I was assuming the modeller reader was out for IP reasons
On the contrary, we should be using whatever we can from Modeller. If
Modeller is in future determined to be deficient in some way, we can
dump that functionality and write a new module in IMP, but if Modeller's
up to the job, we should use it by all means. We're not setting out to
rewrite everything from scratch - that would be silly.
it would be great if someone could write a bridge for it
soon.
import modeller.scripts
e = modeller.environ()
e.libs.topology.read('${LIB}/top_heav.lib')
e.libs.parameters.read('${LIB}/par.lib')
m = modeller.scripts.complete_pdb(e, "my.pdb")
after which all the coordinates are available in m.atoms[], all the
bonds in m.bonds[], angles in m.angles[], etc.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle