Re: r5308 - in /1.3: physical_constants.py prompt/jw_mapping.py specific_fns/jw_mapping.py test_suite/system_tests/jw_mapping.py -- April 04, 2008 - 16:42

Hi,

It may have been best to make separate commits for these different
changes.  The reason is because in the file 'physical_constants.py',
the variable 'nuclues' should not have changed to 'heteronuc_type'.
The proton is not a heteronucleus, this function simply returns the
gyromagnetic ratio for the desired nucleus.  As the changes to these 4
files were committed together, the revision cannot be reverted.
However the changes to the file can be reverted using normal reversion
commands but with the file name at the end.

Cheers,

Edward



On Fri, Apr 4, 2008 at 4:21 PM,  <sebastien.morin.1@xxxxxxxxx> wrote:
> 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)
>
>
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