To follow pdb conventions, a patch that renames the type attribute to
name attribute in both AtomDecerator and ResidueDecerator is attached.
Why should we follow PDB conventions anyway? And I have a couple of
other problems with this proposed patch:
1. The residue type really is a type. All THY residues are thymines, for
example - it's not an arbitrary name.
2. The atom type could be argued to really be 'name', since, for
example, AT_CG1 and AT_CG2 are both carbon, and this is orthogonal from
the CHARMM forcefield type (probably CT2 or CT3). But the name does
determine the element, so could easily be described as 'type'. And if
you go down that route, you have to go all the way, also renaming
AtomType to AtomName. In this patch you end up with methods like
void set_name(AtomType t)
which seems weird to me. Either it should be set_type(AtomType) or
set_name(AtomName).
What do others think?
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle