Help deciphering an input

The primary Rosetta documentation is here: https://www.rosettacommons.org/docs/latest/Home

Your starting point suggests you may benefit from the Meiler Lab recorded tutorials: http://www.meilerlab.org/index.php/rosetta-tutorials

> 1) I get that the ‘fix_bb_monomer_ddg.linuxgccrelease’ is invoking the packer (the syntax used in this code is weird cause I don’t see any underscores in my Rosetta though)

You are on command line.  fix_bb_monomer_ddg.linuxgccrelease is the command.  The remainder of the line is command line flags and arguments to those flags.  fix_bb_monomer_ddg.linuxgccrelease specifically is one compiled rosetta binary – the portion before the . names the binary (there are a few hundred) and the portion after describes how it was compiled.  I guess this command “invokes the packer” in a technical sense, but if all you want to do is repack you should use regular fixbb, as it is simpler and meant for the purpose.  

> 1) What is the ‘ddg’? What does it mean and where does it come from? I have tried searching up Rosetta ddg on google but nothing really comes up for it. 

DDG means delta delta G – the change of free energy of folding upon mutation.  mutation is one delta, folding is one delta, g is gibbs free energy.  DDG of mutation tools tell how how a protein’s energy will change when you mutate the sequence but leave the structure similar.  You say you want to use minimization and repacking; you probably want regular old relax, not this tool that is a preparatory step for a particular ddg pipeline.

> 2) Why are there so many double colons? 

C++ uses a double colon to indicate namespacing.  I will rely on you to google namespacing in programming to learn about it.  Rosetta namespaces its command line options because there are thousands and it’s a good way to resolve name conflicts.  Double or single colons are permitted for command line flag namespacing.  I assume we allow both because some people wanted singular for compactness, and others used double because they were used to C++ and it was easier to allow both.  (It isn’t because the underlying code requires colons because it is C++, it’s just a case of progammers using familiar patterns.)