Author: bugman
Date: Mon Mar 4 18:46:51 2013
New Revision: 18623
URL: http://svn.gna.org/viewcvs/relax?rev=18623&view=rev
Log:
Fixes for the PCS with translations and rotations.
The reverse rotations previously used have been converted to forwards
rotations. This makes more
sense from the perspective of moving the original structures to the average
position.
Modified:
branches/frame_order_testing/maths_fns/frame_order/__init__.py
branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py
branches/frame_order_testing/maths_fns/frame_order/rotor.py
Modified: branches/frame_order_testing/maths_fns/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order/__init__.py?rev=18623&r1=18622&r2=18623&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order/__init__.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order/__init__.py Mon Mar 4
18:46:51 2013
@@ -472,9 +472,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_rotor(sigma_max=pi, c=self.pcs_const[align_index],
r_pivot_atom=r_pivot_atom, r_ln_pivot=self.r_ln_pivot[:, 0],
A=self.A_3D[align_index], R_eigen=self.R_eigen, RT_eigen=RT_eigen,
Ri_prime=self.Ri_prime)
@@ -646,9 +646,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_iso_cone(theta_max=cone_theta, sigma_max=sigma_max,
c=self.pcs_const[align_index], r_pivot_atom=r_pivot_atom,
r_ln_pivot=self.r_ln_pivot[:, 0], A=self.A_3D[align_index],
R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime)
@@ -822,9 +822,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_iso_cone(theta_max=theta_max, sigma_max=pi,
c=self.pcs_const[align_index], r_pivot_atom=r_pivot_atom,
r_ln_pivot=self.r_ln_pivot[:, 0], A=self.A_3D[align_index],
R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime)
@@ -998,9 +998,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_iso_cone_torsionless(theta_max=cone_theta,
c=self.pcs_const[align_index], r_pivot_atom=r_pivot_atom,
r_ln_pivot=self.r_ln_pivot[:, 0], A=self.A_3D[align_index],
R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime)
@@ -1168,9 +1168,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_pseudo_ellipse(theta_x=cone_theta_x, theta_y=cone_theta_y,
sigma_max=cone_sigma_max, c=self.pcs_const[align_index],
r_pivot_atom=r_pivot_atom, r_ln_pivot=self.r_ln_pivot[:, 0],
A=self.A_3D[align_index], R_eigen=self.R_eigen, RT_eigen=RT_eigen,
Ri_prime=self.Ri_prime)
@@ -1335,9 +1335,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_pseudo_ellipse(theta_x=cone_theta_x, theta_y=cone_theta_y,
sigma_max=pi, c=self.pcs_const[align_index], r_pivot_atom=r_pivot_atom,
r_ln_pivot=self.r_ln_pivot[:, 0], A=self.A_3D[align_index],
R_eigen=self.R_eigen, RT_eigen=RT_eigen, Ri_prime=self.Ri_prime)
@@ -1541,9 +1541,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_pseudo_ellipse_torsionless(theta_x=cone_theta_x,
theta_y=cone_theta_y, c=self.pcs_const[align_index],
r_pivot_atom=r_pivot_atom, r_ln_pivot=self.r_ln_pivot[:, 0],
A=self.A_3D[align_index], R_eigen=self.R_eigen, RT_eigen=RT_eigen,
Ri_prime=self.Ri_prime)
@@ -1691,9 +1691,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The PCS calculation.
vect = self.r_ln_pivot[:, 0] + r_pivot_atom
@@ -1784,9 +1784,9 @@
if not self.missing_pcs[align_index, j]:
# Forwards and reverse rotations.
if self.full_in_ref_frame[align_index]:
+ r_pivot_atom = self.r_pivot_atom[:, j]
+ else:
r_pivot_atom = self.r_pivot_atom_rev[:, j]
- else:
- r_pivot_atom = self.r_pivot_atom[:, j]
# The numerical integration.
self.pcs_theta[align_index, j] =
pcs_numeric_int_rotor(sigma_max=sigma_max, c=self.pcs_const[align_index],
r_pivot_atom=r_pivot_atom, r_ln_pivot=self.r_ln_pivot[:, 0],
A=self.A_3D[align_index], R_eigen=self.R_eigen, RT_eigen=RT_eigen,
Ri_prime=self.Ri_prime)
Modified: branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py?rev=18623&r1=18622&r2=18623&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py
(original)
+++ branches/frame_order_testing/maths_fns/frame_order/matrix_ops.py Mon Mar
4 18:46:51 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2009-2012 Edward d'Auvergne
#
+# Copyright (C) 2009-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -212,11 +212,11 @@
# The projection.
if full_in_ref_frame[i]:
+ proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
+ length_i = length
+ else:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
length_i = length_rev
- else:
- proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length
# The PCS.
pcs_theta[i, j] += proj * length_i
@@ -356,11 +356,11 @@
# The projection.
if full_in_ref_frame[i]:
+ proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
+ length_i = length
+ else:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
length_i = length_rev
- else:
- proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length
# The PCS.
pcs_theta[i, j] += proj * length_i
Modified: branches/frame_order_testing/maths_fns/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/frame_order/rotor.py?rev=18623&r1=18622&r2=18623&view=diff
==============================================================================
--- branches/frame_order_testing/maths_fns/frame_order/rotor.py (original)
+++ branches/frame_order_testing/maths_fns/frame_order/rotor.py Mon Mar 4
18:46:51 2013
@@ -303,11 +303,11 @@
# The projection.
if full_in_ref_frame[i]:
+ proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
+ length_i = length
+ else:
proj = dot(rot_vect_rev[j], dot(A[i], rot_vect_rev[j]))
length_i = length_rev
- else:
- proj = dot(rot_vect[j], dot(A[i], rot_vect[j]))
- length_i = length
# The PCS.
pcs_theta[i, j] += proj * length_i
r18623 - in /branches/frame_order_testing/maths_fns/frame_order: __init__.py matrix_ops.py rotor.py