Author: bugman
Date: Tue Apr 28 14:03:25 2009
New Revision: 9018
URL: http://svn.gna.org/viewcvs/relax?rev=9018&view=rev
Log:
Merged revisions 9015-9017 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9015 | bugman | 2009-04-27 15:26:25 +0200 (Mon, 27 Apr 2009) | 5 lines
Bug fix.
The PyMOL code was failing because of the new design of the structural data
object.
........
r9016 | bugman | 2009-04-28 13:47:51 +0200 (Tue, 28 Apr 2009) | 3 lines
Added a catch for bug #13442 (https://gna.org/bugs/index.php?13442) to the
test suite.
........
r9017 | bugman | 2009-04-28 14:02:02 +0200 (Tue, 28 Apr 2009) | 6 lines
Fix for bug #13442 (https://gna.org/bugs/index.php?13442).
The problem was that global minimisation objects were being accessed when
the do not exist. These
are now skipped.
........
Modified:
branches/ave_noe/ (props changed)
branches/ave_noe/generic_fns/pymol.py
branches/ave_noe/specific_fns/model_free/main.py
branches/ave_noe/test_suite/system_tests/model_free.py
Propchange: branches/ave_noe/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Apr 28 14:03:25 2009
@@ -1,1 +1,1 @@
-/1.3:1-9011
+/1.3:1-9017
Modified: branches/ave_noe/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/pymol.py?rev=9018&r1=9017&r2=9018&view=diff
==============================================================================
--- branches/ave_noe/generic_fns/pymol.py (original)
+++ branches/ave_noe/generic_fns/pymol.py Tue Apr 28 14:03:25 2009
@@ -71,14 +71,23 @@
self.pipe_write("reinitialize")
# Open the PDB files.
- for i in xrange(cdp.structure.num):
- # The file path.
- file = cdp.structure.file[i]
- if cdp.structure.path[i]:
- file = cdp.structure.path[i] + sep + file
-
- # Open the file in PyMOL.
- self.pipe_write("load " + file)
+ open_files = []
+ for model in cdp.structure.structural_data:
+ for mol in model.mol:
+ # The file path.
+ file = mol.file_name
+ if mol.file_path:
+ file = mol.file_path + sep + file
+
+ # Already loaded.
+ if file in open_files:
+ continue
+
+ # Open the file in PyMOL.
+ self.pipe_write("load " + file)
+
+ # Add to the open file list.
+ open_files.append(file)
def pipe_open(self):
@@ -155,21 +164,30 @@
cdp = pipes.get_pipe()
# Loop over the PDB files.
- for i in xrange(cdp.structure.num):
- # Identifier.
- pdb_file = cdp.structure.file[i]
- if cdp.structure.path[i]:
- pdb_file = cdp.structure.path[i] + sep + pdb_file
- id = file_root(pdb_file)
-
- # Hide everything.
- pymol.pipe_write("cmd.hide('everything'," + `id` + ")")
-
- # Show the cartoon style.
- pymol.pipe_write("cmd.show('cartoon'," + `id` + ")")
-
- # Colour by secondary structure.
- pymol.pipe_write("util.cbss(" + `id` + ", 'red', 'yellow', 'green')")
+ open_files = []
+ for model in cdp.structure.structural_data:
+ for mol in model.mol:
+ # Identifier.
+ pdb_file = mol.file_name
+ if mol.file_path:
+ pdb_file = mol.file_path + sep + pdb_file
+ id = file_root(pdb_file)
+
+ # Already loaded.
+ if file in open_files:
+ continue
+
+ # Add to the open file list.
+ open_files.append(file)
+
+ # Hide everything.
+ pymol.pipe_write("cmd.hide('everything'," + `id` + ")")
+
+ # Show the cartoon style.
+ pymol.pipe_write("cmd.show('cartoon'," + `id` + ")")
+
+ # Colour by secondary structure.
+ pymol.pipe_write("util.cbss(" + `id` + ", 'red', 'yellow',
'green')")
def command(command):
Modified: branches/ave_noe/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/model_free/main.py?rev=9018&r1=9017&r2=9018&view=diff
==============================================================================
--- branches/ave_noe/specific_fns/model_free/main.py (original)
+++ branches/ave_noe/specific_fns/model_free/main.py Tue Apr 28 14:03:25 2009
@@ -2971,6 +2971,10 @@
# Loop over the global minimisation stats objects.
for object_name in min_names:
+ # Skip non-existent objects.
+ if not hasattr(cdp, object_name):
+ continue
+
# Name for the simulation object.
sim_object_name = object_name + '_sim'
Modified: branches/ave_noe/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/test_suite/system_tests/model_free.py?rev=9018&r1=9017&r2=9018&view=diff
==============================================================================
--- branches/ave_noe/test_suite/system_tests/model_free.py (original)
+++ branches/ave_noe/test_suite/system_tests/model_free.py Tue Apr 28
14:03:25 2009
@@ -109,6 +109,18 @@
return string
+ def monte_carlo(self):
+ """Run Monte Carlo simulations for the optimised model-free model."""
+
+ # Monte Carlo simulations.
+ self.relax.interpreter._Monte_carlo.setup(number=3)
+ self.relax.interpreter._Monte_carlo.create_data()
+ self.relax.interpreter._Monte_carlo.initial_values()
+ self.relax.interpreter._Minimise('newton')
+ self.relax.interpreter._Eliminate()
+ self.relax.interpreter._Monte_carlo.error_analysis()
+
+
def object_comparison(self, obj1=None, obj2=None, skip=None):
"""Check if the contents of 2 objects are the same."""
@@ -559,6 +571,9 @@
# Minimise.
self.relax.interpreter._Minimisation.minimise('newton', 'gmw', 'mt')
+
+ # Monte Carlo simulations.
+ self.monte_carlo()
# Alias the relevent spin container.
spin = cdp.mol[0].res[1].spin[0]
r9018 - in /branches/ave_noe: ./ generic_fns/pymol.py specific_fns/model_free/main.py test_suite/system_tests/model_free.py