r21737 - /trunk/test_suite/system_tests/relax_disp.py
Author: bugman Date: Tue Dec 3 09:03:31 2013 New Revision: 21737 URL: http://svn.gna.org/viewcvs/relax?rev=21737view=rev Log: Basic fix for the Relax_disp.test_r2eff_read_spin system test - the CPMG frequencies are now set. This was identified in the post http://thread.gmane.org/gmane.science.nmr.relax.devel/4773/focus=4774. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21737r1=21736r2=21737view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 09:03:31 2013 @@ -2576,6 +2576,10 @@ for id in ids: self.interpreter.spectrometer.frequency(id=id, frq=500e6) self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG') +for value in H_disp_points: +self.interpreter.relax_disp.cpmg_frq(spectrum_id='1H_CPMG_%s' % value, cpmg_frq=value) +for value in N_disp_points: +self.interpreter.relax_disp.cpmg_frq(spectrum_id='15N_CPMG_%s' % value, cpmg_frq=value) # Loop over the experiments. for id, file, spin_id in [['1H_CPMG', 'hs_500.res', ':9@H'], ['15N_CPMG', 'ns_500.res', ':9@N']]: ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21738 - /trunk/lib/text/gui.py
Author: bugman Date: Tue Dec 3 11:58:57 2013 New Revision: 21738 URL: http://svn.gna.org/viewcvs/relax?rev=21738view=rev Log: Added support for the 'NS MMQ 3-site' model parameters to the lib.text.gui module. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax Modified: trunk/lib/text/gui.py Modified: trunk/lib/text/gui.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/text/gui.py?rev=21738r1=21737r2=21738view=diff == --- trunk/lib/text/gui.py (original) +++ trunk/lib/text/gui.py Tue Dec 3 11:58:57 2013 @@ -65,9 +65,18 @@ # Relaxation dispersion GUI text elements. dw = u(d\u03C9) +dw_AB = u(d\u03C9(AB)) +dw_AC = u(d\u03C9(AC)) +dw_BC = u(d\u03C9(BC)) dwH = u(d\u03C9H) +dwH_AB = u(d\u03C9H(AB)) +dwH_AC = u(d\u03C9H(AC)) +dwH_BC = u(d\u03C9H(BC)) i0 = u(I\u2080) kex = u(k\u2091\u2093) +kAB = u(k\u2091\u2093(AB)) +kAC = u(k\u2091\u2093(AC)) +kBC = u(k\u2091\u2093(BC)) padw2 = u(pA.d\u03C9\u00B2) phi_ex = u(\u03D5\u2091\u2093) phi_exB = u(\u03D5\u2091\u2093B) @@ -80,6 +89,9 @@ if win: i0 = I0 kex = kex +kAB = kex(AB) +kAC = kex(AC) +kBC = kex(BC) phi_ex = u(phi_ex) phi_exB = u(phi_exB) phi_exC = u(phi_exC) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21739 - /trunk/user_functions/relax_disp.py
Author: bugman
Date: Tue Dec 3 12:04:30 2013
New Revision: 21739
URL: http://svn.gna.org/viewcvs/relax?rev=21739view=rev
Log:
Added the 'NS MMQ 3-site' models to the relax_disp.select_model user function
frontend.
This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_front_end
Modified:
trunk/user_functions/relax_disp.py
Modified: trunk/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/relax_disp.py?rev=21739r1=21738r2=21739view=diff
==
--- trunk/user_functions/relax_disp.py (original)
+++ trunk/user_functions/relax_disp.py Tue Dec 3 12:04:30 2013
@@ -32,7 +32,7 @@
FD_SAVE = -1
# relax module imports.
-from lib.text.gui import dw, dwH, i0, kex, padw2, phi_ex, phi_exB, phi_exC,
r1rho, r1rho_prime, r2, r2a, r2b, r2eff
+from lib.text.gui import dw, dw_AB, dw_BC, dwH, dwH_AB, dwH_BC, i0, kex, kAB,
kBC, kAC, padw2, phi_ex, phi_exB, phi_exC, r1rho, r1rho_prime, r2, r2a, r2b,
r2eff
from graphics import ANALYSIS_IMAGE_PATH, WIZARD_IMAGE_PATH
from pipe_control import pipes, spectrum
from pipe_control.mol_res_spin import get_spin_ids
@@ -42,7 +42,7 @@
from specific_analyses.relax_disp.nessy import nessy_input
from specific_analyses.relax_disp.parameters import copy
from specific_analyses.relax_disp.sherekhan import sherekhan_input
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_R2EFF,
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR,
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_TAP03, MODEL_TP02,
MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_CPMG_PROTON_MQ,
EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL,
MODEL_DPL94, MODEL_IT99, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B,
MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_R2EFF, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE,
MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
from specific_analyses.setup import relax_disp_obj
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -808,7 +808,9 @@
%s: {%s, ..., pA, %s, %s} % (MODEL_MP05, r1rho_prime, dw, kex),
%s: {%s, ..., pA, %s, %s} % (MODEL_NS_R1RHO_2SITE, r1rho_prime, dw,
kex),
%s: {%s, ..., pA, %s, %s, %s} % (MODEL_MQ_CR72, r2, dw, dwH, kex),
-%s: {%s, ..., pA, %s, %s, %s} % (MODEL_MMQ_2SITE, r2, dw, dwH, kex)
+%s: {%s, ..., pA, %s, %s, %s} % (MODEL_MMQ_2SITE, r2, dw, dwH, kex),
+%s: {%s, ..., pA, %s, %s, %s, pB, %s, %s, %s} %
(MODEL_NS_MMQ_3SITE_LINEAR, r2, dw_AB, dwH_AB, kAB, dw_BC, dwH_BC, kBC),
+%s: {%s, ..., pA, %s, %s, %s, pB, %s, %s, %s, %s} %
(MODEL_NS_MMQ_3SITE, r2, dw_AB, dwH_AB, kAB, dw_BC, dwH_BC, kBC, kAC)
],
wiz_combo_data = [
MODEL_R2EFF,
@@ -832,7 +834,9 @@
MODEL_MP05,
MODEL_NS_R1RHO_2SITE,
MODEL_MQ_CR72,
-MODEL_MMQ_2SITE
+MODEL_MMQ_2SITE,
+MODEL_NS_MMQ_3SITE_LINEAR,
+MODEL_NS_MMQ_3SITE
],
wiz_read_only = True
)
@@ -872,6 +876,8 @@
uf.desc[-1].add_paragraph(The currently supported models are:)
uf.desc[-1].add_item_list_element('%s' % MODEL_MQ_CR72, The the Carver and
Richards (1972) 2-site model for most time scales expanded for MQ CPMG data by
Korzhnev et al., 2004, whereby the simplification R20A = R20B is assumed. Its
parameters are {R20, ..., pA, dw, dwH, kex}.)
uf.desc[-1].add_item_list_element('%s' % MODEL_MMQ_2SITE, The numerical
solution for the 2-site Bloch-McConnell equations for combined
proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG data whereby the simplification
R20A = R20B is assumed. Its parameters are {R20, ..., pA, dw, dwH, kex}.)
+uf.desc[-1].add_item_list_element('%s' % MODEL_NS_MMQ_3SITE_LINEAR, The
numerical solution for the 3-site Bloch-McConnell equations linearised with kAC
= kCA = 0 for combined proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG data
whereby the simplification R20A = R20B = R20C is assumed. Its parameters are
{R20, ..., pA, dw(AB), dwH(AB), kex(AB), pB, dw(BC), dwH(BC), kex(BC)}.)
r21740 - /trunk/specific_analyses/relax_disp/api.py
Author: bugman Date: Tue Dec 3 12:09:28 2013 New Revision: 21740 URL: http://svn.gna.org/viewcvs/relax?rev=21740view=rev Log: Added support for the 'NS MMQ 3-site' models to the relax_disp.select_model user function back end. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_disp.select_model_user_function_back_end. Modified: trunk/specific_analyses/relax_disp/api.py Modified: trunk/specific_analyses/relax_disp/api.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=21740r1=21739r2=21740view=diff == --- trunk/specific_analyses/relax_disp/api.py (original) +++ trunk/specific_analyses/relax_disp/api.py Tue Dec 3 12:09:28 2013 @@ -48,7 +48,7 @@ from specific_analyses.relax_disp.disp_data import average_intensity, find_intensity_keys, get_curve_type, has_exponential_exp_type, has_proton_mmq_cpmg, loop_cluster, loop_exp_frq_point, loop_exp_frq_point_time, loop_frq, loop_time, pack_back_calc_r2eff, return_cpmg_frqs, return_index_from_disp_point, return_index_from_exp_type, return_index_from_frq, return_offset_data, return_param_key_from_data, return_r1_data, return_r2eff_arrays, return_spin_lock_nu1, spin_ids_to_containers from specific_analyses.relax_disp.optimisation import Disp_memo, Disp_minimise_command, back_calc_r2eff, grid_search_setup from specific_analyses.relax_disp.parameters import assemble_param_vector, assemble_scaling_matrix, disassemble_param_vector, get_param_names, get_value, linear_constraints, loop_parameters, param_index_to_param_info, param_num -from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_MMQ, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 +from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, MODEL_LIST_FULL, MODEL_LM63, MODEL_LM63_3SITE, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_MMQ, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 from target_functions.relax_disp import Dispersion from user_functions.data import Uf_tables; uf_tables = Uf_tables() from user_functions.objects import Desc_container @@ -602,6 +602,16 @@ print(The reduced numerical solution for the 2-site Bloch-McConnell equations for MQ CPMG data using 3D magnetisation vectors, whereby the simplification R20A = R20B is assumed.) params = ['r2', 'pA', 'dw', 'dwH', 'kex'] +# NS MMQ CPMG 3-site model. +elif model == MODEL_NS_MMQ_3SITE: +print(The numerical solution for the 3-site Bloch-McConnell equations for MMQ CPMG data whereby the simplification R20A = R20B = R20C is assumed.) +params = ['r2', 'pA', 'dw_AB', 'dwH_AB', 'kex_AB', 'pB', 'dw_BC', 'dwH_BC', 'kex_BC', 'kex_AC'] + +# NS MMQ CPMG 3-site linearised model. +elif model == MODEL_NS_MMQ_3SITE_LINEAR: +print(The numerical solution for the 3-site Bloch-McConnell equations for MMQ CPMG data linearised with kAC = kCA = 0 whereby the simplification R20A = R20B = R20C is assumed.) +params = ['r2', 'pA', 'dw_AB', 'dwH_AB', 'kex_AB', 'pB', 'dw_BC', 'dwH_BC', 'kex_BC'] + # Invalid model. else: raise RelaxError(The model '%s' must be one of %s. % (model, MODEL_LIST_FULL)) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21741 - in /trunk/specific_analyses/relax_disp: api.py optimisation.py parameters.py
Author: bugman Date: Tue Dec 3 12:42:30 2013 New Revision: 21741 URL: http://svn.gna.org/viewcvs/relax?rev=21741view=rev Log: Added support for the new 3-site exchange dispersion parameters. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Adding_support_for_the_parameters. Modified: trunk/specific_analyses/relax_disp/api.py trunk/specific_analyses/relax_disp/optimisation.py trunk/specific_analyses/relax_disp/parameters.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/specific_analyses/relax_disp/api.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/api.py?rev=21741r1=21740r2=21741view=diff Modified: trunk/specific_analyses/relax_disp/optimisation.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=21741r1=21740r2=21741view=diff Modified: trunk/specific_analyses/relax_disp/parameters.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=21741r1=21740r2=21741view=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21742 - /trunk/specific_analyses/relax_disp/variables.py
