"""Tests for superpose.py""" from __future__ import absolute_import, division, print_function import random import os import unittest import iotbx.pdb import libtbx.load_env import libtbx.test_utils import mmtbx.superpose as superpose from six.moves import range if (1): # Fix random seed to avoid rare failures random.seed(0) def get_filename(filename): return libtbx.env.find_in_repositories(relative_path="phenix_regression/pdb/%s"%filename, test=os.path.isfile) def random_pair(left, right): assert left < right x = random.randrange(left, right) y = random.randrange(left, right) if(y < x): tmp = x x = y y = tmp return x,y # Don't test yet. # class SuperposeTestExamples(unittest.TestCase): class SuperposeExamples(object): def test_example_presets(self): # Do a basic Ca fitting (default) fixed = superpose.SuperposePDB(filename="1CBS.pdb", desc='fixed', preset='ca') moving = superpose.SuperposePDB(filename="1HMT.pdb", desc='moving', preset='ca') rmsd, lsq = moving.superpose(fixed) # ... or will all atoms moving.select_update(preset="all") rmsd, lsq = moving.superpose(fixed) # ... or with a specific selection string. moving.select_update(selection="""pepnames and (name ca) chain A""") rmsd, lsq = moving.superpose(fixed) # ... or use the Select-o-matic. moving.selectomatic(fixed) rmsd, lsq = moving.superpose(fixed) # Write output. # moving.output(lsq, filename="1HMT-fit-1CBS.pdb") def test_example_na(self): # Fit nucleic acid -- note the default settings will realize it's NA. fixed = superpose.SuperposePDB(filename="na1.pdb", desc='fixed') moving = superpose.SuperposePDB(filename="na2.pdb", desc='moving') rmsd, lsq = moving.superpose(fixed) # moving.output(lsq, filename="na-fit.pdb") def test_example_multiple(self): # Open multiple models for fitting and align chain A Ca's. fixed = superpose.SuperposePDB(filename="1OAN.pdb", desc='fixed', preset='ca') models = superpose.SuperposePDB.open_models(filename="1S6N.pdb", desc='moving', preset='ca') for model in models: rmsd, lsq = model.superpose(fixed) def test_example_pairwise(self): result = {} moving = superpose.SuperposePDB(filename="1AON.pdb") fixed = superpose.SuperposePDB(filename="1AON.pdb") for moving_chain in list(moving.pdb.chains())[:7]: for fixed_chain in list(fixed.pdb.chains())[:7]: fixed.select_update(preset='ca', chain=fixed_chain.id) moving.select_update(preset='ca', chain=moving_chain.id) result[(moving_chain.id, fixed_chain.id)] = moving.superpose(fixed) keys = set([i[0] for i in sorted(result.keys())]) print("\t"+"\t".join(keys)) for key1 in keys: rmsds = [result[(key1,key2)][0] for key2 in keys] print("%s:\t"%key1, "\t".join(["%0.2f"%i for i in rmsds])) def test_example_sieve(self): pass # Use an alternate fitting method. # fixed = SuperposePDBSieve(filename="1CBS.pdb", desc='fixed', preset='ca') # moving = superpose.SuperposePDBSieve(filename="1HMT.pdb", desc='moving', preset='ca') # rmsd, lsq = moving.superpose(fixed) # moving.output(lsq, filename="1HMT-fit-1CBS-sieve.pdb") class SuperposeTest(unittest.TestCase): # OK! def test_alignment_used_1(self, filename='fab_a_cut_1.pdb', test='test_alignment_used_1', tolerance=0.003): filename = get_filename(filename) filename_shifted = "%s.shifted.pdb"%test cmd = """phenix.pdbtools %(filename)s suffix=none output.prefix=%(filename_shifted)s remove="%(gap_selection)s" %(shift)s"""%{ 'filename': filename, 'filename_shifted': filename_shifted.replace(".pdb",""), 