Author: bugman
Date: Fri Mar 22 17:27:05 2013
New Revision: 18999
URL: http://svn.gna.org/viewcvs/relax?rev=18999&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18640:18641
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18641:18642
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18642:18643
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18643:18644
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18644:18645
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18647:18648
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18648:18649
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18649:18650
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18640:18641
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
[edau@localhost relax-trunk]$ svn merge -r18641:18642
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18642 into '.':
U test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
[edau@localhost relax-trunk]$ svn merge -r18642:18643
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18643 into '.':
A test_suite/shared_data/frame_order/displacements/optimisation.py
[edau@localhost relax-trunk]$ svn merge -r18643:18644
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18644 into '.':
U test_suite/shared_data/frame_order/cam/full_analysis.py
[edau@localhost relax-trunk]$ svn merge -r18644:18645
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18645 into '.':
U test_suite/system_tests/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18647:18648
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18648 into '.':
U test_suite/shared_data/frame_order/cam/generate_base.py
[edau@localhost relax-trunk]$ svn merge -r18648:18649
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18649 into '.':
G test_suite/shared_data/frame_order/cam/generate_base.py
[edau@localhost relax-trunk]$ svn merge -r18649:18650
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18650 into '.':
G test_suite/system_tests/frame_order.py
[edau@localhost relax-trunk]$
Added:
trunk/test_suite/shared_data/frame_order/displacements/optimisation.py
- copied unchanged from r18643,
branches/frame_order_testing/test_suite/shared_data/frame_order/displacements/optimisation.py
Modified:
trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
Modified: trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/full_analysis.py?rev=18999&r1=18998&r2=18999&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/full_analysis.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/full_analysis.py Fri Mar 22
17:27:05 2013
@@ -185,8 +185,8 @@
frame_order.domain_to_pdb(domain='N', pdb='1J7O_1st_NH.pdb')
frame_order.domain_to_pdb(domain='C', pdb='1J7P_1st_NH_rot.pdb')
-# Allow the average domain to be translated during optimisation.
-#frame_order.ave_pos_translate()
+# Set up the mechanics of the displacement to the average domain position.
+frame_order.average_position(pivot='motional', translation=False)
# Set the initial pivot point.
pivot = array([ 37.254, 0.5, 16.7465])
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=18999&r1=18998&r2=18999&view=diff
==============================================================================
--- trunk/test_suite/shared_data/frame_order/cam/generate_base.py (original)
+++ trunk/test_suite/shared_data/frame_order/cam/generate_base.py Fri Mar 22
17:27:05 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2012 Edward d'Auvergne
#
+# Copyright (C) 2012-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -33,6 +33,7 @@
from generic_fns.angles import wrap_angles
from generic_fns.frame_order import print_frame_order_2nd_degree
from generic_fns.mol_res_spin import spin_loop
+from generic_fns.interatomic import interatomic_loop
from maths_fns.coord_transform import cartesian_to_spherical
from maths_fns.kronecker_product import kron_prod
from maths_fns.rotation_matrix import axis_angle_to_R, R_to_euler_zyz
@@ -118,17 +119,17 @@
def _backup_pos(self):
"""Back up the positional data prior to the rotations."""
- # Loop over the spins.
+ # Store and then reinitalise the atomic position.
for spin in spin_loop():
- # Store and then reinitalise the atomic position.
if hasattr(spin, 'pos'):
spin.orig_pos = array(spin.pos, float16)
spin.pos = zeros((self.N, 3), float16)
- # Store and then reinitalise the bond vector.
- if hasattr(spin, 'xh_vect'):
- spin.orig_vect = array(spin.xh_vect[0], float16)
- spin.xh_vect = zeros((self.N, 3), float16)
+ # Store and then reinitalise the bond vector.
+ for interatom in interatomic_loop():
+ if hasattr(interatom, 'vector'):
+ interatom.orig_vect = array(interatom.vector, float16)
+ interatom.vector = zeros((self.N, 3), float16)
def _create_distribution(self):
@@ -138,7 +139,7 @@
self.interpreter.pipe.create('distribution', 'N-state')
# Load the original PDB.
- self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir='..')
+ self.interpreter.structure.read_pdb('1J7P_1st_NH.pdb', dir='..',
set_mol_name='C-dom')
# Set up the 15N and 1H spins.
self.interpreter.structure.load_spins(spin_id='@N', ave_pos=False)
@@ -161,7 +162,7 @@
# Open the output files.
rot_file = open_write_file('rotations', compress_type=1, force=True)
- # Print out.
