Mercurial > repos > bgruening > sucos_docking_scoring
changeset 4:3b20a6bf613a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837"
| author | bgruening |
|---|---|
| date | Wed, 15 Apr 2020 13:25:24 +0000 |
| parents | 4e75edcf9513 |
| children | 070f0e96733b |
| files | sucos_max.py |
| diffstat | 1 files changed, 11 insertions(+), 3 deletions(-) [+] |
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--- a/sucos_max.py Mon Apr 06 13:08:18 2020 +0000 +++ b/sucos_max.py Wed Apr 15 13:25:24 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__":