Author: bugman Date: Tue Dec 3 14:13:52 2013 New Revision: 21742 URL: http://svn.gna.org/viewcvs/relax?rev=21742view=rev Log: Removed the brackets from the 'NS MMQ 3-site (linear)' dispersion model name. Modified: trunk/specific_analyses/relax_disp/variables.py Modified: trunk/specific_analyses/relax_disp/variables.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/variables.py?rev=21742r1=21741r2=21742view=diff == --- trunk/specific_analyses/relax_disp/variables.py (original) +++ trunk/specific_analyses/relax_disp/variables.py Tue Dec 3 14:13:52 2013 @@ -127,7 +127,7 @@ MODEL_NS_MMQ_3SITE = 'NS MMQ 3-site' The numerical solution for the 3-site Bloch-McConnell equations for combined proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG data. -MODEL_NS_MMQ_3SITE_LINEAR = 'NS MMQ 3-site (linear)' +MODEL_NS_MMQ_3SITE_LINEAR = 'NS MMQ 3-site linear' The numerical solution for the 3-site Bloch-McConnell equations with kAC = kCA = 0 for combined proton-heteronuclear SQ, ZQ, DQ, and MQ CPMG data. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21744 - /trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py
Author: bugman Date: Tue Dec 3 14:53:32 2013 New Revision: 21744 URL: http://svn.gna.org/viewcvs/relax?rev=21744view=rev Log: Fixes for the parameters in the Relax_disp.test_ns_mmq_3site system test script. Modified: trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py Modified: trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py?rev=21744r1=21743r2=21744view=diff == --- trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py (original) +++ trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py Tue Dec 3 14:53:32 2013 @@ -169,9 +169,9 @@ spin_N.pA = 0.85 spin_N.pB = 0.05 spin_N.pC = 0.10 -spin_N.kAB = 500.0 -spin_N.kAC = 0.0 -spin_N.kBC = 2000.0 +spin_N.kex_AB = 500.0 +spin_N.kex_AC = 0.0 +spin_N.kex_BC = 2000.0 spin_N.dw_AB = -3.0 spin_N.dw_AC = 8.0 spin_N.dw_BC = 11.0 ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21745 - /trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py
Author: bugman Date: Tue Dec 3 16:49:02 2013 New Revision: 21745 URL: http://svn.gna.org/viewcvs/relax?rev=21745view=rev Log: Missing import for the Relax_disp.test_ns_mmq_3site system test script. Modified: trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py Modified: trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py?rev=21745r1=21744r2=21745view=diff == --- trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py (original) +++ trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py Tue Dec 3 16:49:02 2013 @@ -4,6 +4,7 @@ from os import sep # relax module imports. +from data_store import Relax_data_store; ds = Relax_data_store() from specific_analyses.relax_disp.disp_data import generate_r20_key from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ from status import Status; status = Status() ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21746 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet Date: Tue Dec 3 16:57:35 2013 New Revision: 21746 URL: http://svn.gna.org/viewcvs/relax?rev=21746view=rev Log: Fix for Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model. Fix for bug #21322, (https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0 Reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Adjusted pA, dw, kex, chi2. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21746r1=21745r2=21746view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 16:57:35 2013 @@ -1325,10 +1325,10 @@ # Checks for residue :71. self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1) -self.assertAlmostEqual(spin71.pA, 0.992258541625787, 3) -self.assertAlmostEqual(spin71.dw, 2.75140650899058, 1) -self.assertAlmostEqual(spin71.kex/1000, 2106.60885247431/1000, 1) -self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 2) +self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2) +self.assertAlmostEqual(spin71.dw, 2.75140650899058, 0) +self.assertAlmostEqual(spin71.kex/1000, 2106.60885247431/1000, 0) +self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 1) # Test the conversion to k_AB from kex and pA. self.assertEqual(spin70.k_AB, spin70.kex * (1.0 - spin70.pA)) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21747 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet Date: Tue Dec 3 16:58:33 2013 New Revision: 21747 URL: http://svn.gna.org/viewcvs/relax?rev=21747view=rev Log: Fix for Optimisation of the Korzhnev et al., 2005 15N DQ CPMG data using the 'MMQ 2-site' model. Fix for bug #21322, (https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0 Reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21747r1=21746r2=21747view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 16:58:33 2013 @@ -1581,13 +1581,13 @@ print(%-20s %20.15g\n % (chi2, spin.chi2)) # Checks for residue :9. -self.assertAlmostEqual(spin.r2[r20_key1], 9.48527908326952, 3) +self.assertAlmostEqual(spin.r2[r20_key1], 9.48527908326952, 2) self.assertAlmostEqual(spin.r2[r20_key2], 11.7135951595536, 3) -self.assertAlmostEqual(spin.r2[r20_key3], 13.6153887849344, 3) +self.assertAlmostEqual(spin.r2[r20_key3], 13.6153887849344, 2) self.assertAlmostEqual(spin.pA, 0.965638501551899, 4) -self.assertAlmostEqual(spin.dw, 2.8537583461577, 4) -self.assertAlmostEqual(spin.dwH, -0.387633062766635, 4) -self.assertAlmostEqual(spin.kex/1000, 573.704033851592/1000, 4) +self.assertAlmostEqual(spin.dw, 