from __future__ import absolute_import, division, print_function from scitbx.array_family import flex import iotbx.pdb import mmtbx.model from libtbx.utils import null_out from libtbx.test_utils import show_diff from mmtbx.model.utils import merge_models import time cryst_info = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 """ cryst_info_2 = """\ CRYST1 21.937 5.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 """ pdb_str_1 = """\ ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O """ pdb_str_2 = """\ ATOM 1 N GLY B 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY B 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY B 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY B 1 -7.523 2.521 5.381 1.00 16.78 O """ pdb_str_2_1 = """\ ATOM 1 N GLY C 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY C 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY C 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY C 1 -7.523 2.521 5.381 1.00 16.78 O """ pdb_str_3 = """\ MODEL 1 ATOM 1 N GLY B 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY B 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY B 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY B 1 -7.523 2.521 5.381 1.00 16.78 O TER ENDMDL MODEL 2 ATOM 1 N GLY B 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY B 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY B 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY B 1 -7.523 2.521 5.381 1.00 16.78 O TER ENDMDL """ pdb_str_3_1 = """\ MODEL 1 ATOM 1 N GLY C 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY C 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY C 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY C 1 -7.523 2.521 5.381 1.00 16.78 O TER ENDMDL MODEL 2 ATOM 1 N GLY D 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY D 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY D 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY D 1 -7.523 2.521 5.381 1.00 16.78 O TER ENDMDL """ pdb_str_4 = """\ ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 CA GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O """ def tst_1(): """ testing assertions """ m1 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_1, source_info=None), log = null_out()) m2 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_2, source_info=None), log = null_out()) m2_1 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info_2+pdb_str_2, source_info=None), log = null_out()) m2.process(make_restraints=True) m3 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_3, source_info=None), log = null_out()) m4 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_4, source_info=None), log = null_out()) try: new_model = merge_models([m1, m3]) except AssertionError as e: assert not show_diff(str(e), """\ Cannot merge models that have differing numbers of hierarchy 'models'""") try: new_model = merge_models([m1, m2]) except AssertionError as e: assert not show_diff(str(e), """\ Model #2 has GRM initialized.""") try: new_model = merge_models([m1, m2_1]) except AssertionError as e: assert not show_diff(str(e), """\ Cannot merge models with different crystal symmetries (#2)""") try: new_model = merge_models([m1, m1]) except AssertionError as e: assert not show_diff(str(e), """\ Duplicated chain ids are present.""") try: new_model = merge_models([m1, m4]) except AssertionError as e: assert not show_diff(str(e), """\ Model #2 has erros: ['### ERROR: duplicate atom labels ###']""") def tst_2(): """ Normal operation """ answer = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O TER ATOM 5 N GLY B 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 6 CA GLY B 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 7 C GLY B 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 8 O GLY B 1 -7.523 2.521 5.381 1.00 16.78 O TER END """ m1 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_1, source_info=None), log = null_out()) m2 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_2, source_info=None), log = null_out()) new_model = merge_models([m1, m2]) assert not show_diff(new_model.model_as_pdb(), answer) # make sure that new_model is detached from original models m1.get_hierarchy().atoms().set_b(flex.double([10]*4)) m2.get_hierarchy().atoms().set_b(flex.double([20]*4)) assert m1.get_hierarchy().atoms().extract_b() == flex.double([10]*4) assert m2.get_hierarchy().atoms().extract_b() == flex.double([20]*4) assert new_model.get_hierarchy().atoms().extract_b() == flex.double([16.77, 16.57, 16.16, 16.78]*2) # print(new_model.model_as_pdb()) def tst_3(): """ 3 models """ m1 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_1, source_info=None), log = null_out()) m2 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_2, source_info=None), log = null_out()) m3 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_2_1, source_info=None), log = null_out()) new_model = merge_models([m1, m2, m3]) assert len(new_model.get_hierarchy().only_model().chains()) == 3, len(new_model.get_hierarchy().only_model().chains()) def tst_4(): """ 2 models with 2 hierarchy models """ m1 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_3, source_info=None), log = null_out()) m2 = mmtbx.model.manager( model_input = iotbx.pdb.input(lines=cryst_info+pdb_str_3_1, source_info=None), log = null_out()) new_model = merge_models([m1, m2]) assert len(new_model.get_hierarchy().models()) == 2 assert len(new_model.get_hierarchy().models()[0].chains()) == 2 assert len(new_model.get_hierarchy().models()[1].chains()) == 2 assert [c.id for c in new_model.get_hierarchy().models()[0].chains()] == ['B', 'C'] assert [c.id for c in new_model.get_hierarchy().models()[1].chains()] == ['B', 'D'] print(new_model.model_as_pdb()) if (__name__ == "__main__"): t0 = time.time() tst_1() tst_2() tst_3() tst_4() print("Total time: %-8.4f"%(time.time()-t0)) print("OK")