Author: bugman
Date: Sat Mar 23 20:51:12 2013
New Revision: 19081
URL: http://svn.gna.org/viewcvs/relax?rev=19081&view=rev
Log:
Renamed the pipe_control.frame_order module to lib.frame_order.format.
Added:
trunk/lib/frame_order/format.py
- copied unchanged from r19080, trunk/pipe_control/frame_order.py
Removed:
trunk/pipe_control/frame_order.py
Modified:
trunk/target_functions/frame_order/__init__.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
Removed: trunk/pipe_control/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/frame_order.py?rev=19080&view=auto
==============================================================================
--- trunk/pipe_control/frame_order.py (original)
+++ trunk/pipe_control/frame_order.py (removed)
@@ -1,127 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2009-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program 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 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module containing functions related to the Frame Order theories."""
-
-# Python module imports.
-from numpy import array, matrix
-import sys
-
-# relax module imports.
-from lib.float import isNaN
-
-
-def print_frame_order_2nd_degree(daeg, name=None, epsilon=1e-15,
integer=False, dot=False, comma=True, file=None):
- """Nicely print out the Frame Order matrix of the 2nd degree.
-
- @param daeg: The 3D, rank-4 Frame Order matrix.
- @type daeg: numpy 3D, rank-4 array
- @keyword name: The name of the matrix.
- @type name: None or str
- @keyword epsilon: The minimum value, below which is considered zero.
- @type epsilon: float
- @keyword integer: A flag which if true will only print the integer
part of the number.
- @type integer: bool
- @keyword dot: A flag which if true replaces all zeros with dot
characters.
- @type dot: bool
- @keyword comma: A flag which if true causes commas to be printed
between the elements.
- @type comma: bool
- @keyword file: The file object to write to.
- @type file: file object
- """
-
- # Default name.
- if not name:
- name = 'Frame Order matrix, 2nd degree'
-
- # No file given, so send to STDOUT.
- if file == None:
- file = sys.stdout
-
- # Header and first row start.
- file.write("\n%s:\n" % name)
- file.write('[[')
-
- # Convert to an array, if necessary.
- if isinstance(daeg, matrix):
- daeg = array(daeg)
-
- # Loop over the rows.
- for i in range(len(daeg)):
- # 2nd to last row start.
- if i != 0:
- file.write(' [')
-
- # Row end character.
- char2 = ''
- if comma:
- char2 = ','
- if i == len(daeg) - 1:
- char2 = ']'
-
- # Loop over the columns.
- for j in range(len(daeg[i])):
- # Column end character.
- char1 = ''
- if comma:
- char1 = ','
- if j == len(daeg[i]) - 1:
- char1 = ']%s\n' % char2
-
- # Write out the elements.
- if abs(daeg[i, j]) > epsilon:
- # Integer printout.
- if integer:
- val = int(daeg[i, j])
- format = "%4i%s"
-
- # Float printout.
- else:
- val = daeg[i, j]
- format = "%10.4f%s"
-
- # NaN.
- elif isNaN(daeg[i, j]):
- val = 'NaN'
- if integer:
- format = "%4i%s"
- else:
- format = "%10s%s"
-
- # Write out the zero elements.
- else:
- # Integer printout.
- if integer:
- format = "%4s%s"
-
- # Float printout.
- else:
- format = "%10s%s"
-
- # The character.
- if dot:
- val = '.'
- else:
- val = '0'
-
- # Write.
- file.write(format % (val, char1))
Modified: trunk/target_functions/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order/__init__.py?rev=19081&r1=19080&r2=19081&view=diff
==============================================================================
--- trunk/target_functions/frame_order/__init__.py (original)
+++ trunk/target_functions/frame_order/__init__.py Sat Mar 23 20:51:12 2013
@@ -30,7 +30,7 @@
# relax module imports.
from lib.float import isNaN
-from pipe_control.frame_order import print_frame_order_2nd_degree
+from lib.frame_order.format import print_frame_order_2nd_degree
from extern.sobol.sobol_lib import i4_sobol
from lib.alignment.alignment_tensor import to_5D, to_tensor
from target_functions.chi2 import chi2
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=19081&r1=19080&r2=19081&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/generate_base.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/generate_base.py Sat Mar 23
20:51:12 2013
@@ -31,7 +31,7 @@
# relax module imports.
from pipe_control.angles import wrap_angles
-from pipe_control.frame_order import print_frame_order_2nd_degree
+from lib.frame_order.format import print_frame_order_2nd_degree
from pipe_control.mol_res_spin import spin_loop
from pipe_control.interatomic import interatomic_loop
from lib.geometry.coord_transform import cartesian_to_spherical
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py?rev=19081&r1=19080&r2=19081&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order_matrix.py
Sat Mar 23 20:51:12 2013
@@ -5,7 +5,7 @@
# relax module imports.
from lib.algebra.kronecker_product import kron_prod
-from pipe_control.frame_order import print_frame_order_2nd_degree
+from lib.frame_order.format import print_frame_order_2nd_degree
# Load the matrices.
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py?rev=19081&r1=19080&r2=19081&view=diff
==============================================================================
---
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py
(original)
+++
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix.py
Sat Mar 23 20:51:12 2013
@@ -1,6 +1,6 @@
from numpy import array, float64, zeros
-from pipe_control.frame_order import print_frame_order_2nd_degree
+from lib.frame_order.format import print_frame_order_2nd_degree
from lib.algebra.kronecker_product import kron_prod
Modified:
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py?rev=19081&r1=19080&r2=19081&view=diff
==============================================================================
---
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
(original)
+++
trunk/test_suite/unit_tests/_target_functions/_frame_order/test_matrix_ops.py
Sat Mar 23 20:51:12 2013
@@ -25,7 +25,7 @@
from unittest import TestCase
# relax module imports.
-from pipe_control.frame_order import print_frame_order_2nd_degree
+from lib.frame_order.format import print_frame_order_2nd_degree
from lib.geometry.coord_transform import cartesian_to_spherical
from target_functions.frame_order import *
from lib.algebra.kronecker_product import transpose_23
r19081 - in /trunk: lib/frame_order/ pipe_control/ target_functions/frame_order/ test_suite/shared_data/frame_order/cam/ tes...