Author: bugman
Date: Thu Oct 1 21:08:55 2015
New Revision: 27925
URL: http://svn.gna.org/viewcvs/relax?rev=27925&view=rev
Log:
Merged revisions 23613-23615 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23613 | bugman | 2014-06-03 08:53:25 +0200 (Tue, 03 Jun 2014) | 5 lines
Optimisation of the rotor model to the rigid CaM frame order test data.
The optimisation script and all results files have been added to the
repository.
........
r23614 | bugman | 2014-06-03 09:00:25 +0200 (Tue, 03 Jun 2014) | 4 lines
Increased the grid search bounds for the frame order average domain
translation.
Instead of being a 10 Angstrom box centred at {0, 0, 0}, now the
translation search has been
increased to a 100 Angstrom box.
........
r23615 | bugman | 2014-06-03 09:16:09 +0200 (Tue, 03 Jun 2014) | 8 lines
Proper edge case handling and slight speed up of the frame order PCS
integration functions.
The case whereby no Sobol' points in the numerical integration lie within
the motional distribution
is now caught and the rotation matrix set to the motional eigenframe to
simulate the rigid state.
As the code for averaging the PCS was changed, it was also simplified by
removing an unnecessary
loop over all spins. This should speed up the PCS integration by a tiny
amount.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/
- copied from r23615,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rigid/rotor_analysis/
Modified:
trunk/ (props changed)
trunk/lib/frame_order/double_rotor.py
trunk/lib/frame_order/iso_cone.py
trunk/lib/frame_order/iso_cone_torsionless.py
trunk/lib/frame_order/pseudo_ellipse.py
trunk/lib/frame_order/pseudo_ellipse_torsionless.py
trunk/lib/frame_order/rotor.py
trunk/specific_analyses/frame_order/api.py
Propchange: trunk/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Oct 1 21:08:55 2015
@@ -1 +1 @@
-/branches/frame_order_cleanup:1-23195,23197-23205,23208-23612
+/branches/frame_order_cleanup:1-23195,23197-23205,23208-23615
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/double_rotor.py (original)
+++ trunk/lib/frame_order/double_rotor.py Thu Oct 1 21:08:55 2015
@@ -129,11 +129,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ pcs_pivot_motion_double_rotor(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def pcs_pivot_motion_double_rotor(full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None,
Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
Modified: trunk/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/iso_cone.py (original)
+++ trunk/lib/frame_order/iso_cone.py Thu Oct 1 21:08:55 2015
@@ -109,11 +109,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ pcs_pivot_motion_full_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def populate_1st_eigenframe_iso_cone(matrix, angle):
Modified: trunk/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone_torsionless.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/iso_cone_torsionless.py (original)
+++ trunk/lib/frame_order/iso_cone_torsionless.py Thu Oct 1 21:08:55
2015
@@ -128,8 +128,11 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+
pcs_pivot_motion_torsionless_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
Modified: trunk/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/pseudo_ellipse.py (original)
+++ trunk/lib/frame_order/pseudo_ellipse.py Thu Oct 1 21:08:55 2015
@@ -653,11 +653,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ pcs_pivot_motion_full_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def tmax_pseudo_ellipse(phi, theta_x, theta_y):
Modified: trunk/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse_torsionless.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/pseudo_ellipse_torsionless.py (original)
+++ trunk/lib/frame_order/pseudo_ellipse_torsionless.py Thu Oct 1 21:08:55
2015
@@ -314,8 +314,11 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+
pcs_pivot_motion_torsionless_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
+
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/lib/frame_order/rotor.py (original)
+++ trunk/lib/frame_order/rotor.py Thu Oct 1 21:08:55 2015
@@ -130,14 +130,14 @@
# Increment the number of points.
num += 1
- # Calculate the PCS and error.
- for i in range(len(pcs_theta)):
- for j in range(len(pcs_theta[i])):
- if num == 0:
- continue
+ # Default to the rigid state if no points lie in the distribution.
+ if num == 0:
+ pcs_pivot_motion_rotor_qrint(full_in_ref_frame=full_in_ref_frame,
r_pivot_atom=r_pivot_atom, r_pivot_atom_rev=r_pivot_atom_rev,
r_ln_pivot=r_ln_pivot, A=A, R_eigen=R_eigen, RT_eigen=RT_eigen,
Ri_prime=R_eigen, pcs_theta=pcs_theta, pcs_theta_err=pcs_theta_err,
missing_pcs=missing_pcs)
- # The average PCS.
- pcs_theta[i, j] = c[i] * pcs_theta[i, j] / float(num)
+ # Average the PCS.
+ else:
+ for i in range(len(pcs_theta)):
+ pcs_theta[i] = c[i] * pcs_theta[i] / float(num)
def pcs_pivot_motion_rotor_qrint(full_in_ref_frame=None, r_pivot_atom=None,
r_pivot_atom_rev=None, r_ln_pivot=None, A=None, R_eigen=None, RT_eigen=None,
Ri_prime=None, pcs_theta=None, pcs_theta_err=None, missing_pcs=None):
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27925&r1=27924&r2=27925&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/api.py (original)
+++ trunk/specific_analyses/frame_order/api.py Thu Oct 1 21:08:55 2015
@@ -376,6 +376,27 @@
# Reset.
dist_type = None
end_point = True
+
+ # The pivot point.
+ if cdp.params[i] in ['pivot_x', 'pivot_y', 'pivot_z']:
+ val = getattr(cdp, cdp.params[i])
+ lower = val - 10.0
+ upper = val + 10.0
+
+ # Average domain position translation (in a +/- 5 Angstrom box).
+ if cdp.params[i] in ['ave_pos_x', 'ave_pos_y', 'ave_pos_z']:
+ lower = -50
+ upper = 50
+
+ # Linear angle grid from 0 to one inc before 2pi.
+ if cdp.params[i] in ['ave_pos_alpha', 'ave_pos_gamma',
'eigen_alpha', 'eigen_gamma', 'axis_phi']:
+ lower = 0.0
+ upper = 2*pi * (1.0 - 1.0/incs[i])
+
+ # Linear angle grid from -pi to one inc before pi.
+ if cdp.params[i] in ['axis_alpha']:
+ lower = -pi
+ upper = pi * (1.0 - 1.0/incs[i])
# Arccos grid from 0 to pi.
if cdp.params[i] in ['ave_pos_beta', 'eigen_beta', 'axis_theta']:
r27925 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/rigid/rotor_an...