from __future__ import absolute_import, division, print_function import mmtbx.model import iotbx.pdb from cctbx.array_family import flex from libtbx.utils import format_cpu_times from libtbx.test_utils import approx_equal, show_diff from iotbx.regression.ncs.tst_ncs import pdb_str_5 from mmtbx.regression.ncs.tst_ncs_search import test_pdb_6 def exercise_set_sites_cart_ncs(): """ No extra atoms """ inp = iotbx.pdb.input(lines=pdb_str_5, source_info=None) model = mmtbx.model.manager(model_input=inp) model.search_for_ncs() nrgl = model.get_ncs_groups() nrgl._show() print ('n model atoms:', model.get_number_of_atoms()) print ('n master atoms:', model.get_master_selection().count(True)) print ('n master atoms:', model.get_master_selection().iselection().size()) print ('n master atoms:', model.get_master_hierarchy().atoms_size()) assert model.get_master_selection().count(True) ==\ model.get_master_selection().iselection().size() ==\ model.get_master_hierarchy().atoms_size() h = model.get_hierarchy() # print('h sites:', list(h.atoms().extract_xyz())) # Warning: here here mh is not deep-copy, therefore when we change atom coords # they are changing in model.get_hierarchy() as well mh = model.get_master_hierarchy() new_sites_cart = flex.vec3_double([(1.0, 1.0, 1.0)]*42) mh.atoms().set_xyz(new_sites_cart) model.set_sites_cart_from_hierarchy(multiply_ncs=True) h = model.get_hierarchy() new_xyz=h.atoms().extract_xyz() # print('h sites:', list(new_xyz)) # checking if setting went as supposed: assert approx_equal(new_xyz[0], (1.0, 1.0, 1.0), eps=1e-4) assert approx_equal(new_xyz[42], (-0.6420293330506949, 1.2600792663765976, 7.999997229451341), eps=1e-4) assert approx_equal(new_xyz[84], (-1.396802536808536, -0.22123285934616377, 1.000000038694047), eps=1e-4) for i in range(3): for j in range(42): assert approx_equal(new_xyz[42*i+j], new_xyz[42*i], eps=1e-4) def exercise_set_sites_cart_ncs_with_extra_atoms(): inp = iotbx.pdb.input(lines=test_pdb_6, source_info=None) model = mmtbx.model.manager(model_input=inp) model.search_for_ncs() nrgl = model.get_ncs_groups() nrgl._show(brief=False) print ('n model atoms:', model.get_number_of_atoms()) print ('n master atoms:', model.get_master_selection().count(True)) print ('n master atoms:', model.get_master_selection().iselection().size()) print ('n master isel:', list(model.get_master_selection().iselection())) print ('n master atoms:', model.get_master_hierarchy().atoms_size()) print ('n master hierarchy:\n', model.get_master_hierarchy().as_pdb_string()) # Note that "HETATM 32 C2 NDG H" and "HETATM 35 C2 NDG L" # don't belong to any master/copy assert not show_diff(model.get_master_hierarchy().as_pdb_string(),"""\ ATOM 1 N ASP H 5 91.286 -31.834 73.572 1.00 77.83 N ATOM 2 CA ASP H 5 90.511 -32.072 72.317 1.00 78.04 C ATOM 3 C ASP H 5 90.136 -30.762 71.617 1.00 77.70 C ATOM 4 O ASP H 5 89.553 -29.857 72.225 1.00 77.56 O ATOM 5 N THR H 6 91.286 -31.834 73.572 1.00 77.83 N ATOM 6 CA THR H 6 90.511 -32.072 72.317 1.00 78.04 C TER ATOM 7 N GLY I 501 91.286 -31.834 