osp {fibos} | R Documentation |
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
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"))