PDBencode: Encode PDB structures into Structural Alphabet sequences

The package provides the functionality to encode given PDB structures into Structural Alphabet (SA) strings.

Installation

There are several ways to install the PDBencode package, please choose one of the following. For the Install options you need to have R installed and the bio3d package. Alternatively the Docker container provides a mode to run PDBencode without explicit installation.

Install on Linux shell

Download the latest PDBencode release (.tar.gz) and install on the shell with (example for version 0.4):

R CMD INSTALL PDBencode-v.0.4.tar.gz

Install on R console

Download the latest PDBencode release (.tar.gz) and install from the R console (example for version 0.1, assuming it is located in the current directory):

install.packages("./PDBencode-v.0.4.tar.gz")

Install on R console with devtools

Install the devtools package and install PDBencode directly from GitHub:

library("devtools")
install_github("Fraternalilab/PDBencode")

Docker container

Run PDBencode in a Docker container. Use the bash provided in PDBencode/inst/tools:

./buildDockerImage.bash
./pdbencode.bash <path_to_data> <path_to_script>

In most cases the user wants to provide the path to the (structure) data, while that path to the script is optional in case a modified script is to be used.

Usage

Option 1 (not for Docker container)

Run the R script Rscripts/pdbencode.R in the directory containing PDB file(s):

Rscript pdbencode.R 

All PDB files (with extension ".pdb") in that directory will be processed. Each structure <ID>.pdb yields an encoded <ID>.sasta file containing one SA sequence per chain. The format of SA sequence headers is <ID>|<chain>.

You may run this command on the Docker container as well, but it will only process the example data in extdata.

Option 2

Provide the path to the data directory as command line parameter. The R script accepts 3 command line options:

• --data : Path to the data directory
• --script : Path to the directory containing the R script
• --help : Help for command line arguments

Rscript pdbencode.R --data <path_to_data>

The script path is intended to be used for a modified pdbencode.R script. For most purposes the built-in script should suffice.

Copyright Holders, Authors and Maintainers

• 2021 Jens Kleinjung (author, maintainer) [email protected]
• 2021 Franca Fraternali (author, maintainer) [email protected]