I am looking for a script and/or code that calls a docking tool starting from a CDK data model. The parts I am most interested in, is how to set up the input for that docking tool automatically (using that script and/or code), such as initial position of the ligand. Surely this will be a non-trivial piece of code, and any tips towards a full solution would also be much appreciated. Obviously, I have a preference for an Open Source docking tool, but could live with a free docking tool too.
Imported from: http://blueobelisk.stackexchange.com/questions/93