2.8537583461577, 2) +self.assertAlmostEqual(spin.dwH, -0.387633062766635, 3) +self.assertAlmostEqual(spin.kex/1000, 573.704033851592/1000, 3) self.assertAlmostEqual(spin.chi2, 9.29563496654824, 2) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21748 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet Date: Tue Dec 3 16:59:37 2013 New Revision: 21748 URL: http://svn.gna.org/viewcvs/relax?rev=21748view=rev Log: Fix for Optimisation of the Korzhnev et al., 2005 15N MQ CPMG data using the 'MMQ 2-site' model. Fix for bug #21322, (https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0 Reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21748r1=21747r2=21748view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 16:59:37 2013 @@ -1656,7 +1656,7 @@ self.assertAlmostEqual(spin.r2[r20_key1], 6.02016436619016, 1) self.assertAlmostEqual(spin.r2[r20_key2], 6.65421500772308, 1) self.assertAlmostEqual(spin.r2[r20_key3], 8.6729591487622, 1) -self.assertAlmostEqual(spin.pA, 0.930083249288083, 4) +self.assertAlmostEqual(spin.pA, 0.930083249288083, 3) self.assertAlmostEqual(spin.dw, 4.33890689462363, 2) self.assertAlmostEqual(spin.dwH, -0.274316585638047, 3) self.assertAlmostEqual(spin.kex/1000, 344.329651956132/1000, 3) ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21749 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet Date: Tue Dec 3 17:00:43 2013 New Revision: 21749 URL: http://svn.gna.org/viewcvs/relax?rev=21749view=rev Log: Fix for Optimisation of the Korzhnev et al., 2005 15N ZQ CPMG data using the 'MMQ 2-site' model. Fix for bug #21322, (https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0 Reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21749r1=21748r2=21749view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 17:00:43 2013 @@ -1800,7 +1800,7 @@ self.assertAlmostEqual(spin.dw, 0.850592422908884, 1) self.assertAlmostEqual(spin.dwH, 0.0881272284455416, 3) self.assertAlmostEqual(spin.kex/1000, 372.745483351305/1000, 3) -self.assertAlmostEqual(spin.chi2, 23.8464637019392, 2) +self.assertAlmostEqual(spin.chi2, 23.8464637019392, 1) def test_korzhnev_2005_1h_mq_data(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21751 - /trunk/specific_analyses/relax_disp/parameters.py
Author: bugman Date: Tue Dec 3 17:09:43 2013 New Revision: 21751 URL: http://svn.gna.org/viewcvs/relax?rev=21751view=rev Log: Fixes for the loop_parameters() dispersion function for the new 'NS MMQ 3-site' model parameters. The new parameters were not being handled by this function. Modified: trunk/specific_analyses/relax_disp/parameters.py Modified: trunk/specific_analyses/relax_disp/parameters.py URL: http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameters.py?rev=21751r1=21750r2=21751view=diff == --- trunk/specific_analyses/relax_disp/parameters.py (original) +++ trunk/specific_analyses/relax_disp/parameters.py Tue Dec 3 17:09:43 2013 @@ -704,7 +704,7 @@ param_index += 1 yield 'r2b', param_index, spin_index, generate_r20_key(exp_type=exp_type, frq=frq) -# Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2' and 'dw' (one per spin). +# Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin). for spin_index in range(len(spins)): # Yield the data. if 'phi_ex' in spins[spin_index].params: @@ -722,16 +722,34 @@ if 'dw' in spins[spin_index].params: param_index += 1 yield 'dw', param_index, spin_index, None +if 'dw_AB' in spins[spin_index].params: +param_index += 1 +yield 'dw_AB', param_index, spin_index, None +if 'dw_BC' in spins[spin_index].params: +param_index += 1 +yield 'dw_BC', param_index, spin_index, None +if 'dw_AC' in spins[spin_index].params: +param_index += 1 +yield 'dw_AC', param_index, spin_index, None # Then a separate block for the proton chemical shift difference parameters for the MQ models (one per spin). for spin_index in range(len(spins)): if 'dwH' in spins[spin_index].params: param_index += 1 yield 'dwH', param_index, spin_index, None +if 'dwH_AB' in spins[spin_index].params: +param_index += 1 +yield 'dwH_AB', param_index, spin_index, None +if 'dwH_BC' in spins[spin_index].params: +param_index += 1 +yield 'dwH_BC', param_index, spin_index, None +if 'dwH_AC' in spins[spin_index].params: +param_index += 1 +yield 'dwH_AC', param_index, spin_index, None # All other parameters (one per spin cluster). for param in spins[0].params: -if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dwH']: +if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 'dwH_BC', 'dwH_AB']: param_index += 1 yield param, param_index, None, None ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21752 - /trunk/test_suite/system_tests/relax_disp.py
