Author: bugman
Date: Wed Jan 18 15:40:42 2012
New Revision: 15172
URL: http://svn.gna.org/viewcvs/relax?rev=15172&view=rev
Log:
The reduced spectral density analysis code now uses the SPIN_PARAMS API
object.
Modified:
branches/spec_api/specific_fns/jw_mapping.py
branches/spec_api/test_suite/system_tests/jw_mapping.py
branches/spec_api/test_suite/system_tests/scripts/jw_mapping.py
Modified: branches/spec_api/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/jw_mapping.py?rev=15172&r1=15171&r2=15172&view=diff
==============================================================================
--- branches/spec_api/specific_fns/jw_mapping.py (original)
+++ branches/spec_api/specific_fns/jw_mapping.py Wed Jan 18 15:40:42 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2011 Edward d'Auvergne
#
+# Copyright (C) 2004-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -46,11 +46,23 @@
self.create_mc_data = self._create_mc_relax_data
self.model_loop = self._model_loop_spin
self.return_conversion_factor = self._return_no_conversion_factor
+ self.return_data_name = self._return_data_name_spin
self.return_error = self._return_error_relax_data
+ self.return_grace_string = self._return_grace_string_spin
+ self.return_units = self._return_units_spin
self.return_value = self._return_value_general
self.set_param_values = self._set_param_values_spin
self.set_selected_sim = self._set_selected_sim_spin
self.sim_pack_data = self._sim_pack_relax_data
+
+ # Set up the spin parameters.
+ self.SPIN_PARAMS.add('j0', string='J(0)', grace_string='\\qJ(0)\\Q')
+ self.SPIN_PARAMS.add('jwx', grace_string='\\qJ(\\xw\\f{}\\sX\\N)\\Q')
+ self.SPIN_PARAMS.add('jwh', grace_string='\\qJ(\\xw\\f{}\\sH\\N)\\Q')
+ self.SPIN_PARAMS.add('r', default=NH_BOND_LENGTH, units='Angstrom',
grace_string='Bond length')
+ self.SPIN_PARAMS.add('csa', default=N15_CSA, units='ppm',
grace_string='\\qCSA\\Q')
+ self.SPIN_PARAMS.add('heteronuc_type', default='15N')
+ self.SPIN_PARAMS.add('proton_type', default='1H')
def _set_frq(self, frq=None):
@@ -278,31 +290,6 @@
"""]
- def default_value(self, param):
- """The default J(w) mapping parameter values.
-
- @param param: The J(w) mapping parameter.
- @type param: str
- @return: The default value.
- @rtype: float
- """
-
- # Bond length.
- if param == 'r':
- return NH_BOND_LENGTH
-
- # CSA.
- elif param == 'csa':
- return N15_CSA
-
- # Heteronucleus type.
- elif param == 'heteronuc_type':
- return '15N'
-
- # Proton type.
- elif param == 'proton_type':
- return '1H'
-
def overfit_deselect(self):
"""Deselect spins which have insufficient data to support
calculation."""
@@ -332,128 +319,27 @@
return_data_name_doc = ["Reduced spectral density mapping data type
string matching patterns", """
-
____________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Patterns
|
-
|________________________|__________________|______________________________________________|
- | | |
|
- | J(0) | 'j0' | '^[Jj]0$' or
'[Jj]\(0\)' |
- | | |
|
- | J(wX) | 'jwx' | '^[Jj]w[Xx]$' or
'[Jj]\(w[Xx]\)' |
- | | |
|
- | J(wH) | 'jwh' | '^[Jj]w[Hh]$' or
'[Jj]\(w[Hh]\)' |
- | | |
|
- | Bond length | 'r' | '^r$' or '[Bb]ond[
-_][Ll]ength' |
- | | |
|
- | CSA | 'csa' | '^[Cc][Ss][Aa]$'
|
- | | |
|
- | Heteronucleus type | 'heteronuc_type' | '^[Hh]eteronucleus$'
|
- | | |
|
- | Proton type | 'proton_type' | '^[Pp]roton$'
|
-
|________________________|__________________|______________________________________________|
+ _____________________________________________
+ | | |
+ | Data type | Object name |
+ |________________________|__________________|
+ | | |
+ | J(0) | 'j0' |
+ | | |
+ | J(wX) | 'jwx' |
+ | | |
+ | J(wH) | 'jwh' |
+ | | |
+ | Bond length | 'r' |
+ | | |
+ | CSA | 'csa' |
+ | | |
+ | Heteronucleus type | 'heteronuc_type' |
+ | | |
+ | Proton type | 'proton_type' |
+ |________________________|__________________|
"""]
-
- def return_data_name(self, param):
- """Return a unique identifying string for the J(w) mapping parameter.
