modeller_test_energy3.py

from modeller import *
from modeller.scripts import complete_pdb

log.none()

env = environ()
env.io.atom_files_directory = '../atom_files'
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

mdl = complete_pdb(env, "PDB/pdb2a3d.ent")

def make_restranints(sel):
    mdl.restraints.make(sel, restraint_type='LJ', spline_on_site=False)
    mdl.restraints.make(sel, restraint_type='LJ14', spline_on_site=False)
    mdl.restraints.make(sel, restraint_type='COULOMB14', spline_on_site=False)
    return sel
    
s0 = selection(mdl.residue_range('%s:A'%str(2),'%s:A'%str(20)))
s1 = selection(mdl.residue_range('%s:A'%str(24),'%s:A'%str(43)))
s0s1 = s0 | s1

for sel in [s0, s1, s0s1]:
    sel = make_restranints(sel)
    (molpdf, terms) = sel.energy(edat=energy_data(dynamic_sphere=True))
    print terms
    print