Author: tlinnet Date: Tue Dec 3 17:19:16 2013 New Revision: 21752 URL: http://svn.gna.org/viewcvs/relax?rev=21752view=rev Log: Fix for Optimisation of Dr. Flemming Hansen's CPMG data to the 'NS CPMG 2-site star' dispersion model. Changed so assertAlmostEqual matches 2 digits. Fix for bug #21322, (https://gna.org/bugs/?21322) - 5x Test suite fail for version 3.1.0 Reported for system CentOS 2.6.32-358.18.1.el6.x86_64. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21752r1=21751r2=21752view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 17:19:16 2013 @@ -1326,8 +1326,8 @@ # Checks for residue :71. self.assertAlmostEqual(spin71.r2[r20_key1], 4.992594256544, 1) self.assertAlmostEqual(spin71.pA, 0.992258541625787, 2) -self.assertAlmostEqual(spin71.dw, 2.75140650899058, 0) -self.assertAlmostEqual(spin71.kex/1000, 2106.60885247431/1000, 0) +self.assertAlmostEqual(spin71.dw/100, 2.75140650899058/100, 2) +self.assertAlmostEqual(spin71.kex/10, 2106.60885247431/10, 2) self.assertAlmostEqual(spin71.chi2/100, 17.3293856656588/100, 1) # Test the conversion to k_AB from kex and pA. ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21753 - /trunk/target_functions/relax_disp.py
Author: bugman Date: Tue Dec 3 17:23:43 2013 New Revision: 21753 URL: http://svn.gna.org/viewcvs/relax?rev=21753view=rev Log: Created the target functions for the 'NS MMQ 3-site' models. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site (linear)' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_target_function Modified: trunk/target_functions/relax_disp.py Modified: trunk/target_functions/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=21753r1=21752r2=21753view=diff == --- trunk/target_functions/relax_disp.py (original) +++ trunk/target_functions/relax_disp.py Tue Dec 3 17:23:43 2013 @@ -42,6 +42,7 @@ from lib.dispersion.ns_cpmg_2site_3d import r2eff_ns_cpmg_2site_3D from lib.dispersion.ns_cpmg_2site_expanded import r2eff_ns_cpmg_2site_expanded from lib.dispersion.ns_cpmg_2site_star import r2eff_ns_cpmg_2site_star +from lib.dispersion.ns_mmq_3site import r2eff_ns_mmq_3site_mq, r2eff_ns_mmq_3site_sq_dq_zq from lib.dispersion.ns_r1rho_2site import ns_r1rho_2site from lib.dispersion.ns_matrices import r180x_3d from lib.dispersion.tp02 import r1rho_TP02 @@ -50,7 +51,7 @@ from lib.errors import RelaxError from lib.float import isNaN from target_functions.chi2 import chi2 -from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL, MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 +from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_FULL, MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 class Dispersion: @@ -84,6 +85,8 @@ - 'NS CPMG 2-site star full': The full numerical solution for the 2-site Bloch-McConnell equations for CPMG data using complex conjugate matrices. - 'NS CPMG 2-site expanded': The numerical solution for the 2-site Bloch-McConnell equations for CPMG data expanded using Maple by Nikolai Skrynnikov. - 'MMQ 2-site': The numerical solution for the 2-site Bloch-McConnell equations for combined proton-heteronuclear SQ, ZD, DQ, and MQ CPMG data with R20A = R20B. +- 'NS MMQ 3-site linear': The numerical solution for the 3-site Bloch-McConnell equations linearised with kAC = kCA = 0 for combined proton-heteronuclear SQ, ZD, DQ, and MQ CPMG data with R20A = R20B = R20C. +- 'NS MMQ 3-site': The numerical solution for the 3-site Bloch-McConnell equations for combined proton-heteronuclear SQ, ZD, DQ, and MQ CPMG data with R20A = R20B = R20C. @keyword model: The relaxation dispersion model to fit. @@ -195,6 +198,10 @@ self.end_index.append(self.end_index[-1] + self.num_spins) if model in [MODEL_IT99, MODEL_LM63_3SITE, MODEL_MQ_CR72, MODEL_MMQ_2SITE]: self.end_index.append(self.end_index[-1] + self.num_spins) +elif model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: +self.end_index.append(self.end_index[-1] + self.num_spins) +self.end_index.append(self.end_index[-1] + self.num_spins) +self.end_index.append(self.end_index[-1] + self.num_spins) # Set up the matrices for the numerical solutions. if model in [MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL]: @@ -217,6 +224,8 @@ # This is a vector that contains the initial magnetizations corresponding to the A and B state transverse magnetizations. if model in [MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL]: self.M0 = zeros(2, float64) +if model in [MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: +self.M0 = zeros(3, float64) if model in
r21754 - in /trunk/lib/dispersion: __init__.py ns_mmq_3site.py
Author: bugman Date: Tue Dec 3 17:27:34 2013 New Revision: 21754 URL: http://svn.gna.org/viewcvs/relax?rev=21754view=rev Log: Added the R2eff calculating functions for the 'NS MMQ 3-site' models to the relax library. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_library. Added: trunk/lib/dispersion/ns_mmq_3site.py - copied, changed from r21737, trunk/lib/dispersion/mmq_2site.py Modified: trunk/lib/dispersion/__init__.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/lib/dispersion/__init__.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/__init__.py?rev=21754r1=21753r2=21754view=diff Copied: trunk/lib/dispersion/ns_mmq_3site.py (from r21737, trunk/lib/dispersion/mmq_2site.py) URL: http://svn.gna.org/viewcvs/relax/trunk/lib/dispersion/ns_mmq_3site.py?p2=trunk/lib/dispersion/ns_mmq_3site.pyp1=trunk/lib/dispersion/mmq_2site.pyr1=21737r2=21754rev=21754view=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21755 - /trunk/auto_analyses/relax_disp.py
