Author: bugman
Date: Mon Dec 10 17:33:32 2012
New Revision: 18095
URL: http://svn.gna.org/viewcvs/relax?rev=18095&view=rev
Log:
Merged revisions 18087-18091 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18087 | bugman | 2012-12-10 15:11:12 +0100 (Mon, 10 Dec 2012) | 5 lines
Created the interatomic.copy and interatomic.create user functions.
This is simply new front ends for the user for the functions of
generic_fns.interatomic.
........
r18088 | bugman | 2012-12-10 15:12:10 +0100 (Mon, 10 Dec 2012) | 3 lines
The generic_fns.interatomic.copy() function now accepts spin IDs as
arguments to partially copy the data.
........
r18089 | bugman | 2012-12-10 17:20:45 +0100 (Mon, 10 Dec 2012) | 3 lines
Expanded the RelaxNoSpinError class to accept the data pipe name for the
error printout.
........
r18090 | bugman | 2012-12-10 17:29:16 +0100 (Mon, 10 Dec 2012) | 3 lines
Created the Interatomic.test_copy system test to check the interatomic.copy
user function.
........
r18091 | bugman | 2012-12-10 17:30:10 +0100 (Mon, 10 Dec 2012) | 3 lines
Fixes for the checks in the interatomic.copy user function backend.
........
Added:
branches/relax_disp/user_functions/interatomic.py
- copied unchanged from r18091, trunk/user_functions/interatomic.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/generic_fns/interatomic.py
branches/relax_disp/relax_errors.py
branches/relax_disp/test_suite/system_tests/interatomic.py
branches/relax_disp/user_functions/__init__.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Dec 10 17:33:32 2012
@@ -1,1 +1,1 @@
-/trunk:1-18081
+/trunk:1-18091
Modified: branches/relax_disp/generic_fns/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/interatomic.py?rev=18095&r1=18094&r2=18095&view=diff
==============================================================================
--- branches/relax_disp/generic_fns/interatomic.py (original)
+++ branches/relax_disp/generic_fns/interatomic.py Mon Dec 10 17:33:32 2012
@@ -29,19 +29,22 @@
# relax module imports.
from generic_fns import pipes
-from generic_fns.mol_res_spin import Selection, return_spin
-from relax_errors import RelaxError, RelaxInteratomError,
RelaxNoInteratomError
+from generic_fns.mol_res_spin import Selection, count_spins, return_spin
+from relax_errors import RelaxError, RelaxInteratomError,
RelaxNoInteratomError, RelaxNoSpinError
from relax_io import write_data
-from relax_warnings import RelaxNoSpinWarning
-
-
-def copy(pipe_from=None, pipe_to=None, verbose=True):
+
+
+def copy(pipe_from=None, pipe_to=None, spin_id1=None, spin_id2=None,
verbose=True):
"""Copy the interatomic data from one data pipe to another.
@keyword pipe_from: The data pipe to copy the interatomic data
from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the interatomic data
to. This defaults to the current data pipe.
@type pipe_to: str
+ @keyword spin_id1: The spin ID string of the first atom.
+ @type spin_id1: str
+ @keyword spin_id2: The spin ID string of the second atom.
+ @type spin_id2: str
@keyword verbose: A flag which if True will cause info about
each spin pair to be printed out.
@type verbose: bool
"""
@@ -58,17 +61,25 @@
pipes.test(pipe_from)
pipes.test(pipe_to)
+ # Check that the spin IDs exist.
+ if spin_id1:
+ if count_spins(selection=spin_id1, pipe=pipe_from, skip_desel=False)
== 0:
+ raise RelaxNoSpinError(spin_id1, pipe_from)
+ if count_spins(selection=spin_id1, pipe=pipe_to, skip_desel=False)
== 0:
+ raise RelaxNoSpinError(spin_id1, pipe_to)
+ if spin_id2:
+ if count_spins(selection=spin_id2, pipe=pipe_from, skip_desel=False)
== 0:
+ raise RelaxNoSpinError(spin_id2, pipe_from)
+ if count_spins(selection=spin_id2, pipe=pipe_to, skip_desel=False)
== 0:
+ raise RelaxNoSpinError(spin_id2, pipe_to)
+
# Test if pipe_from contains interatomic data (skipping the rest of the
function if it is missing).
if not exists_data(pipe_from):
return
- # Test if pipe_to contains interatomic data.
- if exists_data(pipe_to):
- raise RelaxInteratomError
-
# Loop over the interatomic data of the pipe_from data pipe.
ids = []
- for interatom in interatomic_loop(pipe=pipe_from):
+ for interatom in interatomic_loop(selection1=spin_id1,
selection2=spin_id2, pipe=pipe_from):
# Create a new container.
new_interatom = create_interatom(spin_id1=interatom.spin_id1,
spin_id2=interatom.spin_id2, pipe=pipe_to)
@@ -103,7 +114,7 @@
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
- @keyword spin_id2: The spin ID string of the first atom.
+ @keyword spin_id2: The spin ID string of the second atom.
