# Example for: model.rotate_dihedrals()

# This will optimize and randomize dihedrals in a MODEL
env = environ()
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

# Select dihedral angle types for optimization and randomization:
dih = 'phi psi omega chi1 chi2 chi3 chi4 chi5'

# Read the sequence, get its topology and coordinates:
code='1fas'
mdl = model(env, file=code)
aln = alignment(env)
aln.append_model(mdl, align_codes=code, atom_files=code)
aln.append_model(mdl, align_codes=code+'_ini', atom_files=code+'_ini')
mdl.generate_topology(aln, sequence=code+'_ini')
mdl.transfer_xyz(aln)
mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES')
mdl.rotate_dihedrals(change='RANDOMIZE', deviation=90.0, dihedrals=dih)
mdl.write(file='1fas.ini1')

# Get restraints from somewhere and optimize dihedrals:
mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False)
mdl.rotate_dihedrals(change='OPTIMIZE', deviation=90.0, dihedrals=dih)
mdl.write(file='1fas.ini2')