Author: bugman Date: Tue Dec 3 17:36:11 2013 New Revision: 21755 URL: http://svn.gna.org/viewcvs/relax?rev=21755view=rev Log: Added the 'NS MMQ 3-site' models to the dispersion auto-analysis. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_auto-analysis. Modified: trunk/auto_analyses/relax_disp.py Modified: trunk/auto_analyses/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp.py?rev=21755r1=21754r2=21755view=diff == --- trunk/auto_analyses/relax_disp.py (original) +++ trunk/auto_analyses/relax_disp.py Tue Dec 3 17:36:11 2013 @@ -36,7 +36,7 @@ from pipe_control.pipes import has_pipe from prompt.interpreter import Interpreter from specific_analyses.relax_disp.disp_data import has_exponential_exp_type, has_cpmg_exp_type, has_fixed_time_exp_type, has_r1rho_exp_type, loop_frq -from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE, MODEL_LIST_NUMERIC, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 +from specific_analyses.relax_disp.variables import MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_ANALYTIC, MODEL_LIST_CPMG, MODEL_LIST_R1RHO, MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE, MODEL_MP05, MODEL_MQ_CR72, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_LIST_NUMERIC, MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01 from status import Status; status = Status() @@ -236,6 +236,13 @@ nested_pipe = MODEL_NS_CPMG_2SITE_3D if model == MODEL_NS_CPMG_2SITE_STAR_FULL and MODEL_NS_CPMG_2SITE_STAR in self.models: nested_pipe = MODEL_NS_CPMG_2SITE_STAR +if model == MODEL_NS_MMQ_3SITE_LINEAR and MODEL_MMQ_2SITE in self.models: +nested_pipe = MODEL_MMQ_2SITE +if model == MODEL_NS_MMQ_3SITE: +if MODEL_NS_MMQ_3SITE_LINEAR in self.models: +nested_pipe = MODEL_NS_MMQ_3SITE_LINEAR +elif MODEL_MMQ_2SITE in self.models: +nested_pipe = MODEL_MMQ_2SITE # Using the analytic solution. analytic = False @@ -476,7 +483,7 @@ self.interpreter.grace.write(x_data_type='res_num', y_data_type='i0', file='i0.agr', dir=path, force=True) ## The R20 parameter. -#if has_cpmg_exp_type() and model in [None, MODEL_LM63, MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_EXPANDED]: +#if has_cpmg_exp_type() and model in [None, MODEL_LM63, MODEL_CR72, MODEL_IT99, MODEL_M61, MODEL_DPL94, MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: #self.interpreter.value.write(param='r2', file='r20.out', dir=path, force=True) #self.interpreter.grace.write(x_data_type='res_num', y_data_type='r2', file='r20.agr', dir=path, force=True) @@ -492,12 +499,15 @@ #self.interpreter.value.write(param='r2', file='r1rho0.out', dir=path, force=True) #self.interpreter.grace.write(x_data_type='res_num', y_data_type='r2', file='r1rho0.agr', dir=path, force=True) -# The pA and pB parameters. -if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE, MODEL_TP02, MODEL_TAP03, MODEL_MP05]: +# The pA, pB, and pC parameters. +if model in [None, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, MODEL_M61B, MODEL_MQ_CR72, MODEL_MMQ_2SITE, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_R1RHO_2SITE, MODEL_TP02, MODEL_TAP03, MODEL_MP05, MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR]: self.interpreter.value.write(param='pA', file='pA.out', dir=path, force=True) self.interpreter.value.write(param='pB', file='pB.out', dir=path, force=True)
r21756 - /trunk/test_suite/system_tests/relax_disp.py
Author: bugman Date: Tue Dec 3 17:41:17 2013 New Revision: 21756 URL: http://svn.gna.org/viewcvs/relax?rev=21756view=rev Log: Fix for the Relax_disp.test_ns_mmq_3site system test. The wrong spin was being checked. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21756r1=21755r2=21756view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 17:41:17 2013 @@ -2427,7 +2427,7 @@ self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site.py') # Check the chi-squared value. -self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.0, 5) +self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 5) def test_r2eff_read(self): ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21757 - /trunk/test_suite/system_tests/relax_disp.py
Author: bugman Date: Tue Dec 3 17:41:51 2013 New Revision: 21757 URL: http://svn.gna.org/viewcvs/relax?rev=21757view=rev Log: Updated the docstring of the Relax_disp.test_ns_mmq_3site system test. Modified: trunk/test_suite/system_tests/relax_disp.py Modified: trunk/test_suite/system_tests/relax_disp.py URL: http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21757r1=21756r2=21757view=diff == --- trunk/test_suite/system_tests/relax_disp.py (original) +++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 17:41:51 2013 @@ -2421,7 +2421,7 @@ def test_ns_mmq_3site(self): -Compare the 'NS MMQ 3-site (branched)' dispersion model to synthetic data from cpmg_fit. +Compare the 'NS MMQ 3-site' dispersion model to synthetic data from cpmg_fit. # Execute the script. self.interpreter.run(script_file=status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site.py') ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21758 - /trunk/gui/analyses/auto_relax_disp.py
Author: bugman
Date: Tue Dec 3 17:44:43 2013
New Revision: 21758
URL: http://svn.gna.org/viewcvs/relax?rev=21758view=rev
Log:
Added the 'NS MMQ 3-site' models to the GUI model list.
