De novo water predictions using SPaDES

I wanted to give it a go for a misbehaving protein-protein interface and I found out the following —I know this post is over a year old, but someone else may be looking for info.

Hydrate
The SPADES protocol is called `hydrate/SPADES` in `rosetta/main/documentation/Release-Notes.md`. So hydrate must be SPADES...

Hydrate appears in pyrosetta as a module in protocols with a class with several functions.

The class is a mover, but does not have a citation ref associated with it so I cannot verify SPADES == hydrate:

def get_citation(mover) -> str:
    ci = mover.provide_citation_info()
    if len(ci) == 0:
        return ''
    else:
        cc = ed.provide_citation_info().pop()
        #print(cc.module_name(), cc.module_type())
        buffer = pyrosetta.rosetta.std.stringbuf()
        cc.get_citations_formatted(pyrosetta.rosetta.std.ostream(buffer))
        return buffer.str().strip()
    
Hydrate = pyrosetta.rosetta.protocols.hydrate.Hydrate
get_citation(Hydrate())

But it is the only module to do with hydration and its functionality is the same. So SPADES must be hydrate.

EDIT — I forgot to just check that the authors matched in the source files with the paper ones. And they do. So hydrate is SPaDES.

Usage

The wiki documentation is lacking, but there is a solid amount of info in places.

Firstly, there are two folders in `rosetta/main/tests/integration/tests`, one called hydrate, the other hydrate relax.

One runs the binary `hydrate` and the other (`hydrate_relax`) runs relax. The former accepts a resfile, so is a packer.
The commands have some interesting flags —which basically explain the basic usage— and require a "hyfile", which is a list of HYD and numbers.

In terms of the many functions (which appear in pyrosetta), these are well documented in the header file `hydrate_functions.cc` in `rosetta/main/source/src/protocols/hydrate` as comments above each function —My utterly clueless guess is that they did not go into the documentation of pyrosetta as they lack the @brief tag. In the case of `read_hyfile`, it explains what a hyfile is:

// Read hyfile;
// Hyfile should be a list with two columns:
// 1st with one of the keywords:
//  "HYD" to hydrate that residue (only residues)
//  "ENF" to enforce that water molecule, to ensure it will be present at the end of the simulation (only water molecules)
// 2nd with the residue or water molecule number