I feel as though it would be best to just rename the function to centres_ppRoll
On Thu, Sep 11, 2025, 14:57 Leo Mada via R-package-devel < r-package-devel@r-project.org> wrote: > Dear All, > > I have some problems and some questions regarding how to pass some checks > (run on my computer - new version not yet submitted). > > There are 2 important notes: > > 1. Note 1: > checking S3 generic/method consistency ... NOTE > Apparent methods for exported generics not registered: > centres.ppRoll > > 2. Note 2: > checking Rd \usage sections ... NOTE > S3 methods shown with full name in Rd file 'centres.ppRoll.Rd': > 'centres.ppRoll' > > The current code is on GitHub: > https://github.com/discoleo/Rpdb > > But let me first explain the reason and reasoning. > > There are 2 generic functions: centres and centres.ppRoll, each with 3 > methods for pdb objects, atoms and coords (default). > > Generic function centres: > The 1st generic function, centres, computes the centres of a molecule and > has methods for 3 objects: pdb molecule, atoms and xyz-coordinates > (default). It acts on an object of type coords, while the objects atoms and > pdb include such a coords-object in their structure. > > I would like to write various "specialised" versions: > - they still compute the centre, as it's the simplest summary possible for > 3D objects; > - however, there are many types of molecules: proteins, nucleic acids, > other types of molecules; and each may benefit from more "specialised" > methods; > Note: all molecules are still coded as a pdb object. It's the user who > selects which method is most appropriate for a specific situation/molecule. > > E.g. proteins consist of long linear chains. One such variant would be a > "rolling mean": it makes sense for polypeptide chains and nucleic acids, > but little (or no) sense for other molecules. > > I wrote therefore a generic function centres.ppRoll with 3 methods for the > 3 base-objects. > > I would like to reuse the centres-skeleton for the name: users can then > easily check which methods are available to compute centres: > methods(centres) > # [1] centres.atoms centres.coords centres.pdb > # centres.ppRoll > # [5] centres.ppRoll.atoms centres.ppRoll.default centres.ppRoll.pdb > > I would like to avoid having hundreds of function names which no-one > remembers and which would be cumbersome to search for. Each method would be > useful only in particular situations and users are likely to forget the > exact names between uses. > > I get the above 2 notes with this approach: > - I did not register centres.ppRoll as an S3 method to avoid the 2nd note; > - I get the 2nd note anyway (and it gets silently registered, which may be > necessary for the methods-search to work); > > Another pseudo-solution would be to add a methods argument. This solution > is misused at times; unfortunately, it is really ugly here because some of > the methods may have particular arguments (e.g. window-size for the > roll-method). > > Ultimately, I may end up with 50 or 100 arguments in the function, which I > also need to replicate to all the 3 methods (pdb, atoms, default/coords). > > I really don't like this pseudo-solution and prefer one based on the 1st > approach. > > I did not count how many function name variants are in the > 20,000 > packages on CRAN. But I think that a more structured approach would be > beneficial to everyone. > > Thanks in advance for any support, > > Leonard > > ########## > > ### Note > - Proteins have a backbone and the amino-acids also have side chains; > - It is useful in certain situations to have additional types of centres > computed; > - The initial developer of Rpdb used it mainly for other types of > molecules (not proteins); > > The code actually functions: > > # pdb2z81.ent can be downloaded from the Protein Data Bank; > setwd(...) > x = read.pdb("pdb2z81.ent") > # Number of models: 0 > # Warning message: > # In read.pdb("pdb2z81.ent") : The pdb contains a Caveat record! > tmp = centres.ppRoll(x) > visualize(x, type="p", pbc.box = FALSE) > # Draw a peptide-"Skeleton" > lines3d(tmp, lwd = 5, col = "red") > > # A new version of the pdb-format is also out, > # but that's a horror-story in itself. > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
