Author: bugman
Date: Tue Jul 3 23:20:26 2012
New Revision: 17171
URL: http://svn.gna.org/viewcvs/relax?rev=17171&view=rev
Log:
Converted the Dasha system test to the interatomic data design.
Modified:
branches/interatomic/test_suite/system_tests/dasha.py
branches/interatomic/test_suite/system_tests/scripts/dasha.py
Modified: branches/interatomic/test_suite/system_tests/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/dasha.py?rev=17171&r1=17170&r2=17171&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/dasha.py (original)
+++ branches/interatomic/test_suite/system_tests/dasha.py Tue Jul 3 23:20:26
2012
@@ -22,6 +22,7 @@
###############################################################################
# Python module imports.
+from math import pi
from os import sep
import sys
from tempfile import mkdtemp
@@ -29,6 +30,7 @@
# relax module imports.
from base_classes import SystemTestCase
from data import Relax_data_store; ds = Relax_data_store()
+from generic_fns.interatomic import interatomic_loop
from generic_fns.mol_res_spin import spin_loop
from relax_io import test_binary
from status import Status; status = Status()
@@ -69,14 +71,11 @@
# The spin data.
select = [True, True, False, False]
- fixed = [None, None, None, None]
- proton_type = [None, None, None, None]
- heteronuc_type = ['15N', '15N', '15N', '15N']
- attached_proton = [None, None, None, None]
+ fixed = [False, False, False, False]
+ isotope = ['15N', '15N', '15N', '15N']
model = ['m3', 'm3', 'm3', 'm3']
equation = ['mf_orig', 'mf_orig', 'mf_orig', 'mf_orig']
params = [['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex'], ['s2', 'rex']]
- xh_vect = [None, None, None, None]
s2 = [0.71510, 0.64359, None, None]
s2f = [None, None, None, None]
s2s = [None, None, None, None]
@@ -84,8 +83,8 @@
te = [None, None, None, None]
tf = [None, None, None, None]
ts = [None, None, None, None]
- rex = [4.32701, 4.29432, None, None]
- r = [1.02e-10, 1.02e-10, 1.02e-10, 1.02e-10]
+ rex_scale = 1.0 / (2.0 * pi * cdp.frq[cdp.ri_ids[0]]) ** 2
+ rex = [4.32701*rex_scale, 4.29432*rex_scale, None, None]
csa = [-172e-6, -172e-6, -172e-6, -172e-6]
chi2 = [1.9657, 0.63673, None, None]
ri_data = [{'R1_600': 1.0, 'R2_600': 15.0, 'NOE_600': 0.9},
@@ -100,16 +99,19 @@
# Check the spin data.
i = 0
for spin in spin_loop():
+ # Protons.
+ if spin.isotope == '1H':
+ self.assertEqual(spin.select, False)
+ continue
+
# Check the data.
+ print spin
self.assertEqual(spin.select, select[i])
self.assertEqual(spin.fixed, fixed[i])
- self.assertEqual(spin.proton_type, proton_type[i])
- self.assertEqual(spin.heteronuc_type, heteronuc_type[i])
- self.assertEqual(spin.attached_proton, attached_proton[i])
+ self.assertEqual(spin.isotope, isotope[i])
self.assertEqual(spin.model, model[i])
self.assertEqual(spin.equation, equation[i])
self.assertEqual(spin.params, params[i])
- self.assertEqual(spin.xh_vect, xh_vect[i])
self.assertEqual(spin.s2, s2[i])
self.assertEqual(spin.s2f, s2f[i])
self.assertEqual(spin.s2s, s2s[i])
@@ -118,7 +120,6 @@
self.assertEqual(spin.tf, tf[i])
self.assertEqual(spin.ts, ts[i])
self.assertEqual(spin.rex, rex[i])
- self.assertAlmostEqual(spin.r, r[i])
self.assertAlmostEqual(spin.csa, csa[i])
self.assertEqual(spin.chi2, chi2[i])
for ri_id in cdp.ri_ids:
@@ -127,3 +128,10 @@
# Increment the spin index.
i += 1
+
+ # Check the interatomic data.
+ r = [1.02e-10, 1.02e-10, 1.02e-10, 1.02e-10]
+ i = 0
+ for interatom in interatomic_loop():
+ self.assertAlmostEqual(interatom.r, r[i])
+ i += 1
Modified: branches/interatomic/test_suite/system_tests/scripts/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/dasha.py?rev=17171&r1=17170&r2=17171&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/dasha.py (original)
+++ branches/interatomic/test_suite/system_tests/scripts/dasha.py Tue Jul 3
23:20:26 2012
@@ -32,11 +32,25 @@
relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R2.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
+ # Name the spins, then attach some protons.
+ spin.name('N')
+ sequence.attach_protons()
+
# Setup other values.
diffusion_tensor.init(1e-8, fixed=True)
- value.set('15N', 'heteronuc_type')
- value.set(1.02 * 1e-10, 'r')
- value.set(-172 * 1e-6, 'csa')
+
+ # Define the magnetic dipole-dipole relaxation interaction.
+ spin.element(element='N', spin_id='@N')
+ spin.element(element='H', spin_id='@H')
+ dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+ dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
+
+ # Define the chemical shift relaxation interaction.
+ value.set(-172 * 1e-6, 'csa', spin_id='@N')
+
+ # Set the nuclear isotope type.
+ spin.isotope('15N', spin_id='@N')
+ spin.isotope('1H', spin_id='@H')
# Select the model-free model.
model_free.select_model(model=name)
r17171 - in /branches/interatomic/test_suite/system_tests: dasha.py scripts/dasha.py