Read Protein Sequences in PDB Format

Usage

readPDB(file = system.file("protseq/4HHB.pdb", package = "Rcpi"))

Arguments

file: The name of the file which the sequences in PDB format are to be read from. If it does not contain an absolute or relative path, the file name is relative to the current working directory, getwd. The default here is to read the 4HHB.PDB file which is present in the protseq directory of the Rcpi package.

Value

A character vector, representing the amino acid sequence of the single-letter code.

Details

This function reads protein sequences in PDB (Protein Data Bank) format, and return the amino acid sequences represented by single-letter code.

References

Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description, Version 3.30. Accessed 2013-06-26. https://files.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_Letter.pdf

Examples

Seq4HHB = readPDB(system.file('protseq/4HHB.pdb', package = 'Rcpi'))
Seq4HHB
#> $chain_A
#> [1] "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR"
#> 
#> $chain_B
#> [1] "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"
#> 
#> $chain_C
#> [1] "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR"
#> 
#> $chain_D
#> [1] "VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"
#>