Author: bugman
Date: Wed Mar 10 18:31:25 2010
New Revision: 10969
URL: http://svn.gna.org/viewcvs/relax?rev=10969&view=rev
Log:
Updated the generate_ri.py sample script to work with the current relax code
base.
This code was old and broken. A copyright notice has been added.
Modified:
1.3/sample_scripts/generate_ri.py
Modified: 1.3/sample_scripts/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/generate_ri.py?rev=10969&r1=10968&r2=10969&view=diff
==============================================================================
--- 1.3/sample_scripts/generate_ri.py (original)
+++ 1.3/sample_scripts/generate_ri.py Wed Mar 10 18:31:25 2010
@@ -1,7 +1,29 @@
-# Script for generating synthetic relaxation data.
+###############################################################################
+#
#
+# Copyright (C) 2004-2010 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
#
+#
#
+###############################################################################
+
+"""Script for back-calculating the relaxation data."""
# relax module imports.
-from generic.selection import spin_loop
+from generic_fns.mol_res_spin import spin_loop
def back_calc():
@@ -22,6 +44,10 @@
for spin in spin_loop():
# Loop over the relaxation data.
for j in xrange(len(spin.relax_data)):
+ # No data.
+ if spin.relax_data[j] == None:
+ continue
+
# 600 MHz NOE.
if spin.ri_labels[j] == 'NOE' and
spin.frq_labels[spin.remap_table[j]] == '600':
spin.relax_error[j] = 0.04
@@ -46,25 +72,28 @@
relax_data.write(ri_label='R2', frq_label='500', file='r2.500.out',
force=True)
-# Create the run
+# Create the data pipe.
pipe.create('test', 'mf')
-# Set the nucleus type to nitrogen.
+# Load a PDB file.
+structure.read_pdb('example.pdb')
+
+# Load the backbone amide nitrogen spins from the structure.
+structure.load_spins(spin_id='@N')
+
+# Set the spin name and then load the NH vectors.
+structure.vectors(spin_id='@N', attached='H*', ave=False)
+
+# Set the diffusion tensor in the PDB frame (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
+diffusion_tensor.init((1.340e7, 1.516e7, 1.691e7, 0.000e7, 0.000e7,
0.000e7), param_types=3)
+
+# Set the required values.
+value.set(val=-172e-6, param='CSA')
+value.set(val=1.02e-10, param='r')
value.set('15N', 'heteronucleus')
-
-# Set the diffusion tensor to isotropic with tm set to 10 ns.
-diffusion_tensor.init(10e-9)
-
-# Add a residue.
-sequence.add(1, 'ALA')
-
-# Set the CSA and bond lengths.
-value.set(value=-172e-6, param='CSA')
-value.set(value=1.02e-10, param='r')
-
-# Set the model-free parameters.
-value.set(value=0.8, param='S2')
-value.set(value=20e-12, param='te')
+value.set('1H', 'proton')
+value.set(val=0.8, param='S2')
+value.set(val=20e-12, param='te')
# Select model-free model m2.
model_free.select_model(model='m2')
r10969 - /1.3/sample_scripts/generate_ri.py