Author: bugman
Date: Fri May 16 16:32:44 2014
New Revision: 23207
URL: http://svn.gna.org/viewcvs/relax?rev=23207&view=rev
Log:
Merged revisions 23206 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23206 | bugman | 2014-05-16 16:32:03 +0200 (Fri, 16 May 2014) | 5 lines
Added the 'centre_type' argument to the structure.superimpose user function.
This allows the default 'centroid' superimposition to be replaced by a
centre of mass (CoM)
superimposition instead. As the CoM and centroid position do not match,
the translation vector and
Euler rotation angles will be different.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/superimpose.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/user_functions/structure.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri May 16 16:32:44 2014
@@ -1 +1 @@
-/trunk:1-23194
+/trunk:1-23206
Modified: branches/frame_order_cleanup/lib/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/superimpose.py?rev=23207&r1=23206&r2=23207&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/superimpose.py (original)
+++ branches/frame_order_cleanup/lib/structure/superimpose.py Fri May 16
16:32:44 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2011-2013 Edward d'Auvergne
#
+# Copyright (C) 2011-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -29,6 +29,7 @@
from numpy.linalg import det, norm, svd
# relax module import.
+from lib.structure.mass import centre_of_mass
from lib.structure.statistics import calc_mean_structure
from lib.geometry.rotations import R_to_axis_angle, R_to_euler_zyz
@@ -49,17 +50,21 @@
return centroid
-def fit_to_first(models=None, coord=None, centroid=None):
+def fit_to_first(models=None, coord=None, centre_type="centroid",
elements=None, centroid=None):
"""Superimpose a set of structural models using the fit to first
algorithm.
- @keyword models: The list of models to superimpose.
- @type models: list of int
- @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
- @type coord: list of numpy rank-2, Nx3 arrays
- @keyword centroid: An alternative position of the centroid to allow for
different superpositions, for example of pivot point motions.
- @type centroid: list of float or numpy rank-1, 3D array
- @return: The lists of translation vectors, rotation matrices,
and rotation pivots.
- @rtype: list of numpy rank-1 3D arrays, list of numpy rank-2
3D arrays, list of numpy rank-1 3D arrays
+ @keyword models: The list of models to superimpose.
+ @type models: list of int
+ @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
+ @type coord: list of numpy rank-2, Nx3 arrays
+ @keyword centroid: An alternative position of the centroid to allow
for different superpositions, for example of pivot point motions.
+ @type centroid: list of float or numpy rank-1, 3D array
+ @keyword centre_type: The type of centre to superimpose over. This
can either be the standard centroid superimposition or the CoM could be used
instead.
+ @type centre_type: str
+ @keyword elements: The list of elements corresponding to the atoms.
+ @type elements: list of str
+ @return: The lists of translation vectors, rotation
matrices, and rotation pivots.
+ @rtype: list of numpy rank-1 3D arrays, list of numpy
rank-2 3D arrays, list of numpy rank-1 3D arrays
"""
# Print out.
@@ -73,7 +78,7 @@
# Loop over the ending models.
for i in range(1, len(models)):
# Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%models[i],
coord_from=coord[i], coord_to=coord[0], centroid=centroid)
+ trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%models[i],
coord_from=coord[i], coord_to=coord[0], centre_type=centre_type,
elements=elements, centroid=centroid)
# Store the transforms.
T_list.append(trans_vect)
@@ -84,19 +89,23 @@
return T_list, R_list, pivot_list
-def fit_to_mean(models=None, coord=None, centroid=None, verbosity=1):
+def fit_to_mean(models=None, coord=None, centre_type="centroid",
elements=None, centroid=None, verbosity=1):
"""Superimpose a set of structural models using the fit to first
algorithm.
- @keyword models: The list of models to superimpose.
- @type models: list of int
- @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
- @type coord: list of numpy rank-2, Nx3 arrays
- @keyword centroid: An alternative position of the centroid to allow for
different superpositions, for example of pivot point motions.
- @type centroid: list of float or numpy rank-1, 3D array
- @keyword verbosity: The amount of information to print out. If 0,
nothing will be printed.
- @type verbosity: int
- @return: The lists of translation vectors, rotation matrices,
and rotation pivots.