This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_GUI.
Modified:
trunk/gui/analyses/auto_relax_disp.py
Modified: trunk/gui/analyses/auto_relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/gui/analyses/auto_relax_disp.py?rev=21758r1=21757r2=21758view=diff
==
--- trunk/gui/analyses/auto_relax_disp.py (original)
+++ trunk/gui/analyses/auto_relax_disp.py Tue Dec 3 17:44:43 2013
@@ -44,11 +44,11 @@
from gui.string_conv import float_to_gui, gui_to_bool, gui_to_float,
gui_to_int, gui_to_str, str_to_gui
from gui.uf_objects import Uf_storage; uf_store = Uf_storage()
from gui.wizards.peak_intensity import Peak_intensity_wizard
-from lib.text.gui import dw, dwH, i0, kex, padw2, phi_ex, phi_exB, phi_exC,
r1, r1rho, r1rho_prime, r2, r2a, r2b, r2eff
+from lib.text.gui import dw, dw_AB, dw_BC, dwH, dwH_AB, dwH_BC, i0, kex, kAB,
kBC, kAC, padw2, phi_ex, phi_exB, phi_exC, r1, r1rho, r1rho_prime, r2, r2a,
r2b, r2eff
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
from pipe_control.pipes import has_bundle, has_pipe
from specific_analyses.relax_disp.disp_data import has_cpmg_exp_type,
has_r1rho_exp_type
-from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_R1RHO,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE,
MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_R1RHO_2SITE,
MODEL_R2EFF, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_R1RHO,
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MMQ_2SITE,
MODEL_MP05, MODEL_MQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D,
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED,
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_3SITE,
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_R2EFF, MODEL_TAP03,
MODEL_TP02, MODEL_TSMFK01
from status import Status; status = Status()
@@ -733,7 +733,9 @@
MODEL_NS_R1RHO_2SITE,
None,
MODEL_MQ_CR72,
-MODEL_MMQ_2SITE
+MODEL_MMQ_2SITE,
+MODEL_NS_MMQ_3SITE_LINEAR,
+MODEL_NS_MMQ_3SITE
]
params = [
{%s/%s, %s} % (r2eff, r1rho, i0),
@@ -761,7 +763,9 @@
{%s, ..., pA, %s, %s} % (r1rho_prime, dw, kex),
None,
{%s, ..., pA, %s, %s, %s} % (r2, dw, dwH, kex),
-{%s, ..., pA, %s, %s, %s} % (r2, dw, dwH, kex)
+{%s, ..., pA, %s, %s, %s} % (r2, dw, dwH, kex),
+{%s, ..., pA, %s, %s, %s, pB, %s, %s, %s} % (r2, dw_AB, dwH_AB, kAB,
dw_BC, dwH_BC, kBC),
+{%s, ..., pA, %s, %s, %s, pB, %s, %s, %s, %s} % (r2, dw_AB, dwH_AB,
kAB, dw_BC, dwH_BC, kBC, kAC)
]
model_desc = [
The base model for determining the %s/%s values and errors for all
other models. % (r2eff, r1rho),
@@ -789,7 +793,9 @@
The 2-site numerical solution using 3D magnetisation vectors.,
None,
The CR72 2-site model extended to MQ CPMG data by Korzhnev et al.,
2004.,
-The 2-site numerical solution of Korzhnev et al. (2004) from
multi-quantum CPMG data.
+The 2-site numerical solution of Korzhnev et al. (2004) from
multi-quantum CPMG data.,
+The 3-site linearised numerical solution of Korzhnev et al. (2005)
for MMQ CPMG data.,
+The 3-site numerical solution of Korzhnev et al. (2005) for MMQ CPMG
data.
]
size = wx.Size(1024, 750)
tooltip = The list of all relaxation dispersion models to be optimised as
part of the protocol.
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r21759 - /trunk/docs/latex/dispersion.tex
Author: bugman
Date: Tue Dec 3 19:33:17 2013
New Revision: 21759
URL: http://svn.gna.org/viewcvs/relax?rev=21759view=rev
Log:
Updated the 'MMQ 2-site' model description in the manual.
The R2_DQ = R2_ZQ = R20 assumption is now explained.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21759r1=21758r2=21759view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Dec 3 19:33:17 2013
@@ -914,6 +914,7 @@
\end{align}
\end{subequations}
+For the model it is assumed that $\RtwoDQA = \RtwoZQA = \RtwozeroA$ and
$\RtwoDQB = \RtwoZQB = \RtwozeroB$.
