Classifiers

Classifiers assign van der Waals radii and polarity classes to atoms based on residue and atom names. The choice of classifier directly affects SASA values, so understanding the differences is important.

Quick Recommendation

• ProtOr: CLI default for PDB/mmCIF. Hybridization-based radii (Tsai et al. 1999).
• NACCESS: Widely used, compatible with FreeSASA. Use when comparing with NACCESS-based studies.
• OONS: Larger aliphatic carbon radii. Use when comparing with OONS-based studies.

How Classifiers Work

1. Residue-specific match: Exact match of (residue name, atom name) pair
2. ANY fallback: Generic atom definitions shared across residues (NACCESS and OONS only)
3. Element estimation: Estimate radius from element symbol if no match found

Classifier Comparison

Radius Differences

Atom Type	NACCESS	ProtOr	OONS
Aliphatic C (e.g., CA, CB)	1.87 Å	1.88 Å	2.00 Å
Aromatic C	1.76 Å	1.76 Å	1.75 Å
Nitrogen	1.65 Å	1.64 Å	1.55 Å
Oxygen	1.40 Å	1.42-1.46 Å	1.40 Å
Sulfur	1.85 Å (apolar)	1.77 Å (polar)	2.00 Å (polar)

Sulfur polarity varies

NACCESS treats sulfur as apolar, while ProtOr and OONS treat it as polar. This affects polar/nonpolar SASA classification for CYS and MET residues.

Key Differences

Property	NACCESS	ProtOr	OONS
ANY fallback	Yes	No	Yes
Classification basis	Atom type	Hybridization state	Atom type
Reference	Hubbard & Thornton 1993	Tsai et al. 1999	Ooi et al. 1987

Usage

CLI

# NACCESS (recommended)
zsasa calc --classifier=naccess structure.cif output.json

# ProtOr
zsasa calc --classifier=protor structure.cif output.json

# OONS
zsasa calc --classifier=oons structure.cif output.json

# Custom config file
zsasa calc --config=my_radii.toml structure.cif output.json

Python

from zsasa import classify_atoms, calculate_sasa, ClassifierType

# Step 1: Classify atoms to get radii
classification = classify_atoms(residue_names, atom_names, ClassifierType.NACCESS)

# Step 2: Calculate SASA using classified radii
result = calculate_sasa(coords, classification.radii)

Python (Gemmi)

from zsasa.core import ClassifierType
from zsasa.integrations.gemmi import calculate_sasa_from_structure

# Classifier is applied automatically
result = calculate_sasa_from_structure(
    "protein.cif",
    classifier=ClassifierType.NACCESS,
)

Custom Classifier

You can define custom atom radii using a config file.

TOML Format

name = "my-classifier"

[types]
C_ALI = { radius = 1.87, class = "apolar" }
C_CAR = { radius = 1.76, class = "apolar" }
N     = { radius = 1.65, class = "polar" }
O     = { radius = 1.40, class = "polar" }
S     = { radius = 1.85, class = "apolar" }

[[atoms]]
residue = "ANY"
atom = "CA"
type = "C_ALI"

[[atoms]]
residue = "ALA"
atom = "CB"
type = "C_ALI"

FreeSASA Format

name: my-classifier

types:
C_ALI 1.87 apolar
C_CAR 1.76 apolar
O     1.40 polar

atoms:
ANY CA  C_ALI
ALA CB  C_ALI

The format is auto-detected by file extension: .toml for TOML, all others for FreeSASA format.

Supported Residues

Amino Acids

All 20 standard amino acids plus SEC (selenocysteine) and MSE (selenomethionine).

Nucleic Acids

RNA: A, C, G, I, T, U DNA: DA, DC, DG, DI, DT, DU

Handling Unknown Atoms

When a classifier cannot find a matching (residue, atom name) pair:

1. NACCESS/OONS check the ANY fallback entries
2. If still unmatched, the element is extracted from the atom name and a generic van der Waals radius is assigned

To avoid ambiguity (e.g., "CA" = Carbon-alpha vs Calcium), include an element field (atomic numbers) in JSON input:

{
  "atom_name": ["CA", "CA"],
  "element": [6, 20]
}

• Atomic number 6 = Carbon (Cα)
• Atomic number 20 = Calcium (metal ion)

References

• Hubbard, S. J.; Thornton, J. M. NACCESS, Computer Program. UCL, 1993.
• Tsai, J.; Taylor, R.; Chothia, C.; Gerstein, M. The Packing Density in Proteins. J. Mol. Biol. 1999, 290(1), 253-266.
• Ooi, T.; Oobatake, M.; Némethy, G.; Scheraga, H. A. Accessible Surface Areas. Proc. Natl. Acad. Sci. 1987, 84(10), 3086-3090.
• Mantina, M. et al. Consistent van der Waals Radii. J. Phys. Chem. A 2009, 113(19), 5806-5812.