Output & Analysis

Output Formats

JSON (default)

Pretty-printed JSON with 2-space indentation:

{
  "total_area": 18923.28,
  "atom_areas": [
    32.47,
    0.25,
    15.82
  ]
}

Compact JSON

Single-line JSON without whitespace:

{"total_area":18923.28,"atom_areas":[32.47,0.25,15.82]}

CSV

Basic CSV with atom index and area:

atom_index,area
0,32.470000
1,0.250000
2,15.820000
total,18923.280000

When input has structural info (mmCIF/PDB), rich CSV is generated:

chain,residue,resnum,atom_name,x,y,z,radius,area
A,ALA,1,N,1.000,3.000,5.000,1.500,32.470000
A,ALA,1,CA,2.000,4.000,6.000,1.700,0.250000
,,,,,,,,18923.280000

Trajectory Output (CSV)

The traj subcommand outputs CSV with per-frame total SASA:

frame,step,time,total_sasa
0,1,1.000,1866.44
1,2,2.000,1977.96
2,3,3.000,1884.93
...

Analysis Features

Per-Residue Aggregation (--per-residue)

Groups atom SASA by residue (chain + residue number + insertion code):

Per-residue SASA:
Chain  Res    Num       SASA  Atoms
----- ---- ------ ---------- ------
    A  MET      1     198.52     19
    A  LYS      2     142.31     22
    A  ALA      3      45.67      5

RSA Calculation (--rsa)

Calculates Relative Solvent Accessibility (RSA = SASA / MaxSASA).

MaxSASA reference values from Tien et al. (2013):

Residue	MaxSASA (Ų)	Residue	MaxSASA (Ų)
ALA	129.0	LEU	201.0
ARG	274.0	LYS	236.0
ASN	195.0	MET	224.0
ASP	193.0	PHE	240.0
CYS	167.0	PRO	159.0
GLN	225.0	SER	155.0
GLU	223.0	THR	172.0
GLY	104.0	TRP	285.0
HIS	224.0	TYR	263.0
ILE	197.0	VAL	174.0

Output with RSA values (can exceed 1.0 for exposed terminal residues):

Per-residue SASA with RSA:
Chain  Res    Num       SASA    RSA  Atoms
----- ---- ------ ---------- ------ ------
    A  MET      1     198.52   0.89     19
    A  LYS      2     142.31   0.60     22
    A  ALA      3      45.67   0.35      5

Polar/Nonpolar Summary (--polar)

Classifies residues and shows SASA breakdown. Automatically enables --per-residue.

• Polar: ARG, ASN, ASP, GLN, GLU, HIS, LYS, SER, THR, TYR
• Nonpolar: ALA, CYS, PHE, GLY, ILE, LEU, MET, PRO, TRP, VAL
• Unknown: Non-standard residues (ligands, modified residues, etc.)

Polar/Nonpolar SASA:
  Polar:       2345.67 Ų ( 45.2%) - 42 residues
  Nonpolar:    2845.23 Ų ( 54.8%) - 58 residues
  Unknown:        0.00 Ų (  0.0%) -  0 residues