README

		INSTALLATION AND IMPLEMENTATION OF ResPRE
(Copyright 2018 by Zhang Lab, University of Michigan, All rights reserved)

1. What is ResPRE?
    ResPRE is a program for protein contact-map prediction by coupling PREcision matrix
    with fully Residual neurl networks. 

2. How to install the ResPRE?

    1) Prerequisites
        Python3 with numpy and scipy should be installed
        pytorch-0.3.0 (https://pytorch.org/get-started/previous-versions/)
        Anaconda is recommended to set up python environments
    2) There is an executable file under 'bin' path, Maybe you also need set 
        executable permission to the bin file.

3. Bug report:
    Please visit https://zhanglab.ccmb.med.umich.edu/bbs/?q=forum/2

4. How to run the ResPRE?
	python respre.py [msa_file] [outfile]
		msa_file: Multiple Sequence Alignment file
		outfile:  Output file, each line in this format: [position1 position2 score]
		where position index start from 1 [NOT 0]

5. Example
	You can test by fowllowing commands:
		' python respre.py test/T0759-D1.aln test/T0759-D1.out '
	It will generate 2 files:
		' T0759-D1.out.weight ': Weights for each sequence in msa, you can just ignore it.
		' T0759-D1.out '       : Output file 


Reference
Yang Li, Jun Hu, Chengxin Zhang, Dong-Jun Yu, and Yang Zhang, ResPRE: high-accuracy protein 
contact prediction by coupling precision matrix with deep residual neural networks.Bioinformatics.