NAME
	PPSampler (Proteins' Partition Sampler) - predict protein complexes

SYNOPSIS
	PPSampler [OPTIONS]

OPTIONS
	-f, --file
		specify a file of protein-protein interactions with their weights, 
        where each line should contain two protein IDs and the 
        corresponding interaction weight, which are tab-deliminated.
	-h, --help
		show help document and exit.
	--output <output>
		set an output file to be <output>. The default is "output.txt" in 
        the working directory.
	--maxClusterSize <maxClusterSize>
		set the possible maximum size of clusters to be predicted to be 
        <maxClusterSize>. The default is 100.
	--temperature <temperature>
		set the temperature parameter to be <temperature>. This parameter 
        controls acceptance rate of candidate state. The default is 5.
	--gamma <gamma> 
		set the parameter, gamma, of the score subfunction, f_2, to be 
        <gamma>. The default is 2.
	--lambda <lambda>
		set the parameter, lambda, of the score subfunction, f_3, to be 
        <lambda>. The default is 2000.
    --maxIterationCount <maxIterationCount>
        set the repeat count to be <maxIterationCount>. The default is 
        100,000, in which case, PPSampler will stop in 80 seconds.  
    --proposalDitribution <proposalDitribution>
    	specify a proposal distribution. <proposalDitribution> is either 1 
        or 2. 1 corresponds to the proposal distribution given in [1]. The 
        other proposal distribution, specified by the option 2, is a 
        modification of the former one. This is more efficient in time than 
        the former. We recommend to use the option of 2. Details of this 
        new option will be explain somewhere. The default is 2. 
    --beta <beta>  
        set the parameter, beta, of both proposal distribuitions. <beta> 
        should be in [0..1]. The default is 0.01.
    --noPlot
        makes no graphs of historical scores. Without this option, graphs 
        are given.
    -v, --version
        output version information and exit.

REFERENCE
	[1] Daisuke Tatsuke and Osamu Maruyama, Sampling strategy for protein 
    complex prediction using cluster size frequency, Gene, 2012.