Author: bugman
Date: Tue Nov 24 13:49:42 2009
New Revision: 9920
URL: http://svn.gna.org/viewcvs/relax?rev=9920&view=rev
Log:
Alphabetical ordering of methods, and separation of the private from the API
methods.
Modified:
1.3/specific_fns/noe.py
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=9920&r1=9919&r2=9920&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Tue Nov 24 13:49:42 2009
@@ -56,87 +56,6 @@
spin.sat = intensity
else:
raise RelaxError("The spectrum type '%s' is unknown." %
spectrum_type)
-
-
- 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::
- ___________________________________________
- \/ {sd(sat)*I(unsat)}^2 + {sd(unsat)*I(sat)}^2
- 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.
- pipes.test()
-
- # The spectrum types have not been set.
- if not hasattr(cdp, 'spectrum_type'):
- raise RelaxError("The spectrum types have not been set.")
-
- # Test if the 2 spectra types 'ref' and 'sat' exist.
- if not 'ref' in cdp.spectrum_type or not 'sat' in cdp.spectrum_type:
- raise RelaxError("The reference and saturated NOE spectra have
not been loaded.")
-
- # Loop over the spins.
- for spin in spin_loop():
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Average intensities (if required).
- sat = 0.0
- sat_err = 0.0
- ref = 0.0
- ref_err = 0.0
- for i in xrange(len(cdp.spectrum_type)):
- # Sat spectra.
- if cdp.spectrum_type[i] == 'sat':
- sat = sat + spin.intensities[i]
- sat_err = sat_err + spin.intensity_err[i]
-
- # Ref spectra.
- if cdp.spectrum_type[i] == 'ref':
- ref = ref + spin.intensities[i]
- ref_err = ref_err + spin.intensity_err[i]
-
- # Calculate the NOE.
- spin.noe = sat / ref
-
- # Calculate the error.
- spin.noe_err = sqrt((sat_err * ref)**2 + (ref_err * sat)**2) /
ref**2
-
-
- def overfit_deselect(self):
- """Deselect spins which have insufficient data to support
calculation"""
-
- # Test the sequence data exists.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Loop over spin data.
- for spin, spin_id in spin_loop(return_id=True):
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Check for sufficient data.
- if not hasattr(spin, 'intensities') or not len(spin.intensities)
== 2:
- warn(RelaxDeselectWarning(spin_id, 'insufficient data'))
- spin.select = False
-
- # Check for sufficient errors.
- elif not hasattr(spin, 'intensity_err') or not
len(spin.intensity_err) == 2:
- warn(RelaxDeselectWarning(spin_id, 'missing errors'))
- spin.select = False
def _read(self, file=None, dir=None, spectrum_type=None, format=None,
heteronuc=None, proton=None, int_col=None):
@@ -175,6 +94,116 @@
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)
+ 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'.
+ @type spectrum_type: str
+ @keyword spectrum_id: The spectrum id string.
+ @type spectrum_id: str
+ """
+
+ # Test if the current pipe exists
+ pipes.test()
+
+ # Test the spectrum id string.
+ if spectrum_id not in cdp.spectrum_ids:
+ raise RelaxError("The peak intensities corresponding to the
spectrum id '%s' does not exist." % spectrum_id)
+
+ # The spectrum id index.
+ spect_index = cdp.spectrum_ids.index(spectrum_id)
+
+ # Initialise or update the spectrum_type data structure as necessary.
+ if not hasattr(cdp, 'spectrum_type'):
+ cdp.spectrum_type = [None] * len(cdp.spectrum_ids)
+ elif len(cdp.spectrum_type) < len(cdp.spectrum_ids):
+ cdp.spectrum_type.append([None] * (len(cdp.spectrum_ids) -
len(cdp.spectrum_type)))
+
+ # Set the error.
+ cdp.spectrum_type[spect_index] = spectrum_type
+
+
+ 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::
+ ___________________________________________
+ \/ {sd(sat)*I(unsat)}^2 + {sd(unsat)*I(sat)}^2
+ 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.
+ pipes.test()
+
+ # The spectrum types have not been set.
+ if not hasattr(cdp, 'spectrum_type'):
+ raise RelaxError("The spectrum types have not been set.")
+
+ # Test if the 2 spectra types 'ref' and 'sat' exist.
+ if not 'ref' in cdp.spectrum_type or not 'sat' in cdp.spectrum_type:
+ raise RelaxError("The reference and saturated NOE spectra have
not been loaded.")
+
+ # Loop over the spins.
+ for spin in spin_loop():
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Average intensities (if required).
+ sat = 0.0
+ sat_err = 0.0
+ ref = 0.0
+ ref_err = 0.0
+ for i in xrange(len(cdp.spectrum_type)):
+ # Sat spectra.
+ if cdp.spectrum_type[i] == 'sat':
+ sat = sat + spin.intensities[i]
+ sat_err = sat_err + spin.intensity_err[i]
+
+ # Ref spectra.
+ if cdp.spectrum_type[i] == 'ref':
+ ref = ref + spin.intensities[i]
+ ref_err = ref_err + spin.intensity_err[i]
+
+ # Calculate the NOE.
+ spin.noe = sat / ref
+
+ # Calculate the error.
+ spin.noe_err = sqrt((sat_err * ref)**2 + (ref_err * sat)**2) /
ref**2
+
+
+ def overfit_deselect(self):
+ """Deselect spins which have insufficient data to support
calculation"""
+
+ # Test the sequence data exists.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Loop over spin data.
+ for spin, spin_id in spin_loop(return_id=True):
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Check for sufficient data.
+ if not hasattr(spin, 'intensities') or not len(spin.intensities)
== 2:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient data'))
+ spin.select = False
+
+ # Check for sufficient errors.
+ elif not hasattr(spin, 'intensity_err') or not
len(spin.intensity_err) == 2:
+ warn(RelaxDeselectWarning(spin_id, 'missing errors'))
+ spin.select = False
+
+
return_data_name_doc = """
NOE calculation data type string matching patterns
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -259,32 +288,3 @@
"""
return 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'.
- @type spectrum_type: str
- @keyword spectrum_id: The spectrum id string.
- @type spectrum_id: str
- """
-
- # Test if the current pipe exists
- pipes.test()
-
- # Test the spectrum id string.
- if spectrum_id not in cdp.spectrum_ids:
- raise RelaxError("The peak intensities corresponding to the
spectrum id '%s' does not exist." % spectrum_id)
-
- # The spectrum id index.
- spect_index = cdp.spectrum_ids.index(spectrum_id)
-
- # Initialise or update the spectrum_type data structure as necessary.
- if not hasattr(cdp, 'spectrum_type'):
- cdp.spectrum_type = [None] * len(cdp.spectrum_ids)
- elif len(cdp.spectrum_type) < len(cdp.spectrum_ids):
- cdp.spectrum_type.append([None] * (len(cdp.spectrum_ids) -
len(cdp.spectrum_type)))
-
- # Set the error.
- cdp.spectrum_type[spect_index] = spectrum_type
r9920 - /1.3/specific_fns/noe.py