Author: bugman
Date: Thu Feb 19 14:19:02 2015
New Revision: 27666
URL: http://svn.gna.org/viewcvs/relax?rev=27666&view=rev
Log:
Merged revisions 27661-27662,27664 via svnmerge from
svn+ssh://bug...@svn.gna.org/svn/relax/trunk
........
r27661 | bugman | 2015-02-17 16:27:20 +0100 (Tue, 17 Feb 2015) | 6 lines
Added some error checking for the monte_carlo.setup user function.
A RelaxError is now raised if the number of simulations is less than 3. This
prevents Python errors
when later calling the monte_carlo.error_analysis user function.
........
r27662 | bugman | 2015-02-17 16:48:45 +0100 (Tue, 17 Feb 2015) | 6 lines
Test suite fixes for the error checking in the monte_carlo.setup user
function.
The number of simulations has been increased from either 1 or 2 in all tests
to the minimal number
of simulations (3).
........
r27664 | bugman | 2015-02-18 17:55:35 +0100 (Wed, 18 Feb 2015) | 3 lines
Small fix for the structure.write_pdb user function for handling old relax
state and results files.
........
Modified:
branches/nmrglue/ (props changed)
branches/nmrglue/lib/structure/internal/object.py
branches/nmrglue/pipe_control/error_analysis.py
branches/nmrglue/test_suite/gui_tests/model_free.py
branches/nmrglue/test_suite/system_tests/relax_disp.py
branches/nmrglue/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
branches/nmrglue/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
branches/nmrglue/test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py
Propchange: branches/nmrglue/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Feb 19 14:19:02 2015
@@ -1 +1 @@
-/trunk:1-27659
+/trunk:1-27665
Modified: branches/nmrglue/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/structure/internal/object.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
--- branches/nmrglue/lib/structure/internal/object.py (original)
+++ branches/nmrglue/lib/structure/internal/object.py Thu Feb 19 14:19:02 2015
@@ -2970,6 +2970,12 @@
# Loop over and unpack the helix data.
index = 1
for helix_id, mol_init_index, init_res_name, init_seq_num,
mol_end_index, end_res_name, end_seq_num, helix_class, length in self.helices:
+ # The chain IDs.
+ if mol_init_index == None:
+ mol_init_index = 0
+ if mol_end_index == None:
+ mol_end_index = 0
+
pdb_write.helix(file, ser_num=index, helix_id=helix_id,
init_chain_id=CHAIN_ID_LIST[mol_init_index], init_res_name=init_res_name,
init_seq_num=init_seq_num, end_chain_id=CHAIN_ID_LIST[mol_end_index],
end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class,
length=length)
index += 1
@@ -2984,6 +2990,10 @@
index = 1
for strand, sheet_id, num_strands, init_res_name, mol_init_index,
init_seq_num, init_icode, end_res_name, mol_end_index, end_seq_num, end_icode,
sense, cur_atom, cur_res_name, mol_cur_index, cur_res_seq, cur_icode,
prev_atom, prev_res_name, mol_prev_index, prev_res_seq, prev_icode in
self.sheets:
# Translate molecule indices to chain IDs.
+ if mol_init_index == None:
+ mol_init_index = 0
+ if mol_end_index == None:
+ mol_end_index = 0
init_chain_id = CHAIN_ID_LIST[mol_init_index]
end_chain_id = CHAIN_ID_LIST[mol_end_index]
cur_chain_id = None
Modified: branches/nmrglue/pipe_control/error_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/pipe_control/error_analysis.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
--- branches/nmrglue/pipe_control/error_analysis.py (original)
+++ branches/nmrglue/pipe_control/error_analysis.py Thu Feb 19 14:19:02 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2004-2014 Edward d'Auvergne #
+# Copyright (C) 2004-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -362,18 +362,20 @@
def monte_carlo_setup(number=None, all_select_sim=None):
- """Function for setting up Monte Carlo simulations.
+ """Store the Monte Carlo simulation number.
@keyword number: The number of Monte Carlo simulations to set
up.
@type number: int
- @keyword all_select_sim: The selection status of the Monte Carlo
simulations. The first
- dimension of this matrix corresponds to the
simulation and the
- second corresponds to the instance.
+ @keyword all_select_sim: The selection status of the Monte Carlo
simulations. The first dimension of this matrix corresponds to the simulation
and the second corresponds to the instance.
@type all_select_sim: list of lists of bool
"""
# Test if the current data pipe exists.
check_pipe()
+
+ # Check the value.
+ if number < 3:
+ raise RelaxError("A minimum of 3 Monte Carlo simulations is required.")
