Author: bugman
Date: Thu Nov 5 13:23:26 2009
New Revision: 9868
URL: http://svn.gna.org/viewcvs/relax?rev=9868&view=rev
Log:
The relax_data.peak_intensity_type() user function is now fully operational.
The BMRB system test has been repaired for the user function argument name
change.
Modified:
branches/bmrb/data/exp_info.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py
Modified: branches/bmrb/data/exp_info.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/exp_info.py?rev=9868&r1=9867&r2=9868&view=diff
==============================================================================
--- branches/bmrb/data/exp_info.py (original)
+++ branches/bmrb/data/exp_info.py Thu Nov 5 13:23:26 2009
@@ -169,6 +169,51 @@
return self.temp_control[i].method
+ def setup_peak_intensity_type(self, ri_label, frq_label, type):
+ """Store the peak intensity type.
+
+ @param ri_label: The relaxation data type, ie 'R1', 'R2', or
'NOE'.
+ @type ri_label: str
+ @param frq_label: The field strength label.
+ @type frq_label: str
+ @param type: The peak intensity type, one of 'height' or
'volume'.
+ @type type: str
+ """
+
+ # Initialise the container if needed.
+ if not hasattr(self, "peak_intensity_type"):
+ # The list.
+ self.peak_intensity_type = ContainerList()
+
+ # The name of the container.
+ self.peak_intensity_type.container_name =
"peak_intensity_type_list"
+
+ # The description of the container.
+ self.peak_intensity_type.container_desc = "List of peak
intensity types."
+
+ # Find if the type has already been set.
+ for i in range(len(self.peak_intensity_type)):
+ if self.peak_intensity_type[i].ri_label == ri_label and
self.peak_intensity_type[i].frq_label == frq_label:
+ raise RelaxError("The peak intensity type for the '%s'
ri_label and '%s' frq_label has already been set.")
+
+ # Init the container.
+ peak_intensity_type = Element()
+
+ # The name of the container.
+ peak_intensity_type.element_name = "peak_intensity_type"
+
+ # The description of the container.
+ peak_intensity_type.element_desc = "Temperature control methods for
the relaxation data."
+
+ # Set the attributes.
+ peak_intensity_type.ri_label = ri_label
+ peak_intensity_type.frq_label = frq_label
+ peak_intensity_type.type = type
+
+ # Append the container.
+ self.peak_intensity_type.append(peak_intensity_type)
+
+
def setup_thiol(self, state):
"""Set up the thiol state of the system.
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9868&r1=9867&r2=9868&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Thu Nov 5 13:23:26 2009
@@ -767,6 +767,41 @@
# Update all data structures.
update_data_structures_spin(spin, ri_label, frq_label, frq,
values[i], errors[i])
+
+
+def peak_intensity_type(ri_label=None, frq_label=None, type=None):
+ """Set the type of intensity measured for the peaks.
+
+ @param ri_label: The relaxation data type, ie 'R1', 'R2', or 'NOE'.
+ @type ri_label: str
+ @param frq_label: The field strength label.
+ @type frq_label: str
+ @param type: The peak intensity type, one of 'height' or 'volume'.
+ @type type: str
+ """
+
+ # Test if the current pipe exists.
+ pipes.test()
+
+ # Test if sequence data is loaded.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Test if relaxation data corresponding to 'ri_label' and 'frq_label'
already exists.
+ if not test_labels(ri_label, frq_label):
+ raise RelaxNoRiError(ri_label, frq_label)
+
+ # Check the values, and warn if not in the list.
+ valid = ['height', 'volume']
+ if type not in valid:
+ raise RelaxError("The '%s' peak intensity type is unknown. Please
select one of %s." % (type, valid))
+
+ # Set up the experimental info data container, if needed.
+ if not hasattr(cdp, 'exp_info'):
+ cdp.exp_info = ExpInfo()
+
+ # Store the type.
+ cdp.exp_info.setup_peak_intensity_type(ri_label, frq_label, type)
def read(ri_label=None, frq_label=None, frq=None, file=None, dir=None,
file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=None,
error_col=None, sep=None, spin_id=None):
Modified: branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py?rev=9868&r1=9867&r2=9868&view=diff
==============================================================================
--- branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py (original)
+++ branches/bmrb/test_suite/system_tests/scripts/bmrb_rw.py Thu Nov 5
13:23:26 2009
@@ -43,7 +43,7 @@
for i in range(6):
relax_data.temp_calibration(ri_label=ri_labels[i],
frq_label=frq_labels[i], method='methanol')
relax_data.temp_control(ri_label=ri_labels[i], frq_label=frq_labels[i],
method='single fid interleaving')
- relax_data.peak_intensity_type(ri_label=ri_labels[i],
frq_label=frq_labels[i], intensity='height')
+ relax_data.peak_intensity_type(ri_label=ri_labels[i],
frq_label=frq_labels[i], type='height')
# Set up some BMRB information.
bmrb.software_select('NMRPipe')
r9868 - in /branches/bmrb: data/exp_info.py generic_fns/relax_data.py test_suite/system_tests/scripts/bmrb_rw.py