Author: semor
Date: Fri Apr 17 17:45:55 2009
New Revision: 9014
URL: http://svn.gna.org/viewcvs/relax?rev=9014&view=rev
Log:
Merged revisions 8997-9003,9010-9011 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r8997 | bugman | 2009-03-25 16:49:55 -0400 (Wed, 25 Mar 2009) | 5 lines
Modified the model elimination print out to show the data pipe name.
This was picked up while trying to debug bug #13259
(https://gna.org/bugs/index.php?13259).
........
r8998 | bugman | 2009-03-25 17:26:06 -0400 (Wed, 25 Mar 2009) | 3 lines
Clean up of the model_loop() checking.
........
r8999 | bugman | 2009-03-25 17:42:30 -0400 (Wed, 25 Mar 2009) | 6 lines
Removed the check for spin selection so that determine_model_type() works
with nothing selected.
This is a partial response to bug #13259
(https://gna.org/bugs/index.php?13259) reported by
Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca).
........
r9000 | bugman | 2009-03-25 19:21:17 -0400 (Wed, 25 Mar 2009) | 3 lines
Fixes for the MC sim methods for deselected spins.
........
r9001 | bugman | 2009-03-25 19:42:14 -0400 (Wed, 25 Mar 2009) | 5 lines
Modified the structure.vectors() user function to fail if no vectors are
found.
This saves a lot of sanity when debugging a user script which fails.
........
r9002 | bugman | 2009-03-26 10:10:14 -0400 (Thu, 26 Mar 2009) | 7 lines
Bug fix for bug #13259 (https://gna.org/bugs/index.php?13259).
This bug was reported by Pierre-Yves Savard (pierre-yves dot savard att bcm
dot ulaval dot ca).
The bug may not be completely gone yet.
........
r9003 | bugman | 2009-03-26 11:40:57 -0400 (Thu, 26 Mar 2009) | 6 lines
Fix for the regression of bug #12607 (https://gna.org/bugs/?12607).
The determine_model_type() method now handles the strange case where no
spins are selected
(gracefully).
........
r9010 | bugman | 2009-04-15 08:33:53 -0400 (Wed, 15 Apr 2009) | 5 lines
Expanded the test_read_pdb_internal3() and test_read_pdb_scientific3()
system tests.
Now the reading of atomic positions from different models is tested.
........
r9011 | bugman | 2009-04-15 09:28:15 -0400 (Wed, 15 Apr 2009) | 6 lines
Removed a test in load_spins() causing a bug.
This test is totally unnecessary as the structures are not created if they
already exist. This was
causing only the position from the first model to be extracted, if ave_pos
was False.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/generic_fns/model_selection.py
branches/relax_disp/generic_fns/structure/main.py
branches/relax_disp/sample_scripts/full_analysis.py
branches/relax_disp/specific_fns/model_free/main.py
branches/relax_disp/test_suite/system_tests/structure.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Apr 17 17:45:55 2009
@@ -1,1 +1,1 @@
-/1.3:1-8990
+/1.3:1-9013
Modified: branches/relax_disp/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/model_selection.py?rev=9014&r1=9013&r2=9014&view=diff
==============================================================================
--- branches/relax_disp/generic_fns/model_selection.py (original)
+++ branches/relax_disp/generic_fns/model_selection.py Fri Apr 17 17:45:55
2009
@@ -196,10 +196,9 @@
model_statistics[pipes[i]] = get_specific_fn('model_stats',
get_type(pipes[i]))
skip_function[pipes[i]] = get_specific_fn('skip_function',
get_type(pipes[i]))
- # The model loop should be the same for all data pipes!
- for j in xrange(len(pipes)):
- if model_loop[pipes[0]] != model_loop[pipes[j]]:
- raise RelaxError, "The models for each data pipes should be
the same."
+ # The model loop should be the same for all data pipes!
+ if model_loop[pipes[0]] != model_loop[pipes[i]]:
+ raise RelaxError, "Bug: The model loop for each data pipes
should be the same!"
model_loop = model_loop[pipes[0]]
# The model description.
Modified: branches/relax_disp/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/main.py?rev=9014&r1=9013&r2=9014&view=diff
==============================================================================
--- branches/relax_disp/generic_fns/structure/main.py (original)
+++ branches/relax_disp/generic_fns/structure/main.py Fri Apr 17 17:45:55 2009
@@ -80,10 +80,6 @@
if last_model != model_num:
model_index = model_index + 1
last_model = model_num
-
- # Only load one set of spins if combine_models is set.
- if combine_models and model_index >= 1:
- break
# Remove the '+' regular expression character from the mol, res, and
spin names!
if mol_name and search('\+', mol_name):
@@ -340,6 +336,7 @@
object_name = 'bond_vect'
# Loop over the spins.
+ no_vectors = True
for spin, mol_name, res_num, res_name in spin_loop(selection=spin_id,
full_info=True):
# Skip deselected spins.
if not spin.select:
@@ -410,9 +407,16 @@
# Set the vector.
setattr(spin, object_name, vector)
+ # We have a vector!
+ no_vectors = False
+
# Print out of modified spins.
if verbosity:
print "Extracted " + spin.name + "-" + attached_name + " vectors
for " + `id` + '.'
+
+ # Right, catch the problem of missing vectors to prevent massive user
confusion!
