Author: bugman
Date: Tue Jan 11 12:58:33 2011
New Revision: 12202
URL: http://svn.gna.org/viewcvs/relax?rev=12202&view=rev
Log:
Updates for Python 3.0.
The command used from docs/2to3_checklist was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
Modified:
1.3/data/align_tensor.py
1.3/maths_fns/frame_order.py
1.3/sample_scripts/dauvergne_protocol.py
1.3/specific_fns/frame_order.py
1.3/specific_fns/n_state_model.py
1.3/test_suite/system_tests/diffusion_tensor.py
1.3/test_suite/system_tests/model_free.py
1.3/test_suite/system_tests/relax_fit.py
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py
1.3/test_suite/test_suite_runner.py
Modified: 1.3/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/align_tensor.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/data/align_tensor.py (original)
+++ 1.3/data/align_tensor.py Tue Jan 11 12:58:33 2011
@@ -802,7 +802,7 @@
# Switch from the left handed to right handed universe if required.
if abs(det(rot_perm) - 1.0) > 1e-7:
- rot_perm[:,0] = -rot_perm[:,0]
+ rot_perm[:, 0] = -rot_perm[:, 0]
# Return the permuted rotation matrix.
return rot_perm
Modified: 1.3/maths_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/frame_order.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/maths_fns/frame_order.py (original)
+++ 1.3/maths_fns/frame_order.py Tue Jan 11 12:58:33 2011
@@ -31,7 +31,7 @@
from generic_fns.frame_order import print_frame_order_2nd_degree
from maths_fns.alignment_tensor import to_5D, to_tensor
from maths_fns.chi2 import chi2
-from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor,
compile_2nd_matrix_iso_cone,
compile_2nd_matrix_iso_cone_free_rotor,compile_2nd_matrix_iso_cone_torsionless,
compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor,
reduce_alignment_tensor
+from maths_fns.frame_order_matrix_ops import compile_2nd_matrix_free_rotor,
compile_2nd_matrix_iso_cone, compile_2nd_matrix_iso_cone_free_rotor,
compile_2nd_matrix_iso_cone_torsionless, compile_2nd_matrix_pseudo_ellipse,
compile_2nd_matrix_pseudo_ellipse_free_rotor,
compile_2nd_matrix_pseudo_ellipse_torsionless, compile_2nd_matrix_rotor,
reduce_alignment_tensor
from maths_fns.rotation_matrix import euler_to_R_zyz as euler_to_R
from relax_errors import RelaxError
Modified: 1.3/sample_scripts/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/dauvergne_protocol.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/sample_scripts/dauvergne_protocol.py (original)
+++ 1.3/sample_scripts/dauvergne_protocol.py Tue Jan 11 12:58:33 2011
@@ -195,4 +195,4 @@
# Execution (do not change!).
-dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME,attached_name=ATTACHED_NAME, relax_data=RELAX_DATA,
unres=UNRES, exclude=EXCLUDE, bond_length=BOND_LENGTH, csa=CSA,
hetnuc=HETNUC, proton=PROTON, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_num=MC_NUM, conv_loop=CONV_LOOP)
+dAuvergne_protocol(diff_model=DIFF_MODEL, mf_models=MF_MODELS,
local_tm_models=LOCAL_TM_MODELS, pdb_file=PDB_FILE, seq_args=SEQ_ARGS,
het_name=HET_NAME, attached_name=ATTACHED_NAME, relax_data=RELAX_DATA,
unres=UNRES, exclude=EXCLUDE, bond_length=BOND_LENGTH, csa=CSA,
hetnuc=HETNUC, proton=PROTON, grid_inc=GRID_INC, min_algor=MIN_ALGOR,
mc_num=MC_NUM, conv_loop=CONV_LOOP)
Modified: 1.3/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/frame_order.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/specific_fns/frame_order.py (original)
+++ 1.3/specific_fns/frame_order.py Tue Jan 11 12:58:33 2011
@@ -272,7 +272,7 @@
# Fill the structure.
for i in range(cdp.sim_number):
- euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim[:,i])
+ euler_to_R_zyz(cdp.eigen_alpha_sim[i],
cdp.eigen_beta_sim[i], cdp.eigen_gamma_sim[i], axes_sim[:, i])
# Rotation and inversion.
axes_sim_pos = axes_sim
@@ -284,12 +284,12 @@
for i in range(2):
# Simulation structures.
if sim:
- axis_sim_pos = axes_sim_pos[:,i]
- axis_sim_neg = axes_sim_neg[:,i]
+ axis_sim_pos = axes_sim_pos[:, i]
+ axis_sim_neg = axes_sim_neg[:, i]
