Author: bugman
Date: Wed Feb 13 14:33:39 2008
New Revision: 4972
URL: http://svn.gna.org/viewcvs/relax?rev=4972&view=rev
Log:
Merged revisions 4970-4971 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4970 | bugman | 2008-02-13 14:27:32 +0100 (Wed, 13 Feb 2008) | 5 lines
Separated the set up of the specific code into the setup.py module.
The design was crap! It causes massive circular import headaches!
........
r4971 | bugman | 2008-02-13 14:30:07 +0100 (Wed, 13 Feb 2008) | 3 lines
Fixes for the imports of the get_specific_fn function.
........
Added:
branches/N_state_model/specific_fns/setup.py
- copied unchanged from r4971, 1.3/specific_fns/setup.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/minimise.py
branches/N_state_model/generic_fns/molmol.py
branches/N_state_model/generic_fns/value.py
branches/N_state_model/prompt/model_free.py
branches/N_state_model/specific_fns/__init__.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
Binary property 'svnmerge-integrated' - no diff available.
Modified: branches/N_state_model/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/minimise.py?rev=4972&r1=4971&r2=4972&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/minimise.py (original)
+++ branches/N_state_model/generic_fns/minimise.py Wed Feb 13 14:33:39 2008
@@ -27,7 +27,7 @@
from data import Data as relax_data_store
from selection import spin_loop
from relax_errors import RelaxError
-from specific_fns import get_specific_fn
+from specific_fns.setup import get_specific_fn
def reset_min_stats(data_pipe=None, spin=None):
Modified: branches/N_state_model/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/molmol.py?rev=4972&r1=4971&r2=4972&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/molmol.py (original)
+++ branches/N_state_model/generic_fns/molmol.py Wed Feb 13 14:33:39 2008
@@ -29,7 +29,7 @@
from generic_fns.selection import exists_mol_res_spin_data
from relax_errors import RelaxError, RelaxNoPipeError, RelaxNoSequenceError
from relax_io import open_write_file, test_binary
-from specific_fns import get_specific_fn
+from specific_fns.setup import get_specific_fn
command_history = ""
Modified: branches/N_state_model/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/value.py?rev=4972&r1=4971&r2=4972&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/value.py (original)
+++ branches/N_state_model/generic_fns/value.py Wed Feb 13 14:33:39 2008
@@ -31,7 +31,7 @@
from generic_fns.minimise import reset_min_stats
from generic_fns.selection import exists_mol_res_spin_data, spin_loop
from relax_errors import RelaxError, RelaxFileEmptyError, RelaxNoResError,
RelaxNoPipeError, RelaxNoSequenceError, RelaxParamSetError, RelaxRegExpError,
RelaxUnknownParamError, RelaxValueError
-from specific_fns import get_specific_fn
+from specific_fns.setup import get_specific_fn
def partition_params(val, param):
Modified: branches/N_state_model/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/model_free.py?rev=4972&r1=4971&r2=4972&view=diff
==============================================================================
--- branches/N_state_model/prompt/model_free.py (original)
+++ branches/N_state_model/prompt/model_free.py Wed Feb 13 14:33:39 2008
@@ -26,7 +26,7 @@
# relax module imports.
import help
from relax_errors import RelaxIntError, RelaxListError, RelaxListStrError,
RelaxNoneStrError, RelaxStrError
-from specific_fns import model_free_obj
+from specific_fns.setup import model_free_obj
class Model_free:
Modified: branches/N_state_model/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/__init__.py?rev=4972&r1=4971&r2=4972&view=diff
==============================================================================
--- branches/N_state_model/specific_fns/__init__.py (original)
+++ branches/N_state_model/specific_fns/__init__.py Wed Feb 13 14:33:39 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -24,278 +24,11 @@
"""This package consists of modules which are specific to the type of the
data pipe."""
-
-# relax module imports.
-from specific_fns.hybrid import Hybrid
-from specific_fns.jw_mapping import Jw_mapping
-from specific_fns.model_free import Model_free
-from specific_fns.n_state_model import N_state_model
-from specific_fns.noe import Noe
-from specific_fns.relax_fit import Relax_fit
-from relax_errors import RelaxError, RelaxFuncSetupError
-
-
# The available modules.
__all__ = [ 'base_class',
'hybrid',
'jw_mapping',
'model_free',
- 'n_state_model',
'noe',
'relax_data',
'relax_fit']
-
-# Instantiate all classes.
-hybrid_obj = Hybrid()
-jw_mapping_obj = Jw_mapping()
-model_free_obj = Model_free()
-noe_obj = Noe()
-n_state_model_obj = N_state_model()
-relax_fit_obj = Relax_fit()
-
-
-# The function for returning the requested specific function.
-def get_specific_fn(eqi, function_type, raise_error=1):
- """The function for returning the requested specific function."""
-
- # Initialise.
- function = None
-
- # Get the class instance corresponding to function_type.
- inst = get_instance(function_type)
-
- # Attempt to retrieve the function.
- try:
- # Back-calculate function.
- if eqi == 'back_calc':
- function = inst.back_calc
-
- # Calculate function.
- if eqi == 'calculate':
- function = inst.calculate
-
- # Copy function.
- if eqi == 'copy':
- function = inst.copy
-
- # Create Monte Carlo data function.
- if eqi == 'create_mc_data':
- function = inst.create_mc_data
-
- # Data structure initialisation function.
- if eqi == 'data_init':
- function = inst.data_init
-
- # Default parameter value returning function.
