osp: Occluded Surface Packing (OSP)

In fibos: Occlusion Surface Using the Occluded Surface and Fibonacci Occluded Surface

Occluded Surface Packing (OSP)

Description

Implements the 'occluded surface' packing density metric (OSP) averaged by residue, as described in (Fleming and Richards 2000).

Usage

osp(file)

Arguments

file	a SRF File (.srf) generated by 'occluded_surface' in fibos_files folder.

Value

A table containing:

Resnum

residue id.

Resname

residue name.

OS

the summed areas of dots in residue.

`os*[1-raylen]`

'OS' areas weighted by (1-raylen). Raylen is the average lengths of normals normalized by 2.8 \text{\AA} (water diameter). So, raylen is a value between 0 and 1. A raylen close to 1 indicates worse packaging, and the 'OS' will be reduced.

OSP

average occluded surface packing value (OSP) by residue.

Author(s)

Herson Soares

Joao Romanelli

Patrick Fleming

Carlos Silveira.

References

Fleming PJ, Richards FM (2000). "Protein packing: Dependence on protein size, secondary structure and amino acid composition." doi:10.1006/jmbi.2000.3750

Pattabiraman N, Ward KB, Fleming PJ (1995). "Occluded molecular surface: Analysis of protein packing." doi:10.1002/jmr.300080603

Soares HHM, Romanelli JPR, Fleming PJ, da Silveira CH (2024). "bioRxiv, 2024.11.01.621530." doi:10.1101/2024.11.01.621530

See Also

occluded_surface()

Examples

library(fibos)

#Configure the Environment
fibos_config() 

# Calculate FIBOS per atom and create .srf files in fibos_files folder
pdb_fibos <- occluded_surface("1ptx", method = "FIBOS", density_dots = 5.0)
# Calculate OSP metric per residue from .srf file in fibos_files folder
pdb_osp <- osp(fs::path("fibos_files","prot_1ptx.srf"))

fibos documentation built on June 8, 2025, 10:11 a.m.