execute {fibos}R Documentation

Surface Calculation

Description

The function executes the implemented methods. Using this function, it is possible to calculate occluded areas through the traditional methodology, 'Occluded Surface', or by applying the 'Fibonacci OS' methodology. At the end of the method execution, the 'prot.srf' file is generated, and returned for the function. The data in this file refers to all contacts between atoms of molecules present in a protein's PDB.

Usage

execute(pdb, method, density_dots)

Arguments

pdb

4-digit PDB id (will fetch it from the RCSB repository) or the path to a PDB local file.

method

Method to be used: 'OS' (classic) or 'FIBOS' (default). The classic 'OS' covers the surface radially with one of the axes as a reference when allocating the dots. In 'FIBOS', Fibonacci spirals were used to allocate the dots, which is known to produce lower axial anisotropy as well as more evenly spaced points on a sphere.

density_dots

Distribution density of atomic dots for surface occlusion calculation.

Value

A data frame containing the protein surface data read from the generated SRF file.

Author(s)

Carlos Henrique da Silveira (carlos.silveira@unifei.edu.br)

Herson Hebert Mendes Soares (hersonhebert@hotmail.com)

Joao Paulo Roquim Romanelli (joaoromanelli@unifei.edu.br)

Patrick Fleming (Pat.Fleming@jhu.edu)


[Package fibos version 2.0.1 Index]