Author: bugman
Date: Tue Nov 23 14:02:38 2010
New Revision: 11698
URL: http://svn.gna.org/viewcvs/relax?rev=11698&view=rev
Log:
Brought the relaxation dispersion branch into sync with the 1.3 line.
There were many design changes within the 1.3 line that required that the old
relaxation dispersion
code be updated.
Modified:
branches/relax_disp/dep_check.py
branches/relax_disp/prompt/relax_disp.py
branches/relax_disp/specific_fns/relax_disp.py
branches/relax_disp/specific_fns/relax_fit.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
Modified: branches/relax_disp/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/dep_check.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/dep_check.py (original)
+++ branches/relax_disp/dep_check.py Tue Nov 23 14:02:38 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2009 Edward d'Auvergne
#
+# Copyright (C) 2008-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -173,7 +173,7 @@
try:
from maths_fns.relax_fit import setup
del setup
- C_module_fit = True
+ C_module_exp_fn = True
except ImportError, message:
# The OS.
system = platform.system()
@@ -183,14 +183,14 @@
if system == 'Windows' or system == 'Microsoft':
file = 'relax_fit.pyd'
if not access('maths_fns' + sep + file, F_OK):
- C_module_fit_mesg = "ImportError: relaxation curve fitting is
unavailable, the corresponding C modules have not been compiled."
+ C_module_exp_fn_mesg = "ImportError: relaxation curve fitting is
unavailable, the corresponding C modules have not been compiled."
# Show the full error.
else:
- C_module_fit_mesg = "ImportError: " + message[0] + "\nRelaxation
curve fitting is unavailable, try compiling the C modules."
+ C_module_exp_fn_mesg = "ImportError: " + message[0] + "\nRelaxation
curve fitting is unavailable, try compiling the C modules."
# Set the flag.
- C_module_fit = False
+ C_module_exp_fn = False
# Relaxation dispersion.
try:
Modified: branches/relax_disp/prompt/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/relax_disp.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/prompt/relax_disp.py (original)
+++ branches/relax_disp/prompt/relax_disp.py Tue Nov 23 14:02:38 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2010 Edward d'Auvergne
#
# Copyright (C) 2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
@@ -25,27 +25,14 @@
"""Module containing the 'relax_disp' user function class."""
__docformat__ = 'plaintext'
-# Python module imports.
-import sys
-
# relax module imports.
-import help
+from base_class import User_fn_class
from relax_errors import RelaxNoneNumError, RelaxNumError, RelaxStrError
from specific_fns.setup import relax_disp_obj
-class Relax_disp:
- def __init__(self, relax):
- # Help.
- self.__relax_help__ = \
- """Class for relaxation dispersion curve fitting."""
-
- # Add the generic help string.
- self.__relax_help__ = self.__relax_help__ + "\n" +
help.relax_class_help
-
- # Place relax in the class namespace.
- self.__relax__ = relax
-
+class Relax_disp(User_fn_class):
+ """Class for relaxation dispersion user functions."""
def calc_r2eff(self, exp_type='cpmg', id=None, delayT=None,
int_cpmg=1.0, int_ref=1.0):
"""Calculate the effective transversal relaxation rate from the peak
intensities.
@@ -89,8 +76,8 @@
"""
# Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_disp.calc_r2eff("
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "relax_disp.calc_r2eff("
text = text + "exp_type=" + `exp_type`
text = text + ", id=" + `id`
text = text + ", delayT=" + `delayT`
@@ -149,8 +136,8 @@
"""
# Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "delayT("
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "delayT("
text = text + "id=" + `id`
text = text + ", delayT=" + `delayT` + ")"
print text
@@ -201,8 +188,8 @@
"""
# Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_disp.cpmg_frq("
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "relax_disp.cpmg_frq("
text = text + ", cpmg_frq=" + `cpmg_frq`
text = text + "spectrum_id=" + `spectrum_id` + ")"
print text
@@ -244,8 +231,8 @@
"""
# Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_disp.exp_type("
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "relax_disp.exp_type("
text = text + "exp_type=" + `exp_type` + ")"
print text
@@ -303,8 +290,8 @@
"""
# Function intro text.
- if self.__relax__.interpreter.intro:
- text = sys.ps3 + "relax_disp.select_model("
+ if self._exec_info.intro:
+ text = self._exec_info.ps3 + "relax_disp.select_model("
text = text + "model=" + `model` + ")"
print text
Modified: branches/relax_disp/specific_fns/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_disp.py (original)
+++ branches/relax_disp/specific_fns/relax_disp.py Tue Nov 23 14:02:38 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2010 Edward d'Auvergne
#
# Copyright (C) 2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
@@ -30,8 +30,9 @@
from re import match, search
# relax module imports.
+from api_base import API_base
+from api_common import API_common
from dep_check import C_module_disp
-from base_class import Common_functions
from generic_fns import pipes
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_loop
from minfx.generic import generic_minimise
@@ -42,7 +43,7 @@
from maths_fns.relax_disp import setup, func, dfunc, d2func, back_calc_I
-class Relax_disp(Common_functions):
+class Relax_disp(API_base, API_common):
"""Class containing functions for relaxation dispersion curve fitting."""
