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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