+ # Printout.
sys.stdout.write("\n\nRotating %s states:\n\n" % self.N)
# Load N copies of the original C-domain.
@@ -172,15 +173,15 @@
# Generate the distribution specific rotation.
self.rotation(i)
- # Loop over the spins to rotate the vectors and positions.
+ # Rotate the atomic position.
for spin in spin_loop():
- # Rotate the atomic position.
if hasattr(spin, 'pos'):
- spin.pos[i] = dot(self.R, (spin.orig_pos - self.pivot))
+ self.pivot
-
- # Rotate the NH vector.
- if hasattr(spin, 'xh_vect'):
- spin.xh_vect[i] = dot(self.R, spin.orig_vect)
+ spin.pos[i] = dot(self.R, (spin.orig_pos[0] -
self.pivot)) + self.pivot
+
+ # Rotate the NH vector.
+ for interatom in interatomic_loop():
+ if hasattr(interatom, 'vector'):
+ interatom.vector[i] = dot(self.R, interatom.orig_vect)
# Decompose the rotation into Euler angles and store them.
a, b, g = R_to_euler_zyz(self.R)
@@ -236,19 +237,19 @@
def _progress(self, i, a=5, b=100):
- """A simple progress write out."""
+ """A simple progress write out (which goes to the terminal
STDERR)."""
# The spinner characters.
chars = ['-', '\\', '|', '/']
# A spinner.
if i % a == 0:
- sys.stdout.write('\b%s' % chars[i%4])
- sys.stdout.flush()
+ sys.__stderr__.write('\b%s' % chars[i%4])
+ sys.__stderr__.flush()
# Dump the progress.
if i % b == 0:
- sys.stdout.write('\b%i\n' % i)
+ sys.__stderr__.write('\b%i\n' % i)
def axes_to_pdb_full(self):
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=18999&r1=18998&r2=18999&view=diff
==============================================================================
--- trunk/test_suite/system_tests/frame_order.py (original)
+++ trunk/test_suite/system_tests/frame_order.py Fri Mar 22 17:27:05 2013
@@ -225,7 +225,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'free_rotor.py')
- self.check_chi2(0.5010702982403058)
+ self.check_chi2(26.111745902046135)
def test_cam_free_rotor_missing_data(self):
@@ -234,7 +234,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'free_rotor_missing_data.py')
- self.check_chi2(0.39693993157977275)
+ self.check_chi2(19.769652316529044)
def test_cam_free_rotor_pcs(self):
@@ -243,7 +243,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'free_rotor.py')
- self.check_chi2(0.0038077166507876079)
+ self.check_chi2(26.0561429411961)
def test_cam_free_rotor_rdc(self):
@@ -252,7 +252,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(pcs=False)
self.interpreter.run(script_file=self.cam_path+'free_rotor.py')
- self.check_chi2(0.49726258158951819)
+ self.check_chi2(0.055602960850032274)
def test_cam_free_rotor2(self):
@@ -261,7 +261,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'free_rotor2.py')
- self.check_chi2(0.16009718934343264)
+ self.check_chi2(20.036591746561481)
def test_cam_free_rotor2_pcs(self):
@@ -270,7 +270,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'free_rotor2.py')
- self.check_chi2(0.0022059688975884064)
+ self.check_chi2(19.974062558612736)
def test_cam_free_rotor2_rdc(self):
@@ -279,7 +279,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(pcs=False)
self.interpreter.run(script_file=self.cam_path+'free_rotor2.py')
- self.check_chi2(0.15789122044584425)
+ self.check_chi2(0.062529187948743833)
def test_cam_iso_cone(self):
@@ -288,7 +288,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'iso_cone.py')
- self.check_chi2(275.91311056249037)
+ self.check_chi2(4.4891048094666539)
def test_cam_iso_cone_pcs(self):
@@ -297,7 +297,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone.py')
- self.check_chi2(275.86580651838085)
+ self.check_chi2(4.4418007653570815)
def test_cam_iso_cone_rdc(self):
@@ -315,7 +315,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor.py')
- self.check_chi2(25.809427534465456)
+ self.check_chi2(48.623418841452626)
def test_cam_iso_cone_free_rotor_pcs(self):
@@ -324,7 +324,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor.py')
- self.check_chi2(25.611019294716833)
+ self.check_chi2(31.340571886727734)
def test_cam_iso_cone_free_rotor_rdc(self):
@@ -333,7 +333,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(pcs=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor.py')
