This is a fairly large PR that covers three aspects: reactive docking, ligand seeding, and the RosettaScripts overhaul. See descriptions of each component:
reactive docking: the dock_reactants() method has been significantly overhauled. It is streamlined, debugged, and fully implemented in terms of options
ligand seeding: critical to reactive docking is the initial "seeding" of ligands. This refers to the initial placement of the ligand in an unrefined, energetically unfavorable way. This functionality is accessed via the enzy_htp.preparation.seed_ligand() method. It works on the Structure before dock_reactants() and allows a variety of strategies.
RosettaScripts overhaul: The RosettaInterface class now works much better when using RosettaScripts through the creation of RosettaOptions, RosettaScriptsElement, and RosettaScriptsProtocol classes. These classes make the creation and execution of RosettaScripts very easy and intuitive in python. This functionality is also put back into various functions to improve overall code readabilty.
This is a fairly large PR that covers three aspects: reactive docking, ligand seeding, and the RosettaScripts overhaul. See descriptions of each component:
reactive docking: the
dock_reactants()method has been significantly overhauled. It is streamlined, debugged, and fully implemented in terms of optionsligand seeding: critical to reactive docking is the initial "seeding" of ligands. This refers to the initial placement of the ligand in an unrefined, energetically unfavorable way. This functionality is accessed via the
enzy_htp.preparation.seed_ligand()method. It works on theStructurebeforedock_reactants()and allows a variety of strategies.RosettaScripts overhaul: The
RosettaInterfaceclass now works much better when using RosettaScripts through the creation ofRosettaOptions,RosettaScriptsElement, andRosettaScriptsProtocolclasses. These classes make the creation and execution of RosettaScripts very easy and intuitive in python. This functionality is also put back into various functions to improve overall code readabilty.