Author: tlinnet
Date: Sun Nov 22 18:02:12 2015
New Revision: 28087
URL: http://svn.gna.org/viewcvs/relax?rev=28087&view=rev
Log:
Extended the systemtest -s Relax_disp.test_paul_schanda_nov_2015 to include
auto analysis and clustered fits.
This should show that the analysis is now possible.
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=28087&r1=28086&r2=28087&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Sun Nov 22 18:02:12 2015
@@ -36,7 +36,7 @@
from auto_analyses.relax_disp_repeat_cpmg import DIC_KEY_FORMAT,
Relax_disp_rep
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
-from lib.dispersion.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_LIST, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_FULL, MODEL_LM63,
MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03
+from lib.dispersion.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_LIST, EXP_TYPE_R1RHO, MODEL_B14_FULL, MODEL_CR72,
MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_FULL, MODEL_LM63,
MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D_FULL,
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR_FULL,
MODEL_NS_R1RHO_2SITE, MODEL_PARAMS, MODEL_R2EFF, MODEL_TP02, MODEL_TAP03
from lib.errors import RelaxError
from lib.io import extract_data, get_file_path
from lib.spectrum.nmrpipe import show_apod_extract, show_apod_rmsd,
show_apod_rmsd_dir_to_files, show_apod_rmsd_to_file
@@ -6428,6 +6428,75 @@
self.interpreter.relax_disp.plot_disp_curves(dir=outdir,
y_axis='r2_eff', x_axis='disp', num_points=1000, extend_hz=500.0,
extend_ppm=500.0, interpolate='disp', force=True)
+ # Number of grid search increments. If set to None, then the grid
search will be turned off and the default parameter values will be used
instead.
+ #GRID_INC = None
+ GRID_INC = 21
+ # The number of Monte Carlo simulations to be used for error
analysis at the end of the analysis.
+ MC_NUM = 3
+ # Model selection technique.
+ MODSEL = 'AIC'
+ # Which models to analyse ?
+ MODELS = [MODEL_NOREX, MODEL_M61]
+ # Fit, instead of read. Off for On-resonance.
+ r1_fit = False
+ # Set the initial guess from the minimum R2eff point
+ set_grid_r20=True
+
+ # Execute the auto-analysis (fast).
+ # Standard parameters are: func_tol = 1e-25, grad_tol = None,
max_iter = 10000000,
+ OPT_FUNC_TOL = 1e-1
+ relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
+ OPT_MAX_ITERATIONS = 1000
+ relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS
+
+ # Go
+ relax_disp.Relax_disp(pipe_name="relax_disp",
pipe_bundle="relax_disp", results_dir=outdir, models=MODELS,
grid_inc=GRID_INC, mc_sim_num=MC_NUM, exp_mc_sim_num=None, modsel=MODSEL,
pre_run_dir=None, optimise_r2eff=False, insignificance=0.0,
numeric_only=False, mc_sim_all_models=False, eliminate=True,
set_grid_r20=set_grid_r20, r1_fit=r1_fit)
+
+ # Now simulate that all spins are first deselected, and then
selected.
+ self.interpreter.deselect.all()
+ sel_ids = [
+ ":12",
+ ":51",
+ ]
+ for sel_spin in sel_ids:
+ print("Selecting spin %s"%sel_spin)
+ self.interpreter.select.spin(spin_id=sel_spin, change_all=False)
+
+ # Inspect which residues should be analysed together for a
clustered/global fit.
+ cluster_ids = sel_ids
+
+ # Cluster spins
+ for curspin in cluster_ids:
+ print("Adding spin %s to cluster"%curspin)
+ self.interpreter.relax_disp.cluster('model_cluster', curspin)
+
+ # Show the pipe
+ print("\nPrinting all the available pipes.")
+ self.interpreter.pipe.display()
+
+ # Get the selected models
+ print("\nChecking which model is stored per spin.")
+ for curspin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=False):
+ print("For spin_id '%s the model is '%s''"%(spin_id,
curspin.model))
+
+ # Copy pipe and switch to it.
+ self.interpreter.pipe.copy(pipe_from="final - relax_disp",
pipe_to="relax_disp_cluster", bundle_to="relax_disp_cluster")
+ self.interpreter.pipe.switch(pipe_name="relax_disp_cluster")
+ self.interpreter.pipe.display()
+
+ # Go again with clustered spins.
+ relax_disp.Relax_disp(pipe_name="relax_disp_cluster",
pipe_bundle="relax_disp_cluster", results_dir=outdir+sep+"cluster",
models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM, exp_mc_sim_num=None,
modsel=MODSEL, pre_run_dir=None, optimise_r2eff=False, insignificance=0.0,
numeric_only=False, mc_sim_all_models=False, eliminate=True,
set_grid_r20=set_grid_r20, r1_fit=r1_fit)
+
+ # Get the clustered fitted values
+ print("\nChecking which value is stored per spin.")
+ kex = None
+ for curspin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=False):
+ if kex == None:
+ kex = curspin.kex
+ self.assertEqual(curspin.kex, kex)
+ print("For spin_id %s the kex is %.3f"%(spin_id, kex))
+
+
def test_repeat_cpmg(self):
"""Test the protocol for repeated dispersion analysis. The class:
relax_disp_repeat_cpmg.
r28087 - /trunk/test_suite/system_tests/relax_disp.py