Author: bugman
Date: Thu Oct 23 15:06:11 2014
New Revision: 26387
URL: http://svn.gna.org/viewcvs/relax?rev=26387&view=rev
Log:
Merged revisions 26380-26383 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26380 | bugman | 2014-10-23 14:27:05 +0200 (Thu, 23 Oct 2014) | 6 lines
Created the Structure.test_bug_22861_PDB_writing_chainID_fail system test.
This is to catch bug #22861 (https://gna.org/bugs/?22861), the chain IDs in
the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.
........
r26381 | bugman | 2014-10-23 14:45:25 +0200 (Thu, 23 Oct 2014) | 13 lines
The structure.write_pdb user function can now handle empty molecules.
This fixes bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the
structure.write_pdb user
function PDB files are incorrect after calling structure.delete.
To handle this consistently, the internal structural object
ModelContainer.mol_loop() generator
method has been created. This loops over the molecules, yielding those
that are not empty. The
MolContainer.is_empty() method has been fixed by not checking for the
molecule name, as that remains
after the structure.delete user function call while all other information
has been removed. And
finally the write_pdb() structural object method has been modified to use
the mol_loop() method
rather than performing the loop itself.
........
r26382 | bugman | 2014-10-23 14:55:09 +0200 (Thu, 23 Oct 2014) | 6 lines
Small modification of the Structure.test_bug_22861_PDB_writing_chainID_fail
system test.
File metadata is now being set to demonstrate that the structure.delete
user function does not
remove this once there is no more data left for the molecule.
........
r26383 | bugman | 2014-10-23 14:56:54 +0200 (Thu, 23 Oct 2014) | 8 lines
Fix for the structure.delete user function for molecule metadata once no
more data exists.
This relates to bug #22861 (https://gna.org/bugs/?22861), the chain IDs in
the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.
The metadata, when it exists, is now deleted for the molecule once no more
data is present.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/internal/models.py
branches/frame_order_cleanup/lib/structure/internal/molecules.py
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Oct 23 15:06:11 2014
@@ -1 +1 @@
-/trunk:1-26370,26373-26374,26379
+/trunk:1-26385
Modified: branches/frame_order_cleanup/lib/structure/internal/models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/models.py?rev=26387&r1=26386&r2=26387&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/models.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/models.py Thu
Oct 23 15:06:11 2014
@@ -263,3 +263,20 @@
# The ModelContainer is unmodified.
return True
+
+
+ def mol_loop(self):
+ """Generator method to loop over the molecules of this model.
+
+ @return: The molecules of this model.
+ @rtype: MolContainer instance
+ """
+
+ # Loop over all molecules.
+ for mol in self.mol:
+ # No data, so do not yield the molecule.
+ if mol.is_empty():
+ continue
+
+ # Yield the molecule.
+ yield mol
Modified: branches/frame_order_cleanup/lib/structure/internal/molecules.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/molecules.py?rev=26387&r1=26386&r2=26387&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/molecules.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/molecules.py Thu
Oct 23 15:06:11 2014
@@ -453,7 +453,6 @@
"""Check if the container is empty."""
# Set attributes.
- if hasattr(self, 'mol_name'): return False
if hasattr(self, 'file_name'): return False
if hasattr(self, 'file_path'): return False
if hasattr(self, 'file_mol_num'): return False
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=26387&r1=26386&r2=26387&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Thu
Oct 23 15:06:11 2014
@@ -1622,6 +1622,17 @@
for k in range(len(mol.bonded[j])):
mol.bonded[j][k] -= 1
+ # Reset the metadata if nothing remains.
+ if mol.atom_num == []:
+ if hasattr(mol, 'file_name'):
+ del mol.file_name
+ if hasattr(mol, 'file_path'):
+ del mol.file_path
+ if hasattr(mol, 'file_mol_num'):
+ del mol.file_mol_num
+ if hasattr(mol, 'file_model'):
+ del mol.file_model
+
# Nothing more to do.
if not len(del_res_nums):
return
@@ -2628,7 +2639,7 @@
# Loop over the molecules of the first model.
index = 0
- for mol in self.structural_data[0].mol:
+ for mol in self.structural_data[0].mol_loop():
# Check the validity of the data.
self._validate_data_arrays(mol)
@@ -2816,7 +2827,7 @@
# Loop over the molecules.
index = 0
atom_serial = 0
- for mol in model.mol:
+ for mol in model.mol_loop():
# Print out.
print("ATOM, HETATM, TER")
@@ -2897,7 +2908,7 @@
# The per molecule incremented atom counts.
atom_counts = [0]
index = 0
- for mol in self.structural_data[0].mol:
+ for mol in self.structural_data[0].mol_loop():
if index == 0:
atom_counts.append(len(mol.atom_name))
else:
@@ -2906,7 +2917,7 @@
# Loop over the molecules of the first model.
index = 0
- for mol in self.structural_data[0].mol:
+ for mol in self.structural_data[0].mol_loop():
# Loop over the atoms.
for i in range(len(mol.atom_name)):
# No bonded atoms, hence no CONECT record is required.
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=26387&r1=26386&r2=26387&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/structure.py Thu
Oct 23 15:06:11 2014
@@ -377,6 +377,40 @@
# CoM.
self.assertRaises(RelaxNoPdbError, self.interpreter.structure.com)
+
+
+ def test_bug_22861_PDB_writing_chainID_fail(self):
+ """Catch U{bug #22861<https://gna.org/bugs/?22861>}, the chain IDs
in the structure.write_pdb user function PDB files are incorrect after
calling structure.delete."""
+
+ # Add one atom to two different molecules.
+ self.interpreter.structure.add_atom(mol_name='A', atom_name='N',
res_name='Phe', res_num=1, pos=[1.0, 1.0, 1.0], element='N')
+ self.interpreter.structure.add_atom(mol_name='B', atom_name='N',
res_name='Phe', res_num=1, pos=[1.0, 1.0, 1.0], element='N')
+
+ # Add some metadata to demonstrate a problem with the
structure.delete user function.
+ cdp.structure.structural_data[0].mol[0].file_name = 'test.pdb'
+ cdp.structure.structural_data[0].mol[1].file_name = 'test2.pdb'
+
+ # Delete the first molecule.
+ self.interpreter.structure.delete('#A')
+
+ # Create a PDB file.
+ file = DummyFileObject()
+ self.interpreter.structure.write_pdb(file=file, force=True)
+
+ # The file contents, without remarks, as they should be.
+ contents = [
+ "ATOM 1 N Phe A 1 1.000 1.000 1.000 1.00
0.00 N \n",
+ "TER 2 Phe A 1
\n",
+ "MASTER 0 0 0 0 0 0 0 0 1 1
0 0 \n",
+ "END
\n"
+ ]
+
+ # Check the created PDB file.
+ lines = file.readlines()
+ self.strip_remarks(lines)
+ self.assertEqual(len(contents), len(lines))
+ for i in range(len(lines)):
+ self.assertEqual(contents[i], lines[i])
def test_collapse_ensemble(self):
r26387 - in /branches/frame_order_cleanup: ./ lib/structure/internal/ test_suite/system_tests/