- self.check_chi2(0.1984082397486189)
+ self.check_chi2(17.282846954724896)
def test_cam_iso_cone_free_rotor2(self):
@@ -342,7 +342,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor2.py')
- self.check_chi2(14.592812979256083)
+ self.check_chi2(25.367430594567658)
def test_cam_iso_cone_free_rotor2_pcs(self):
@@ -351,7 +351,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone_free_rotor2.py')
- self.check_chi2(14.558536687064853)
+ self.check_chi2(25.326543785930376)
def test_cam_iso_cone_free_rotor2_rdc(self):
@@ -369,7 +369,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'iso_cone_torsionless.py')
- self.check_chi2(10.580880766157209)
+ self.check_chi2(0.18003434152054845)
def test_cam_iso_cone_torsionless_pcs(self):
@@ -378,7 +378,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'iso_cone_torsionless.py')
- self.check_chi2(10.531962619247517)
+ self.check_chi2(0.13111619461084989)
def test_cam_iso_cone_torsionless_rdc(self):
@@ -396,7 +396,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(opt=True)
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse.py')
- self.check_chi2(0.41620996733974391)
+ self.check_chi2(1.8246387150578596)
def test_cam_pseudo_ellipse_pcs(self):
@@ -405,7 +405,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse.py')
- self.check_chi2(0.32074844336329322)
+ self.check_chi2(1.7291771910814087)
def test_cam_pseudo_ellipse_rdc(self):
@@ -423,7 +423,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse2.py')
- self.check_chi2(215.4218668866402)
+ self.check_chi2(1.3234054898860625)
def test_cam_pseudo_ellipse2_pcs(self):
@@ -432,7 +432,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse2.py')
- self.check_chi2(215.39087557831226)
+ self.check_chi2(1.2924141815581189)
def test_cam_pseudo_ellipse2_rdc(self):
@@ -450,7 +450,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse_free_rotor.py')
- self.check_chi2(313.28994761021153)
+ self.check_chi2(3.1209520727818716)
def test_cam_pseudo_ellipse_free_rotor_pcs(self):
@@ -459,7 +459,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'pseudo_ellipse_free_rotor.py')
- self.check_chi2(313.24702804423549)
+ self.check_chi2(3.0780325068058922)
def test_cam_pseudo_ellipse_free_rotor_rdc(self):
@@ -531,7 +531,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'rotor.py')
- self.check_chi2(0.13723126588106613)
+ self.check_chi2(0.081540635994869701)
def test_cam_rotor_pcs(self):
@@ -540,7 +540,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'rotor.py')
- self.check_chi2(0.056425405173228374)
+ self.check_chi2(0.00073477528703013134)
def test_cam_rotor_rdc(self):
@@ -558,7 +558,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'rotor_2_state.py')
- self.check_chi2(2.4871012333020976)
+ self.check_chi2(1.0043926000277981)
def test_cam_rotor_2_state_pcs(self):
@@ -567,7 +567,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'rotor_2_state.py')
- self.check_chi2(1.5019518682995305)
+ self.check_chi2(0.019243235025296658)
def test_cam_rotor_2_state_rdc(self):
@@ -585,7 +585,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags()
self.interpreter.run(script_file=self.cam_path+'rotor2.py')
- self.check_chi2(0.14648723257135565)
+ self.check_chi2(0.081769384900455433)
def test_cam_rotor2_pcs(self):
@@ -594,7 +594,7 @@
# The flags, execute the script, and then check the chi2 value.
self.flags(rdc=False)
self.interpreter.run(script_file=self.cam_path+'rotor2.py')
- self.check_chi2(0.065817693413976419)
+ self.check_chi2(0.0010998457430728529)
def test_cam_rotor2_rdc(self):
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py?rev=18999&r1=18998&r2=18999&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
(original)
+++ trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse.py
Fri Mar 22 17:27:05 2013
@@ -40,7 +40,7 @@
cone_theta_y = 50.0 * 2.0 * pi / 360.0
cone_sigma_max = 60.0 * 2.0 * pi / 360.0
cone = True
- num_int_pts = 1000
+ num_int_pts = 15
# Execute the analysis.
r18999 - in /trunk/test_suite: shared_data/frame_order/cam/ shared_data/frame_order/displacements/ system_tests/ system_test...