Author: bugman
Date: Wed Jun 20 15:40:00 2012
New Revision: 17006
URL: http://svn.gna.org/viewcvs/relax?rev=17006&view=rev
Log:
Lots of fixes for the model-free system tests.
Modified:
branches/interatomic/test_suite/system_tests/model_free.py
branches/interatomic/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
branches/interatomic/test_suite/system_tests/scripts/model_free/latex_mf_table.py
branches/interatomic/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
branches/interatomic/test_suite/system_tests/scripts/model_free/tylers_peptide.py
Modified: branches/interatomic/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/model_free.py?rev=17006&r1=17005&r2=17006&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/model_free.py (original)
+++ branches/interatomic/test_suite/system_tests/model_free.py Wed Jun 20
15:40:00 2012
@@ -396,7 +396,7 @@
# Load the relaxation data.
for i in range(len(frq)):
- self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE',
float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
+ self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE',
float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1',
float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2',
float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py?rev=17006&r1=17005&r2=17006&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
Wed Jun 20 15:40:00 2012
@@ -22,6 +22,8 @@
# Local tm data.
pipe.create(pipe_name='local_tm', pipe_type='mf')
results.read(file='local_tm_trunc', dir=path)
+spin.element('N', '@N')
+spin.element('H', '@H')
# Sphere data.
pipe.create(pipe_name='sphere', pipe_type='mf')
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/latex_mf_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/latex_mf_table.py?rev=17006&r1=17005&r2=17006&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/latex_mf_table.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/latex_mf_table.py
Wed Jun 20 15:40:00 2012
@@ -38,11 +38,9 @@
# Python module imports.
from os import sep
from string import replace
-import sys
# relax module imports.
from generic_fns.mol_res_spin import spin_loop
-from generic_fns import pipes
from relax_io import open_write_file
from status import Status; status = Status()
@@ -139,25 +137,12 @@
# End the font size.
self.file.write("\\end{small}\n")
- # Terminate the document.
- self.file.write("\\end{document}\n")
-
def latex_header(self):
"""Create the LaTeX header.
This function will need to be heavily modified to suit your needs.
"""
-
- # Document class - to allow for compilation tests.
- self.file.write("\documentclass[a4paper, 12pt, twoside]{book}\n\n")
-
- # Package inclusion.
- self.file.write("\usepackage{longtable}\n")
- self.file.write("\usepackage{booktabs}\n\n")
-
- # Start the document.
- self.file.write("\\begin{document}\n\n")
# Font size.
self.file.write("% Small font.\n")
@@ -193,10 +178,15 @@
# The spin is not selected.
if not spin.select:
- self.file.write("\\\n")
+ self.file.write("\\multicolumn{11}{c}{} \\\\\n")
+ continue
# The model-free model.
- self.file.write("$%s$ & " % spin.model)
+ if hasattr(spin, 'model'):
+ self.file.write("$%s$ & " % spin.model)
+ else:
+ self.file.write("\\multicolumn{11}{c}{} \\\\\n")
+ continue
# S2.
if spin.s2 == None:
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py?rev=17006&r1=17005&r2=17006&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
Wed Jun 20 15:40:00 2012
@@ -20,6 +20,10 @@
# Create the two spins.
spin.create(res_num=5, res_name='GLU', spin_name='N')
spin.create(res_num=5, res_name='GLU', spin_name='H')
+spin.element('N', '@N')
+spin.element('H', '@H')
+spin.isotope('15N', spin_id='@N')
+spin.isotope('1H', spin_id='@H')
# Define the magnetic dipole-dipole relaxation interaction.
dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
@@ -28,9 +32,5 @@
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa')
-# Set the spin information.
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
-
# Select the model-free model.
model_free.select_model(model='tm2')
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/tylers_peptide.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/tylers_peptide.py?rev=17006&r1=17005&r2=17006&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/tylers_peptide.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/tylers_peptide.py
Wed Jun 20 15:40:00 2012
@@ -18,6 +18,8 @@
model_free.remove_tm(spin_id=None)
sequence.display()
structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=DATA_PATH+'structures', parser='internal')
+structure.get_pos("@N")
+structure.get_pos("@H")
dipole_pair.unit_vectors()
diffusion_tensor.init(params=(1e-08, 0, 0, 0, 0, 0), time_scale=1.0,
d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None,
fixed=False)
fix(element='all_spins', fixed=True)
r17006 - in /branches/interatomic/test_suite/system_tests: ./ scripts/model_free/