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.
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