- @rtype: list of numpy rank-1 3D arrays, list of numpy rank-2
3D arrays, list of numpy rank-1 3D arrays
+ @keyword models: The list of models to superimpose.
+ @type models: list of int
+ @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
+ @type coord: list of numpy rank-2, Nx3 arrays
+ @keyword centre_type: The type of centre to superimpose over. This
can either be the standard centroid superimposition or the CoM could be used
instead.
+ @type centre_type: str
+ @keyword elements: The list of elements corresponding to the atoms.
+ @type elements: list of str
+ @keyword centroid: An alternative position of the centroid to allow
for different superpositions, for example of pivot point motions.
+ @type centroid: list of float or numpy rank-1, 3D array
+ @keyword verbosity: The amount of information to print out. If 0,
nothing will be printed.
+ @type verbosity: int
+ @return: The lists of translation vectors, rotation
matrices, and rotation pivots.
+ @rtype: list of numpy rank-1 3D arrays, list of numpy
rank-2 3D arrays, list of numpy rank-1 3D arrays
"""
# Print out.
@@ -131,7 +140,7 @@
converged = True
for i in range(len(models)):
# Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='mean', coord_from=coord[i],
coord_to=mean, centroid=centroid, verbosity=0)
+ trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='mean', coord_from=coord[i],
coord_to=mean, centre_type=centre_type, elements=elements, centroid=centroid,
verbosity=0)
# Table printout.
if verbosity:
@@ -161,7 +170,7 @@
# Perform the fit once from the original coordinates to obtain the full
transforms.
for i in range(len(models)):
# Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[i], name_to='the mean structure',
coord_from=orig_coord[i], coord_to=mean, centroid=centroid, verbosity=0)
+ trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[i], name_to='the mean structure',
coord_from=orig_coord[i], coord_to=mean, centre_type=centre_type,
elements=elements, centroid=centroid, verbosity=0)
# Store the transforms.
T_list.append(trans_vect)
@@ -172,7 +181,7 @@
return T_list, R_list, pivot_list
-def kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None,
centroid=None, verbosity=1):
+def kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None,
centre_type="centroid", elements=None, centroid=None, verbosity=1):
"""Calculate the rotational and translational displacements between the
two given coordinate sets.
This uses the U{Kabsch
algorithm<http://en.wikipedia.org/wiki/Kabsch_algorithm>}.
@@ -186,6 +195,10 @@
@type coord_from: numpy rank-2, Nx3 array
@keyword coord_to: The list of atomic coordinates for the ending
structure.
@type coord_to: numpy rank-2, Nx3 array
+ @keyword centre_type: The type of centre to superimpose over. This
can either be the standard centroid superimposition or the CoM could be used
instead.
+ @type centre_type: str
+ @keyword elements: The list of elements corresponding to the atoms.
+ @type elements: list of str
@keyword centroid: An alternative position of the centroid, used
for studying pivoted systems.
@type centroid: list of float or numpy rank-1, 3D array
@return: The translation vector T, translation distance
d, rotation matrix R, rotation axis r, rotation angle theta, and the
rotational pivot defined as the centroid of the ending structure.
@@ -196,9 +209,12 @@
if centroid != None:
centroid_from = centroid
centroid_to = centroid
- else:
+ elif centre_type == 'centroid':
centroid_from = find_centroid(coord_from)
centroid_to = find_centroid(coord_to)
+ else:
+ centroid_from, mass_from = centre_of_mass(pos=coord_from,
elements=elements)
+ centroid_to, mass_to = centre_of_mass(pos=coord_to,
elements=elements)
