pLink-SS is a software dedicated for the identification of disulfide bond peptides. This readme text file gives the guide to compile and configure pLink-SS. For the usage of pLink-SS, please check the user guide in the setup kit.

Table of Contents
=================

- Needed Software
- Compile
- Extra Needed Files
- Python Interface

=================


Needed Software
===============

pLink-SS is developed by C++ and Python. For the C++ part, G++ is used as the compiler, and msys is also needed in Windows system for the support of Makefile. 

Software list:

G++: version 4.6.2 or above.
msys: version 1.0 or above.
Python: version 2.7 or above.


Compile
=======

The source code of pLink-SS is organized by Makefile. Usage:

1 Modify the file make.include. Change the following line:

BUILD_DIR :=
INSTALL_DIR :=

to appoint the build directory and the install directory.

2 Use the following command:

> make

to automatically compile the whole source code. The binary files will be generated at the build directory.

3 Use the following command:

> make install

to copy the files from the build directory to release directory.


Extra Needed Files
==================

Some extra configuration files are needed for the usage of the software. The files needed are:

dbconf.ini
aa.ini
modify.ini
enzyme.ini
xlink.ini
pthreadGC2.dll
pthreadGCE2.dll


These files can be found in the setup kit. For the format and configuration of these files, please check the user guide.


Python Interface
================

To facilitate the whole searching process, a Python interface is provided. The python code are provided under the folder python_plink. Numpy and Matplotlib Python package may also be needed.

With Python installed, use the following command:

>python flow.py pLink.ini

to run the whole process. The format of pLink.ini is descripted in the user guide.