Author: bugman
Date: Tue Sep 29 13:51:04 2015
New Revision: 27887
URL: http://svn.gna.org/viewcvs/relax?rev=27887&view=rev
Log:
Added the frame order sample scripts used in the CaM-IQ analysis.
Added:
branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py
branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py
branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py
branches/frame_order_cleanup/sample_scripts/frame_order/summarise.py
Added:
branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py?rev=27887&view=auto
==============================================================================
---
branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py
(added)
+++
branches/frame_order_cleanup/sample_scripts/frame_order/count_sobol_points.py
Tue Sep 29 13:51:04 2015
@@ -0,0 +1,7 @@
+"""Create a table of the total number of Sobol' points used in the PCS
integration."""
+
+# relax module imports.
+from auto_analyses.frame_order import count_sobol_points
+
+# The table.
+count_sobol_points(file_name='sobol_point_count')
Added:
branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py?rev=27887&view=auto
==============================================================================
--- branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py
(added)
+++ branches/frame_order_cleanup/sample_scripts/frame_order/full_analysis.py
Tue Sep 29 13:51:04 2015
@@ -0,0 +1,220 @@
+"""Script for black-box Frame Order analysis.
+
+This is for the CaM-IQ data.
+
+The free rotor pseudo-elliptic cone model is not used in this script as the
cone X and Y opening angles cannot be differentiated with simply RDC and PCS
data, hence this model is perfectly approximated by the free rotor isotropic
cone.
+"""
+
+# Python module imports.
+from numpy import array
+from time import asctime, localtime
+
+# relax module imports.
+from auto_analyses.frame_order import Frame_order_analysis,
Optimisation_settings
+
+
+# Analysis variables.
+#####################
+
+# The frame order models to use.
+MODELS = [
+ 'rigid',
+ 'rotor',
+ 'iso cone',
+ 'pseudo-ellipse',
+ 'iso cone, torsionless',
+ 'pseudo-ellipse, torsionless',
+ 'double rotor'
+]
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the protocol.
+MC_NUM = 10
+
+# Rigid model optimisation setup.
+OPT_RIGID = Optimisation_settings()
+OPT_RIGID.add_grid(inc=21, zoom=0)
+OPT_RIGID.add_grid(inc=21, zoom=1)
+OPT_RIGID.add_grid(inc=21, zoom=2)
+OPT_RIGID.add_grid(inc=21, zoom=3)
+OPT_RIGID.add_min(min_algor='simplex')
+
+# PCS subset optimisation setup.
+OPT_SUBSET = Optimisation_settings()
+OPT_SUBSET.add_grid(inc=11, zoom=0, sobol_max_points=100)
+OPT_SUBSET.add_grid(inc=11, zoom=1, sobol_max_points=100)
+OPT_SUBSET.add_grid(inc=11, zoom=2, sobol_max_points=100)
+OPT_SUBSET.add_min(min_algor='simplex', func_tol=1e-2, sobol_max_points=100)
+
+# Full data set optimisation setup.
+OPT_FULL = Optimisation_settings()
+OPT_FULL.add_grid(inc=11, zoom=2, sobol_max_points=100)
+OPT_FULL.add_grid(inc=11, zoom=3, sobol_max_points=100)
+OPT_FULL.add_min(min_algor='simplex', func_tol=1e-2, sobol_max_points=100)
+OPT_FULL.add_min(min_algor='simplex', func_tol=1e-3, sobol_max_points=1000)
+OPT_FULL.add_min(min_algor='simplex', func_tol=1e-4, sobol_max_points=10000)
+
+# Monte Carlo simulation optimisation setup.
+OPT_MC = Optimisation_settings()
+OPT_MC.add_min(min_algor='simplex', func_tol=1e-3, sobol_max_points=100)
+
+
+# Set up the base data pipes.
+#############################
+
+# The data pipe bundle to group all data pipes.
+PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())
+
+# Create the base data pipe containing only a subset of the PCS data.