# The translation.
trans_vect = centroid_to - centroid_from
@@ -212,8 +228,12 @@
# Print out.
if verbosity >= 1:
print("\n\nCalculating the rotational and translational
displacements from %s to %s using the Kabsch algorithm.\n" % (name_from,
name_to))
- print("Start centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_from[0], centroid_from[1], centroid_from[2]))
- print("End centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_to[0], centroid_to[1], centroid_to[2]))
+ if centre_type == 'centroid':
+ print("Start centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_from[0], centroid_from[1], centroid_from[2]))
+ print("End centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_to[0], centroid_to[1], centroid_to[2]))
+ else:
+ print("Start CoM: [%20.15f, %20.15f, %20.15f]" %
(centroid_from[0], centroid_from[1], centroid_from[2]))
+ print("End CoM: [%20.15f, %20.15f, %20.15f]" %
(centroid_to[0], centroid_to[1], centroid_to[2]))
print("Translation vector: [%20.15f, %20.15f, %20.15f]" %
(trans_vect[0], trans_vect[1], trans_vect[2]))
print("Translation distance: %.15f" % trans_dist)
print("Rotation matrix:")
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=23207&r1=23206&r2=23207&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/structure/main.py (original)
+++ branches/frame_order_cleanup/pipe_control/structure/main.py Fri May 16
16:32:44 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
+# Copyright (C) 2003-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -867,23 +867,30 @@
spin.xh_vect = xh_vect
-def superimpose(models=None, method='fit to mean', atom_id=None,
centroid=None):
+def superimpose(models=None, method='fit to mean', atom_id=None,
centre_type="centroid", centroid=None):
"""Superimpose a set of structural models.
- @keyword models: The list of models to superimpose. If set to None,
then all models will be used.
- @type models: list of int or None
- @keyword method: The superimposition method. It must be one of 'fit
to mean' or 'fit to first'.
- @type method: str
- @keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
- @type atom_id: str or None
- @keyword centroid: An alternative position of the centroid to allow for
different superpositions, for example of pivot point motions.
- @type centroid: list of float or numpy rank-1, 3D array
+ @keyword models: The list of models to superimpose. If set to
None, then all models will be used.
+ @type models: list of int or None
+ @keyword method: The superimposition method. It must be one of
'fit to mean' or 'fit to first'.
+ @type method: str
+ @keyword atom_id: The molecule, residue, and atom identifier
string. This matches the spin ID string format.
+ @type atom_id: str or None
+ @keyword centre_type: The type of centre to superimpose over. This
can either be the standard centroid superimposition or the CoM could be used
instead.
+ @type centre_type: str
+ @keyword centroid: An alternative position of the centroid to allow
for different superpositions, for example of pivot point motions.
+ @type centroid: list of float or numpy rank-1, 3D array
"""
# Check the method.
allowed = ['fit to mean', 'fit to first']
if method not in allowed:
raise RelaxError("The superimposition method '%s' is unknown. It
must be one of %s." % (method, allowed))
+
+ # Check the type.
+ allowed = ['centroid', 'CoM']
+ if centre_type not in allowed:
+ raise RelaxError("The superimposition centre type '%s' is unknown.
It must be one of %s." % (centre_type, allowed))
# Test if the current data pipe exists.
pipes.test()
@@ -905,11 +912,16 @@
coord[-1].append(pos[0])
coord[-1] = array(coord[-1])
+ # Assemble the element types.
+ elements = []
+ for elem in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
element_flag=True):
+ elements.append(elem)
+
# The different algorithms.
if method == 'fit to mean':
- T, R, pivot = fit_to_mean(models=models, coord=coord,
centroid=centroid)
+ T, R, pivot = fit_to_mean(models=models, coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
elif method == 'fit to first':
- T, R, pivot = fit_to_first(models=models, coord=coord,
centroid=centroid)
+ T, R, pivot = fit_to_first(models=models, coord=coord,
centre_type=centre_type, elements=elements, centroid=centroid)
# Update to the new coordinates.
Modified: branches/frame_order_cleanup/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=23207&r1=23206&r2=23207&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/structure.py (original)
+++ branches/frame_order_cleanup/user_functions/structure.py Fri May 16
16:32:44 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2013 Edward d'Auvergne
#
+# Copyright (C) 2003-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -932,6 +932,16 @@
can_be_none = True
)
uf.add_keyarg(
+ name = "centre_type",
+ py_type = "str",
+ default = "centroid",
+ desc_short = "centre type",
+ desc = "The type of centre to user for the superimposition, i.e. either
the standard centroid superimposition or a superimposition using the centre
of mass (CoM).",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["The centroid", "The centre of mass (CoM)"],
+ wiz_combo_data = ["centroid", "CoM"]
+)
+uf.add_keyarg(
name = "centroid",
py_type = "float_array",
desc_short = "centroid position",
r23207 - in /branches/frame_order_cleanup: ./ lib/structure/ pipe_control/structure/ user_functions/