@type spin_id2: str
@keyword pipe: The data pipe to create the interatomic data
container for. This defaults to the current data pipe if not supplied.
@type pipe: str or None
Modified: branches/relax_disp/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/relax_errors.py?rev=18095&r1=18094&r2=18095&view=diff
==============================================================================
--- branches/relax_disp/relax_errors.py (original)
+++ branches/relax_disp/relax_errors.py Mon Dec 10 17:33:32 2012
@@ -672,8 +672,11 @@
# Cannot find the spin in the sequence.
class RelaxNoSpinError(BaseError):
- def __init__(self, id):
- self.text = "The spin " + repr(id) + " does not exist."
+ def __init__(self, id, pipe=None):
+ if pipe == None:
+ self.text = "The spin '%s' does not exist." % id
+ else:
+ self.text = "The spin '%s' does not exist in the '%s' data
pipe." % (id, pipe)
# The sequence data is not valid.
class RelaxInvalidSeqError(BaseError):
Modified: branches/relax_disp/test_suite/system_tests/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/interatomic.py?rev=18095&r1=18094&r2=18095&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/interatomic.py (original)
+++ branches/relax_disp/test_suite/system_tests/interatomic.py Mon Dec 10
17:33:32 2012
@@ -35,6 +35,55 @@
class Interatomic(SystemTestCase):
"""Class for testing the interatomic functions."""
+ def test_copy(self):
+ """Test the operation of the interatomic.copy user function."""
+
+ # Create an initial data pipe.
+ self.interpreter.pipe.create(pipe_name="orig", pipe_type='N-state')
+
+ # Create some sequence data.
+ self.interpreter.molecule.create(mol_name='Test mol')
+ self.interpreter.residue.create(mol_name='Test mol', res_name='His',
res_num=1)
+ self.interpreter.residue.create(mol_name='Test mol', res_name='His',
res_num=2)
+ self.interpreter.spin.create(res_num=1, spin_name='N')
+ self.interpreter.spin.create(res_num=1, spin_name='H')
+ self.interpreter.spin.create(res_num=2, spin_name='N')
+ self.interpreter.spin.create(res_num=2, spin_name='H')
+
+ # Define the interatomic interaction.
+ self.interpreter.interatomic.create(spin_id1=':1@N', spin_id2=':1@H')
+ self.interpreter.interatomic.create(spin_id1=':2@N', spin_id2=':2@H')
+
+ # Add some test data.
+ cdp.interatomic[0].x = 1
+ cdp.interatomic[1].y = 2
+
+ # Create a new data pipe to copy the data to.
+ self.interpreter.pipe.create(pipe_name="new", pipe_type='N-state')
+
+ # Copy the data.
+ self.interpreter.sequence.copy(pipe_from='orig')
+ self.interpreter.interatomic.copy(pipe_from='orig', spin_id1=':2@N',
spin_id2=':2@H')
+ self.interpreter.interatomic.copy(pipe_from='orig', spin_id1=':1@H',
spin_id2=':1@N')
+
+ # Check the sequence data.
+ self.assertEqual(cdp.mol[0].name, 'Test mol')
+ self.assertEqual(cdp.mol[0].res[0].name, 'His')
+ self.assertEqual(cdp.mol[0].res[0].spin[0].name, 'N')
+ self.assertEqual(cdp.mol[0].res[0].spin[1].name, 'H')
+ self.assertEqual(cdp.mol[0].res[1].name, 'His')
+ self.assertEqual(cdp.mol[0].res[1].spin[0].name, 'N')
+ self.assertEqual(cdp.mol[0].res[1].spin[1].name, 'H')
+
+ # Check the interatomic data.
+ self.assertEqual(cdp.interatomic[0].spin_id1, ':2@N')
+ self.assertEqual(cdp.interatomic[0].spin_id2, ':2@H')
+ self.assertEqual(cdp.interatomic[0].y, 2)
+ self.assertEqual(cdp.interatomic[1].spin_id1, ':1@N')
+ self.assertEqual(cdp.interatomic[1].spin_id2, ':1@H')
+ self.assertEqual(cdp.interatomic[1].x, 1)
+
+
def test_manipulation(self):
"""Test the manipulation of interatomic data containers."""
Modified: branches/relax_disp/user_functions/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/__init__.py?rev=18095&r1=18094&r2=18095&view=diff
==============================================================================
--- branches/relax_disp/user_functions/__init__.py (original)
+++ branches/relax_disp/user_functions/__init__.py Mon Dec 10 17:33:32 2012
@@ -48,6 +48,7 @@
'frame_order',
'frq',
'grace',
+ 'interatomic',
'jw_mapping',
'minimisation',
'model_free',
@@ -97,6 +98,7 @@
import user_functions.frame_order
import user_functions.frq
import user_functions.grace
+import user_functions.interatomic
import user_functions.jw_mapping
import user_functions.minimisation
import user_functions.model_free
r18095 - in /branches/relax_disp: ./ generic_fns/ test_suite/system_tests/ user_functions/