Integration Modules

All integration modules provide a consistent interface for calculating SASA from structure files.

Available Integrations

Module	Library	Formats	Best For
gemmi	gemmi	mmCIF, PDB	Fast parsing, large files
biopython	BioPython	PDB, mmCIF	Existing BioPython workflows
biotite	Biotite	PDB, mmCIF, BinaryCIF	AtomWorks compatibility
mdtraj	MDTraj	XTC, TRR, DCD, etc.	MD trajectory analysis
mdanalysis	MDAnalysis	XTC, TRR, DCD, etc.	MD trajectory analysis

Common Functions

All structure file integrations (gemmi, biopython, biotite) provide:

Function	Description
extract_atoms_from_model(model)	Extract atom data from model
calculate_sasa_from_model(model)	Calculate SASA from model
calculate_sasa_from_structure(source)	Calculate SASA from file or structure

Biotite uses atom_array instead of model:

Function	Description
extract_atoms_from_atom_array(atom_array)	Extract atom data from AtomArray
calculate_sasa_from_atom_array(atom_array)	Calculate SASA from AtomArray

Common Parameters

Parameter	Type	Default	Description
classifier	ClassifierType	NACCESS	Atom radius classifier
algorithm	"sr" or "lr"	"sr"	SASA algorithm
n_points	int	100	Test points (SR)
n_slices	int	20	Slices (LR)
probe_radius	float	1.4	Probe radius in Å
n_threads	int	0	Threads (0 = auto)
include_hetatm	bool	True	Include HETATM records
include_hydrogens	bool	False	Include hydrogen atoms
model_index	int	0	Model index (NMR)

SasaResultWithAtoms

Extended result class with atom metadata:

@dataclass
class SasaResultWithAtoms(SasaResult):
    atom_classes: NDArray[int32]  # Per-atom polarity classes
    atom_data: AtomData           # Atom metadata
    polar_area: float             # Total polar SASA
    apolar_area: float            # Total apolar SASA

AtomData

@dataclass
class AtomData:
    coords: NDArray[float64]   # (N, 3) coordinates
    residue_names: list[str]   # Residue names
    atom_names: list[str]      # Atom names
    chain_ids: list[str]       # Chain IDs
    residue_ids: list[int]     # Residue numbers
    elements: list[str]        # Element symbols