| Previous changeset 3:bd12f4b4c3a8 (2020-03-28) Next changeset 5:12725d4b90f3 (2020-07-28) |
|
Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837" |
|
modified:
sucos_max.py |
| b |
| diff -r bd12f4b4c3a8 -r 791c86130585 sucos_max.py --- a/sucos_max.py Sat Mar 28 05:16:44 2020 -0400 +++ b/sucos_max.py Wed Apr 15 09:26:30 2020 -0400 |
| [ |
| @@ -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 = [] @@ -80,6 +80,7 @@ continue scores_max = [0, 0, 0] scores_cum = [0, 0, 0] + cluster_name = None for clusterfilename in all_clusters: cluster = all_clusters[clusterfilename] index = 0 @@ -104,21 +105,28 @@ scores_cum[2] += vol_score - cluster_file_name_only = cluster_name.split(os.sep)[-1] - # utils.log("Max SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2],"File:", cluster_file_name_only, "Index:", cluster_index) mol.SetDoubleProp("Max_SuCOS_Score", scores_max[0] if scores_max[0] > 0 else 0) mol.SetDoubleProp("Max_SuCOS_FeatureMap_Score", scores_max[1] if scores_max[1] > 0 else 0) mol.SetDoubleProp("Max_SuCOS_Protrude_Score", scores_max[2] if scores_max[2] > 0 else 0) - mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only) - mol.SetIntProp("Max_SuCOS_Index", cluster_index) + + if cluster_name: + cluster_file_name_only = cluster_name.split(os.sep)[-1] + mol.SetProp("Max_SuCOS_Cluster", cluster_file_name_only) + mol.SetIntProp("Max_SuCOS_Index", cluster_index) # utils.log("Cum SuCOS:", scores[0], "FM:", scores[1], "P:", scores[2]) mol.SetDoubleProp("Cum_SuCOS_Score", scores_cum[0] if scores_cum[0] > 0 else 0) 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() @@ -135,11 +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__": |