# The vectors.
- res_num = generate_vector_residues(mol=mol,
vector=axes_pos[:,i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_pos,
res_num=res_num+1, origin=cdp.pivot, scale=size)
- res_num = generate_vector_residues(mol=mol,
vector=axes_neg[:,i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_neg,
res_num=res_num+1, origin=cdp.pivot, scale=size)
+ res_num = generate_vector_residues(mol=mol,
vector=axes_pos[:, i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_pos,
res_num=res_num+1, origin=cdp.pivot, scale=size)
+ res_num = generate_vector_residues(mol=mol,
vector=axes_neg[:, i], atom_name='%s-ax'%label[i],
res_name_vect='%sAX'%upper(label[i]), sim_vectors=axis_sim_neg,
res_num=res_num+1, origin=cdp.pivot, scale=size)
# The cone object.
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Tue Jan 11 12:58:33 2011
@@ -569,7 +569,7 @@
# Loop over the structures.
i = 0
- while 1:
+ while True:
# End condition.
if i == cdp.N - 1:
break
Modified: 1.3/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/diffusion_tensor.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Tue Jan 11 12:58:33 2011
@@ -225,8 +225,8 @@
vects = array(vects)
for vect in vects:
# The projections.
- proj1 = dot(vect,dot(cdp.diff_tensor.tensor, vect))
- proj2 = dot(vect,dot(D, vect))
+ proj1 = dot(vect, dot(cdp.diff_tensor.tensor, vect))
+ proj2 = dot(vect, dot(D, vect))
# Compare projections.
self.assertAlmostEqual(proj1, proj2)
@@ -268,8 +268,8 @@
vects = array(vects)
for vect in vects:
# The projections.
- proj1 = dot(vect,dot(cdp.diff_tensor.tensor, vect))
- proj2 = dot(vect,dot(D, vect))
+ proj1 = dot(vect, dot(cdp.diff_tensor.tensor, vect))
+ proj2 = dot(vect, dot(D, vect))
# Print out.
print("\nVector: %s" % vect)
@@ -295,8 +295,8 @@
gamma = 0.5
# The actual tensor in the PDB frame.
- D = array([[ 22758858.4088357 , -7267400.1700938 ,
6272205.75829415],
- [ -7267400.1700938 , 17923072.3436445 ,
1284270.53726401],
+ D = array([[ 22758858.4088357, -7267400.1700938,
6272205.75829415],
+ [ -7267400.1700938, 17923072.3436445,
1284270.53726401],
[ 6272205.75829415, 1284270.53726401,
19318069.2475198 ]], float64)
# The tensor in the eigenframe.
Modified: 1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Tue Jan 11 12:58:33 2011
@@ -1573,7 +1573,7 @@
eqi = [None, 'mf_ext']
select = [False, True]
model = [None, 'm5']
- params = [[], ['S2f','S2','ts']]
+ params = [[], ['S2f', 'S2', 'ts']]
s2 = [None, 0.86578779694713515]
s2f = [None, 0.88618694421409949]
s2s = [None, 0.97698098871784322]
@@ -1635,7 +1635,7 @@
self.assertEqual(cdp.warning_sim[2], None)
# Global relaxation data tests.
- self.assertEqual(cdp.ri_labels,
['R1','NOE','R1','R2','NOE','R1','R2','NOE'])
+ self.assertEqual(cdp.ri_labels, ['R1', 'NOE', 'R1', 'R2', 'NOE',
'R1', 'R2', 'NOE'])
self.assertEqual(cdp.remap_table, [0, 0, 1, 1, 1, 2, 2, 2])
self.assertEqual(cdp.frq_labels, ['800', '600', '500'])
self.assertEqual(cdp.frq, [799744000.0, 599737000.0, 499719000.0])
@@ -1722,7 +1722,7 @@
eqi = [None, None, None, 'mf_ext', 'mf_orig', 'mf_orig', None,
'mf_orig']
select = [False, False, False, True, True, True, False, True]
model = [None, None, None, 'm5', 'm2', 'm1', None, 'm1']
- params = [None, None, None, ['S2f','S2','ts'], ['S2', 'te'], ['S2'],
None, ['S2']]
+ params = [None, None, None, ['S2f', 'S2', 'ts'], ['S2', 'te'],
['S2'], None, ['S2']]
s2 = [None, None, None, 0.85674161305142216, 0.89462664243726608,
0.90201790111143165, None, 0.92099297347361675]
s2f = [None, None, None, 0.88220054271390302, None, None, None, None]
s2s = [None, None, None, 0.97114156200339452, None, None, None, None]
@@ -1732,7 +1732,7 @@
rex = [None, None, None, None, None, None, None, None]
r = [None, None, None, 1.0200000000000001e-10,
1.0200000000000001e-10, 1.0200000000000001e-10, None, 1.0200000000000001e-10]
csa = [None, None, None, -0.00017199999999999998,
-0.00017199999999999998, -0.00017199999999999998, None,
-0.00017199999999999998]
- ri_labels = [[], [], [],
['R1','R2','R1','R2','NOE','R1','R2','NOE'],
['R1','R2','R1','R2','NOE','R1','R2','NOE'],
['R1','R2','R1','R2','NOE','R1','R2','NOE'], [],
['R1','R2','R1','R2','NOE','R1','R2','NOE']]
+ ri_labels = [[], [], [], ['R1', 'R2', 'R1', 'R2', 'NOE', 'R1', 'R2',
'NOE'], ['R1', 'R2', 'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'], ['R1', 'R2',
'R1', 'R2', 'NOE', 'R1', 'R2', 'NOE'], [], ['R1', 'R2', 'R1', 'R2', 'NOE',
'R1', 'R2', 'NOE']]
remap_table = [[], [], [], [0, 0, 1, 1, 1, 2, 2, 2], [0, 0, 1, 1, 1,
2, 2, 2], [0, 0, 1, 1, 1, 2, 2, 2], [], [0, 0, 1, 1, 1, 2, 2, 2]]
frq_labels = [[], [], [], ['800', '600', '500'], ['800', '600',
'500'], ['800', '600', '500'], [], ['800', '600', '500']]
frq = [[], [], [], [799812000.0, 599739000.0, 499827000.0],
[799812000.0, 599739000.0, 499827000.0], [799812000.0, 599739000.0,
499827000.0], [], [799812000.0, 599739000.0, 499827000.0]]
@@ -1776,7 +1776,7 @@
self.assertEqual(cdp.diff_tensor.gamma, 42.15815798778408 / 360.0 *
2.0 * pi)
