URL:
<http://gna.org/bugs/?22961>
Summary: Loading of relaxation data fails with "IndexError:
list index out of range".
Project: relax
Submitted by: bugman
Submitted on: Mon 17 Nov 2014 07:55:51 AM UTC
Category: relax's source code
Specific analysis category: Model-free analysis
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: bugman
Originator Name:
Originator Email:
Open/Closed: Open
Release: 3.3.2
Discussion Lock: Any
Operating System: All systems
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Details:
The loading of relaxation data, in some rare cases, fails with and IndexError.
This is now caught by the Mf.test_data_loading_failures system test:
======================================================================
ERROR: test_data_loading_failures (test_suite.system_tests.model_free.Mf)
Catch a failure when loading relaxation data.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)
relax> sequence.read(file='noe.500.out',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere/noe.500.out'
for reading.
# mol_name res_num res_name spin_num spin_name
sphere_mol1 1 GLY 1 N
sphere_mol1 1 GLY 2 H
sphere_mol1 2 GLY 3 N
sphere_mol1 2 GLY 4 H
sphere_mol1 3 GLY 5 N
sphere_mol1 3 GLY 6 H
sphere_mol1 4 GLY 7 N
sphere_mol1 4 GLY 8 H
sphere_mol1 5 GLY 9 N
sphere_mol1 5 GLY 10 H
sphere_mol1 6 GLY 11 N
sphere_mol1 6 GLY 12 H
sphere_mol1 7 GLY 13 N
sphere_mol1 7 GLY 14 H
sphere_mol1 8 GLY 15 N
sphere_mol1 8 GLY 16 H
sphere_mol1 9 GLY 17 N
sphere_mol1 9 GLY 18 H
sphere_mol1 9 GLY 19 NE1
sphere_mol1 9 GLY 20 HE1
relax> relax_data.read(ri_id='noe500', ri_type='NOE', frq=500000000.0,
file='noe.500.out',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere',
spin_id_col=None, mol_name_col=1, 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='@N')
RelaxWarning: The precise spectrometer frequency should be supplied, a value
such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the
Bruker acqus file.
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/sphere/noe.500.out'
for reading.
RelaxWarning: The precise spectrometer frequency should be supplied, a value
such as 500000000 or 5e8 for a 500 MHz machine is not acceptable. Please see
the 'sfrq' parameter in the Varian procpar file or the 'SFO1' parameter in the
Bruker acqus file.
Traceback (most recent call last):
File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py", line
503, in test_data_loading_failures
self.interpreter.relax_data.read(ri_id='noe500', ri_type='NOE',
frq=500000000.0, file='noe.500.out', dir=dir, spin_id_col=None,
mol_name_col=1, 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='@N')
File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 938, in
read
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 772, in
pack_data
new_id = new_ids[0]
IndexError: list index out of range
----------------------------------------------------------------------
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[bug #22961] Loading of relaxation data fails with "IndexError: list index out of range".