On 10/6/10 11:16 AM, Daniel Russel wrote:
I propose a new standard type of interface, namely, simply taking all the XYZR particles of interest, whether or not they happen to be part of a rigid body. That is, if you have some rigid proteins and some non-rigid proteins and are representing everything with all atoms, you simply pass all the atoms.
Sounds reasonable and less confusing for users to me. My only concern is: what happens in the above case if the user passes a list that contains only some atoms from a given rigid body? (e.g. protein A is rigid, protein B is non-rigid, and the user passes in just a few of the atoms from protein A) Any code that currently makes the assumption that an entire rigid body is involved (e.g. I suspect FitRestraint) would have to do the right thing (or maybe throw an exception and require that all members of a rigid body go in).
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle