Author: semor
Date: Fri Apr 4 16:21:27 2008
New Revision: 5308
URL: http://svn.gna.org/viewcvs/relax?rev=5308&view=rev
Log:
Partially fixed the code so the Jw mapping system test can go further before
failure.
Modified:
1.3/physical_constants.py
1.3/prompt/jw_mapping.py
1.3/specific_fns/jw_mapping.py
1.3/test_suite/system_tests/jw_mapping.py
Modified: 1.3/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/physical_constants.py?rev=5308&r1=5307&r2=5308&view=diff
==============================================================================
--- 1.3/physical_constants.py (original)
+++ 1.3/physical_constants.py Fri Apr 4 16:21:27 2008
@@ -70,29 +70,29 @@
"""The 31P gyromagnetic ratio."""
# Function for returning the desired gyromagnetic ratio.
-def return_gyromagnetic_ratio(nucleus=None):
- """Return the gyromagnetic ratio for the given nucleus type.
+def return_gyromagnetic_ratio(heteronuc_type=None):
+ """Return the gyromagnetic ratio for the given heteronucleus type.
- @keyword nucleus: The nucleus type.
- @type nucleus: str
- @raises RelaxError: If the nucleus type is unknown.
- @returns: The desired gyromagnetic ratio.
- @rtype: float
+ @keyword heteronuc_type: The heteronucleus type.
+ @type heteronucleus: str
+ @raises RelaxError: If the nucleus type is unknown.
+ @returns: The desired gyromagnetic ratio.
+ @rtype: float
"""
# Matching loop.
- if nucleus == '13C':
+ if heteronuc_type == '13C':
return g13C
- elif nucleus == '1H':
+ elif heteronuc_type == '1H':
return g1H
- elif nucleus == '15N':
+ elif heteronuc_type == '15N':
return g15N
- elif nucleus == '17O':
+ elif heteronuc_type == '17O':
return g17O
- elif nucleus == '31P':
+ elif heteronuc_type == '31P':
return g31P
else:
- raise RelaxError, "The nucleus type " + `nucleus` + " is unknown."
+ raise RelaxError, "The heteronucleus type " + `heteronuc_type` + "
is unknown."
# Relative atomic masses.
Modified: 1.3/prompt/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/jw_mapping.py?rev=5308&r1=5307&r2=5308&view=diff
==============================================================================
--- 1.3/prompt/jw_mapping.py (original)
+++ 1.3/prompt/jw_mapping.py Fri Apr 4 16:21:27 2008
@@ -26,6 +26,7 @@
# relax module imports.
import help
from relax_errors import RelaxStrError
+from specific_fns.setup import jw_mapping_obj
class Jw_mapping:
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=5308&r1=5307&r2=5308&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Fri Apr 4 16:21:27 2008
@@ -174,7 +174,7 @@
csa: CSA value.
- nucleus: The heteronucleus type.
+ heteronuc_type: The heteronucleus type.
j0: Spectral density value at 0 MHz.
@@ -189,7 +189,7 @@
# Values.
names.append('r')
names.append('csa')
- names.append('nucleus')
+ names.append('heteronuc_type')
# Spectral density values.
names.append('j0')
@@ -381,10 +381,6 @@
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
-
# Test if the run type is set to 'jw'.
function_type = relax_data_store.run_types[cdp.run_names.index]
if function_type != 'jw':
@@ -475,7 +471,7 @@
relax_data_store.res[run][i].relax_sim_data = sim_data
- def write_columnar_line(self, file=None, num=None, name=None,
select=None, data_set=None, nucleus=None, wH=None, j0=None, jwx=None,
jwh=None, r=None, csa=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, ri=None, ri_error=None):
+ def write_columnar_line(self, file=None, num=None, name=None,
select=None, data_set=None, heteronuc_type=None, wH=None, j0=None, jwx=None,
jwh=None, r=None, csa=None, ri_labels=None, remap_table=None,
frq_labels=None, frq=None, ri=None, ri_error=None):
"""Function for printing a single line of the columnar formatted
results."""
# Residue number and name.
@@ -485,7 +481,7 @@
file.write("%-9s %-9s " % (select, data_set))
# Nucleus.
- file.write("%-7s " % nucleus)
+ file.write("%-7s " % heteronuc_type)
# Proton frequency.
file.write("%-25s " % wH)
@@ -551,14 +547,14 @@
ri_error.append('Ri_error_(' + cdp.ri_labels[i] + "_" +
cdp.frq_labels[cdp.remap_table[i]] + ")")
# Write the header line.
- self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', data_set='Data_set', nucleus='Nucleus',
wH='Proton_frq_(MHz)', j0='J(0)', jwx='J(wX)', jwh='J(wH)',
r='Bond_length_(A)', csa='CSA_(ppm)', ri_labels='Ri_labels',
remap_table='Remap_table', frq_labels='Frq_labels', frq='Frequencies', ri=ri,
ri_error=ri_error)
+ self.write_columnar_line(file=file, num='Num', name='Name',
select='Selected', data_set='Data_set', heteronuc_type='Nucleus',
wH='Proton_frq_(MHz)', j0='J(0)', jwx='J(wX)', jwh='J(wH)',
r='Bond_length_(A)', csa='CSA_(ppm)', ri_labels='Ri_labels',
remap_table='Remap_table', frq_labels='Frq_labels', frq='Frequencies', ri=ri,
ri_error=ri_error)
# Values.
#########
# Nucleus.
- nucleus = self.relax.generic.nuclei.find_nucleus()
+ heteronuc_type = self.relax.generic.nuclei.find_heteronuc_type()
# The proton frequency in MHz.
wH = cdp.jw_frq / 1e6
@@ -628,7 +624,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='value', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='value',
heteronuc_type=heteronuc_type, wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`,
csa=`csa`, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
# Errors.
@@ -676,7 +672,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='error', nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='error',
heteronuc_type=heteronuc_type, wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`,
csa=`csa`, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
# Simulation values.
@@ -734,4 +730,4 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='sim_'+`i`, nucleus=nucleus,
wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`, csa=`csa`,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=spin.num,
name=spin.name, select=spin.select, spin_set='sim_'+`i`,
heteronuc_type=heteronuc_type, wH=`wH`, j0=`j0`, jwx=`jwx`, jwh=`jwh`, r=`r`,
csa=`csa`, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
Modified: 1.3/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/jw_mapping.py?rev=5308&r1=5307&r2=5308&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/jw_mapping.py (original)
+++ 1.3/test_suite/system_tests/jw_mapping.py Fri Apr 4 16:21:27 2008
@@ -78,7 +78,7 @@
# Set r, csa, and the nucleus type.
self.relax.interpreter._Value.set(NH_BOND_LENGTH, 'bond_length')
self.relax.interpreter._Value.set(N15_CSA, 'csa')
- self.relax.interpreter._Value.set('N', 'nucleus')
+ self.relax.interpreter._Value.set('15N', 'heteronucleus')
# Select the frequency.
self.relax.interpreter._Jw_mapping.set_frq(frq=600.0 * 1e6)
r5308 - in /1.3: physical_constants.py prompt/jw_mapping.py specific_fns/jw_mapping.py test_suite/system_tests/jw_mapping.py