Author: bugman
Date: Wed Feb 13 16:44:09 2013
New Revision: 18466
URL: http://svn.gna.org/viewcvs/relax?rev=18466&view=rev
Log:
Merged revisions 18462-18465 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18462 | bugman | 2013-02-13 16:05:19 +0100 (Wed, 13 Feb 2013) | 3 lines
Created the Mol_res_spin.test_metadata_molecule_rename system test to
demonstrate a spin ID metadata bug.
........
r18463 | bugman | 2013-02-13 16:25:36 +0100 (Wed, 13 Feb 2013) | 14 lines
Reverted r18462 as the Mol_res_spin.test_metadata_molecule_rename system
test logic is rubbish.
The command used was:
svn merge -r18462:r18461 .
.....
r18462 | bugman | 2013-02-13 16:05:19 +0100 (Wed, 13 Feb 2013) | 3 lines
Changed paths:
M /trunk/test_suite/system_tests/mol_res_spin.py
Created the Mol_res_spin.test_metadata_molecule_rename system test to
demonstrate a spin ID metadata bug.
.....
........
r18464 | bugman | 2013-02-13 16:41:21 +0100 (Wed, 13 Feb 2013) | 6 lines
Created the Structure.test_load_spins_mol_cat system test.
This will be used to test a new 'mol_name_target' argument to the
structure.load_spins user
function.
........
r18465 | bugman | 2013-02-13 16:42:50 +0100 (Wed, 13 Feb 2013) | 6 lines
Added the mol_name_target argument to the structure.load_spins user
function.
This allows spins from different molecules to be placed together in the
same molecule container in
the relax data store.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/structure/main.py
branches/frame_order_testing/test_suite/system_tests/structure.py
branches/frame_order_testing/user_functions/structure.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Feb 13 16:44:09 2013
@@ -1,1 +1,1 @@
-/trunk:1-18459
+/trunk:1-18465
Modified: branches/frame_order_testing/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/main.py?rev=18466&r1=18465&r2=18466&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/main.py (original)
+++ branches/frame_order_testing/generic_fns/structure/main.py Wed Feb 13
16:44:09 2013
@@ -322,13 +322,15 @@
write_data(out=sys.stdout, headings=["Spin_ID", "Position"], data=data)
-def load_spins(spin_id=None, str_id=None, ave_pos=False):
+def load_spins(spin_id=None, str_id=None, mol_name_target=None,
ave_pos=False):
"""Load the spins from the structural object into the relax data store.
@keyword spin_id: The molecule, residue, and spin identifier
string.
@type spin_id: str
@keyword str_id: The structure identifier. This can be the
file name, model number, or structure number.
@type str_id: int or str
+ @keyword mol_name: The name of target molecule container,
overriding the name of the loaded structures
+ @type mol_name: str or None
@keyword ave_pos: A flag specifying if the average atom
position or the atom position from all loaded structures is loaded into the
SpinContainer.
@type ave_pos: bool
"""
@@ -352,6 +354,10 @@
# Loop over all atoms of the spin_id selection.
for mol_name, res_num, res_name, atom_num, atom_name, element, pos in
cdp.structure.atom_loop(atom_id=spin_id, str_id=str_id, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_num_flag=True,
atom_name_flag=True, element_flag=True, pos_flag=True, ave=ave_pos):
+ # Override the molecule name.
+ if mol_name_target:
+ mol_name = mol_name_target
+
# Remove the '+' regular expression character from the mol, res, and
spin names!
if mol_name and search('\+', mol_name):
mol_name = mol_name.replace('+', '')
@@ -371,12 +377,25 @@
except RelaxError:
spin_cont = return_spin(id)
+<<<<<<< .working
# Append all the spin ID info for printing later.
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(atom_num)
spin_names.append(atom_name)
+=======
+ # Append all the spin ID info for the first model for printing later.
+ if model_index == 0:
+ if mol_name_target:
+ mol_names.append(mol_name_target)
+ else:
+ mol_names.append(mol_name)
+ res_nums.append(res_num)
+ res_names.append(res_name)
+ spin_nums.append(atom_num)
+ spin_names.append(atom_name)
+>>>>>>> .merge-right.r18465
# Position vector.
spin_cont.pos = pos
Modified: branches/frame_order_testing/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/structure.py?rev=18466&r1=18465&r2=18466&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/structure.py Wed Feb
13 16:44:09 2013
@@ -184,6 +184,33 @@
self.assertAlmostEqual(cdp.structure.displacements._rotation_axis[models[i]][models[j]][k],
rot_axis[i][j][k])
+ def test_load_spins_mol_cat(self):
+ """Test the loading of spins from different molecules into one
molecule container."""
+
+ # Path of the files.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
+
+ # Read the PDBs.
+ self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, set_mol_name='L1', parser='internal')
+ self.interpreter.structure.read_pdb(file='lactose_MCMM4_S1_2.pdb',
dir=path, set_mol_name='L2', parser='internal')
+
+ # Load a few protons.
+ self.interpreter.structure.load_spins('#L1:900@C1',
mol_name_target='Lactose')
+ self.interpreter.structure.load_spins('#L2:900@C2',
mol_name_target='Lactose')
+
+ # Check the spin data.
+ self.assertEqual(len(cdp.mol), 1)
+ self.assertEqual(cdp.mol[0].name, 'Lactose')
+ self.assertEqual(len(cdp.mol[0].res), 1)
+ self.assertEqual(cdp.mol[0].res[0].name, 'UNK')
+ self.assertEqual(cdp.mol[0].res[0].num, 900)
+ self.assertEqual(len(cdp.mol[0].res[0].spin), 2)
+ self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'C1')
+ self.assertEqual(cdp.mol[0].res[0].spin[0].num, 1)
+ self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'C2')
+ self.assertEqual(cdp.mol[0].res[0].spin[1].num, 2)
+
+
def test_load_internal_results(self):
"""Load the PDB file using the information in a results file (using
the internal structural object)."""
Modified: branches/frame_order_testing/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/structure.py?rev=18466&r1=18465&r2=18466&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/structure.py (original)
+++ branches/frame_order_testing/user_functions/structure.py Wed Feb 13
16:44:09 2013
@@ -428,6 +428,12 @@
desc = "The spin identification string for the selective loading of
certain spins into the relax data store.",
wiz_combo_choices = ["@N", "@C", "@H", "@O", "@P", "@NE1", "@HE1",
":A@C2", ":A@C8", ":G@N1", ":G@C8", ":C@C5", ":C@C5", ":U@N3", ":U@C5",
":U@C6"],
can_be_none = True
+)
+uf.add_keyarg(
+ name = "mol_name_target",
+ py_type = "str",
+ desc_short = "target molecule name",
+ desc = "The name of target molecule container, overriding the name of
the loaded structures."
)
uf.add_keyarg(
name = "ave_pos",
r18466 - in /branches/frame_order_testing: ./ generic_fns/structure/ test_suite/system_tests/ user_functions/