue name parsed from CHARMM `RESI`. |
| `charmm_residue_charge` | Residue charge parsed from CHARMM `RESI`. |
| `charmm_residue_comment` | Comment attached to the CHARMM `RESI` line. |
| `charmm_atom_names` | Atom names from CHARMM topology. |
| `charmm_atom_types` | Atom types from CHARMM topology. |
| `charmm_atom_charges` | Atom charges from CHARMM topology. |
| `charmm_atom_count` | Number of CHARMM atoms. |
| `charmm_bond_count` | Number of CHARMM bond pairs. |
| `gromacs_residue_name` | Residue name from GROMACS RTP. |
| `gromacs_residue_comment` | Comment attached to the GROMACS residue header. |
| `gromacs_atom_names` | Atom names from GROMACS RTP. |
| `gromacs_atom_types` | Atom types from GROMACS RTP. |
| `gromacs_atom_charges` | Atom charges from GROMACS RTP. |
| `gromacs_atom_count` | Number of GROMACS RTP atoms. |
| `gromacs_bond_count` | Number of GROMACS RTP bonds. |
| `gromacs_improper_count` | Number of GROMACS RTP impropers. |
| `hdb_rule_count` | Number of hydrogen database rules. |
| `hdb_declared_rule_count` | Rule count declared in the HDB header. |
| `bbind_rotamer_rows` | Rows in the backbone-independent rotamer library for this residue code. |
| `bbdep_rotamer_rows` | Rows in the backbone-dependent rotamer library for this residue code. |
| `split_bucket` | Deterministic split bucket from `sha256(entry_id) % 10`. |

# Citation

```
@article{gfeller2013swisssidechain,
  title   = {{SwissSidechain}: a molecular and structural database of non-natural sidechains},
  author  = {Gfeller, David and Michielin, Olivier and Zoete, Vincent},
  journal = {Nucleic Acids Research},
  volume  = {41},
  number  = {D1},
  pages   = {D327--D332},
  year    = {2013},
  doi     = {10.1093/nar/gks991}
}
```