# Global relaxation data tests.
- self.assertEqual(cdp.ri_labels,
['R1','R2','R1','R2','NOE','R1','R2','NOE'])
+ self.assertEqual(cdp.ri_labels, ['R1', 'R2', 'R1', 'R2', 'NOE',
'R1', 'R2', 'NOE'])
self.assertEqual(cdp.remap_table, [0, 0, 1, 1, 1, 2, 2, 2])
self.assertEqual(cdp.frq_labels, ['800', '600', '500'])
self.assertEqual(cdp.frq, [799812000.0, 599739000.0, 499827000.0])
Modified: 1.3/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/relax_fit.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/relax_fit.py (original)
+++ 1.3/test_suite/system_tests/relax_fit.py Tue Jan 11 12:58:33 2011
@@ -72,8 +72,7 @@
self.assertEqual(cdp.curve_type, 'exp')
self.assertEqual(cdp.int_method, ds.int_type)
self.assertEqual(len(cdp.relax_times), 10)
- cdp_relax_times = cdp.relax_times.values()
- cdp_relax_times.sort()
+ cdp_relax_times = sorted(cdp.relax_times.values())
for i in range(10):
self.assertEqual(cdp_relax_times[i], relax_times[i])
Modified:
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
---
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py
(original)
+++
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py
Tue Jan 11 12:58:33 2011
@@ -42,9 +42,9 @@
# Build the frame.
EIG_FRAME = zeros((3, 3), float64)
-EIG_FRAME[:,0] = vect_x
-EIG_FRAME[:,1] = vect_y
-EIG_FRAME[:,2] = vect_z
+EIG_FRAME[:, 0] = vect_x
+EIG_FRAME[:, 1] = vect_y
+EIG_FRAME[:, 2] = vect_z
a, b, g = R_to_euler_zyz(EIG_FRAME)
# Load the tensors.
Modified:
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
---
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py
(original)
+++
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py
Tue Jan 11 12:58:33 2011
@@ -42,9 +42,9 @@
# Build the frame.
EIG_FRAME = zeros((3, 3), float64)
-EIG_FRAME[:,0] = vect_x
-EIG_FRAME[:,1] = vect_y
-EIG_FRAME[:,2] = vect_z
+EIG_FRAME[:, 0] = vect_x
+EIG_FRAME[:, 1] = vect_y
+EIG_FRAME[:, 2] = vect_z
a, b, g = R_to_euler_zyz(EIG_FRAME)
# Load the tensors.
Modified:
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
---
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py
(original)
+++
1.3/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py
Tue Jan 11 12:58:33 2011
@@ -42,9 +42,9 @@
# Build the frame.
EIG_FRAME = zeros((3, 3), float64)
-EIG_FRAME[:,0] = vect_x
-EIG_FRAME[:,1] = vect_y
-EIG_FRAME[:,2] = vect_z
+EIG_FRAME[:, 0] = vect_x
+EIG_FRAME[:, 1] = vect_y
+EIG_FRAME[:, 2] = vect_z
a, b, g = R_to_euler_zyz(EIG_FRAME)
# Load the tensors.
Modified: 1.3/test_suite/test_suite_runner.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/test_suite_runner.py?rev=12202&r1=12201&r2=12202&view=diff
==============================================================================
--- 1.3/test_suite/test_suite_runner.py (original)
+++ 1.3/test_suite/test_suite_runner.py Tue Jan 11 12:58:33 2011
@@ -165,10 +165,7 @@
unit_count[test[1]] += 1
# The missing modules.
- missing_modules = system_count.keys()
- missing_modules.sort()
-
- # Sub-title.
+ missing_modules = sorted(system_count.keys())
subtitle("Optional packages/modules")
# Nothing missing.
r12202 - in /1.3: data/ maths_fns/ sample_scripts/ specific_fns/ test_suite/ test_suite/system_tests/ test_suite/system_test...