Author: bugman
Date: Tue Jul 26 14:49:37 2011
New Revision: 13886
URL: http://svn.gna.org/viewcvs/relax?rev=13886&view=rev
Log:
Modified the dauvergne_protocol.py sample script to use the new design of
accepting a filled data pipe.
The automatic protocol will soon accept a data pipe filled with sequence
data, relaxation data, and
values set.
Modified:
branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py
Modified: branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py?rev=13886&r1=13885&r2=13886&view=diff
==============================================================================
--- branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py
(original)
+++ branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py Tue
Jul 26 14:49:37 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2010 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -139,48 +139,23 @@
The final black-box model-free results will be placed in the file
'final/results'.
"""
+# Python module imports.
+from time import asctime, localtime
+
# relax module imports.
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
+# Analysis variables.
+#####################
+
# The diffusion model.
DIFF_MODEL = 'local_tm'
-# The model-free models (do not change these unless absolutely necessary).
+# The model-free models. Do not change these unless absolutely necessary,
the protocol is likely to fail if these are changed.
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
'tm8', 'tm9']
-# The PDB file (set this to None if no structure is available).
-PDB_FILE = '1f3y.pdb'
-
-# The sequence data (file name, dir, mol_name_col, res_num_col,
res_name_col, spin_num_col, spin_name_col, sep). These are the arguments to
the sequence.read() user function, for more information please see the
documentation for that function.
-SEQ_ARGS = ['noe.600.out', None, None, 1, 2, None, None, None]
-
-# The heteronucleus and attached proton names corresponding to those in the
PDB file (used if the spin name is not in the sequence data).
-HET_NAME = 'N'
-ATTACHED_NAME = 'H'
-
-# The relaxation data (data type, frequency label, frequency, file name,
dir, mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col,
data_col, error_col, sep). These are the arguments to the relax_data.read()
user function, please see the documentation for that function for more
information.
-RELAX_DATA = [['R1', '600', 599.719 * 1e6, 'r1.600.out', None, None, 1, 2,
None, None, 3, 4, None],
- ['R2', '600', 599.719 * 1e6, 'r2.600.out', None, None, 1, 2,
None, None, 3, 4, None],
- ['NOE', '600', 599.719 * 1e6, 'noe.600.out', None, None, 1, 2,
None, None, 3, 4, None],
- ['R1', '500', 500.208 * 1e6, 'r1.500.out', None, None, 1, 2,
None, None, 3, 4, None],
- ['R2', '500', 500.208 * 1e6, 'r2.500.out', None, None, 1, 2,
None, None, 3, 4, None],
- ['NOE', '500', 500.208 * 1e6, 'noe.500.out', None, None, 1, 2,
None, None, 3, 4, None]
-]
-
-# The file containing the list of unresolved spins to exclude from the
analysis (set this to None if no spin is to be excluded).
-UNRES = 'unresolved'
-
-# A file containing a list of spins which can be dynamically excluded at any
point within the analysis (when set to None, this variable is not used).
-EXCLUDE = None
-
-# The bond length, CSA values, heteronucleus type, and proton type.
-BOND_LENGTH = 1.02 * 1e-10
-CSA = -172 * 1e-6
-HETNUC = '15N'
-PROTON = '1H'
-
# The grid search size (the number of increments per dimension).
GRID_INC = 11
@@ -194,5 +169,48 @@
CONV_LOOP = True
-# 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)
+
+# Set up the data pipe.
+#######################
+
+# The following sequence of user function calls can be changed as needed.
+
+# Create the data pipe.
+name = "mf (%s)" % asctime(localtime())
+pipe.create(name, 'mf')
+
+# Load the sequence.
+sequence.read(file='noe.500.out', dir=None, mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None)
+
+# Name the spins.
+spin.name(name='N')
+
+# Load the PDB file.
+structure.read_pdb('1f3y.pdb')
+structure.vectors(attached='H')
+
+# Load the relaxation data.
+relax_data.read(ri_id='R1_600', ri_type='R1', frq=599.719*1e6,
file='r1.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='R2_600', ri_type='R2', frq=599.719*1e6,
file='r2.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=599.719*1e6,
file='noe.600.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='R1_500', ri_type='R1', frq=500.208*1e6,
file='r1.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.208*1e6,
file='r2.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.208*1e6,
file='noe.500.out', mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
+
+# Deselect spins to be excluded (including unresolved and specifically
excluded spins).
+deselect.read(file='unresolved', dir=None, spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=None, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)
+deselect.read(file='exclude', spin_id_col=1)
+
+# Set the bond length, CSA values, heteronucleus type, and proton type.
+value.set(1.02 * 1e-10, 'bond_length')
+value.set(-172 * 1e-6, 'csa')
+value.set('15N', 'heteronucleus')
+value.set('1H', 'proton')
+
+
+
+# Execution.
+############
+
+# Do not change!
+dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL,
mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC,
min_algor=MIN_ALGOR, mc_num=MC_NUM, conv_loop=CONV_LOOP)
r13886 - /branches/gui_testing/sample_scripts/model_free/dauvergne_protocol.py