Author: bugman
Date: Tue Nov 24 13:48:37 2009
New Revision: 9919
URL: http://svn.gna.org/viewcvs/relax?rev=9919&view=rev
Log:
Clean up of the entire NOE API.
Modified:
1.3/prompt/noe.py
1.3/specific_fns/noe.py
Modified: 1.3/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=9919&r1=9918&r2=9919&view=diff
==============================================================================
--- 1.3/prompt/noe.py (original)
+++ 1.3/prompt/noe.py Tue Nov 24 13:48:37 2009
@@ -142,4 +142,4 @@
check.is_str(spectrum_id, 'spectrum identification string')
# Execute the functional code.
- noe_obj.spectrum_type(spectrum_type=spectrum_type,
spectrum_id=spectrum_id)
+ noe_obj._spectrum_type(spectrum_type=spectrum_type,
spectrum_id=spectrum_id)
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=9919&r1=9918&r2=9919&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Tue Nov 24 13:48:37 2009
@@ -36,7 +36,7 @@
class Noe(API_base):
"""Class containing functions for relaxation data."""
- def assign_function(self, spin=None, intensity=None, spectrum_type=None):
+ def _assign_function(self, spin=None, intensity=None,
spectrum_type=None):
"""Place the peak intensity data into the spin container.
The intensity data can be either that of the reference or saturated
spectrum.
@@ -58,7 +58,7 @@
raise RelaxError("The spectrum type '%s' is unknown." %
spectrum_type)
- def calculate(self, verbosity=1):
+ def calculate(self, spin_id=None, verbosity=1, sim_index=None):
"""Calculate the NOE and its error.
The error for each peak is calculated using the formula::
@@ -67,8 +67,12 @@
sd(NOE) = -----------------------------------------------
I(unsat)^2
+ @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 MC simulation index (unused).
+ @type sim_index: None
"""
# Test if the current pipe exists.
@@ -135,7 +139,7 @@
spin.select = False
- def read(self, file=None, dir=None, spectrum_type=None, format=None,
heteronuc=None, proton=None, int_col=None):
+ def _read(self, file=None, dir=None, spectrum_type=None, format=None,
heteronuc=None, proton=None, int_col=None):
"""Read in the peak intensity data.
@keyword file: The name of the file containing the peak
intensities.
@@ -157,6 +161,7 @@
@type int_col: int
"""
+ asdf
# Spectrum type argument.
spect_type_list = ['ref', 'sat']
if spectrum_type not in spect_type_list:
@@ -167,7 +172,7 @@
print("Saturated spectrum.")
# Generic intensity function.
- intensity.read(file=file, dir=dir, format=format,
heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self.assign_function, spectrum_type=spectrum_type)
+ intensity.read(file=file, dir=dir, format=format,
heteronuc=heteronuc, proton=proton, int_col=int_col,
assign_func=self._assign_function, spectrum_type=spectrum_type)
return_data_name_doc = """
@@ -188,33 +193,41 @@
"""
- def return_data_name(self, name):
+ def return_data_name(self, param):
"""Return a unique identifying string for the steady-state NOE
parameter.
- @param name: The steady-state NOE parameter.
- @type name: str
+ @param param: The steady-state NOE parameter.
+ @type param: str
@return: The unique parameter identifying string.
@rtype: str
"""
# Reference intensity.
- if match('^[Rr]ef$', name) or match('[Rr]ef[ -_][Ii]nt', name):
+ if match('^[Rr]ef$', param) or match('[Rr]ef[ -_][Ii]nt', param):
return 'ref'
# Saturated intensity.
- if match('^[Ss]at$', name) or match('[Ss]at[ -_][Ii]nt', name):
+ if match('^[Ss]at$', param) or match('[Ss]at[ -_][Ii]nt', param):
return 'sat'
# NOE.
- if match('^[Nn][Oo][Ee]$', name):
+ if match('^[Nn][Oo][Ee]$', param):
return 'noe'
- 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 representation of 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)
# Reference intensity.
if object_name == 'ref':
@@ -228,57 +241,27 @@
if object_name == 'noe':
return '\\qNOE\\Q'
- # Return the data type as the Grace string.
- return data_type
-
-
- def return_units(self, stat_type, spin_id=None):
+ # Return the parameter as the Grace string.
+ return param
+
+
+ def return_units(self, param, spin=None, spin_id=None):
"""Dummy function which returns None as the stats have no units.
- @param stat_type: Not used.
- @type stat_type: None
- @keyword spin_id: Not used.
- @type spin_id: None
- @return: Nothing.
- @rtype: None
+ @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: Nothing.
+ @rtype: None
"""
return None
- def set_error(self, error=0.0, spectrum_id=None, spin_id=None):
- """Set the peak intensity errors.
-
- @param error: The peak intensity error value defined as
the RMSD of the base plane
- noise.
- @type error: float
- @keyword spectrum_id: The id of spectrum, one of 'ref' or 'sat'.
- @type spectrum_id: str
- @param spin_id: The spin identification string.
- @type spin_id: str
- """
-
- # Test if the current pipe exists
- pipes.test()
-
- # Test if the sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Loop over the spins.
- for spin in spin_loop(spin_id):
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Set the error.
- if spectrum_id == 'ref':
- spin.ref_err = float(error)
- elif spectrum_id == 'sat':
- spin.sat_err = float(error)
-
-
- def spectrum_type(self, spectrum_type=None, spectrum_id=None):
+ def _spectrum_type(self, spectrum_type=None, spectrum_id=None):
"""Set the spectrum type corresponding to the spectrum_id.
@keyword spectrum_type: The type of NOE spectrum, one of 'ref' or
'sat'.
r9919 - in /1.3: prompt/noe.py specific_fns/noe.py