overlap with nma(mass=TRUE)

Barry Grant

I think the warning route would be best as fit.xyz() is already bloated and quite central to many other workflows that are best left undisturbed until we have a robust and useful testsuite.

On a somewhat related note, assigning mass to things not included in aa2mass() is a weak point that I have been thinking about. The way aa321() goes about this is to use a wild card "X" that is setup in substitution matrices to score well with any other residue.

If we have a missing residue definition in aa2mass() could we have an option that attempt to calculate the mass based on a corresponding pdb structure?

2013-10-11T14:33:27+00:00

Lars Skjærven reporter

Agree that we can leave fix.xyz alone for now, but with time we could consider it. I'll see how I can update the rmsip and overlap functions. perhaps just noting in the .Rd files is enough...?

We can calculate residue mass for any given set of atoms with atom2mass. i.e.:

atom2mass(c("C", "O", "CA", "NH1"))
[1] 12.01 16.00 12.01 14.01

atom2mass(pdb, inds=atom.select(pdb, resno=10))

Build selection from input components

      segid  chain  resno resid  eleno  elety 
Stest ""     ""     "10"  ""     ""     ""    
Natom "3888" "3888" "8"   "3888" "3888" "3888"
 *  Selected a total of: 8 intersecting atoms  *
[1] 14.01 12.01 12.01 16.00 12.01 12.01 16.00 14.01

There is also a grpby argument for the purpose of extracting residue masses from atom2mass. However, aa2mass provides amino acid masses including the weights of the hydrogens -- which atom2mass would not pick up unless they are present in the structure.