Author: bugman
Date: Tue Jun 3 11:47:09 2014
New Revision: 23621
URL: http://svn.gna.org/viewcvs/relax?rev=23621&view=rev
Log:
Updated the parameters in all of the frame_order.py scripts for the CaM test
data.
The parameters are now specified at the top of the script as variables. All
scripts now handle the
change to the translation + CoM rotation for the average domain position
rather than having a pure
rotation about a fixed pivot, which is no longer supported.
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,14 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_BETA = 0.19740471457956135
+AVE_POS_GAMMA = 4.6622313104265416
+AXIS_THETA = 0.96007997859534299767
+AXIS_PHI = 4.03227550621962294031
+CONE_S1 = iso_cone_theta_to_S(1.0)
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,13 +82,15 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_beta', val=1.1824796065148637)
-value.set(param='ave_pos_gamma', val=0.35360993689599368)
-value.set(param='axis_theta', val=0.96007997859534299767)
-value.set(param='axis_phi', val=4.03227550621962294031)
-value.set(param='cone_s1', val=iso_cone_theta_to_S(1.0))
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='axis_theta', val=AXIS_THETA)
+value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='cone_s1', val=CONE_S1)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,14 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_BETA = 0.19740471457956135
+AVE_POS_GAMMA = 4.6622313104265416
+AXIS_THETA = 0.69828059079619353433
+AXIS_PHI = 4.03227550621962294031
+CONE_S1 = iso_cone_theta_to_S(1.1)
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,13 +82,15 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_beta', val=0.77485244603476433)
-value.set(param='ave_pos_gamma', val=0.1420704587263735)
-value.set(param='axis_theta', val=0.69828059079619353433)
-value.set(param='axis_phi', val=4.03227550621962294031)
-value.set(param='cone_s1', val=iso_cone_theta_to_S(1.2))
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='axis_theta', val=AXIS_THETA)
+value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='cone_s1', val=CONE_S1)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,13 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
+AXIS_THETA = 0.96007997859534299767
+AXIS_PHI = 4.03227550621962294031
+CONE_THETA = 1.3
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,14 +81,16 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_alpha', val=4.3434999280669997)
-value.set(param='ave_pos_beta', val=0.43544332764249905)
-value.set(param='ave_pos_gamma', val=3.8013235235956007)
-value.set(param='axis_theta', val=0.9600799785953431)
-value.set(param='axis_phi', val=4.0322755062196229)
-value.set(param='cone_theta', val=1.3)
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='axis_theta', val=AXIS_THETA)
+value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='cone_theta', val=CONE_THETA)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,16 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
+EIGEN_ALPHA = 3.14159265358979311600
+EIGEN_BETA = 0.69828059079619364535
+EIGEN_GAMMA = 4.03227550621962294031
+CONE_THETA_X = 0.8
+CONE_THETA_Y = 1.2
+CONE_SIGMA_MAX = 0.9
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,17 +84,19 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_alpha', val=4.3434999280669997)
-value.set(param='ave_pos_beta', val=0.43544332764249905)
-value.set(param='ave_pos_gamma', val=3.8013235235956007)
-value.set(param='eigen_alpha', val=3.14159265358979311600)
-value.set(param='eigen_beta', val=0.69828059079619364535)
-value.set(param='eigen_gamma', val=4.03227550621962294031)
-value.set(param='cone_theta_x', val=0.8)
-value.set(param='cone_theta_y', val=1.2)
-value.set(param='cone_sigma_max', val=0.9)
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='eigen_alpha', val=EIGEN_ALPHA)
+value.set(param='eigen_beta', val=EIGEN_BETA)
+value.set(param='eigen_gamma', val=EIGEN_GAMMA)
+value.set(param='cone_theta_x', val=CONE_THETA_X)
+value.set(param='cone_theta_y', val=CONE_THETA_Y)
+value.set(param='cone_sigma_max', val=CONE_SIGMA_MAX)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,16 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_BETA = 0.19740471457956135
+AVE_POS_GAMMA = 4.6622313104265416
+EIGEN_ALPHA = 3.1415926535897931
+EIGEN_BETA = 0.96007997859534311
+EIGEN_GAMMA = 4.0322755062196229
+CONE_THETA_X = 0.5
+CONE_THETA_Y = 0.3
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,16 +84,17 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_alpha', val=4.3434999280669997)
-value.set(param='ave_pos_beta', val=0.43544332764249905)
-value.set(param='ave_pos_gamma', val=3.8013235235956007)
-value.set(param='eigen_alpha', val=3.1415926535897931)
-value.set(param='eigen_beta', val=0.96007997859534311)
-value.set(param='eigen_gamma', val=4.0322755062196229)
-value.set(param='cone_theta_x', val=0.5)
-value.set(param='cone_theta_y', val=0.3)
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='eigen_alpha', val=EIGEN_ALPHA)
+value.set(param='eigen_beta', val=EIGEN_BETA)
+value.set(param='eigen_gamma', val=EIGEN_GAMMA)
+value.set(param='cone_theta_x', val=CONE_THETA_X)
+value.set(param='cone_theta_y', val=CONE_THETA_Y)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,15 @@