The references for this model are:
\begin{itemize}
\item \bibentry{Korzhnev04a}
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r21760 - in /trunk/docs/latex: dispersion.tex dispersion_models.tex dispersion_params.tex dispersion_software.tex relax.tex
Author: bugman Date: Tue Dec 3 19:54:12 2013 New Revision: 21760 URL: http://svn.gna.org/viewcvs/relax?rev=21760view=rev Log: Added the 'NS MMQ 3-site' models to the relax user manual. This is for the 'NS MMQ 3-site' and 'NS MMQ 3-site linear' CPMG dispersion models. This follows the tutorial for adding relaxation dispersion models at: http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_relax_manual. Modified: trunk/docs/latex/dispersion.tex trunk/docs/latex/dispersion_models.tex trunk/docs/latex/dispersion_params.tex trunk/docs/latex/dispersion_software.tex trunk/docs/latex/relax.tex [This mail would be too long, it was shortened to contain the URLs only.] Modified: trunk/docs/latex/dispersion.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21760r1=21759r2=21760view=diff Modified: trunk/docs/latex/dispersion_models.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion_models.tex?rev=21760r1=21759r2=21760view=diff Modified: trunk/docs/latex/dispersion_params.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion_params.tex?rev=21760r1=21759r2=21760view=diff Modified: trunk/docs/latex/dispersion_software.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion_software.tex?rev=21760r1=21759r2=21760view=diff Modified: trunk/docs/latex/relax.tex URL: http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=21760r1=21759r2=21760view=diff ___ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
r21761 - /trunk/docs/latex/dispersion.tex
Author: bugman
Date: Tue Dec 3 20:15:13 2013
New Revision: 21761
URL: http://svn.gna.org/viewcvs/relax?rev=21761view=rev
Log:
Completed the 'MMQ 2-site' documentation in the manual.
The equations for the numeric evolution of SQ, ZQ and DQ data was missing.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=21761r1=21760r2=21761view=diff
==
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Dec 3 20:15:13 2013
@@ -859,7 +859,43 @@
This is the numerical model for 2-site exchange for proton-heteronuclear SQ,
ZQ, DQ and MQ CPMG data, as derived in
\citep{Korzhnev04a,Korzhnev04b,Korzhnev05}.
It is selected by setting the model to `MMQ 2-site'.
The simple constraint $\pA \pB$ is used to halve the optimisation space, as
both sides of the limit are mirror image spaces.
-The equation for the exchange process is
+Different sets of equations are used for the different data types.
+
+
+% The SQ, ZD and DQ equations.
+\subsubsection{The SQ, ZD and DQ equations}
+
+The basic evolution matrices for single, zero and double quantum CPMG-type
data for this model are
+\begin{equation}
+\Rtwoeff = - \frac{1}{T_\textrm{relax}} \log
\frac{\mathbf{M}_A(T_\textrm{relax})}{\mathbf{M}_A(0)},
+\end{equation}
+
+where $\mathbf{M}_A(0)$ is proportional to the vector $[\pA, \pB]^T$ and
+\begin{equation}
+\mathbf{M}_A(T_\textrm{relax}) = \left(
\mathbf{A_\pm}\mathbf{A_\mp}\mathbf{A_\mp}\mathbf{A_\pm} \right)^n
\mathbf{M}_A(0)
+\end{equation}
+
+The evolution matrix $\mathbf{A}$ is defined as
+\begin{equation}
+\mathbf{A_\pm} = e^{\mathbf{a_\pm} \cdot \taucpmg},
+\end{equation}
+
+where
+\begin{equation}
+\mathbf{a_\pm} = \begin{pmatrix}
+ -\kAB -\RtwozeroA \kBA \\
+ \kAB -\kBA \pm\imath\dw - \RtwozeroB
+ \end{pmatrix}.
+\end{equation}
+
+For different data types $\dw$ is defined as: $\dw$ ($^{15}$N SQ-type data);
$\dwH$ ($^1$H SQ-type data); $\dwH - \dw$ (ZQ-type data); and $\dwH + \dw$
(DQ-type data).
+
+
+
+% The MQ equations.
+\subsubsection{The MQ equations}
+
+The equation for the exchange process for multiple quantum CPMG-type data is
\begin{equation}
\Rtwoeff = - \frac{1}{T}
\log \left\{ Re \left[ \frac{0.5}{\pA}
@@ -942,7 +978,7 @@
% The SQ, ZD and DQ equations.
\subsubsection{The SQ, ZD and DQ equations}
-The basic evolution matrices for this model are
+The basic evolution matrices for single, zero and double quantum CPMG-type
data for this model are
\begin{equation}
\mathbf{A_\pm} = e^{\mathbf{a_\pm} \cdot \taucpmg},
\end{equation}
@@ -1018,7 +1054,7 @@
% The SQ, ZD and DQ equations.
\subsubsection{The SQ, ZD and DQ equations}
-The basic evolution matrices for this model are
+The basic evolution matrices for single, zero and double quantum CPMG-type
data for this model are
\begin{equation}
\mathbf{A_\pm} = e^{\mathbf{a_\pm} \cdot \taucpmg},
\end{equation}
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