Author: bugman
Date: Tue Oct 21 16:01:01 2008
New Revision: 7881
URL: http://svn.gna.org/viewcvs/relax?rev=7881&view=rev
Log:
Created the empty user function class 'spectrum'.
Added:
branches/spectral_errors/prompt/spectrum.py
- copied, changed from r7879,
branches/spectral_errors/prompt/model_free.py
Modified:
branches/spectral_errors/prompt/interpreter.py
Modified: branches/spectral_errors/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/interpreter.py?rev=7881&r1=7880&r2=7881&view=diff
==============================================================================
--- branches/spectral_errors/prompt/interpreter.py (original)
+++ branches/spectral_errors/prompt/interpreter.py Tue Oct 21 16:01:01 2008
@@ -82,6 +82,7 @@
from pipe import Pipe
from select import Select
from sequence import Sequence
+from spectrum import Spectrum
from spin import Spin
from state import State
from deselect import Deselect
@@ -166,6 +167,7 @@
self._Pipe = Pipe(relax)
self._Select = Select(relax)
self._Sequence = Sequence(relax)
+ self._Spectrum = Spectrum(relax)
self._Spin = Spin(relax)
self._State = State(relax)
self._Deselect = Deselect(relax)
@@ -235,6 +237,7 @@
pipe = self._Pipe
select = self._Select
sequence = self._Sequence
+ spectrum = self._Spectrum
spin = self._Spin
state = self._State
deselect = self._Deselect
Copied: branches/spectral_errors/prompt/spectrum.py (from r7879,
branches/spectral_errors/prompt/model_free.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/prompt/spectrum.py?p2=branches/spectral_errors/prompt/spectrum.py&p1=branches/spectral_errors/prompt/model_free.py&r1=7879&r2=7881&rev=7881&view=diff
==============================================================================
--- branches/spectral_errors/prompt/model_free.py (original)
+++ branches/spectral_errors/prompt/spectrum.py Tue Oct 21 16:01:01 2008
@@ -26,10 +26,9 @@
# relax module imports.
import help
from relax_errors import RelaxIntError, RelaxListError, RelaxListStrError,
RelaxNoneStrError, RelaxStrError
-from specific_fns.setup import model_free_obj
-class Model_free:
+class Spectrum:
def __init__(self, relax):
# Help.
self.__relax_help__ = \
@@ -40,333 +39,3 @@
# Place relax in the class namespace.
self.__relax__ = relax
-
-
- def create_model(self, model=None, equation=None, params=None,
spin_id=None):
- """Function to create a model-free model.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- model: The name of the model-free model.
-
- equation: The model-free equation.
-
- params: The array of parameter names of the model.
-
- spin_id: The spin identification string.
-
-
- Model-free equation
- ~~~~~~~~~~~~~~~~~~~
-
- 'mf_orig' selects the original model-free equations with parameters
{S2, te}.
- 'mf_ext' selects the extended model-free equations with parameters
{S2f, tf, S2, ts}.
- 'mf_ext2' selects the extended model-free equations with parameters
{S2f, tf, S2s, ts}.
-
-
- Model-free parameters
- ~~~~~~~~~~~~~~~~~~~~~
-
- The following parameters are accepted for the original model-free
equation:
-
- 'S2': The square of the generalised order parameter.
- 'te': The effective correlation time.
-
- The following parameters are accepted for the extended model-free
equation:
-
- 'S2f': The square of the generalised order parameter of the
faster motion.
- 'tf': The effective correlation time of the faster motion.
- 'S2': The square of the generalised order parameter S2 = S2f *
S2s.
- 'ts': The effective correlation time of the slower motion.
-
- The following parameters are accepted for the extended 2 model-free
equation:
-
- 'S2f': The square of the generalised order parameter of the
faster motion.
- 'tf': The effective correlation time of the faster motion.
- 'S2s': The square of the generalised order parameter of the
slower motion.
- 'ts': The effective correlation time of the slower motion.
-
- The following parameters are accepted for all equations:
-
- 'Rex': The chemical exchange relaxation.
- 'r': The average bond length <r>.
- 'CSA': The chemical shift anisotropy.
-
-
- Spin identification string
- ~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- If 'spin_id' is supplied then the model will only be created for the
corresponding spins.
- Otherwise the model will be created for all spins.
-
-
- Examples
- ~~~~~~~~
-
- The following commands will create the model-free model 'm1' which
is based on the original
- model-free equation and contains the single parameter 'S2'.
