I had a large folder of ConQuest CON files that I wanted to run substructure searches for and then collate the results together in some kind of summary for review in Excel afterwards.

This script takes as input the path to the folder of files and outputs both refcode list files (GCDs) for each of the searches as well as a CSV file containing the summary of the searches (numbers of hits), one line per search file. Various search filters are set by default, but these can be turned off using command-line arguments (see the script comments for details). Note that you could edit the script to carry out the same kind of analysis using a set of SDF, MOL or MOL2 files for example to run searches.

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