from __future__ import absolute_import, division, print_function from mmtbx.validation import clashscore from iotbx import pdb from libtbx.test_utils import approx_equal from libtbx.utils import null_out from libtbx.easy_pickle import loads, dumps import libtbx.load_env import time #protein pdb_str_1 = """ ATOM 556 N LEU A 71 32.763 35.831 23.090 1.00 12.71 N ATOM 557 CA LEU A 71 34.145 35.472 23.481 1.00 16.06 C ATOM 558 C LEU A 71 34.239 35.353 24.979 1.00 18.09 C ATOM 559 O LEU A 71 33.707 36.197 25.728 1.00 19.26 O ATOM 560 CB LEU A 71 35.114 36.564 22.907 1.00 17.10 C ATOM 561 CG LEU A 71 35.926 35.979 21.737 1.00 19.37 C ATOM 562 CD1 LEU A 71 35.003 35.084 20.920 1.00 17.51 C ATOM 563 CD2 LEU A 71 36.533 37.087 20.917 1.00 19.57 C ATOM 564 N ARG A 72 34.930 34.384 25.451 1.00 21.47 N ATOM 565 CA ARG A 72 35.161 34.174 26.896 1.00 25.83 C ATOM 566 C ARG A 72 36.671 34.296 27.089 1.00 27.74 C ATOM 567 O ARG A 72 37.305 33.233 26.795 1.00 30.65 O ATOM 568 CB ARG A 72 34.717 32.760 27.286 1.00 28.49 C ATOM 569 CG ARG A 72 35.752 32.054 28.160 1.00 31.79 C ATOM 570 CD ARG A 72 35.612 30.577 28.044 1.00 34.05 C ATOM 571 NE ARG A 72 35.040 30.252 26.730 1.00 35.08 N ATOM 572 CZ ARG A 72 34.338 29.103 26.650 1.00 34.67 C ATOM 573 NH1 ARG A 72 34.110 28.437 27.768 1.00 35.02 N ATOM 574 NH2 ARG A 72 34.014 28.657 25.457 1.00 34.97 N ATOM 575 N LEU A 73 37.197 35.397 27.513 0.45 28.93 N ATOM 576 CA LEU A 73 38.668 35.502 27.680 0.45 30.76 C ATOM 577 C LEU A 73 39.076 34.931 29.031 0.45 32.18 C ATOM 578 O LEU A 73 38.297 34.946 29.996 0.45 32.31 O ATOM 579 CB LEU A 73 39.080 36.941 27.406 0.45 30.53 C ATOM 580 CG LEU A 73 39.502 37.340 26.002 0.45 30.16 C ATOM 581 CD1 LEU A 73 38.684 36.647 24.923 0.45 29.57 C ATOM 582 CD2 LEU A 73 39.337 38.854 25.862 0.45 29.11 C ATOM 583 N ARG A 74 40.294 34.412 29.045 0.45 33.82 N ATOM 584 CA ARG A 74 40.873 33.802 30.253 0.45 35.33 C ATOM 585 C ARG A 74 41.765 34.829 30.944 0.45 36.22 C ATOM 586 O ARG A 74 42.945 34.994 30.583 0.45 36.70 O ATOM 587 CB ARG A 74 41.651 32.529 29.923 0.45 36.91 C ATOM 588 CG ARG A 74 41.608 31.444 30.989 0.45 38.62 C ATOM 589 CD ARG A 74 41.896 30.080 30.456 0.45 39.75 C ATOM 590 NE ARG A 74 43.311 29.735 30.563 0.45 41.13 N ATOM 591 CZ ARG A 74 44.174 29.905 29.554 0.45 41.91 C ATOM 592 NH1 ARG A 74 43.754 30.312 28.356 0.45 42.75 N ATOM 593 NH2 ARG A 74 45.477 29.726 29.763 0.45 41.93 N END """ def exercise_clashscore(): for cp in [True, False]: pdb_io = pdb.input(source_info=None, lines=pdb_str_1) pdb_hierarchy = pdb_io.construct_hierarchy() cs = clashscore.clashscore( pdb_hierarchy=pdb_hierarchy, fast = False, condensed_probe=cp, out=null_out()) for unpickle in [False, True] : if (unpickle): cs = loads(dumps(cs)) c_score = cs.get_clashscore() assert approx_equal(c_score, 35.29, eps=0.01) bad_clashes_list = cs.results assert ([ c.format_old() for c in bad_clashes_list ] == [' A 72 ARG HG2 A 72 ARG O :1.038', ' A 72 ARG CG A 72 ARG O :0.465', ' A 71 LEU HA A 71 LEU HD12 :0.446']), [ c.format_old() for c in bad_clashes_list ] #test nuclear distances cs = clashscore.clashscore( pdb_hierarchy=pdb_hierarchy, fast = False, condensed_probe=cp, nuclear=True) for unpickle in [False, True] : if (unpickle): cs = loads(dumps(cs)) c_score = cs.get_clashscore() assert approx_equal(c_score, 58.82, eps=0.01) bad_clashes_list = cs.results assert ([ c.format_old() for c in bad_clashes_list ] == [ ' A 72 ARG HG2 A 72 ARG O :1.082', ' A 72 ARG CG A 72 ARG O :0.622', ' A 71 LEU HA A 71 LEU HD12 :0.535', ' A 72 ARG HB3 A 72 ARG HE :0.475', ' A 72 ARG HD3 A 72 ARG HH11 :0.451']) #test B factor cutoff cs = clashscore.clashscore( pdb_hierarchy=pdb_hierarchy, fast = False, condensed_probe=cp, b_factor_cutoff=40) for unpickle in [False, True] : if (unpickle): cs = loads(dumps(cs)) c_score = cs.get_clashscore() assert approx_equal(c_score, 35.29, eps=0.01) c_score_b_cutoff = cs.get_clashscore_b_cutoff() assert approx_equal(c_score_b_cutoff, 39.47, eps=0.01) bad_clashes_list = cs.results assert ([ c.format_old() for c in bad_clashes_list ] == [' A 72 ARG HG2 A 72 ARG O :1.038', ' A 72 ARG CG A 72 ARG O :0.465', ' A 71 LEU HA A 71 LEU HD12 :0.446']) def exercise_fast_clashscore(): for fast_clash in [True, False]: pdb_io = pdb.input(source_info=None, lines=pdb_str_1) pdb_hierarchy = pdb_io.construct_hierarchy() cs = clashscore.clashscore( pdb_hierarchy=pdb_hierarchy, fast = fast_clash, condensed_probe=True, out=null_out()) for unpickle in [False, True] : if (unpickle): cs = loads(dumps(cs)) c_score = cs.get_clashscore() assert approx_equal(c_score, 35.29, eps=0.01) #test nuclear distances cs = clashscore.clashscore( pdb_hierarchy=pdb_hierarchy, fast = fast_clash, condensed_probe=True, nuclear=True) for unpickle in [False, True] : if (unpickle): cs = loads(dumps(cs)) c_score = cs.get_clashscore() assert approx_equal(c_score, 58.82, eps=0.01) if (__name__ == "__main__"): if (not libtbx.env.has_module(name="probe")): print("Skipping exercise_clashscore(): probe not configured") print("OK") else: t0 = time.time() exercise_clashscore() exercise_fast_clashscore() print("OK. Time: %8.3f"%(time.time()-t0))