readPDB: Read Protein Sequences in PDB Format

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

Read Protein Sequences in PDB Format

Description

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

Usage

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

Arguments

file	Path to the file containing the protein sequences in PDB format. 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 protr package.

Value

Character vector of the protein sequence.

Author(s)

Nan Xiao <https://nanx.me>

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

See Also

See readFASTA for reading protein sequences in FASTA format.

Examples

Seq4HHB <- readPDB(system.file("protseq/4HHB.pdb", package = "protr"))

protr documentation built on Sept. 12, 2024, 6:44 a.m.