-
- relax> model_free.create_model('m1', 'mf_orig', ['S2'])
- relax> model_free.create_model(model='m1', params=['S2'],
equation='mf_orig')
-
-
- The following commands will create the model-free model
'large_model' which is based on the
- extended model-free equation and contains the seven parameters
'S2f', 'tf', 'S2', 'ts',
- 'Rex', 'CSA', 'r'.
-
- relax> model_free.create_model('large_model', 'mf_ext', ['S2f',
'tf', 'S2', 'ts', 'Rex',
- 'CSA', 'r'])
- relax> model_free.create_model(model='large_model', params=['S2f',
'tf', 'S2', 'ts', 'Rex',
- 'CSA', 'r'], equation='mf_ext')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "model_free.create_model("
- text = text + "model=" + `model`
- text = text + ", equation=" + `equation`
- text = text + ", params=" + `params`
- text = text + ", spin_id=" + `spin_id` + ")"
- print text
-
- # Model argument.
- if type(model) != str:
- raise RelaxStrError, ('model', model)
-
- # Equation.
- if type(equation) != str:
- raise RelaxStrError, ('model-free equation', equation)
-
- # Parameter types.
- if type(params) != list:
- raise RelaxListStrError, ('parameters', params)
- else:
- # Empty list.
- if params == []:
- raise RelaxListStrError, ('parameters', params)
-
- # Check the values.
- for i in xrange(len(params)):
- if type(params[i]) != str:
- raise RelaxListStrError, ('parameters', params)
-
- # Spin identification string.
- if spin_id != None and type(spin_id) != str:
- raise RelaxNoneStrError, ('spin identification string', spin_id)
-
- # Execute the functional code.
- model_free_obj.create_model(model=model, equation=equation,
params=params, spin_id=spin_id)
-
-
- def delete(self):
- """Function for deleting all model-free data from the current data
pipe.
-
- Examples
- ~~~~~~~~
-
- To delete all model-free data, type:
-
- relax> model_free.delete()
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "model_free.delete()"
- print text
-
- # Execute the functional code.
- model_free_obj.delete()
-
-
- def remove_tm(self, spin_id=None):
- """Function for removing the local tm parameter from a model.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- spin_id: The spin identification string.
-
-
- Description
- ~~~~~~~~~~~
-
- This function will remove the local tm parameter from the model-free
parameter set. If
- there is no local tm parameter within the set nothing will happen.
-
- If no spin identification string is given, then the function will
apply to all spins.
-
-
- Examples
- ~~~~~~~~
-
- The following command will remove the parameter 'tm':
-
- relax> model_free.remove_tm()
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "model_free.remove_tm("
- text = text + "spin_id=" + `spin_id` + ")"
- print text
-
- # Spin identification string.
- if spin_id != None and type(spin_id) != str:
- raise RelaxNoneStrError, ('spin identification string', spin_id)
-
- # Execute the functional code.
- model_free_obj.remove_tm(spin_id=spin_id)
-
-
- def select_model(self, model=None, spin_id=None):
- """Function for the selection of a preset model-free model.
-
- Keyword Arguments
- ~~~~~~~~~~~~~~~~~
-
- model: The name of the preset model.
-
-
- The preset models
- ~~~~~~~~~~~~~~~~~
-
- The standard preset model-free models are
- 'm0' = {},
- 'm1' = {S2},
- 'm2' = {S2, te},
- 'm3' = {S2, Rex},
- 'm4' = {S2, te, Rex},
- 'm5' = {S2f, S2, ts},
- 'm6' = {S2f, tf, S2, ts},
- 'm7' = {S2f, S2, ts, Rex},
- 'm8' = {S2f, tf, S2, ts, Rex},
- 'm9' = {Rex}.
-
- The preset model-free models with optimisation of the CSA value are
- 'm10' = {CSA},
- 'm11' = {CSA, S2},
- 'm12' = {CSA, S2, te},
- 'm13' = {CSA, S2, Rex},
- 'm14' = {CSA, S2, te, Rex},
- 'm15' = {CSA, S2f, S2, ts},
- 'm16' = {CSA, S2f, tf, S2, ts},
- 'm17' = {CSA, S2f, S2, ts, Rex},
- 'm18' = {CSA, S2f, tf, S2, ts, Rex},
- 'm19' = {CSA, Rex}.
-
- The preset model-free models with optimisation of the bond length are
- 'm20' = {r},
- 'm21' = {r, S2},
- 'm22' = {r, S2, te},
- 'm23' = {r, S2, Rex},
- 'm24' = {r, S2, te, Rex},
- 'm25' = {r, S2f, S2, ts},
- 'm26' = {r, S2f, tf, S2, ts},
- 'm27' = {r, S2f, S2, ts, Rex},
- 'm28' = {r, S2f, tf, S2, ts, Rex},
- 'm29' = {r, CSA, Rex}.
