I think anybody that has used any other package will be rather
confused that our atom "type" is what PDB calls the "name", and not
the forcefield type,
PDB happened to pick the word "name" and charmm the word "type" for
the equivalent concepts in their two systems. We are conflicting with
one either way we choose. Since "name" is already taken in IMP to be
a label for objects for the purpose of user inspection and having
prettier log messages, we are stuck with type (or could switch all
Type to Label throughout the code if it makes you happier).
I think it will be clearer once we have charmm working, since then we
will have both AtomTypes and CharmmTypes floating around. We already
have FormFactorAtomType.
particularly given that we already have a particle attribute called
"name".
No there isn't. All IMP::Objects have names, but it is not an attribute.