'gap_selection': "chain A and (resid 5:30 or resid 32:50)", 'shift': 'sites.rotate="10 20 30" sites.translate="10 20 30"' } libtbx.test_utils.run_command(command=cmd, result_file_names=[filename_shifted]) moving = superpose.SuperposePDB(filename_shifted) target = superpose.SuperposePDB(filename) rmsd, lsq = moving.superpose(target) self.assertLess(rmsd, tolerance) # OK! def test_alignment_used_2(self, filename='fab_a_cut.pdb', test='test_alignment_used_2', tolerance=0.003): filename = get_filename(filename) for attempt in range(1): filename_shifted = '%s.%s.shifted.pdb'%(test, attempt) gap_selection = "chain A and (resid %s:%s or resid %s:%s or resid %s:%s)"%(tuple( random_pair(0, 15)+ random_pair(16, 35)+ random_pair(36, 50))) cmd = """phenix.pdbtools %(filename)s suffix=none output.prefix=%(filename_shifted)s remove="%(gap_selection)s" %(shift)s"""%{ 'filename': filename, 'filename_shifted': filename_shifted.replace(".pdb",""), 'gap_selection': gap_selection, 'shift': 'sites.rotate="10 20 30" sites.translate="10 20 30"' } libtbx.test_utils.run_command(command=cmd, result_file_names=[filename_shifted]) moving = superpose.SuperposePDB(filename_shifted) target = superpose.SuperposePDB(filename) rmsd, lsq = moving.superpose(target) self.assertLess(rmsd, tolerance) return # TODO: Not quite OK def test_comprehensive(self, filename='enk_gm.pdb', test='test_comprehensive'): filename = get_filename(filename) tests = [ ["", "None", "None"], # OK ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "None", "None"], # OK ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "chain A or resname HOH", "not (chain A or resname HOH)"], # OK ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "chain A or chain C", "not (chain A or chain C)"], # OK # ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "resname HOH", "not (resname HOH)"], # FAILED ["""sites.rotate="1 2 3" sites.translate="4 5 6" """, "name CA", "not (name CA)"] # OK ] count = 0 for shift, shift_selection, remove_selection in tests: print("========= shift: %s -- shift_selection: %s -- remove_selection: %s"%(shift, shift_selection, remove_selection)) filename_shifted = '%s.%s.shifted.pdb'%(test, count) filename_fitted = '%s.%s.fitted.pdb'%(test, count) cmd = """phenix.pdbtools %(filename)s suffix=none output.prefix=%(filename_shifted)s selection="%(shift_selection)s" remove="%(remove_selection)s" %(shift)s"""%{ 'filename': filename, 'filename_shifted': filename_shifted.replace(".pdb",""), 'shift': shift, 'shift_selection': shift_selection, 'remove_selection': remove_selection } libtbx.test_utils.run_command(command=cmd) moving = superpose.SuperposePDB(filename_shifted, selection=shift_selection) target = superpose.SuperposePDB(filename, selection=shift_selection) rmsd, lsq = moving.superpose(target) moving.output(lsq, filename=filename_fitted) xs_shifted = iotbx.pdb.input(file_name=filename_shifted).xray_structure_simple() xs_fitted = iotbx.pdb.input(file_name=filename_fitted).xray_structure_simple() check = xs_fitted.mean_distance(other=xs_shifted) if shift: self.assertGreater(check, 5.0) else: self.assertAlmostEqual(check, 0) count += 1 return # OK! def test_assert_anisou_warning_message(self, filename='phe_a.pdb', test='test_assert_anisou_warning_message'): filename = get_filename(filename) filename_output = '%s.noaniso.pdb'%test moving = superpose.SuperposePDB(filename) target = superpose.SuperposePDB(filename) rmsd, lsq = moving.superpose(target) moving.output(lsq, filename=filename_output) pi = iotbx.pdb.input(file_name=filename_output) ph = pi.construct_hierarchy() pa = ph.atoms() uij = pa.extract_uij().as_double() print(uij.all_eq(-1.0)) assert uij.all_eq(-1.0) # Mostly OK! def test_erik_vogan_case(self, test='test_erik_vogan_case'): filename1 = get_filename('rebuild03_ckpt04.pdb') filename2 = get_filename('2C30.pdb') filename_output = '%s.fitted.pdb'%test moving = superpose.SuperposePDB(filename2) target = superpose.SuperposePDB(filename1) rmsd, lsq = moving.superpose(target) moving.output(lsq, filename=filename_output) # ["Number of atoms for LS fitting = 36", # "RMSD (all matching atoms) (start): 60.830 (number of atoms: 99)", # "RMSD (all matching atoms) (final): 0.992 (number of atoms: 99)"]: self.assertLess(rmsd, 1.0) # Mostly OK! def test_altlocs_1(self, test='test_altlocs_1', tolerance=0.001): filename1 = get_filename("fab_1.pdb") filename2 = get_filename("fab_2.pdb") filename_output = '%s.fitted.pdb'%test moving = superpose.SuperposePDB(filename2) target = superpose.SuperposePDB(filename1) rmsd, lsq = moving.superpose(target) moving.output(lsq, filename=filename_output) # ["Number of atoms for LS fitting = 6", # "RMSD between fixed and moving atoms (start): 12.830", # "RMSD between fixed and moving atoms (final): 0.000", # "RMSD (all matching atoms) (start): 13.164 (number of atoms: 15)", # "RMSD (all matching atoms) (final): 0.001 (number of atoms: 15)"]: self.assertLess(rmsd, tolerance) # OK! def test_same_models_many_differently_ordered_chains_1(self, test='test_same_models_many_differently_ordered_chains_1', tolerance=0.03): filename1 = get_filename("a1.pdb") filename2 = get_filename("b1.pdb") filename_output = '%s.fitted.pdb'%test moving = superpose.SuperposePDB(filename2) target = superpose.SuperposePDB(filename1) rmsd, lsq = moving.superpose(target) rmsd_output = moving.output(lsq, filename=filename_output) # ["Number of atoms for LS fitting = 33", # "RMSD between fixed and moving atoms (start): 153.279", # "RMSD between fixed and moving atoms (final): 0.025"]: self.assertLess(rmsd, tolerance) # OK! def test_same_models_many_differently_ordered_chains_2(self, test='test_same_models_many_differently_ordered_chains_2', tolerance=0.13): filename1 = get_filename("a2.pdb") filename2 = get_filename("b2.pdb") filename_output = '%s.fitted.pdb'%test moving = superpose.SuperposePDB(filename2) target = superpose.SuperposePDB(filename1) rmsd, lsq = moving.superpose(target) rmsd_output = moving.output(lsq, filename=filename_output) # ["Number of atoms for LS fitting = 1284", # "RMSD (all matching atoms) (start): 159.830 (number of atoms: 26184)", # "RMSD (all matching atoms) (final): 67.995 (number of atoms: 26184)"] self.assertLess(rmsd, tolerance) # OK! def test_rna_dna(self, test='test_rna_dna', tolerance=0.7): filename1 = get_filename('superpose_pdbs_a.pdb') filename2 = get_filename('superpose_pdbs_b.pdb') filename_output = '%s.fitted.pdb'%test moving = superpose.SuperposePDB(filename2) target = superpose.SuperposePDB(filename1) rmsd, lsq = moving.superpose(target) rmsd_output = moving.output(lsq, filename=filename_output) # ["Number of atoms for LS fitting = 8142", # "RMSD (all matching atoms) (start): 405.009 (number of atoms: 8142)", # "RMSD (all matching atoms) (final): 0.607 (number of atoms: 8142)"]: self.assertLess(rmsd, tolerance) if __name__ == '__main__': unittest.main(verbosity=0)