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]
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