+ if no_vectors:
+ raise RelaxError, "No vectors could be extracted."
def write_pdb(file=None, dir=None, model_num=None, force=False):
Modified: branches/relax_disp/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/sample_scripts/full_analysis.py?rev=9014&r1=9013&r2=9014&view=diff
==============================================================================
--- branches/relax_disp/sample_scripts/full_analysis.py (original)
+++ branches/relax_disp/sample_scripts/full_analysis.py Fri Apr 17 17:45:55
2009
@@ -297,7 +297,7 @@
self.multi_model()
# Model selection.
- self.model_selection(modsel_pipe='final',
dir=self.base_dir + 'aic')
+ self.model_selection(modsel_pipe='aic',
dir=self.base_dir + 'aic')
# Final optimisation of all diffusion and model-free
parameters.
fix('all', fixed=False)
Modified: branches/relax_disp/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/model_free/main.py?rev=9014&r1=9013&r2=9014&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/model_free/main.py (original)
+++ branches/relax_disp/specific_fns/model_free/main.py Fri Apr 17 17:45:55
2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2008 Edward d'Auvergne
#
+# Copyright (C) 2003-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -992,10 +992,14 @@
# Check if any model-free parameters are allowed to vary.
mf_all_fixed = True
+ mf_all_deselected = True
for spin in spin_loop():
# Skip deselected spins.
if not spin.select:
continue
+
+ # At least one spin is selected.
+ mf_all_deselected = False
# Test the fixed flag.
if not hasattr(spin, 'fixed'):
@@ -1004,6 +1008,14 @@
if not spin.fixed:
mf_all_fixed = False
break
+
+ # No spins selected?!?
+ if mf_all_deselected:
+ # All parameters fixed!
+ if cdp.diff_tensor.fixed:
+ raise RelaxError, "All parameters are fixed."
+
+ return 'diff'
# Local tm.
if local_tm:
@@ -1254,17 +1266,17 @@
# Local tm.
if name == 'local_tm' and value >= c1:
if sim == None:
- print "The local tm parameter of %.5g is greater than %.5g,
eliminating spin system '%s'." % (value, c1, spin_id)
+ print "Data pipe '%s': The local tm parameter of %.5g is
greater than %.5g, eliminating spin system '%s'." % (pipes.cdp_name(), value,
c1, spin_id)
else:
- print "The local tm parameter of %.5g is greater than %.5g,
eliminating simulation %i of spin system '%s'." % (value, c1, sim, spin_id)
+ print "Data pipe '%s': The local tm parameter of %.5g is
greater than %.5g, eliminating simulation %i of spin system '%s'." %
(pipes.cdp_name(), value, c1, sim, spin_id)
return True
# Internal correlation times.
if match('t[efs]', name) and value >= c2 * tm:
if sim == None:
- print "The %s value of %.5g is greater than %.5g,
eliminating spin system '%s'." % (name, value, c2*tm, spin_id)
+ print "Data pipe '%s': The %s value of %.5g is greater than
%.5g, eliminating spin system '%s'." % (pipes.cdp_name(), name, value, c2*tm,
spin_id)
else:
- print "The %s value of %.5g is greater than %.5g,
eliminating simulation %i of spin system '%s'." % (name, value, c2*tm, sim,
spin_id)
+ print "Data pipe '%s': The %s value of %.5g is greater than
%.5g, eliminating simulation %i of spin system '%s'." % (pipes.cdp_name(),
name, value, c2*tm, sim, spin_id)
return True
# Accept model.
@@ -1786,10 +1798,6 @@
for spin in spin_loop():
# Increment the global spin index.
global_index = global_index + 1
-
- # Skip deselected spins.
- if not spin.select:
- continue
# Yield the spin index.
yield global_index
@@ -2857,6 +2865,10 @@
# Get the spin container.
spin = return_spin_from_index(model_index)
+ # Skip if deselected.
+ if not spin.select:
+ return
+
# Set the simulation flags.
spin.select_sim = deepcopy(select_sim)
@@ -3227,6 +3239,10 @@
# Get the spin container.
spin = return_spin_from_index(model_index)
+ # Skip if deselected.
+ if not spin.select:
+ return
+
# Return the list.
return spin.select_sim
Modified: branches/relax_disp/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/structure.py?rev=9014&r1=9013&r2=9014&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/structure.py (original)
+++ branches/relax_disp/test_suite/system_tests/structure.py Fri Apr 17
17:45:55 2009
@@ -200,14 +200,20 @@
def test_read_pdb_internal3(self):
"""Load the 'gromacs_phthalic_acid.pdb' PDB file (using the internal
structural object PDB reader)."""
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
# Path of the files.
path = sys.path[-1] + '/test_suite/shared_data/structures'
# Read the PDB.
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='internal')
- # Try loading a few protons.
- self.relax.interpreter._Structure.load_spins('@*H*')
+ # Try loading a few protons, without positions averaging across
models.
+ self.relax.interpreter._Structure.load_spins('@*H*', ave_pos=False)
+
+ # A test.
+ self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2)
# And now all the rest of the atoms.
self.relax.interpreter._Structure.load_spins()
@@ -443,6 +449,9 @@
def test_read_pdb_scientific3(self):
"""Load the 'gromacs_phthalic_acid.pdb' PDB file (using the
Scientific python structural object PDB reader)."""
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
# Path of the files.
path = sys.path[-1] + '/test_suite/shared_data/structures'
@@ -450,7 +459,10 @@
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific')
# Try loading a few protons.
- self.relax.interpreter._Structure.load_spins('@*H*')
+ self.relax.interpreter._Structure.load_spins('@*H*', ave_pos=False)
+
+ # A test.
+ self.assertEqual(len(cdp.mol[0].res[0].spin[0].pos), 2)
# And now all the rest of the atoms.
self.relax.interpreter._Structure.load_spins()
r9014 - in /branches/relax_disp: ./ generic_fns/ generic_fns/structure/ sample_scripts/ specific_fns/model_free/ test_suite/...