pdb2sse: Obtain An SSE Sequence Vector From A PDB Object

In bio3d: Biological Structure Analysis

Obtain An SSE Sequence Vector From A PDB Object

Description

Results are similar to that returned by stride(pdb)$sse and dssp(pdb)$sse.

Usage

pdb2sse(pdb, verbose = TRUE)

Arguments

pdb	an object of class pdb as obtained from function read.pdb.
verbose	logical, if TRUE warnings and other messages will be printed.

Details

call for its effects.

Value

a character vector indicating SSE elements for each amino acide residue. The 'names' attribute of the vector contains 'resno', 'chain', 'insert', and 'SSE segment number', seperated by the character '_'.

Author(s)

Barry Grant & Xin-Qiu Yao

See Also

dssp, stride, bounds.sse

Examples

   #PDB server connection required - testing excluded
   try({

   pdb <- read.pdb("1a7l")
   sse <- pdb2sse(pdb)
   sse

   }, silent=TRUE)
   if(inherits(.Last.value, "try-error")) {
      message("Need internet to run the example")
   }  
 

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.