fibos (version 2.0.1)

osp: 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)

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.

Arguments

file

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

Author

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

# \donttest{
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"))
# }