Author: bugman Date: Tue Jan 11 16:32:31 2011 New Revision: 12218 URL: http://svn.gna.org/viewcvs/relax?rev=12218&view=rev Log: Merged revisions 12202 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r12202 | bugman | 2011-01-11 12:58:33 +0100 (Tue, 11 Jan 2011) | 18 lines 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: branches/multi_processor_merge/ (props changed) branches/multi_processor_merge/data/align_tensor.py branches/multi_processor_merge/maths_fns/frame_order.py branches/multi_processor_merge/sample_scripts/dauvergne_protocol.py branches/multi_processor_merge/specific_fns/frame_order.py branches/multi_processor_merge/specific_fns/n_state_model.py branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py branches/multi_processor_merge/test_suite/system_tests/model_free.py branches/multi_processor_merge/test_suite/system_tests/relax_fit.py branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py branches/multi_processor_merge/test_suite/test_suite_runner.py Propchange: branches/multi_processor_merge/ ------------------------------------------------------------------------------ --- svnmerge-integrated (original) +++ svnmerge-integrated Tue Jan 11 16:32:31 2011 @@ -1,1 +1,1 @@ -/1.3:1-12187 +/1.3:1-12215 Modified: branches/multi_processor_merge/data/align_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/align_tensor.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/data/align_tensor.py (original) +++ branches/multi_processor_merge/data/align_tensor.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/maths_fns/frame_order.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/frame_order.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/maths_fns/frame_order.py (original) +++ branches/multi_processor_merge/maths_fns/frame_order.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/sample_scripts/dauvergne_protocol.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/sample_scripts/dauvergne_protocol.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/sample_scripts/dauvergne_protocol.py (original) +++ branches/multi_processor_merge/sample_scripts/dauvergne_protocol.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/specific_fns/frame_order.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/frame_order.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/specific_fns/frame_order.py (original) +++ branches/multi_processor_merge/specific_fns/frame_order.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/specific_fns/n_state_model.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/n_state_model.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/specific_fns/n_state_model.py (original) +++ branches/multi_processor_merge/specific_fns/n_state_model.py Tue Jan 11 16:32:31 2011 @@ -569,7 +569,7 @@ # Loop over the structures. i = 0 - while 1: + while True: # End condition. if i == cdp.N - 1: break Modified: branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/diffusion_tensor.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/test_suite/system_tests/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/model_free.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/model_free.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/model_free.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/test_suite/system_tests/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/relax_fit.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/relax_fit.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/relax_fit.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/iso_cone_to_iso_cone_free_rotor.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/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/branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_free_rotor_to_iso_cone_free_rotor.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py (original) +++ branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/parametric_restriction/pseudo_ellipse_to_iso_cone_free_rotor.py Tue Jan 11 16:32:31 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: branches/multi_processor_merge/test_suite/test_suite_runner.py URL: http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/test_suite_runner.py?rev=12218&r1=12217&r2=12218&view=diff ============================================================================== --- branches/multi_processor_merge/test_suite/test_suite_runner.py (original) +++ branches/multi_processor_merge/test_suite/test_suite_runner.py Tue Jan 11 16:32:31 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.