+SUBSET = "Data subset - " + PIPE_BUNDLE
+pipe.create(pipe_name=SUBSET, pipe_type='frame order', bundle=PIPE_BUNDLE)
+
+# Read the structures.
+structure.read_pdb('2BE6_ndom_truncN.pdb',
dir='../../../structures/2BE6_superimpose', set_mol_name='N-dom')
+structure.read_pdb('2BE6_cdom_truncC.pdb',
dir='../../../structures/2BE6_superimpose', set_mol_name='C-dom')
+
+# Set up the 15N and 1H spins.
+structure.load_spins(spin_id='@N', mol_name_target='CaM', ave_pos=False)
+structure.load_spins(spin_id='@H', mol_name_target='CaM', ave_pos=False)
+spin.isotope(isotope='15N', spin_id='@N')
+spin.isotope(isotope='1H', spin_id='@H')
+
+# Define the magnetic dipole-dipole relaxation interaction.
+interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+interatom.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+interatom.unit_vectors()
+
+# Deselect mobile spins and vectors (from the CaM model-free order
parameters from the BMRB).
+deselect.spin(':2-4')
+deselect.spin(':42')
+deselect.spin(':56-57')
+deselect.spin(':76-82')
+deselect.spin(':114-117')
+deselect.spin(':129-130')
+deselect.spin(':146-148')
+deselect.interatom(':2-4')
+deselect.interatom(':42')
+deselect.interatom(':56-57')
+deselect.interatom(':76-82')
+deselect.interatom(':114-117')
+deselect.interatom(':129-130')
+deselect.interatom(':146-148')
+
+# The lanthanides and data files.
+ln = ['dy', 'tb', 'tm', 'er', 'yb', 'ho']
+pcs_files = [
+ 'PCS_DY_200911.txt',
+ 'PCS_TB_200911.txt',
+ 'PCS_TM_200911.txt',
+ 'PCS_ER_200911.txt',
+ 'PCS_YB_211111.txt',
+ 'PCS_HO_300412.txt'
+]
+pcs_files_subset = [
+ 'PCS_DY_200911_subset.txt',
+ 'PCS_TB_200911_subset.txt',
+ 'PCS_TM_200911_subset.txt',
+ 'PCS_ER_200911_subset.txt',
+ 'PCS_YB_211111_subset.txt',
+ 'PCS_HO_300412_subset.txt'
+]
+rdc_files = [
+ 'RDC_DY_111011_spinID.txt',
+ 'RDC_TB_111011_spinID.txt',
+ 'RDC_TM_111011_spinID.txt',
+ 'RDC_ER_111011_spinID.txt',
+ 'RDC_YB_110112_spinID.txt',
+ 'RDC_HO_300512_spinID.txt'
+]
+
+# The spectrometer frequencies for Luigi's measurements (matching the above
lanthanide ordering, taken from the acqus SFO1 parameter).
+pcs_frq = [
+ 701.2533001, # Dy3+.
+ 701.2533002, # Tb3+.
+ 701.2533005, # Tm3+.
+ 701.2533003, # Er3+.
+ 701.2533004, # Yb3+.
+ 701.2533005 # Ho3+.
+]
+rdc_frq = [
+ 900.00423401, # Dy3+.
+ 900.00423381, # Tb3+.
+ 900.00423431, # Tm3+.
+ 899.90423151, # Er3+.
+ 899.90423111, # Yb3+.
+ 899.80423481, # Ho3+.
+]
+
+# Loop over the alignments.
+for i in range(len(ln)):
+ # Load the RDCs.
+ rdc.read(align_id=ln[i], file=rdc_files[i],
dir='../../../align_data/CaM_IQ/', spin_id1_col=1, spin_id2_col=2,
data_col=3, error_col=4)
+
+ # The 1H PCS (only a subset of ~5 spins for fast initial optimisations).
+ pcs.read(align_id=ln[i], file=pcs_files_subset[i],
dir='../../../align_data/CaM_IQ/', res_num_col=1, data_col=3, error_col=4,
spin_id='@H')
+
+ # The temperature and field strength.
