Author: bugman
Date: Thu Oct 4 18:20:51 2012
New Revision: 17697
URL: http://svn.gna.org/viewcvs/relax?rev=17697&view=rev
Log:
Added the Mf.test_bug_20213_asn_sidechain() system test to catch bug #20213.
The data and script comes from the files 'sh3-47.2.zip' and 'run.py' attached
to the bug report
https://gna.org/bugs/?20213. The PDB now only contains Asp47, the
optimisation parameters have been
made almost insignificant, and all models but 'tm0' have been removed from
the analysis.
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/600_noe.out
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t1.out
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t2.out
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/750_noe.out
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t1.out
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t2.out
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
Modified:
trunk/test_suite/system_tests/model_free.py
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/1U06-H_trunc.pdb
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,19 @@
+ATOM 350 N ASN A 47 26.457 -1.760 14.960 1.00 28.72
N
+ATOM 351 CA ASN A 47 25.222 -2.490 14.664 1.00 28.76
C
+ATOM 352 C ASN A 47 24.060 -1.634 14.088 1.00 28.64
C
+ATOM 353 O ASN A 47 24.124 -1.142 12.946 1.00 30.21
O
+ATOM 354 CB AASN A 47 24.776 -3.282 15.896 0.50 29.19
C
+ATOM 355 CB BASN A 47 24.816 -3.276 15.931 0.50 29.24
C
+ATOM 356 CG AASN A 47 25.683 -4.436 16.177 0.50 29.53
C
+ATOM 357 CG BASN A 47 23.823 -4.390 15.651 0.50 29.20
C
+ATOM 358 OD1AASN A 47 26.400 -4.453 17.175 0.50 29.20
O
+ATOM 359 OD1BASN A 47 23.653 -4.826 14.513 0.50 29.65
O
+ATOM 360 ND2AASN A 47 25.683 -5.405 15.275 0.50 26.68
N
+ATOM 361 ND2BASN A 47 23.154 -4.853 16.703 0.50 28.74
N
+ATOM 0 H ASN A 47 27.264 -2.151 14.517 1.00 28.72
H new
+ATOM 0 HA ASN A 47 25.475 -3.177 13.843 1.00 28.76
H new
+ATOM 0 HB2AASN A 47 24.751 -2.615 16.770 0.50 29.24
H new
+ATOM 0 HB3AASN A 47 23.751 -3.651 15.743 0.50 29.24
H new
+ATOM 0 HD21AASN A 47 26.285 -6.195 15.390 0.50 28.74
H new
+ATOM 0 HD22AASN A 47 25.081 -5.347 14.478 0.50 28.74
H new
+END
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/600_noe.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/600_noe.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/600_noe.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/600_noe.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,1 @@
+47 ASN 0.73043 0.02653 N
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t1.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t1.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t1.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t1.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,2 @@
+# mol_name res_num res_name spin_num spin_name value
error
+1aey-NMR_mol1 47 ASN 704 N
2.16085360786 0.0337059926952
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t2.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t2.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t2.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/600/rx_t2.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,2 @@
+# mol_name res_num res_name spin_num spin_name value
error
+1aey-NMR_mol1 47 ASN 704 N
4.57140358622 0.0525518669771
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/750_noe.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/750_noe.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/750_noe.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/750_noe.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,1 @@
+47 ASN 0.7339 0.03428 N
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t1.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t1.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t1.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t1.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,2 @@
+# mol_name res_num res_name spin_num spin_name value
error
+1aey-NMR_mol1 47 ASN 704 N
1.91890847158 0.0313850811138
Added:
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t2.out
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t2.out?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t2.out
(added)
+++
trunk/test_suite/shared_data/model_free/bug_20213_asn_sidechain/750/rx_t2.out
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,2 @@
+# mol_name res_num res_name spin_num spin_name value
error
+1aey-NMR_mol1 47 ASN 704 N
5.27896458858 0.0502440155185
Modified: trunk/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/model_free.py?rev=17697&r1=17696&r2=17697&view=diff
==============================================================================
--- trunk/test_suite/system_tests/model_free.py (original)