73.572 1.00 77.83 N ATOM 8 CA GLY I 501 90.511 -32.072 72.317 1.00 78.04 C ATOM 9 C GLY I 501 90.136 -30.762 71.617 1.00 77.70 C ATOM 10 O GLY I 501 89.553 -29.857 72.225 1.00 77.56 O TER HETATM 31 C1 NDG H 640 91.286 -31.834 73.572 1.00 77.83 C HETATM 32 C2 NDG H 640 91.286 -31.834 73.572 1.00 77.83 C HETATM 35 C2 NDG L 646 61.028 -14.273 81.262 1.00 69.80 C """) mh = model.get_master_hierarchy() # Note that atoms outside NCS are getting 2.0 as xyz new_sites_cart = flex.vec3_double([ (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0), (1.0, 1.0, 1.0)] + [(3.0, 3.0, 3.0)]*4 + [(1.0, 1.0, 1.0), # <--- Note this atom belongs the first NCS group (2.0, 2.0, 2.0), (2.0, 2.0, 2.0)] ) mh.atoms().set_xyz(new_sites_cart) # print('='*80) # print (mh.as_pdb_string()) model.set_sites_cart_from_hierarchy(multiply_ncs=True) h = model.get_hierarchy() new_xyz=h.atoms().extract_xyz() # print(model.model_as_pdb()) # print (list(new_xyz)) assert approx_equal(new_xyz[31], (2.0, 2.0, 2.0), eps=1e-4) assert approx_equal(new_xyz[34], (2.0, 2.0, 2.0), eps=1e-4) assert approx_equal(new_xyz[0], (1.0, 1.0, 1.0), eps=1e-4) assert approx_equal(new_xyz[5], (1.0, 1.0, 1.0), eps=1e-4) assert approx_equal(new_xyz[6], (3.0, 3.0, 3.0), eps=1e-4) assert approx_equal(new_xyz[9], (3.0, 3.0, 3.0), eps=1e-4) assert nrgl.check_for_max_rmsd(sites_cart=new_xyz, chain_max_rmsd=0.0) for i in [[0, 1, 2, 3, 4, 5, 30], [10, 11, 12, 13, 14, 15, 32], [20, 21, 22, 23, 24, 25, 33]]: for j in i: assert approx_equal(new_xyz[j], new_xyz[i[0]], eps=1e-4) for i in [[6, 7, 8, 9], [16, 17, 18, 19], [26, 27, 28, 29]]: for j in i: assert approx_equal(new_xyz[j], new_xyz[i[0]], eps=1e-4) def exercise_set_sites_cart_no_ncs(): inp = iotbx.pdb.input(lines=pdb_str_5, source_info=None) model = mmtbx.model.manager(model_input=inp, expand_with_mtrix=False) model.search_for_ncs() nrgl = model.get_ncs_groups() nrgl._show() print ('n model atoms:', model.get_number_of_atoms()) print ('n master atoms:', model.get_master_selection().count(True)) print ('n master atoms:', model.get_master_selection().iselection().size()) print ('n master atoms:', model.get_master_hierarchy().atoms_size()) assert model.get_master_selection().count(True) ==\ model.get_master_selection().iselection().size() ==\ model.get_master_hierarchy().atoms_size() h = model.get_hierarchy() # Warning: here here mh is not deep-copy, therefore when we change atom coords # they are changing in model.get_hierarchy() as well mh = model.get_master_hierarchy() new_sites_cart = flex.vec3_double([(1.0, 1.0, 1.0)]*42) mh.atoms().set_xyz(new_sites_cart) model.set_sites_cart_from_hierarchy(multiply_ncs=True) h = model.get_hierarchy() new_xyz=h.atoms().extract_xyz() # print('h sites:', list(new_xyz)) # checking if setting went as supposed: for j in range(42): assert approx_equal(new_xyz[j], (1.0, 1.0, 1.0), eps=1e-4) def run(): exercise_set_sites_cart_ncs() exercise_set_sites_cart_ncs_with_extra_atoms() exercise_set_sites_cart_no_ncs() print(format_cpu_times()) if (__name__ == "__main__"): run()