Thanks for the replay. I am newie to modeller. Do you have an example
where soap_pp.Assessor class is used? (or where I can find it)
Just to be absolutely clear here - SOAP-PP contains two scoring terms, a
SAS term that is applied to each atom, and an atomistic pairwise
statistical potential that is applied to each *pair* of atoms. IMP does
have classes to apply both terms (and the potentials themselves are also
included with IMP) but the soap_score utility only applies the pairwise
term. If you are only ranking rigid docking solutions, the atomistic
term should cancel out anyway, so it isn't needed. What do you need to
do that isn't handled already by soap_score?
If you want to assess with both terms with Modeller, something like the
following should work (although untested):
import modeller
import modeller.soap_pp
from modeller.scripts import complete_pdb
env = modeller.environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')
sp = modeller.soap_pp.Asssesor()
mdl = complete_pdb(env, 'my.pdb')
atmsel = modeller.selection(mdl)
score = atmsel.assess(sp)
Ben
--
ben@salilab.orghttps://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle