Author: bugman
Date: Tue Dec 14 11:11:03 2010
New Revision: 11811
URL: http://svn.gna.org/viewcvs/relax?rev=11811&view=rev
Log:
Added a system test for bug #17276.
This bug (https://gna.org/bugs/index.php?17276) was reported by Leanne Minall
<lm7902 att bristol
dot ac dott uk>.
The test passes though as the problem is not in this test data.
Added:
1.3/test_suite/shared_data/peak_lists/bug_17276/
1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt (with
props)
1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt (with props)
1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt (with
props)
1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt (with
props)
1.3/test_suite/shared_data/peak_lists/bug_17276/sequence.out
1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py
Modified:
1.3/test_suite/system_tests/peak_lists.py
Added: 1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt Tue Dec 14
11:11:03 2010
@@ -1,0 +1,5 @@
+ Assignment w1 w2 Intensity
+
+ A1649N-HN 130.724
7.934 1.69E+07
+ R1615N-HN 131.144
7.235 1.23E+06
+
Propchange: 1.3/test_suite/shared_data/peak_lists/bug_17276/T10102Ed.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: 1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt Tue Dec 14
11:11:03 2010
@@ -1,0 +1,4 @@
+ Assignment w1 w2 Intensity
+
+ A1649N-HN 130.724
7.934 1.69E+07
+ R1615N-HN 131.141
7.233 1.23E+06
Propchange: 1.3/test_suite/shared_data/peak_lists/bug_17276/T1010Ed.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: 1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt Tue Dec 14
11:11:03 2010
@@ -1,0 +1,5 @@
+ Assignment w1 w2 Intensity
+
+ A1649N-HN 130.724
7.934 4.69E+06
+ R1615N-HN 120.372
8.206 3.23E+05
+
Propchange: 1.3/test_suite/shared_data/peak_lists/bug_17276/T112002Ed.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: 1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt (added)
+++ 1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt Tue Dec 14
11:11:03 2010
@@ -1,0 +1,4 @@
+ Assignment w1 w2 Intensity
+
+ A1649N-HN 130.724
7.934 4.69E+06
+ R1615N-HN 131.136
7.235 2.23E+05
Propchange: 1.3/test_suite/shared_data/peak_lists/bug_17276/T11200Ed.txt
------------------------------------------------------------------------------
svn:eol-style = native
Added: 1.3/test_suite/shared_data/peak_lists/bug_17276/sequence.out
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/peak_lists/bug_17276/sequence.out?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/peak_lists/bug_17276/sequence.out (added)
+++ 1.3/test_suite/shared_data/peak_lists/bug_17276/sequence.out Tue Dec 14
11:11:03 2010
@@ -1,0 +1,148 @@
+# Res_num Res_name Spin_name
+1508 Met N
+1509 Lys N
+1510 Ser N
+1511 Asn N
+1512 Glu N
+1513 His N
+1514 Asp N
+1515 Asp N
+1516 Cys N
+1517 Gln N
+1518 Val N
+1519 Thr N
+1520 Asn N
+1521 Pro N
+1522 Ser N
+1523 Thr N
+1524 Gly N
+1525 His N
+1526 Leu N
+1527 Phe N
+1528 Asp N
+1529 Leu N
+1530 Ser N
+1531 Ser N
+1532 Leu N
+1533 Ser N
+1534 Gly N
+1535 Arg N
+1536 Ala N
+1537 Gly N
+1538 Phe N
+1539 Thr N
+1540 Ala N
+1541 Ala N
+1542 Tyr N
+1543 Ala N
+1544 Lys N
+1545 Gly N
+1546 Trp N
+1547 Gly N
+1548 Val N
+1549 Tyr N
+1550 Met N
+1551 Ser N
+1552 Ile N
+1553 Cys N
+1554 Gly N
+1555 Glu N
+1556 Asn N
+1557 Glu N
+1558 Asn N
+1559 Cys N
+1560 Pro N
+1561 Pro N
+1562 Gly N
+1563 Val N
+1564 Gly N
+1565 Ala N
+1566 Cys N
+1567 Phe N
+1568 Gly N
+1569 Gln N
+1570 Thr N
+1571 Arg N
+1572 Ile N
+1573 Ser N
+1574 Val N
+1575 Gly N
+1576 Lys N
+1577 Ala N
+1578 Asn N
+1579 Lys N
+1580 Arg N
+1581 Leu N
+1582 Arg N
+1583 Tyr N
+1584 Val N
+1585 Asp N
+1586 Gln N
+1587 Val N
+1588 Leu N
+1589 Gln N
+1590 Leu N
+1591 Val N
+1592 Tyr N
+1593 Lys N
+1594 Asp N
+1595 Gly N
+1596 Ser N
+1597 Pro N
+1598 Cys N
+1599 Pro N
+1600 Ser N
+1601 Lys N
+1602 Ser N
+1603 Gly N
+1604 Leu N
+1605 Ser N
+1606 Tyr N
+1607 Lys N
+1608 Ser N
+1609 Val N
+1610 Ile N
+1611 Ser N
+1612 Phe N
+1613 Val N
+1614 Cys N
+1615 Arg N
+1616 Pro N
+1617 Glu N
+1618 Ala N
+1619 Gly N
+1620 Pro N
+1621 Thr N
+1622 Asn N
+1623 Arg N
+1624 Pro N
+1625 Met N
+1626 Leu N
+1627 Ile N
+1628 Ser N
+1629 Leu N
+1630 Asp N
+1631 Lys N
+1632 Gln N
+1633 Thr N
+1634 Cys N
+1635 Thr N
+1636 Leu N
+1637 Phe N
+1638 Phe N
+1639 Ser N
+1640 Trp N
+1641 His N
+1642 Thr N
+1643 Pro N
+1644 Leu N
+1645 Ala N
+1646 Cys N
+1647 Glu N
+1648 Gln N
+1649 Ala N
+1650 Thr N
+1651 Lys N
+1652 Glu N
+1653 His N
+1654 His N
Modified: 1.3/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/peak_lists.py?rev=11811&r1=11810&r2=11811&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/peak_lists.py (original)
+++ 1.3/test_suite/system_tests/peak_lists.py Tue Dec 14 11:11:03 2010
@@ -45,6 +45,13 @@
"""Reset the relax data storage object."""
