I am writing a python script that will do docking for my antibody-antigen samples, however, I could not find any SnugDock code examples with pyrosetta. Could you please give at least one?
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The hub for Rosetta modeling software
If Google gives you nothing, then the answer is no to public examples.
However, reverse engineering a binary to be used in PyRosetta is not as crazy as it first sounds.
In https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock are listed the settings to expect.
In https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.protocols.antibody.snugdock.html are listed the classes:
The __init__ is unfortunately missing from the documentation (Sphinx default settings), but calling help on it or instantiating the class with some unexpected arguement like Exception will tell you the options.
The first inherits DockingHighRes which is highly documented as its in the tutorial notebooks https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.protocols.docking.html#pyrosetta.rosetta.protocols.docking.DockingHighRes . So most of the settings will be common. Do note how cycles of perturbations and spinings are not part of mover.