Author: bugman
Date: Sun Oct 12 11:57:44 2008
New Revision: 7635
URL: http://svn.gna.org/viewcvs/relax?rev=7635&view=rev
Log:
Updated the ancient palmer.py sample script to the new design.
Modified:
1.3/sample_scripts/palmer.py
Modified: 1.3/sample_scripts/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/palmer.py?rev=7635&r1=7634&r2=7635&view=diff
==============================================================================
--- 1.3/sample_scripts/palmer.py (original)
+++ 1.3/sample_scripts/palmer.py Sun Oct 12 11:57:44 2008
@@ -1,49 +1,72 @@
-# Script for model-free analysis using the program 'Modelfree4'.
+###############################################################################
+#
#
+# Copyright (C) 2001-2008 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
-# The RelaxError system.
+"""Script for model-free analysis using Art Palmer's program 'Modelfree4'.
+
+The three stages in this script, which can be set below, are:
+ Stage 1: Initial model-free minimisation.
+ Stage 2: Model-free model selection.
+ Stage 3: Final optimisation of diffusion tensor parameters together with
model-free parameters.
+"""
+
+# relax module imports.
from relax_errors import RelaxError
+
# Set the stage of analysis.
-#
-# The three stages in this script are:
-# Stage 1: Initial model-free minimisation.
-# Stage 2: Model-free model selection.
-# Stage 3: Final optimisation of diffusion tensor parameters together
with model-free parameters.
-stage = 2
+STAGE = 1
-# Functions.
-
-def exec_stage_1(runs):
+def exec_stage_1(pipes):
"""Stage 1 function.
Initial model-free minimisation.
"""
- # Loop over the runs.
- for name in runs:
- # Create the run.
+ # Loop over the data pipes.
+ for name in pipes:
+ # Create the data pipe.
print "\n\n# " + name + " #"
pipe.create(name, 'mf')
# Load the sequence.
- sequence.read(name, 'noe.500.out')
+ sequence.read('noe.500.out')
# PDB.
- #structure.read_pdb(name, 'Ap4Aase_new_3.pdb')
+ #structure.read_pdb('Ap4Aase_new_3.pdb')
# Load the relaxation data.
- relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')
- relax_data.read(name, 'R2', '600', 600.0 * 1e6, 'r2.600.out')
- relax_data.read(name, 'NOE', '600', 600.0 * 1e6, 'noe.600.out')
- relax_data.read(name, 'R1', '500', 500.0 * 1e6, 'r1.500.out')
- relax_data.read(name, 'R2', '500', 500.0 * 1e6, 'r2.500.out')
- relax_data.read(name, 'NOE', '500', 500.0 * 1e6, 'noe.500.out')
+ relax_data.read('R1', '600', 600.0 * 1e6, 'r1.600.out')
+ relax_data.read('R2', '600', 600.0 * 1e6, 'r2.600.out')
+ relax_data.read('NOE', '600', 600.0 * 1e6, 'noe.600.out')
+ relax_data.read('R1', '500', 500.0 * 1e6, 'r1.500.out')
+ relax_data.read('R2', '500', 500.0 * 1e6, 'r2.500.out')
+ relax_data.read('NOE', '500', 500.0 * 1e6, 'noe.500.out')
# Setup other values.
- diffusion_tensor.init(name, 1e-8)
- value.set(name, 1.02 * 1e-10, 'bond_length')
- value.set(name, -172 * 1e-6, 'csa')
+ diffusion_tensor.init(1e-8)
+ value.set('15N', 'heteronucleus')
+ value.set(1.02 * 1e-10, 'bond_length')
+ value.set(-172 * 1e-6, 'csa')
# Select the model-free model.
model_free.select_model(model=name)
@@ -58,7 +81,7 @@
state.save('stage1.save', force=True)
-def exec_stage_2(runs):
+def exec_stage_2(pipes):
"""Stage 2 function.
Model-free model selection.
@@ -71,8 +94,8 @@
print "\n\nLoading all the Modelfree 4 data."
# Extract the Modelfree4 data from the 'mfout' files.
- for name in runs:
- palmer.extract()
+ for name in pipes:
+ palmer.extract(dir=name)
# Print out.
print "\n\nModel selection."
@@ -96,11 +119,8 @@
# Load the saved state from stage 2.
state.load('stage2.save')
- # Set the run name.
- name = 'aic'
-
# Let the diffusion tensor parameters be optimised.
- fix(name, 'diff', 0)
+ fix('diff', False)
# Create the Modelfree4 files (change sims as needed, see below).
palmer.create(dir='final', force=True, sims=0)
@@ -118,18 +138,15 @@
# Main section of the script.
#############################
-# Nuclei type.
-value.set('15N', 'heteronucleus')
-
-# Set the run name (also the name of a preset model-free model).
-runs = ['m1', 'm2', 'm3', 'm4', 'm5']
+# Set the data pipe names (also the name of a preset model-free model).
+pipes = ['m1', 'm2', 'm3', 'm4', 'm5']
# Run the stages.
-if stage == 1:
- exec_stage_1(runs)
-elif stage == 2:
- exec_stage_2(runs)
-elif stage == 3:
+if STAGE == 1:
+ exec_stage_1(pipes)
+elif STAGE == 2:
+ exec_stage_2(pipes)
+elif STAGE == 3:
exec_stage_3()
else:
raise RelaxError, "The stage value, which is set to " + `stage` + ",
should be either 1, 2, or 3."
r7635 - /1.3/sample_scripts/palmer.py