ds.__reset__()
+
+
+ def test_bug_17276_peak_lists(self):
+ """Test catching bug #17276, the duplicated peak list reading
failure submitted by Leanne Minall."""
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bug_17276_peak_lists.py')
def test_read_peak_list_generic(self):
Added: 1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py?rev=11811&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py (added)
+++ 1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py Tue Dec 14
11:11:03 2010
@@ -1,0 +1,118 @@
+###############################################################################
+#
#
+# Copyright (C) 2004-2008 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+# Script for relaxation curve fitting.
+######################################
+
+
+# Python module imports.
+import __main__
+from os import sep
+
+
+# Path of the files.
+PATH = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'peak_lists'+sep+'bug_17276'
+
+
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
+
+# Load the backbone amide 15N spins from a PDB file.
+sequence.read('sequence.out', dir=PATH, res_num_col=1, res_name_col=2,
spin_name_col=3)
+
+# Spectrum names.
+names = [
+ 'T1010Ed',
+ 'T10102Ed',
+ 'T11200Ed',
+ 'T112002Ed'
+]
+
+# Relaxation times (in seconds).
+times = [
+ 0.01,
+ 0.01,
+ 1.2,
+ 1.2
+]
+
+# Loop over the spectra.
+for i in xrange(len(names)):
+ # Load the peak intensities.
+ spectrum.read_intensities(file=names[i]+'.txt', dir=PATH,
spectrum_id=names[i], int_method='height')
+
+ # Set the relaxation times.
+ relax_fit.relax_time(time=times[i], spectrum_id=names[i])
+
+# Specify the duplicated spectra.
+#spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
+
+# Set the errors.
+spectrum.replicated(spectrum_ids=['T1010Ed', 'T10102Ed'])
+spectrum.replicated(spectrum_ids=['T11200Ed', 'T112002Ed'])
+
+# Peak intensity error analysis.
+spectrum.error_analysis()
+
+# Deselect unresolved spins.
+#deselect.read(file='unresolved')
+
+# Set the relaxation curve type.
+relax_fit.select_model('exp')
+
+# Grid search.
+grid_search(inc=11)
+
+# The following is not functional!
+#
+## Minimise.
+#minimise('simplex', scaling=False, constraints=False)
+#
+## Monte Carlo simulations.
+#monte_carlo.setup(number=500)
+#monte_carlo.create_data()
+#monte_carlo.initial_values()
+#minimise('simplex', scaling=False, constraints=False)
+#monte_carlo.error_analysis()
+#
+## Save the relaxation rates.
+#value.write(param='rx', file='rx.out', force=True)
+#
+## Save the results.
+#results.write(file='results', force=True)
+#
+## Create Grace plots of the data.
+#grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
+#grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
+#grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
+#grace.write(x_data_type='relax_times', y_data_type='int',
file='intensities.agr', force=True) # Average peak intensities.
+#grace.write(x_data_type='relax_times', y_data_type='int', norm=True,
file='intensities_norm.agr', force=True) # Average peak intensities
(normalised).
+#
+## Display the Grace plots.
+#grace.view(file='chi2.agr')
+#grace.view(file='i0.agr')
+#grace.view(file='rx.agr')
+#grace.view(file='intensities.agr')
+#grace.view(file='intensities_norm.agr')
+#
+## Save the program state.
+#state.save('rx.save', force=True)
r11811 - in /1.3/test_suite: shared_data/peak_lists/bug_17276/ system_tests/ system_tests/scripts/