Installation

The model requires several tools to be installed, which are:

• MCL: https://www.micans.org/mcl/
• Python 3.6.7: https://www.python.org/downloads/release/python-367/
• Pytorch: https://pytorch.org/get-started/locally/
• the requried packages in the "requirements.txt"

  # pip install -r requirements.txt
  

Usage Demo

Note: The model needs to be executed in the root directory (i.e. "/Model"). The sample data have existed in the directory "/Model/data/samples".

1. Set the configuration file. The file "config.ini" exists in the directory "/Model/data".

   PARAMETER
     -BetAtomDist           - the threshold that determines whether there are edges between atoms (default: 8.0)
     -alpha                 - the hyperparameter of the weight formula (default: 0.6)
     -thet                  - the hyperparameter of the contrast weight formula (default: 5)
     -gamma                 - the hyperparameter of the contrast weight formula (default: 1)
     -threshold             - the threshold of the boundary edge weight (default: 0.5)
     -clusterMinSize        - the minimum number of nodes in a cluster (default: 3)
     -min_num_Epitopes      - the minimum ratio of epitope residues in the epitope cluster (default: 0.3)
   

2. Run the program. The command line is as follows:

   # python ./script/Main.py <pdb_id> <chain_name>
   

   For example:

   # python ./script/Main.py 1a14 N
   

   The result is stored in the directory "/Model/data/results", i.e.:

   1a14N.clu