Author: bugman
Date: Wed Nov 25 10:18:38 2009
New Revision: 9965
URL: http://svn.gna.org/viewcvs/relax?rev=9965&view=rev
Log:
Updated all the consistency testing analysis specific API methods to match
the base API.
Modified:
1.3/specific_fns/consistency_tests.py
Modified: 1.3/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=9965&r1=9964&r2=9965&view=diff
==============================================================================
--- 1.3/specific_fns/consistency_tests.py (original)
+++ 1.3/specific_fns/consistency_tests.py Wed Nov 25 10:18:38 2009
@@ -59,8 +59,16 @@
cdp.ct_frq = frq
- def calculate(self, verbosity=1, sim_index=None, spin_id=None):
- """Calculation of the consistency functions."""
+ def calculate(self, spin_id=None, verbosity=1, sim_index=None):
+ """Calculation of the consistency functions.
+
+ @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: None or int
+ """
# Test if the frequency has been set.
if not hasattr(cdp, 'ct_frq') or not isinstance(cdp.ct_frq, float):
@@ -193,8 +201,14 @@
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 structures.
+
+ @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()
@@ -207,9 +221,9 @@
name = name + '_sim'
# If the name is not in 'data', add it.
- if not hasattr(data, name):
+ 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):
@@ -370,57 +384,66 @@
|_______________________|__________________|_______________________________________________|
"""
- def return_data_name(self, name):
+ def return_data_name(self, param):
"""Return a unique identifying string for the consistency test
parameter.
- @param name: The consistency test parameter.
- @type name: str
+ @param param: The consistency test 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'
# F_eta.
- if search('^[Ff]_[Ee][Tt][Aa]$', name):
+ if search('^[Ff]_[Ee][Tt][Aa]$', param):
return 'f_eta'
# F_R2.
- if search('^^[Ff]_[Rr]2$', name):
+ if search('^^[Ff]_[Rr]2$', param):
return 'f_r2'
# 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'
# Angle Theta
- if search('^[Oo]rientation$', name):
+ if search('^[Oo]rientation$', param):
return 'orientation'
# Correlation time
- if search('^[Tt]c$', name):
+ if search('^[Tt]c$', param):
return 'tc'
- 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 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':
@@ -451,21 +474,16 @@
return '\\q\\xt\\f{}c\\Q'
- def return_units(self, data_type, 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.
+ def return_units(self, param, spin=None, spin_id=None):
+ """Return a string representing the parameters units.
+
+ @param param: The name of the parameter to return the units
string for.
+ @type param: str
+ @keyword spin: The spin container.
@type spin: SpinContainer instance
- @param spin_id: The spin identification string (ignored if the
spin container is
- supplied).
+ @keyword spin_id: The spin identification string (ignored if the
spin container is supplied).
@type spin_id: str
- @return: The string representation of the units.
+ @return: The parameter units string.
@rtype: str
"""
@@ -500,8 +518,19 @@
"""
- def set_error(self, spin, index, error):
- """Function for setting parameter errors."""
+ def set_error(self, model_info, index, error):
+ """Set the parameter errors.
+
+ @param model_info: The spin container originating from model_loop().
+ @type model_info: SpinContainer instance
+ @param index: The index of the parameter to set the errors for.
+ @type index: int
+ @param error: The error value.
+ @type error: float
+ """
+
+ # Alias.
+ spin = model_info
# Return J(0) sim data.
if index == 0:
@@ -516,8 +545,19 @@
spin.f_r2_err = error
- def sim_return_param(self, spin, index):
- """Function for returning the array of simulation parameter
values."""
+ def sim_return_param(self, model_info, index):
+ """Return the array of simulation parameter values.
+
+ @param model_info: The spin container originating from model_loop().
+ @type model_info: SpinContainer instance
+ @param index: The index of the parameter to return the array
of values for.
+ @type index: int
+ @return: The array of simulation parameter values.
+ @rtype: list of float
+ """
+
+ # Alias.
+ spin = model_info
# Skip deselected residues.
if not spin.select:
@@ -536,8 +576,17 @@
return spin.f_r2_sim
- def sim_return_selected(self, spin):
- """Function for returning the array of selected simulation flags."""
+ def sim_return_selected(self, model_info):
+ """Return the array of selected simulation flags.
+
+ @param model_info: The spin container originating from model_loop().
+ @type model_info: SpinContainer instance
+ @return: The array of selected simulation flags.
+ @rtype: list of int
+ """
+
+ # Alias.
+ spin = model_info
# Multiple spins.
return spin.select_sim
@@ -546,8 +595,7 @@
def sim_pack_data(self, spin_id, sim_data):
"""Pack the Monte Carlo simulation data.
- @param spin_id: The spin identification string, as yielded by
the base_data_loop()
- generator method.
+ @param spin_id: The spin identification string, as yielded by
the base_data_loop() generator method.
@type spin_id: str
@param sim_data: The Monte Carlo simulation data.
@type sim_data: list of float
r9965 - /1.3/specific_fns/consistency_tests.py