ext_prot_lig_score_fcns.conf

%
% NOTE: Each line is required to have exactly three (3) commas or it will be 
% ignored.
%
% Columns with their intended data.
% 1) Identifier (or scoring function name) for the given protein-ligand 
%    external scoring function -- this is the identifier that will be used on 
%    the search_sitemaps command line to select the given line.  Valid 
%    characters are upper and lower case alphanumeric charcters and '_' and '-'.
%    All other characters, including commas (which denote the end of a field) 
%    are likely to have undefined results.
% 2) The identifier for the scoring function type -- for example DrugScore or
%    SFCscore.  This identifier is used internally by search_sitemaps and
%    at present DrugScore, SFCscore and NONE are the supported types.  Support
%    for additional scoring function types requires knowledge of the output
%    method of the scoring function, how to parse that output and overloading
%    the C++ ExternalScoringFunction class (in src/search) to provide that 
%    support.
% 3) Exact commandline to run for the external scoring function with the
%    values of the $PROTEIN and $LIGAND variables determined by your search.  
%    In particular, the $PROTEIN will be the subset of query protein residues 
%    that are within interaction distance of the query protein binding site.
%    Similarly, the $LIGAND will be those database ligand fragments for which 
%    the corresponding database sitemap was similar enough to the query sitemap.
%    Finally, we strongly encourage you to test your external scoring function 
%    on one or more examples of SimSite3D output before adding the external
%    scoring function to this file.
%    
%
NONE,NONE,/bin/false,
DrugScore,DrugScore,/soft/linux/drugscore/bin/drugscore.lnx PAIR $PROTEIN $LIGAND > /dev/null,
Affiscore,ProtLigScore,$SIMSITE3D_INSTALL_DIR/bin/prot_lig_score -p $PROTEIN -l $LIGAND
Orientscore,ProtLigScore,$SIMSITE3D_INSTALL_DIR/bin/prot_lig_score -p $PROTEIN -l $LIGAND
%SFCscore,SFCscore,/path/to/SFCscore/binary/sfcscore -p $PROTEIN -l $LIGAND /path/to/my/SFCscore/my_spf_file.spf,