+++ trunk/test_suite/system_tests/model_free.py Thu Oct 4 18:20:51 2012
@@ -267,6 +267,13 @@
# Execute the script.
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_18790_negative_error.py')
+
+
+ def test_bug_20213_asn_sidechain(self):
+ """Bug #20213 catch, the model selection failure due to the presence
of Asp and Gln sidechain N spins."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_20213_asn_sidechain.py')
def test_create_m4(self):
Added:
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py?rev=17697&view=auto
==============================================================================
---
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
(added)
+++
trunk/test_suite/system_tests/scripts/model_free/bug_20213_asn_sidechain.py
Thu Oct 4 18:20:51 2012
@@ -1,0 +1,90 @@
+# Python module imports.
+from os import sep
+from time import asctime, localtime
+
+# relax module imports.
+from auto_analyses.dauvergne_protocol import dAuvergne_protocol
+from data import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Analysis variables.
+#####################
+
+# The diffusion model.
+DIFF_MODEL = 'local_tm'
+
+# The model-free models. Do not change these unless absolutely necessary,
the protocol is likely to fail if these are changed.
+MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
+LOCAL_TM_MODELS = ['tm0']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 2
+
+# The optimisation technique.
+MIN_ALGOR = 'simplex'
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
+MC_NUM = 3
+
+# Automatic looping over all rounds until convergence (must be a boolean
value of True or False).
+CONV_LOOP = True
+
+
+
+# Set up the data pipe.
+#######################
+
+# Create the data pipe.
+pipe_bundle = "mf (%s)" % asctime(localtime())
+name = "origin - " + pipe_bundle
+pipe.create(name, 'mf', bundle=pipe_bundle)
+
+# The data path.
+data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' +
sep + 'model_free' + sep + 'bug_20213_asn_sidechain' + sep
+
+# Load PDB file
+structure.read_pdb(file='./1U06-H_trunc.pdb', dir=data_path, read_mol=1,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
+
+# Set up spins and isotopes
+structure.load_spins(spin_id=':47@N*', ave_pos=True)
+structure.load_spins(spin_id=':47@H*', ave_pos=True)
+spin.isotope(isotope='15N', spin_id='@N*', force=True)
+spin.isotope(isotope='1H', spin_id='@H*', force=True)
+spin.element(element='N', spin_id=':*@N*', force=True)
+spin.element(element='H', spin_id=':*@H*', force=True)
+
+# Load relaxation files
+relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.17991*1e6,
file='./600/rx_t1.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7, sep=None, spin_id=None)
+relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.17991*1e6,
file='./600/rx_t2.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7, sep=None, spin_id=None)
+relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.17991*1e6,
file='./600/600_noe.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=5,
data_col=3, error_col=4, sep=None, spin_id=None)
+
+relax_data.read(ri_id='R1_750', ri_type='R1', frq=750.04990*1e6,
file='./750/rx_t1.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7, sep=None, spin_id=None)
+relax_data.read(ri_id='R2_750', ri_type='R2', frq=750.04990*1e6,
file='./750/rx_t2.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
error_col=7, sep=None, spin_id=None)
+relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.04990*1e6,
file='./750/750_noe.out', dir=data_path, spin_id_col=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=5,
data_col=3, error_col=4, sep=None, spin_id=None)
+
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02e-10)
+dipole_pair.unit_vectors(ave=True)
+
+# Define the chemical shift relaxation interaction.
+value.set(val=-0.000172, param='csa', spin_id=None)
+
+
+
+# Execution.
+############
+
+# The results dir.
+if not hasattr(ds, 'tmpdir'):
+ results_dir = status.install_path + sep + 'dauvergne_protocol'
+else:
+ results_dir = ds.tmpdir
+
+# Change some opt params.
+dAuvergne_protocol.opt_func_tol = 1e-5
+dAuvergne_protocol.opt_max_iterations = 1000
+
+# Do not change!
+dAuvergne_protocol(pipe_name=name, pipe_bundle=pipe_bundle,
results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_sim_num=MC_NUM, conv_loop=CONV_LOOP)
r17697 - in /trunk/test_suite: shared_data/model_free/bug_20213_asn_sidechain/ shared_data/model_free/bug_20213_asn_sidechai...