# Python module imports.
from numpy import array
+
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
+EIGEN_ALPHA = 3.14159265358979311600
+EIGEN_BETA = 0.96007997859534310869
+EIGEN_GAMMA = 4.03227550621962294031
+CONE_THETA_X = 1.3
+CONE_THETA_Y = 1.1
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,16 +83,18 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_alpha', val=4.3434999280669997)
-value.set(param='ave_pos_beta', val=0.43544332764249905)
-value.set(param='ave_pos_gamma', val=3.8013235235956007)
-value.set(param='eigen_alpha', val=3.1415926535897931)
-value.set(param='eigen_beta', val=0.96007997859534311)
-value.set(param='eigen_gamma', val=4.0322755062196229)
-value.set(param='cone_theta_x', val=1.3)
-value.set(param='cone_theta_y', val=1.1)
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='eigen_alpha', val=EIGEN_ALPHA)
+value.set(param='eigen_beta', val=EIGEN_BETA)
+value.set(param='eigen_gamma', val=EIGEN_GAMMA)
+value.set(param='cone_theta_x', val=CONE_THETA_X)
+value.set(param='cone_theta_y', val=CONE_THETA_Y)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -44,8 +44,8 @@
# The real parameter values.
-AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -21.269217407269576,
-3.122610661328414, -2.400652421655998]
-AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [ 5.623469076122531,
0.435439405668396, 5.081265529106499]
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
AXIS_THETA = 0.69828059079619353433
AXIS_PHI = 4.03227550621962294031
CONE_SIGMA_MAX = 30.0 / 360.0 * 2.0 * pi
Modified:
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py?rev=23621&r1=23620&r2=23621&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
(original)
+++
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
Tue Jun 3 11:47:09 2014
@@ -3,6 +3,12 @@
# Python module imports.
from numpy import array
+# The real parameter values.
+AVE_POS_X, AVE_POS_Y, AVE_POS_Z = [ -20.859750185691549,
-2.450606987447843, -2.191854570352916]
+AVE_POS_ALPHA, AVE_POS_BETA, AVE_POS_GAMMA = [5.623468683852550,
0.435439748282942, 5.081265879629926]
+AXIS_THETA = 0.52344988559983696152
+AXIS_PHI = 0.89068285262982982
+CONE_SIGMA_MAX = 10.0 / 360.0 * 2.0 * pi
# Create the data pipe.
pipe.create(pipe_name='frame order', pipe_type='frame order')
@@ -74,14 +80,16 @@
frame_order.num_int_pts(num=50)
# Check the minimum.
-value.set(param='ave_pos_alpha', val=4.3434999280669997)
-value.set(param='ave_pos_beta', val=0.43544332764249905)
-value.set(param='ave_pos_gamma', val=3.8013235235956007)
-value.set(param='axis_theta', val=0.52344988559983696152)
-value.set(param='axis_phi', val=0.89068285262982982)
-value.set(param='cone_sigma_max', val=10.0 / 360.0 * 2.0 * pi)
+value.set(param='ave_pos_x', val=AVE_POS_X)
+value.set(param='ave_pos_y', val=AVE_POS_Y)
+value.set(param='ave_pos_z', val=AVE_POS_Z)
+value.set(param='ave_pos_alpha', val=AVE_POS_ALPHA)
+value.set(param='ave_pos_beta', val=AVE_POS_BETA)
+value.set(param='ave_pos_gamma', val=AVE_POS_GAMMA)
+value.set(param='axis_theta', val=AXIS_THETA)
+value.set(param='axis_phi', val=AXIS_PHI)
+value.set(param='cone_sigma_max', val=CONE_SIGMA_MAX)
calc()
-print("\nchi2: %s" % repr(cdp.chi2))
# Create the PDB representation of the true state.
frame_order.pdb_model(ave_pos_file='ave_pos_true.pdb.gz',
rep_file='frame_order_true.pdb.gz', dist_file=None, force=True)
r23621 - in /branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam: iso_cone_free_rotor/ iso_cone_free_rotor2/...