+ spectrometer.temperature(id=ln[i], temp=303.0)
+ spectrometer.frequency(id=ln[i], frq=rdc_frq[i], units="MHz")
+
+# Set up the tensors from the CaM-IQ ABC :6-74@N,CA,C,O N-state model fit.
+align_tensor.init(tensor='Dy N-dom', align_id='dy',
params=(-0.000895122969134, 0.000200206126748, 0.000350783562498,
0.000789321179176, -0.000185956794915), param_types=2)
+align_tensor.init(tensor='Dy N-dom', align_id='dy',
params=(1.2293468401e-05, 1.74966511177e-05, 1.07296910627e-05,
1.21471537359e-05, 9.98472771055e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Tb N-dom', align_id='tb',
params=(-0.000386773980249, -0.000252229451755, 0.000289345115245,
0.00077454551221, -0.000411564842864), param_types=2)
+align_tensor.init(tensor='Tb N-dom', align_id='tb',
params=(9.08568851197e-06, 1.25046911688e-05, 9.13279347879e-06,
8.66699785438e-06, 8.17084290029e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Tm N-dom', align_id='tm',
params=(0.000138832563763, 0.00019276873546, -0.000401761891364,
-0.00053984778662, 0.000385156710458), param_types=2)
+align_tensor.init(tensor='Tm N-dom', align_id='tm',
params=(7.45028293534e-06, 1.15087527652e-05, 7.80160598908e-06,
7.48687231235e-06, 8.44077530542e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Er N-dom', align_id='er',
params=(0.00013266928235, 6.08491225722e-05, -0.000249892897607,
-0.000344865388853, 0.000118692962249), param_types=2)
+align_tensor.init(tensor='Er N-dom', align_id='er',
params=(6.24728334522e-06, 8.68937486363e-06, 7.96726504939e-06,
6.43064935791e-06, 1.00354375045e-05), param_types=2, errors=True)
+align_tensor.init(tensor='Yb N-dom', align_id='yb',
params=(0.000150564392882, -7.59743643441e-05, -0.00013958907081,
-0.000188379895441, 0.000102722198261), param_types=2)
+align_tensor.init(tensor='Yb N-dom', align_id='yb',
params=(4.42731599871e-06, 5.1565091874e-06, 5.18051425981e-06,
3.9225664592e-06, 4.49007020445e-06), param_types=2, errors=True)
+align_tensor.init(tensor='Ho N-dom', align_id='ho',
params=(-0.000307522207243, 2.76511812842e-05, 0.000152789357344,
0.000307999279733, -0.000235201851074), param_types=2)
+align_tensor.init(tensor='Ho N-dom', align_id='ho',
params=(6.56971189673e-06, 1.0420422445e-05, 8.05282585054e-06,
7.42469124453e-06, 7.25413636142e-06), param_types=2, errors=True)
+
+# Define the domains.
+domain(id='N', spin_id=":1-78")
+domain(id='C', spin_id=":80-148")
+
+# The tensor domains and reductions.
+full = ['Dy N-dom', 'Tb N-dom', 'Tm N-dom', 'Er N-dom', 'Yb N-dom', 'Ho
N-dom']
+red = ['Dy C-dom', 'Tb C-dom', 'Tm C-dom', 'Er C-dom', 'Yb C-dom', 'Ho
C-dom']
+ids = ['dy', 'tb', 'tm', 'er', 'yb', 'ho']
+for i in range(len(full)):
+ # Initialise the reduced tensors (fitted during optimisation).
+ align_tensor.init(tensor=red[i], align_id=ids[i], params=(0, 0, 0, 0, 0))
+
+ # Set the domain info.
+ align_tensor.set_domain(tensor=full[i], domain='N')
+ align_tensor.set_domain(tensor=red[i], domain='C')
+
+ # Specify which tensor is reduced.
+ align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
+
+# Set the reference domain.
+frame_order.ref_domain('N')
+
+# Set the initial pivot point.
+pivot = array([ 21.863, 5.270, 5.934])
+frame_order.pivot(pivot, fix=False)
+
+# Set the paramagnetic centre position.