-
- @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$', param) or search('[Jj]\(0\)', param):
- return 'j0'
-
- # J(wX).
- if search('^[Jj]w[Xx]$', param) or search('[Jj]\(w[Xx]\)', param):
- return 'jwx'
-
- # J(wH).
- if search('^[Jj]w[Hh]$', param) or search('[Jj]\(w[Hh]\)', param):
- return 'jwh'
-
- # Bond length.
- if search('^r$', param) or search('[Bb]ond[ -_][Ll]ength', param):
- return 'r'
-
- # CSA.
- if search('^[Cc][Ss][Aa]$', param):
- return 'csa'
-
- # Heteronucleus type.
- if search('^[Hh]eteronucleus$', param):
- return 'heteronuc_type'
-
- # Proton type.
- if search('^[Pp]roton$', param):
- return 'proton_type'
-
-
- 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(param)
-
- # J(0).
- if object_name == 'j0':
- return '\\qJ(0)\\Q'
-
- # J(wX).
- elif object_name == 'jwx':
- return '\\qJ(\\xw\\f{}\\sX\\N)\\Q'
-
- # J(wH).
- elif object_name == 'jwh':
- return '\\qJ(\\xw\\f{}\\sH\\N)\\Q'
-
- # Bond length.
- elif object_name == 'r':
- return 'Bond length'
-
- # CSA.
- elif object_name == 'csa':
- return '\\qCSA\\Q'
-
-
- 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 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(param)
-
- # Bond length (Angstrom).
- if object_name == 'r':
- return 'Angstrom'
-
- # CSA (ppm).
- elif object_name == 'csa':
- return 'ppm'
set_doc = ["Reduced spectral density mapping set details", """
Modified: branches/spec_api/test_suite/system_tests/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/jw_mapping.py?rev=15172&r1=15171&r2=15172&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/jw_mapping.py (original)
+++ branches/spec_api/test_suite/system_tests/jw_mapping.py Wed Jan 18
15:40:42 2012
@@ -68,10 +68,10 @@
self.interpreter.relax_data.read(ri_id=ri_ids[i],
ri_type=ri_type[i], frq=frq[i], file=data_paths[i], res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
# Set r, csa, heteronucleus type, and proton type.
- self.interpreter.value.set(NH_BOND_LENGTH, 'bond_length')
+ self.interpreter.value.set(NH_BOND_LENGTH, 'r')
self.interpreter.value.set(N15_CSA, 'csa')
- self.interpreter.value.set('15N', 'heteronucleus')
- self.interpreter.value.set('1H', 'proton')
+ self.interpreter.value.set('15N', 'heteronuc_type')
+ self.interpreter.value.set('1H', 'proton_type')
# Select the frequency.
self.interpreter.jw_mapping.set_frq(frq=600.0 * 1e6)
@@ -104,7 +104,7 @@
# Try to set the values.
bond_length = NH_BOND_LENGTH
csa = N15_CSA
- self.interpreter.value.set(bond_length, 'bond_length')
+ self.interpreter.value.set(bond_length, 'r')
self.interpreter.value.set(csa, 'csa')
# Loop over residues.
Modified: branches/spec_api/test_suite/system_tests/scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/jw_mapping.py?rev=15172&r1=15171&r2=15172&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/scripts/jw_mapping.py (original)
+++ branches/spec_api/test_suite/system_tests/scripts/jw_mapping.py Wed Jan
18 15:40:42 2012
@@ -21,11 +21,11 @@
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
# Set the nuclei types
-value.set('15N', 'heteronucleus')
-value.set('1H', 'proton')
+value.set('15N', 'heteronuc_type')
+value.set('1H', 'proton_type')
# Set the bond length and CSA values.
-value.set(1.02 * 1e-10, 'bond_length')
+value.set(1.02 * 1e-10, 'r')
value.set(-172 * 1e-6, 'csa')
# Set the frequency.
r15172 - in /branches/spec_api: specific_fns/ test_suite/system_tests/ test_suite/system_tests/scripts/