- if eqi == 'default_value':
- function = inst.default_value
-
- # Duplicate data function.
- if eqi == 'duplicate_data':
- function = inst.duplicate_data
-
- # Eliminate models.
- if eqi == 'eliminate':
- function = inst.eliminate
-
- # Grid search function.
- if eqi == 'grid_search':
- function = inst.grid_search
-
- # Initial Monte Carlo parameter value search function.
- if eqi == 'init_sim_values':
- function = inst.sim_init_values
-
- # Spin specific parameter determining function.
- if eqi == 'is_spin_param':
- function = inst.is_spin_param
-
- # Map bounds function.
- if eqi == 'map_bounds':
- function = inst.map_bounds
-
- # Minimise function.
- if eqi == 'minimise':
- function = inst.minimise
-
- # Model statistics.
- if eqi == 'model_stats':
- function = inst.model_statistics
-
- # Molmol macro creation.
- if eqi == 'molmol_macro':
- function = inst.molmol.macro
-
- # Number of instances.
- if eqi == 'num_instances':
- function = inst.num_instances
-
- # Overfit deselect.
- if eqi == 'overfit_deselect':
- function = inst.overfit_deselect
-
- # Pack Monte Carlo simulation data function.
- if eqi == 'pack_sim_data':
- function = inst.sim_pack_data
-
- # Parameter names function.
- if eqi == 'param_names':
- function = inst.get_param_names
-
- # Parameter values function.
- if eqi == 'param_values':
- function = inst.get_param_values
-
- # Read results file function (Columnar format).
- if eqi == 'read_columnar_results':
- function = inst.read_columnar_results
-
- # Read results file function (XML format).
- #if eqi == 'read_xml_results':
- # function = inst.read_xml_results
-
- # Data returning function.
- if eqi == 'return_data':
- function = inst.return_data
-
- # Data or parameter name returning function.
- if eqi == 'return_data_name':
- function = inst.return_data_name
-
- # Data error returning function.
- if eqi == 'return_error':
- function = inst.return_error
-
- # Factor of conversion between different parameter units returning
function.
- if eqi == 'return_conversion_factor':
- function = inst.return_conversion_factor
-
- # Grace string returning function.
- if eqi == 'return_grace_string':
- function = inst.return_grace_string
-
- # Selected simulation array returning function.
- if eqi == 'return_selected_sim':
- function = inst.sim_return_selected
-
- # Simulation chi-squared array returning function.
- if eqi == 'return_sim_chi2':
- function = inst.sim_return_chi2
-
- # Simulation parameter array returning function.
- if eqi == 'return_sim_param':
- function = inst.sim_return_param
-
- # String of the external parameter units returning function.
- if eqi == 'return_units':
- function = inst.return_units
-
- # Value and error returning function.
- if eqi == 'return_value':
- function = inst.return_value
-
- # Set error function.
- if eqi == 'set_error':
- function = inst.set_error
-
- # Set non-spin specific parameters function.
- if eqi == 'set_non_spin_params':
- function = inst.set_non_spin_params
-
- # Set the selected simulations array.
- if eqi == 'set_selected_sim':
- function = inst.set_selected_sim
-
- # Set update function.
- if eqi == 'set_update':
- function = inst.set_update
-
- # Skip function.
- if eqi == 'skip_function':
- function = inst.skip_function
-
- # Unselect function.
- if eqi == 'unselect':
- function = inst.unselect
-
- # Write results function (Columnar format).
- if eqi == 'write_columnar_results':
- function = inst.write_columnar_results
-
- # Write results function (XML format).
- #if eqi == 'write_xml_results':
- # function = inst.write_xml_results
-
- # Catch if the function is missing.
- except AttributeError:
- function = None
-
- # Raise an error if the function doesn't exist.
- if raise_error and function == None:
- # Raise the error.
- raise RelaxFuncSetupError, get_string(function_type)
-
- # Return the function.
- return function
-
-
-def get_instance(function_type):
- """Function for returning the class instance corresponding to the
function type."""
-
- # NOE calculation.
- if function_type == 'noe':
- return noe_obj
-
- # The N-state model.
- if function_type == 'N-state':
- return n_state_model_obj
-
- # Relaxation curve fitting.
- if function_type == 'relax_fit':
- return relax_fit_obj
-
- # Reduced spectral density mapping.
- if function_type == 'jw':
- return jw_mapping_obj
-
- # Model-free analysis.
- if function_type == 'mf':
- return model_free_obj
-
- # Hybrid models.
- if function_type == 'hybrid':
- return hybrid_obj
-
- # Unknown analysis.
- raise RelaxError, "The function_type " + `function_type` + " is unknown."
-
-
-def get_string(function_type):
- """Function for returning a string corresponding to the function type."""
-
- # NOE calculation.
- if function_type == 'noe':
- return "NOE calculations"
-
- # The N-state model.
- if function_type == 'N-state':
- return "the N-state model"
-
- # Relaxation curve fitting.
- if function_type == 'relax_fit':
- return "relaxation curve fitting"
-
- # Reduced spectral density mapping.
- if function_type == 'jw':
- return "reduced spectral density mapping"
-
- # Model-free analysis.
- if function_type == 'mf':
- return "Model-free analysis"
-
- # Hybrid models.
- if function_type == 'hybrid':
- return "hybrid models"
-
- # Unknown analysis.
- raise RelaxError, "The function_type " + `function_type` + " is unknown."
r4972 - in /branches/N_state_model: ./ generic_fns/ prompt/ specific_fns/