Author: bugman Date: Sat Jan 31 10:03:50 2015 New Revision: 27407 URL: http://svn.gna.org/viewcvs/relax?rev=27407&view=rev Log: Updated the Structure system tests for the structure.align and structure.superimpose user function merger. Modified: trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py trunk/test_suite/system_tests/structure.py Modified: trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py?rev=27407&r1=27406&r2=27407&view=diff ============================================================================== --- trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py (original) +++ trunk/test_suite/system_tests/scripts/n_state_model/structure_align.py Sat Jan 31 10:03:50 2015 @@ -16,11 +16,13 @@ # Load the structure. structure.read_pdb('%s.pdb' % code, dir=status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures') -# First align the N-domains - aligning 1OSA onto 1J70 to act as a scaffold. -structure.align(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', method='fit to first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0) +# First align then superimpose the N-domains - aligning 1OSA onto 1J70 to act as a scaffold. +structure.sequence_alignment(pipes=['1J7O', '1OSA'], matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0) +structure.superimpose(pipes=['1J7O', '1OSA'], atom_id='@N,C,CA,O', method='fit to first') -# Then align the C-domains - aligning 1J7P onto the 1OSA scaffold. -structure.align(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', method='fit to first', matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0) +# Then align then superimpose the C-domains - aligning 1J7P onto the 1OSA scaffold. +structure.sequence_alignment(pipes=['1OSA', '1J7P'], matrix='BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0) +structure.superimpose(pipes=['1OSA', '1J7P'], atom_id='@N,C,CA,O', method='fit to first') # Write out the result. structure.write_pdb('devnull', force=True) Modified: trunk/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27407&r1=27406&r2=27407&view=diff ============================================================================== --- trunk/test_suite/system_tests/structure.py (original) +++ trunk/test_suite/system_tests/structure.py Sat Jan 31 10:03:50 2015 @@ -64,7 +64,7 @@ def test_align(self): - """Test the U{structure.align user function<http://www.nmr-relax.com/manual/structure_align.html>}.""" + """Test the U{structure.superimpose user function<http://www.nmr-relax.com/manual/structure_superimpose.html>}.""" # Reset relax. self.interpreter.reset() @@ -107,7 +107,7 @@ self.interpreter.structure.add_atom(mol_name='uniform_mol1', atom_name='Ti', res_name='TST', res_num=1, pos=[[1.0, 2.0, 3.0], [1.0, 2.0, 3.0]], element='Ti', pdb_record='HETATM') # The alignment. - self.interpreter.structure.align(pipes=['ref', 'align'], method='fit to first', atom_id='@N,H', displace_id='@N,H') + self.interpreter.structure.superimpose(pipes=['ref', 'align'], method='fit to first', atom_id='@N,H', displace_id='@N,H') # Output PDB to stdout to help in debugging. self.interpreter.structure.write_pdb(file=sys.stdout) @@ -213,7 +213,7 @@ def test_align_molecules(self): - """Test the U{structure.align user function<http://www.nmr-relax.com/manual/structure_align.html>} for aligning different molecules in one pipe.""" + """Test the U{structure.superimpose user function<http://www.nmr-relax.com/manual/structure_superimpose.html>} for aligning different molecules in one pipe.""" # Reset relax. self.interpreter.reset() @@ -257,7 +257,7 @@ self.interpreter.structure.add_atom(mol_name='2', atom_name='Ti', res_name='TST', res_num=1, pos=[1.0, 2.0, 3.0], element='Ti', pdb_record='HETATM') # The alignment. - self.interpreter.structure.align(pipes=['ref', 'align'], molecules=[['ref'], ['1', '2']], method='fit to first', atom_id='@N,H', displace_id='@N,H') + self.interpreter.structure.superimpose(pipes=['ref', 'align'], molecules=[['ref'], ['1', '2']], method='fit to first', atom_id='@N,H', displace_id='@N,H') # Output PDB to stdout to help in debugging. self.interpreter.structure.write_pdb(file=sys.stdout) @@ -349,7 +349,7 @@ def test_align_molecules2(self): - """Test of the structure.align user function, fitting to the mean structure.""" + """Test of the structure.superimpose user function, fitting to the mean structure.""" # Path of the structure file. path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam' @@ -363,7 +363,7 @@ self.interpreter.structure.add_atom(mol_name='CaM B', atom_name='Ti', res_name='TST', res_num=1, pos=[2.0, 3.0, 4.0], element='Ti', pdb_record='HETATM') # Superimpose the backbone heavy atoms. - self.interpreter.structure.align(method='fit to mean', atom_id='@N,C,CA,O', displace_id=':82-5000') + self.interpreter.structure.superimpose(method='fit to mean', atom_id='@N,C,CA,O', displace_id=':82-5000') # Check that the two structures now have the same atomic coordinates. mol1 = cdp.structure.structural_data[0].mol[0] @@ -382,7 +382,7 @@ def test_align_molecules_end_truncation(self): - """Test of the structure.align user function, fitting to the mean structure.""" + """Test of the structure.superimpose user function, fitting to the mean structure.""" # Path of the structure file. path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'structures' @@ -403,7 +403,7 @@ self.interpreter.pipe.copy('mf', 'comp') # Superimpose the backbone heavy atoms. - self.interpreter.structure.align(method='fit to mean', atom_id='@N,C,CA,O') + self.interpreter.structure.superimpose(method='fit to mean', atom_id='@N,C,CA,O') # Check that nothing has moved. for mol_index in range(3): @@ -776,7 +776,7 @@ self.interpreter.structure.superimpose(method='fit to first', centre_type='CoM') # Align. - self.interpreter.structure.align(method='fit to first', centre_type='CoM') + self.interpreter.structure.superimpose(method='fit to first', centre_type='CoM') def test_bug_22860_CoM_after_deletion(self): @@ -4789,7 +4789,7 @@ self.interpreter.structure.translate([20.0, 0.0, 0.0], model=3) # Superimpose the backbone heavy atoms. - self.interpreter.structure.superimpose(models=[2, 3], method='fit to mean', atom_id='@N,C,CA,O') + self.interpreter.structure.superimpose(models=[[2, 3]], method='fit to mean', atom_id='@N,C,CA,O') # Check that the two structures now have the same atomic coordinates as the original, but shifted 10 Angstrom in x. model1 = cdp.structure.structural_data[0].mol[0]