/pdb-archive-filter

This script enables users to filter through PDB archive in order to obtain simple data from each file.

Primary LanguagePerl

PDB Archive Filter

Table of Contents

Features

This script allows to process different type of file inputs:

  • Single or an array of CIF files;
  • Single or an array of PDB files;
  • Directory absolute path containing either PDB or CIF files;

The output of this script is:

  • PDB file identification - ID;
  • Year of the publication - YEAR;
  • Experimental method - METHOD;
  • Resolution of the method used (if applicable) - RESOLUTION;
  • Number of atoms - ATOMCOUNT;

CIF and PDB files can be in plain format or in gzipped form with the .gz extension. Also this script returns values in a TAB delimited format:

ID | YEAR | METHOD | RESOLUTION | ATOMCOUNT

Usage

Usage itself is simple. There are 4 possible ways to process a file:

  • For single of batch PDB files:
    ./pdb_archive_filter -pdb filename
  • For single or batch CIF files:
    ./pdb_archive_filter -cif filename
  • For directory containing CIF files:
    ./pdb_archive_filter -d -cif directory
  • For directory containing PDB files:
    ./pdb_archive_filter -d -pdb directory

Options

As it was seen above, this script allows the usage of 3 options. It is important to clarify what type of input is going to be used. This can be achieved by specifying certain options as arguments before running the program.

  • PDB option is used to specify that input file or files are in PDB format;
  • CIF option is used to specify that input file or files are in CIF format;
  • DIRECTORY option is used to specify that input is going to be a directory name or path to that directory. Has to be used together with -pdb or -cif options. The path has to be an absolute path.
  • The script can also take a single option dash "-". This allows the input from the keyboard;

Installation

There is no installation needed. Just download the package and the pdb_archive_filter script is ready to use.

Testing

For testing go to the PDB-Archive-Filter directory and run the following commands:

  • To delete all existing test outputs:
    make clean-tests
  • To run tests after deleting the test outputs:
    make test

Examples

Example of the output format in Linux terminal. This is the command that was run:

    ./pdb_archive_filter -d -pdb ~/Downloads/pdb

TAB