Python get_rotamer_manager Examples

Example #1

File: tst_fix_rotamer_outliers.py Project: zhuligs/cctbx_project

def exercise_2():
  model = get_necessary_inputs(pdb_str_2)
  model = run(
      args=[],
      model = model)
  rotamers = []
  for res in model.get_hierarchy().only_chain().only_conformer().residues():
    rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
  assert rotamers == ['mtt180', 'tttt', 't0', 'pt', 'm', 'pt0', 'm-40',
      'EXCEPTION', 'tt', 'tttt'], rotamers

Example #2

def exercise_2():
    model = get_necessary_inputs(pdb_str_2)
    pdb_h = fix_rotamer_outliers(model=model, radius=5)
    rotamers = []
    for res in pdb_h.only_chain().only_conformer().residues():
        rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
    assert rotamers == [
        'mtt180', 'tttt', 'm-30', 'pt', 'p', 'mt-10', 'm-40', 'EXCEPTION',
        'tt', 'tttt'
    ], rotamers

Example #3

def exercise_1():
    """ 58 is outlier """
    model = get_necessary_inputs(pdb_str_1)
    # pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb")
    pdb_h = fix_rotamer_outliers(model=model, radius=5)
    rotamers = []
    # pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb")
    for res in pdb_h.only_chain().only_conformer().residues():
        rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
    # print rotamers
    assert rotamers == ['m-80', 'p'], rotamers

Example #4

File: tst_fix_rotamer_outliers.py Project: zhuligs/cctbx_project

def exercise_1():
  """ 58 is outlier """
  model = get_necessary_inputs(pdb_str_1)
  # pdb_h.write_pdb_file("fix_rot_out_ex1_start.pdb")
  model = run(
      args=[],
      model=model)
  rotamers = []
  # pdb_h.write_pdb_file("fix_rot_out_ex1_end.pdb")
  for res in model.get_hierarchy().only_chain().only_conformer().residues():
    rotamers.append(model.get_rotamer_manager().evaluate_residue(res))
  # print rotamers
  assert rotamers == ['p90', 'p'], rotamers