Custom Scaffolds

This method generates classes with scaffolds based on user-defined queries contained in an external [query file (*.cqf)], [molfile (*.mol)], or [SD file (*.sdf)].

When selected from the Generate Classes dialog, you should select a file containing these scaffolds. This can be achieved by clicking on the Change Method Options button.

The method operates by iterating over each query contained in the query file, and using it to search all of the molecules contained in the current spreadsheet. If at least one molecule matches the query, a new class is created using all of the matching molecules. If no matching molecules are found, the query is ignored. Note that unlike most other automated methods of class generation, the scaffold method does not involve a post-processing of classes in order to increase homogeneity or limit redundancy. Rather, all queries matching at least one molecule are guaranteed to appear in the final list of classes, and all molecules that match that query will appear in the resulting class.

A Query Wizard is available to assist you in creating query files. See the relevant section for more information. Alternatively, you can draw structures using the integrated MedChem Designer application and export them in SD or CQF format.