On 9/7/17 1:05 AM, Pablo Chacon wrote: > 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