Author: bugman
Date: Fri Sep 17 18:02:20 2010
New Revision: 11609
URL: http://svn.gna.org/viewcvs/relax?rev=11609&view=rev
Log:
Shifted the NOE specific analysis code into its own package.
This is in preparation for splitting up the module and adding new modules.
Added:
1.3/specific_fns/noe/
1.3/specific_fns/noe/__init__.py
- copied, changed from r11592, 1.3/specific_fns/model_free/__init__.py
1.3/specific_fns/noe/main.py
- copied, changed from r11592, 1.3/specific_fns/noe.py
Removed:
1.3/specific_fns/noe.py
Removed: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=11608&view=auto
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py (removed)
@@ -1,266 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2004-2005,2007-2009 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Python module imports.
-from math import sqrt
-from re import match
-from warnings import warn
-
-# relax module imports.
-from api_base import API_base
-from api_common import API_common
-from generic_fns import pipes
-from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
-from relax_errors import RelaxArgNotInListError, RelaxError,
RelaxNoSequenceError
-from relax_warnings import RelaxDeselectWarning
-
-
-class Noe(API_base, API_common):
- """Class containing functions for relaxation data."""
-
- def __init__(self):
- """Initialise the class by placing API_common methods into the
API."""
-
- # Place methods into the API.
- self.return_conversion_factor = self._return_no_conversion_factor
- self.return_value = self._return_value_general
-
-
- 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.
-
- @keyword spin: The spin container.
- @type spin: SpinContainer instance
- @keyword intensity: The intensity value.
- @type intensity: float
- @keyword spectrum_type: The type of spectrum, one of 'ref' or 'sat'.
- @type spectrum_type: str
- """
-
- # Add the data.
- if spectrum_type == 'ref':
- spin.ref = intensity
- elif spectrum_type == 'sat':
- spin.sat = intensity
- else:
- raise RelaxError("The spectrum type '%s' is unknown." %
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."""
-
- # Print out.
- print("\n\nOver-fit spin deselection.\n")
-
- # 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
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-
____________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Patterns
|
-
|________________________|______________|__________________________________________________|
- | | |
|
- | Reference intensity | 'ref' | '^[Rr]ef$' or '[Rr]ef[
-_][Ii]nt' |
- | | |
|
- | Saturated intensity | 'sat' | '^[Ss]at$' or '[Ss]at[
-_][Ii]nt' |
- | | |
|
- | NOE | 'noe' | '^[Nn][Oo][Ee]$'
|
-
|________________________|______________|__________________________________________________|
-
- """
-
- def return_data_name(self, param):
- """Return a unique identifying string for the steady-state NOE
parameter.
-
- @param param: The steady-state NOE parameter.
- @type param: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Reference intensity.
- if match('^[Rr]ef$', param) or match('[Rr]ef[ -_][Ii]nt', param):
- return 'ref'
-
- # Saturated intensity.
- if match('^[Ss]at$', param) or match('[Ss]at[ -_][Ii]nt', param):
- return 'sat'
-
- # NOE.
- if match('^[Nn][Oo][Ee]$', param):
- return 'noe'
-
-
- 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(param)
-
- # Reference intensity.
- if object_name == 'ref':
- return 'Reference intensity'
-
- # Saturated intensity.
- if object_name == 'sat':
- return 'Saturated intensity'
-
- # NOE.
- if object_name == 'noe':
- return '\\qNOE\\Q'
-
- # 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 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
Copied: 1.3/specific_fns/noe/__init__.py (from r11592,
1.3/specific_fns/model_free/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe/__init__.py?p2=1.3/specific_fns/noe/__init__.py&p1=1.3/specific_fns/model_free/__init__.py&r1=11592&r2=11609&rev=11609&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/__init__.py (original)
+++ 1.3/specific_fns/noe/__init__.py Fri Sep 17 18:02:20 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2009 Edward d'Auvergne
#
+# Copyright (C) 2007-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -21,32 +21,25 @@
###############################################################################
# Module docstring.
-"""The model-free specific code."""
+"""The NOE specific code."""
# The available modules.
__all__ = [ 'main',
- 'mf_minimise',
- 'molmol',
- 'results']
+ 'pymol']
# relax module imports.
-from main import Model_free_main
-from mf_minimise import Mf_minimise
-from molmol import Molmol
-from results import Results
+from main import Noe_main
from specific_fns.api_base import API_base
from specific_fns.api_common import API_common
-class Model_free(Model_free_main, Mf_minimise, Molmol, Results, API_base,
API_common):
- """Parent class containing all the model-free specific functions."""
+class Noe(Noe_main, API_base, API_common):
+ """Parent class containing all the NOE specific functions."""
def __init__(self):
"""Initialise the class by placing API_common methods into the
API."""
# Place methods into the API.
- self.base_data_loop = self._base_data_loop_spin
- self.return_error = self._return_error_relax_data
+ self.return_conversion_factor = self._return_no_conversion_factor
self.return_value = self._return_value_general
- self.test_grid_ops = self._test_grid_ops_general
Copied: 1.3/specific_fns/noe/main.py (from r11592, 1.3/specific_fns/noe.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe/main.py?p2=1.3/specific_fns/noe/main.py&p1=1.3/specific_fns/noe.py&r1=11592&r2=11609&rev=11609&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe/main.py Fri Sep 17 18:02:20 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2005,2007-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2005,2007-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -26,24 +26,14 @@
from warnings import warn
# relax module imports.
-from api_base import API_base
-from api_common import API_common
from generic_fns import pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
from relax_errors import RelaxArgNotInListError, RelaxError,
RelaxNoSequenceError
from relax_warnings import RelaxDeselectWarning
-class Noe(API_base, API_common):
+class Noe_main:
"""Class containing functions for relaxation data."""
-
- def __init__(self):
- """Initialise the class by placing API_common methods into the
API."""
-
- # Place methods into the API.
- self.return_conversion_factor = self._return_no_conversion_factor
- self.return_value = self._return_value_general
-
def _assign_function(self, spin=None, intensity=None,
spectrum_type=None):
"""Place the peak intensity data into the spin container.
r11609 - in /1.3/specific_fns: noe.py noe/ noe/__init__.py noe/main.py