-
- The preset model-free models with both optimisation of the bond
length and CSA are
- 'm30' = {r, CSA},
- 'm31' = {r, CSA, S2},
- 'm32' = {r, CSA, S2, te},
- 'm33' = {r, CSA, S2, Rex},
- 'm34' = {r, CSA, S2, te, Rex},
- 'm35' = {r, CSA, S2f, S2, ts},
- 'm36' = {r, CSA, S2f, tf, S2, ts},
- 'm37' = {r, CSA, S2f, S2, ts, Rex},
- 'm38' = {r, CSA, S2f, tf, S2, ts, Rex},
- 'm39' = {r, CSA, Rex}.
-
- Warning: The models in the thirties range fail when using standard
R1, R2, and NOE
- relaxation data. This is due to the extreme flexibly of these
models where a change in the
- parameter 'r' is compensated by a corresponding change in the
parameter 'CSA' and
- vice versa.
-
-
- Additional preset model-free models, which are simply extensions of
the above models with
- the addition of a local tm parameter are:
- 'tm0' = {tm},
- 'tm1' = {tm, S2},
- 'tm2' = {tm, S2, te},
- 'tm3' = {tm, S2, Rex},
- 'tm4' = {tm, S2, te, Rex},
- 'tm5' = {tm, S2f, S2, ts},
- 'tm6' = {tm, S2f, tf, S2, ts},
- 'tm7' = {tm, S2f, S2, ts, Rex},
- 'tm8' = {tm, S2f, tf, S2, ts, Rex},
- 'tm9' = {tm, Rex}.
-
- The preset model-free models with optimisation of the CSA value are
- 'tm10' = {tm, CSA},
- 'tm11' = {tm, CSA, S2},
- 'tm12' = {tm, CSA, S2, te},
- 'tm13' = {tm, CSA, S2, Rex},
- 'tm14' = {tm, CSA, S2, te, Rex},
- 'tm15' = {tm, CSA, S2f, S2, ts},
- 'tm16' = {tm, CSA, S2f, tf, S2, ts},
- 'tm17' = {tm, CSA, S2f, S2, ts, Rex},
- 'tm18' = {tm, CSA, S2f, tf, S2, ts, Rex},
- 'tm19' = {tm, CSA, Rex}.
-
- The preset model-free models with optimisation of the bond length are
- 'tm20' = {tm, r},
- 'tm21' = {tm, r, S2},
- 'tm22' = {tm, r, S2, te},
- 'tm23' = {tm, r, S2, Rex},
- 'tm24' = {tm, r, S2, te, Rex},
- 'tm25' = {tm, r, S2f, S2, ts},
- 'tm26' = {tm, r, S2f, tf, S2, ts},
- 'tm27' = {tm, r, S2f, S2, ts, Rex},
- 'tm28' = {tm, r, S2f, tf, S2, ts, Rex},
- 'tm29' = {tm, r, CSA, Rex}.
-
- The preset model-free models with both optimisation of the bond
length and CSA are
- 'tm30' = {tm, r, CSA},
- 'tm31' = {tm, r, CSA, S2},
- 'tm32' = {tm, r, CSA, S2, te},
- 'tm33' = {tm, r, CSA, S2, Rex},
- 'tm34' = {tm, r, CSA, S2, te, Rex},
- 'tm35' = {tm, r, CSA, S2f, S2, ts},
- 'tm36' = {tm, r, CSA, S2f, tf, S2, ts},
- 'tm37' = {tm, r, CSA, S2f, S2, ts, Rex},
- 'tm38' = {tm, r, CSA, S2f, tf, S2, ts, Rex},
- 'tm39' = {tm, r, CSA, Rex}.
-
-
-
- Spin identification string
- ~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- If 'spin_id' is supplied then the model will only be selected for
the corresponding spins.
- Otherwise the model will be selected for all spins.
-
-
-
- Examples
- ~~~~~~~~
-
- To pick model 'm1' for all selected spins, type:
-
- relax> model_free.select_model('m1')
- relax> model_free.select_model(model='m1')
- """
-
- # Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "model_free.select_model("
- text = text + "model=" + `model`
- text = text + ", spin_id=" + `spin_id` + ")"
- print text
-
- # Model argument.
- if type(model) != str:
- raise RelaxStrError, ('model', model)
-
- # Spin identification string.
- if spin_id != None and type(spin_id) != str:
- raise RelaxNoneStrError, ('spin identification string', spin_id)
-
- # Execute the functional code.
- model_free_obj.select_model(model=model, spin_id=spin_id)
r7881 - in /branches/spectral_errors/prompt: interpreter.py spectrum.py