Author: bugman
Date: Mon Sep 22 10:30:44 2014
New Revision: 25946
URL: http://svn.gna.org/viewcvs/relax?rev=25946&view=rev
Log:
Merged revisions 25942-25945 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25942 | bugman | 2014-09-22 09:59:35 +0200 (Mon, 22 Sep 2014) | 6 lines
Created the Structure.test_collapse_ensemble system test.
This is used to test a planned feature of the internal structural object.
The collapse_ensemble()
method will be created to remove all but one model in the structural
ensemble.
........
r25943 | bugman | 2014-09-22 10:14:25 +0200 (Mon, 22 Sep 2014) | 5 lines
Fixes for the structure.add_atom user function to allow for list of lists
for the atomic position.
This allows different coordinates to be supplied for each model.
........
r25944 | bugman | 2014-09-22 10:16:35 +0200 (Mon, 22 Sep 2014) | 5 lines
Modified the Structure.test_collapse_ensemble system test to check the
initial values.
This is for sanity reasons as the test coverage of the structure.add_atom
user function is poor.
........
r25945 | bugman | 2014-09-22 10:29:55 +0200 (Mon, 22 Sep 2014) | 5 lines
Implemented the internal structural object collapse_ensemble() method.
This allows the Structure.test_collapse_ensemble system test to pass.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/user_functions/structure.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Sep 22 10:30:44 2014
@@ -1 +1 @@
-/trunk:1-25940
+/trunk:1-25945
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=25946&r1=25945&r2=25946&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Mon
Sep 22 10:30:44 2014
@@ -1488,6 +1488,29 @@
return data
+ def collapse_ensemble(self, model_num=None, model_to=1):
+ """Collapse the ensemble into a single model.
+
+ @keyword model_num: The number of the model to keep. All other
models will be removed.
+ @type model_num: int
+ @keyword model_to: The model number for the sole remaining model.
+ @type model_to: int
+ """
+
+ # Store all the model numbers.
+ models = []
+ for model_cont in self.model_loop():
+ if model_cont.num != model_num:
+ models.append(model_cont.num)
+
+ # Delete all models.
+ for model in models:
+ self.delete(model)
+
+ # Renumber the remaining model.
+ self.set_model(model_orig=model_num, model_new=model_to)
+
+
def connect_atom(self, mol_name=None, index1=None, index2=None):
"""Connect two atoms in the structural data object.
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=25946&r1=25945&r2=25946&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/structure.py Mon
Sep 22 10:30:44 2014
@@ -243,6 +243,41 @@
# Superimpose.
self.interpreter.structure.superimpose(method='fit to first',
centre_type='CoM')
+
+
+ def test_collapse_ensemble(self):
+ """Test the collapse_ensemble() method of the internal structural
object."""
+
+ # Create 2 models.
+ self.interpreter.structure.add_model(model_num=1)
+ self.interpreter.structure.add_model(model_num=2)
+
+ # Add an atom.
+ self.interpreter.structure.add_atom(atom_name='H', res_name='Gly',
res_num=1, pos=[[0.0, 1.0, 2.0], [1.0, 2.0, 3.0]], element='H')
+
+ # Check the atomic data.
+ for i in range(2):
+ mol = cdp.structure.structural_data[i].mol[0]
+ self.assertEqual(len(mol.atom_name), 1)
+ self.assertEqual(mol.x[0], 0.0+i)
+ self.assertEqual(mol.y[0], 1.0+i)
+ self.assertEqual(mol.z[0], 2.0+i)
+
+ # Collapse the ensemble to the 2nd model.
+ cdp.structure.collapse_ensemble(model_num=2, model_to=1)
+
+ # Check the collapsed ensemble.
+ self.assert_(hasattr(cdp, 'structure'))
+ self.assertEqual(len(cdp.structure.structural_data), 1)
+ self.assertEqual(cdp.structure.structural_data[0].num, 1)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 1)
+
+ # Check the atomic data.
+ mol = cdp.structure.structural_data[0].mol[0]
+ self.assertEqual(len(mol.atom_name), 1)
+ self.assertEqual(mol.x[0], 1.0)
+ self.assertEqual(mol.y[0], 2.0)
+ self.assertEqual(mol.z[0], 3.0)
def test_create_diff_tensor_pdb(self):
Modified: branches/frame_order_cleanup/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=25946&r1=25945&r2=25946&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/structure.py (original)
+++ branches/frame_order_cleanup/user_functions/structure.py Mon Sep 22
10:30:44 2014
@@ -76,9 +76,8 @@
uf.add_keyarg(
name = "pos",
py_type = "float_object",
- dim = 3,
desc_short = "atomic position",
- desc = "The atomic coordinates.",
+ desc = "The atomic coordinates. For specifying different coordinates
for each model of the ensemble, a list of lists can be supplied.",
list_titles = ['X coordinate', 'Y coordinate', 'Z coordinate']
)
uf.add_keyarg(
r25946 - in /branches/frame_order_cleanup: ./ lib/structure/internal/ test_suite/system_tests/ user_functions/