def assemble_param_vector(self, spin=None, sim_index=None):
Modified: branches/relax_disp/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_fit.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_fit.py (original)
+++ branches/relax_disp/specific_fns/relax_fit.py Tue Nov 23 14:02:38 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2009 Edward d'Auvergne
#
+# Copyright (C) 2004-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -41,7 +41,7 @@
from relax_warnings import RelaxDeselectWarning
# C modules.
-if C_module_fit:
+if C_module_exp_fn:
from maths_fns.relax_fit import setup, func, dfunc, d2func, back_calc_I
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Nov 23
14:02:38 2010
@@ -22,27 +22,24 @@
###############################################################################
# Python module imports.
+import __main__
from os import sep
from shutil import rmtree
-from string import split
-import sys
from tempfile import mkdtemp
-from unittest import TestCase
# relax module imports.
+from base_classes import SystemTestCase
from data import Relax_data_store; ds = Relax_data_store()
-from generic_fns.mol_res_spin import spin_index_loop
-from generic_fns import pipes
-class Relax_disp(TestCase):
+class Relax_disp(SystemTestCase):
"""Class for testing various aspects specific to relaxation dispersion
curve-fitting."""
def setUp(self):
"""Set up for all the functional tests."""
# Create the data pipe.
- self.relax.interpreter._Pipe.create('relax_disp', 'relax_disp')
+ self.interpreter.pipe.create('relax_disp', 'relax_disp')
# Create a temporary directory for dumping files.
ds.tmpdir = mkdtemp()
@@ -64,7 +61,7 @@
fast-exchange limit."""
# Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py')
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_fast.py')
def test_curve_fitting_cpmg_slow(self):
@@ -72,22 +69,19 @@
slow-exchange limit."""
# Execute the script.
- self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py')
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp_cpmg_slow.py')
def test_read_r2eff(self):
"""Test the reading of a file containing r2eff values."""
- # Get the current data pipe.
- cdp = pipes.get_pipe()
-
# Create the sequence data, and name the spins.
- self.relax.interpreter._Residue.create(1, 'Gly')
- self.relax.interpreter._Residue.create(2, 'Gly')
- self.relax.interpreter._Residue.create(3, 'Gly')
+ self.interpreter.residue.create(1, 'Gly')
+ self.interpreter.residue.create(2, 'Gly')
+ self.interpreter.residue.create(3, 'Gly')
# Read the file.
- self.relax.interpreter._Relax_data.read('R2eff', '600', 600 * 1e6,
'r2eff.out', dir=sys.path[-1] +
"/test_suite/shared_data/curve_fitting_disp/r2eff")
+ self.interpreter.relax_data.read('R2eff', '600', 600 * 1e6,
'r2eff.out', dir=__main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'r2eff')
# Test the data.
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_fast.py
Tue Nov 23 14:02:38 2010
@@ -1,17 +1,19 @@
# Script for CPMG relaxation dispersion curve fitting in the fast-exchange
limit.
-import sys
+# Python module imports.
+import __main__
+from os import sep
# Create the data pipe.
pipe.create('rex', 'relax_disp')
# The path to the data files.
-data_path_1 = sys.path[-1] +
'/test_suite/shared_data/curve_fitting_disp/Hansen/500_MHz'
-data_path_2 = sys.path[-1] +
'/test_suite/shared_data/curve_fitting_disp/Hansen/800_MHz'
+data_path1 = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
+data_path2 = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'800_MHz'
# Load the sequence.
-sequence.read('fake_sequence.in', dir=sys.path[-1] +
'/test_suite/shared_data/curve_fitting_disp/Hansen')
+sequence.read('fake_sequence.in', dir=__main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen',
res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
Modified:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp_cpmg_slow.py
Tue Nov 23 14:02:38 2010
@@ -1,16 +1,18 @@
# Script for CPMG relaxation dispersion curve fitting in the slow-exchange
limit.
-import sys
+# Python module imports.
+import __main__
+from os import sep
# Create the data pipe.
pipe.create('rex', 'relax_disp')
# The path to the data files.
-data_path = sys.path[-1] +
'/test_suite/shared_data/curve_fitting_disp/Hansen/500_MHz'
+data_path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen'+sep+'500_MHz'
# Load the sequence.
-sequence.read('fake_sequence.in', dir=sys.path[-1] +
'/test_suite/shared_data/curve_fitting_disp/Hansen')
+sequence.read('fake_sequence.in', dir=__main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting_disp'+sep+'Hansen',
res_num_col=1, res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
Modified: branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py?rev=11698&r1=11697&r2=11698&view=diff
==============================================================================
--- branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py
(original)
+++ branches/relax_disp/test_suite/unit_tests/_prompt/test_relax_disp.py Tue
Nov 23 14:02:38 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
+# Copyright (C) 2008-2010 Edward d'Auvergne
#
# Copyright (C) 2009 Sebastien Morin
#
#
#
# This file is part of the program relax.
#
@@ -30,14 +30,13 @@
# Unit test imports.
from data_types import DATA_TYPES
-import fake_relax
class Test_relax_disp(TestCase):
"""Unit tests for the functions of the 'prompt.relax_disp' module."""
# Instantiate the user function class.
- relax_disp_fns = Relax_disp(fake_relax.fake_instance())
+ relax_disp_fns = Relax_disp()
def test_relax_calc_r2eff_argfail_exp_type(self):
r11698 - in /branches/relax_disp: ./ prompt/ specific_fns/ test_suite/system_tests/ test_suite/system_tests/scripts/ test_su...