Epitope Predictor.

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What does it do?

Given a structure of an antibody, antigen and the paratope information, produce an ordered list of predicted epitopes and the corresponding list of decoys docked by ZDOCK.
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Possible issues:

1. You need numpy installed
2. You need internet access so that we can use Abnum to determine the CDR residues

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Example Usage using the supplied files:

python EpiPred.py --abf 1A2Y.pdb --agf 1A2Y.pdb --abc AB --agc C --epitopes 3 --jobid output_folder --para_ext 0


Explanation:

--abf : the antibody file
--agf : the antigen file (above they are the same)
--abc : the antibody chains to be used for prediction (e.g. 'HL' or 'A' as above) 
--agc : the antigen chains to be used for prediction (e.g. 'CD' or 'B' as above) 
--paratope : the residues assumed to constitute the paratope (see below for the format)
--jobid : the folder that you want the results to be saved in - it will be created in your current directory
--para_ext : OPTIONAL! specify by how much the paratopes should be extended (by defining the radius around the residues declared in paratope.txt)

Other parameters like the percentage cutoff for overlap between epitopes etc. you edit manually in the EpiPred.py or by supplying supplementary options on input (look for 'parameters')

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Output files:

In the folder that you supplied, you will find two folders:

1. epitope_predictions/ where each file [number].txt corresponds to the residues in the epitope in the format [sequence id] [chain id] and files [number].pdb - the corresponding pdb file with BFactor fields colored with the selected epitope. Note however that the pdb files with colored B-factor field are the internal representation with chains and sequence ids renamed!

2. top_decoys/ list of top decoys as ordered by EpiPred in the format complexed[EpiPred ranking].[zdock ranking].pdb