+paramag.centre(pos=[6.518, 8.520, 13.767])
+
+# Duplicate the PCS data subset data pipe to create a data pipe containing
all the PCS data.
+DATA = "Data - " + PIPE_BUNDLE
+pipe.copy(pipe_from=SUBSET, pipe_to=DATA, bundle_to=PIPE_BUNDLE)
+pipe.switch(DATA)
+
+# Load the complete PCS data into the already filled data pipe.
+for i in range(len(ln)):
+ # The 15N PCS.
+ pcs.read(align_id=ln[i], file=pcs_files[i],
dir='../../../align_data/CaM_IQ/', res_num_col=1, data_col=2, error_col=4,
spin_id='@N')
+
+ # The 1H PCS.
+ pcs.read(align_id=ln[i], file=pcs_files[i],
dir='../../../align_data/CaM_IQ/', res_num_col=1, data_col=3, error_col=4,
spin_id='@H')
+
+
+# Execution.
+############
+
+# Do not change!
+Frame_order_analysis(data_pipe_full=DATA, data_pipe_subset=SUBSET,
pipe_bundle=PIPE_BUNDLE, results_dir=None, opt_rigid=OPT_RIGID,
opt_subset=OPT_SUBSET, opt_full=OPT_FULL, opt_mc=OPT_MC, mc_sim_num=MC_NUM,
models=MODELS)
Added: branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py?rev=27887&view=auto
==============================================================================
--- branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py
(added)
+++ branches/frame_order_cleanup/sample_scripts/frame_order/refinement.py
Tue Sep 29 13:51:04 2015
@@ -0,0 +1,52 @@
+"""Script for black-box Frame Order analysis.
+
+This is for the CaM-IQ data.
+
+The free rotor pseudo-elliptic cone model is not used in this script as the
cone X and Y opening angles cannot be differentiated with simply RDC and PCS
data, hence this model is perfectly approximated by the free rotor isotropic
cone.
+"""
+
+# Python module imports.
+from time import asctime, localtime
+
+# relax module imports.
+from auto_analyses.frame_order import Frame_order_analysis,
Optimisation_settings
+
+
+# Analysis variables.
+#####################
+
+# The frame order models to use.
+MODELS = [
+ 'rigid',
+ 'rotor',
+ 'iso cone',
+ 'pseudo-ellipse',
+ 'iso cone, torsionless',
+ 'pseudo-ellipse, torsionless',
+ 'double rotor'
+]
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the protocol.
+MC_NUM = 10
+
+# Full data set optimisation setup.
+OPT_FULL = Optimisation_settings()
+OPT_FULL.add_min(min_algor='simplex', func_tol=1e-4, quad_int=True)
+
+# Monte Carlo simulation optimisation setup.
+OPT_MC = Optimisation_settings()
+OPT_MC.add_min(min_algor='simplex', func_tol=1e-3, quad_int=True)
+
+
+# Set up the base data pipes.
+#############################
+
+# The data pipe bundle to group all data pipes.
+PIPE_BUNDLE = "Frame Order (%s)" % asctime(localtime())
+
+
+# Execution.
+############
+
+# Do not change!
+Frame_order_analysis(pipe_bundle=PIPE_BUNDLE, results_dir='refinement',
pre_run_dir='.', opt_full=OPT_FULL, opt_mc=OPT_MC, mc_sim_num=MC_NUM,
models=MODELS)
Added: branches/frame_order_cleanup/sample_scripts/frame_order/summarise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/sample_scripts/frame_order/summarise.py?rev=27887&view=auto
==============================================================================
--- branches/frame_order_cleanup/sample_scripts/frame_order/summarise.py
(added)
+++ branches/frame_order_cleanup/sample_scripts/frame_order/summarise.py
Tue Sep 29 13:51:04 2015
@@ -0,0 +1,7 @@
+"""Create a summary table of the current frame order results."""
+
+# relax module imports.
+from auto_analyses.frame_order import summarise
+
+# Summarise.
+summarise(file_name='summary')
r27887 - /branches/frame_order_cleanup/sample_scripts/frame_order/