# HG changeset patch
# User bgruening
# Date 1586957101 0
# Node ID 2b60b2b236a4d526f0a35e80796f52db72b30777
# Parent  3bf41c6bd35609b25f0d8b487ae6849ab03e4895
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"

diff -r 3bf41c6bd356 -r 2b60b2b236a4 sucos_max.py
--- a/sucos_max.py	Mon Apr 06 13:07:56 2020 +0000
+++ b/sucos_max.py	Wed Apr 15 13:25:01 2020 +0000
@@ -39,7 +39,7 @@
 from rdkit import Chem
 
 
-def process(inputfilename, clusterfilenames, outputfilename):
+def process(inputfilename, clusterfilenames, outputfilename, filter_value, filter_field):
     all_clusters = {}
     for filename in clusterfilenames:
         cluster = []
@@ -120,7 +120,13 @@
         mol.SetDoubleProp("Cum_SuCOS_FeatureMap_Score", scores_cum[1] if scores_cum[1] > 0 else 0)
         mol.SetDoubleProp("Cum_SuCOS_Protrude_Score", scores_cum[2] if scores_cum[2] > 0 else 0)
 
-        writer.write(mol)
+        if filter_value and filter_field:
+            if mol.HasProp(filter_field):
+                val = mol.GetDoubleProp(filter_field)
+                if val > filter_value:
+                    writer.write(mol)
+        else:
+            writer.write(mol)
 
     input_file.close()
     writer.flush()
@@ -137,11 +143,13 @@
     parser.add_argument('-i', '--input', help='Input file to score in SDF format. Can be gzipped (*.gz).')
     parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).')
     parser.add_argument('clusters', nargs='*', help="One or more SDF files with the clustered hits")
+    parser.add_argument('--filter-value', type=float, help='Filter out values with scores less than this.')
+    parser.add_argument('--filter-field', help='Field to use to filter values.')
 
     args = parser.parse_args()
     utils.log("Max SuCOS Args: ", args)
 
-    process(args.input, args.clusters, args.output)
+    process(args.input, args.clusters, args.output, args.filter_value, args.filter_field)
 
 
 if __name__ == "__main__":