from modeller import * from modeller.automodel import * log.verbose() # for debugging env = environ(rand_seed=-12312) # random seed env.io.atom_files_directory = '.' # Working directory def defsym(mdl, aln, seg1, seg2): """Constrain segments |seg1| and |seg2| to be identical""" for (set,seg) in [(2,seg1), (3,seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='CA', selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) def makealpha(mdl, aln, residue_ids): """Enforce alpha-helical structure on |residue_ids|""" mdl.restraints.make(aln, restraint_type='ALPHA', residue_ids=residue_ids, spline_on_site=False) class mymodel(automodel): def special_restraints(self, aln): segs = [('1', '99'), ('100', '198'), ('199', '297'), ('298', '396')] for n in range(len(segs)): defsym(self, aln, segs[n-1], segs[n]) makealpha(self, aln, ('5', '30')) #M1 region (consensus) makealpha(self, aln, ('40', '53')) #P region (jalview p/out) makealpha(self, aln, ('64', '95')) #M2 region (consensus) makealpha(self, aln, ('104', '129')) makealpha(self, aln, ('139', '152')) makealpha(self, aln, ('163', '194')) makealpha(self, aln, ('203', '228')) makealpha(self, aln, ('238', '251')) makealpha(self, aln, ('262', '293')) makealpha(self, aln, ('302', '327')) makealpha(self, aln, ('337', '350')) makealpha(self, aln, ('361', '392')) a = mymodel(env, alnfile = 'x_vs_y.ali', # The alignment filename knowns = ('template'), # The structure filenames, the pdb # is called filename.atm sequence = 'target') # The sequence filename a.starting_model= 1 # Starting and ending model indices a.ending_model = 4 a.deviation = 4.0 # Deviation in models # Call the routine model which in turn calls all the other routines required. a.make() mdl = model(env, file = ???) mdl.energy() molpdf = mdl.energy(output='VERY_LONG', residue_span_range=(1,9999), normalize_profile=True, edat=energy_data(dynamic_sphere=True)) mdl.seq_id = 90.00 score = mdl.assess_ga341()