# Create a number of MC sim data structures.
cdp.sim_number = number
Modified: branches/nmrglue/test_suite/gui_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/gui_tests/model_free.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
--- branches/nmrglue/test_suite/gui_tests/model_free.py (original)
+++ branches/nmrglue/test_suite/gui_tests/model_free.py Thu Feb 19 14:19:02 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2006-2014 Edward d'Auvergne #
+# Copyright (C) 2006-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -132,7 +132,7 @@
analysis.data.diff_tensor_grid_inc = {'sphere': 5, 'prolate': 5,
'oblate': 5, 'ellipsoid': 3}
# Set the number of Monte Carlo simulations.
- analysis.mc_sim_num.SetValue(2)
+ analysis.mc_sim_num.SetValue(3)
# Set the maximum number of iterations (changing the allowed values).
analysis.max_iter.control.SetRange(0, 100)
@@ -344,7 +344,7 @@
analysis.data.diff_tensor_grid_inc = {'sphere': 5, 'prolate': 5,
'oblate': 5, 'ellipsoid': 3}
# Set the number of Monte Carlo simulations.
- analysis.mc_sim_num.SetValue(2)
+ analysis.mc_sim_num.SetValue(3)
# Set the maximum number of iterations (changing the allowed values).
analysis.max_iter.control.SetRange(0, 100)
@@ -360,7 +360,7 @@
self.assertEqual(analysis.data.local_tm_models, ['tm0', 'tm1'])
self.assertEqual(analysis.data.mf_models, ['m1', 'm2'])
self.assertEqual(analysis.data.grid_inc, 3)
- self.assertEqual(analysis.data.mc_sim_num, 2)
+ self.assertEqual(analysis.data.mc_sim_num, 3)
self.assertEqual(analysis.data.max_iter, 1)
self.assertEqual(analysis.data.diff_tensor_grid_inc['sphere'], 5)
self.assertEqual(analysis.data.diff_tensor_grid_inc['prolate'], 5)
Modified: branches/nmrglue/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/relax_disp.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/relax_disp.py (original)
+++ branches/nmrglue/test_suite/system_tests/relax_disp.py Thu Feb 19
14:19:02 2015
@@ -1344,7 +1344,7 @@
pre_run_dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'bug_21715_clustered_indexerror'+sep+'non_clustered'
relax_disp.Relax_disp.opt_func_tol = 1e-5
relax_disp.Relax_disp.opt_max_iterations = 1000
- relax_disp.Relax_disp(pipe_name='origin - relax_disp (Sun Feb 23
19:36:51 2014)', pipe_bundle='relax_disp (Sun Feb 23 19:36:51 2014)',
results_dir=self.tmpdir, models=['R2eff', 'No Rex'], grid_inc=11, mc_sim_num=2,
modsel='AIC', pre_run_dir=pre_run_dir, insignificance=1.0, numeric_only=True,
mc_sim_all_models=False, eliminate=True)
+ relax_disp.Relax_disp(pipe_name='origin - relax_disp (Sun Feb 23
19:36:51 2014)', pipe_bundle='relax_disp (Sun Feb 23 19:36:51 2014)',
results_dir=self.tmpdir, models=['R2eff', 'No Rex'], grid_inc=11, mc_sim_num=3,
modsel='AIC', pre_run_dir=pre_run_dir, insignificance=1.0, numeric_only=True,
mc_sim_all_models=False, eliminate=True)
def test_bug_22146_unpacking_r2a_r2b_cluster_B14(self):
@@ -5057,7 +5057,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5129,7 +5129,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5199,7 +5199,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5269,7 +5269,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5341,7 +5341,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=100)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5411,7 +5411,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=1000)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
@@ -5508,7 +5508,7 @@
self.interpreter.minimise.execute(min_algor='simplex', func_tol=1e-05,
max_iter=10)
# Monte Carlo simulations.
- self.interpreter.monte_carlo.setup(number=2)
+ self.interpreter.monte_carlo.setup(number=3)
self.interpreter.monte_carlo.create_data(method='back_calc')
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_algor='simplex', max_iter=10)
Modified:
branches/nmrglue/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
---
branches/nmrglue/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
(original)
+++
branches/nmrglue/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
Thu Feb 19 14:19:02 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2004-2013 Edward d'Auvergne #
+# Copyright (C) 2004-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -165,7 +165,7 @@
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
-MC_NUM = 2
+MC_NUM = 3
# Automatic looping over all rounds until convergence (must be a boolean value
of True or False).
CONV_LOOP = True
Modified:
branches/nmrglue/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
---
branches/nmrglue/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
(original)
+++
branches/nmrglue/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
Thu Feb 19 14:19:02 2015
@@ -1,6 +1,6 @@
###############################################################################
# #
-# Copyright (C) 2004-2014 Edward d'Auvergne #
+# Copyright (C) 2004-2015 Edward d'Auvergne #
# #
# This file is part of the program relax (http://www.nmr-relax.com). #
# #
@@ -116,7 +116,7 @@
minimise.execute('simplex', scaling=False, constraints=False)
# Monte Carlo simulations.
-monte_carlo.setup(number=2)
+monte_carlo.setup(number=3)
monte_carlo.create_data()
monte_carlo.initial_values()
minimise.execute('simplex', scaling=False, constraints=False)
Modified:
branches/nmrglue/test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py?rev=27666&r1=27665&r2=27666&view=diff
==============================================================================
---
branches/nmrglue/test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py
(original)
+++
branches/nmrglue/test_suite/system_tests/scripts/relax_disp/r1rho_off_res_tp02.py
Thu Feb 19 14:19:02 2015
@@ -21,7 +21,7 @@
GRID_INC = 4
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
-MC_NUM = 1
+MC_NUM = 3
# Set up the data pipe.
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