Author: bugman
Date: Tue Nov 24 19:59:32 2009
New Revision: 9949
URL: http://svn.gna.org/viewcvs/relax?rev=9949&view=rev
Log:
Updates to the methods of the reduced spectral density mapping API.
Modified:
1.3/prompt/jw_mapping.py
1.3/specific_fns/jw_mapping.py
Modified: 1.3/prompt/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/jw_mapping.py?rev=9949&r1=9948&r2=9949&view=diff
==============================================================================
--- 1.3/prompt/jw_mapping.py (original)
+++ 1.3/prompt/jw_mapping.py Tue Nov 24 19:59:32 2009
@@ -69,4 +69,4 @@
check.is_num(frq, 'spectrometer frequency')
# Execute the functional code.
- jw_mapping_obj.set_frq(frq=frq)
+ jw_mapping_obj._set_frq(frq=frq)
Modified: 1.3/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=9949&r1=9948&r2=9949&view=diff
==============================================================================
--- 1.3/specific_fns/jw_mapping.py (original)
+++ 1.3/specific_fns/jw_mapping.py Tue Nov 24 19:59:32 2009
@@ -35,8 +35,16 @@
class Jw_mapping(API_base):
"""Class containing functions specific to reduced spectral density
mapping."""
- def calculate(self, verbosity=1, sim_index=None, spin_id=None):
- """Calculation of the spectral density values."""
+ def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ """Calculation of the spectral density values.
+
+ @keyword spin_id: The spin identification string.
+ @type spin_id: None or str
+ @keyword verbosity: The amount of information to print. The higher
the value, the greater the verbosity.
+ @type verbosity: int
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ """
# Test if the frequency has been set.
if not hasattr(cdp, 'jw_frq') or not isinstance(cdp.jw_frq, float):
@@ -162,8 +170,14 @@
return spin.relax_data
- def data_init(self, data, sim=0):
- """Function for initialising the data structures."""
+ def data_init(self, data_cont, sim=False):
+ """Initialise the data structure.
+
+ @param data_cont: The data container.
+ @type data_cont: instance
+ @keyword sim: The Monte Carlo simulation flag, which if true
will initialise the simulation data structure.
+ @type sim: bool
+ """
# Get the data names.
data_names = self.data_names()
@@ -175,10 +189,10 @@
# Add '_sim' to the names.
name = name + '_sim'
- # If the name is not in 'data', add it.
- if not hasattr(data, name):
+ # If the name is not in 'data_cont', add it.
+ if not hasattr(data_cont, name):
# Set the attribute.
- setattr(data, name, None)
+ setattr(data_cont, name, None)
def data_names(self, set=None, error_names=False, sim_names=False):
@@ -318,49 +332,57 @@
"""
- def return_data_name(self, name):
+ def return_data_name(self, param):
"""Return a unique identifying string for the J(w) mapping parameter.
- @param name: The J(w) mapping parameter.
- @type name: str
+ @param param: The J(w) mapping parameter name.
+ @type param: str
@return: The unique parameter identifying string.
@rtype: str
"""
# J(0).
- if search('^[Jj]0$', name) or search('[Jj]\(0\)', name):
+ if search('^[Jj]0$', param) or search('[Jj]\(0\)', param):
return 'j0'
# J(wX).
- if search('^[Jj]w[Xx]$', name) or search('[Jj]\(w[Xx]\)', name):
+ if search('^[Jj]w[Xx]$', param) or search('[Jj]\(w[Xx]\)', param):
return 'jwx'
# J(wH).
- if search('^[Jj]w[Hh]$', name) or search('[Jj]\(w[Hh]\)', name):
+ if search('^[Jj]w[Hh]$', param) or search('[Jj]\(w[Hh]\)', param):
return 'jwh'
# Bond length.
- if search('^r$', name) or search('[Bb]ond[ -_][Ll]ength', name):
+ if search('^r$', param) or search('[Bb]ond[ -_][Ll]ength', param):
return 'r'
# CSA.
- if search('^[Cc][Ss][Aa]$', name):
+ if search('^[Cc][Ss][Aa]$', param):
return 'csa'
# Heteronucleus type.
- if search('^[Hh]eteronucleus$', name):
+ if search('^[Hh]eteronucleus$', param):
return 'heteronuc_type'
# Proton type.
- if search('^[Pp]roton$', name):
+ if search('^[Pp]roton$', param):
return 'proton_type'
- def return_grace_string(self, data_type):
- """Function for returning the Grace string representing the data
type for axis labelling."""
+ def return_grace_string(self, param):
+ """Return the Grace string representing the given parameter.
+
+ This is used for axis labelling.
+
+ @param param: The specific analysis parameter.
+ @type param: str
+ @return: The Grace string representation of the parameter.
+ @rtype: str
+ """
# Get the object name.
- object_name = self.return_data_name(data_type)
+ object_name = self.return_data_name(param)
# J(0).
if object_name == 'j0':
@@ -383,26 +405,25 @@
return '\\qCSA\\Q'
- def return_units(self, data_type, spin=None, spin_id=None):
+ def return_units(self, param, spin=None, spin_id=None):
"""Function for returning a string representing the parameters units.
For example, the internal representation of te is in seconds,
whereas the external
representation is in picoseconds, therefore this function will
return the string
'picoseconds' for te.
- @param data_type: The name of the parameter to return the units
string for.
- @type data_type: str
- @param spin: The spin container.
- @type spin: SpinContainer instance
- @param spin_id: The spin identification string (ignored if the
spin container is
- supplied).
- @type spin_id: str
- @return: The string representation of the units.
- @rtype: str
+ @param param: The name of the parameter to return the units string
for.
+ @type param: str
+ @param spin: The spin container.
+ @type spin: SpinContainer instance
+ @param spin_id: The spin identification string (ignored if the spin
container is supplied).
+ @type spin_id: str
+ @return: The string representation of the units.
+ @rtype: str
"""
# Get the object name.
- object_name = self.return_data_name(data_type)
+ object_name = self.return_data_name(param)
# Bond length (Angstrom).
if object_name == 'r':
@@ -422,7 +443,7 @@
"""
- def set_frq(self, frq=None):
+ def _set_frq(self, frq=None):
"""Function for selecting which relaxation data to use in the J(w)
mapping."""
# Test if the current pipe exists.
r9949 - in /1.3: prompt/jw_mapping.py specific_fns/jw_mapping.py