Author: bugman
Date: Tue Mar 5 10:42:14 2013
New Revision: 18627
URL: http://svn.gna.org/viewcvs/relax?rev=18627&view=rev
Log:
Refactored frame_order.ave_pos_translate into the
frame_order.average_position user function.
This is now used to set up all characteristics of the movement to the average
domain position
including which pivot position to use for the rotation and if translation
should be used.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
branches/frame_order_testing/user_functions/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18627&r1=18626&r2=18627&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Tue Mar 5
10:42:14 2013
@@ -240,18 +240,25 @@
return scaling_matrix
- def _ave_pos_translation(self, flag=True):
- """Allow or disallow the translation of the average domain position.
-
- @keyword flag: If True, translation will be allowed. If False,
then translation will not occur.
- @type flag: bool
+ def _average_position(self, pivot='com', translation=True):
+ """Set up the mechanics of the average domain position.
+
+ @keyword pivot: What to use as the motional pivot. This can
be 'com' for the centre of mass of the moving domain, or 'motional' to link
the pivot of the motion to the rotation of the average domain position.
+ @type pivot: str
+ @keyword translation: If True, translation to the average domain
position will be allowed. If False, then translation will not occur.
+ @type translation: bool
"""
# Test if the current data pipe exists.
pipes.test()
- # Store the flag.
- cdp.ave_pos_translation = flag
+ # Check the pivot value.
+ if pivot not in ['com', 'motional']:
+ raise RelaxError("The pivot for the rotation to the average
domain position must be either 'com' or 'motional'.")
+
+ # Store the data.
+ cdp.ave_pos_pivot = pivot
+ cdp.ave_pos_translation = translation
def _base_data_types(self):
Modified: branches/frame_order_testing/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/frame_order.py?rev=18627&r1=18626&r2=18627&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/frame_order.py (original)
+++ branches/frame_order_testing/user_functions/frame_order.py Tue Mar 5
10:42:14 2013
@@ -41,6 +41,56 @@
uf_class.title = "Class containing the user functions of the Frame Order
theories."
uf_class.menu_text = "&frame_order"
uf_class.gui_icon = "relax.frame_order"
+
+
+# The frame_order.average_position user function.
+uf = uf_info.add_uf('frame_order.average_position')
+uf.title = "Define the mechanics of the average domain position."
+uf.title_short = "Average domain position mechanics."
+uf.add_keyarg(
+ name = "pivot",
+ default = "com",
+ py_type = "str",
+ desc_short = "average position pivot",
+ desc = "The type of pivot to use for the rotation to the average domain
position. This can be one of 'com' or 'motional'.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = [
+ "Centre of Mass (CoM)",
+ "Motional pivot"
+ ],
+ wiz_combo_data = [
+ "com",
+ "motional"
+ ],
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "translation",
+ default = False,
+ py_type = "bool",
+ desc_short = "translation flag",
+ desc = "A flag specifying if the average domain position should be
allowed to translate during optimisation. If False, then translation can be
disabled."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("Prior to optimisation, the mechanics of the
average moving domain position must be specified. Having the domain shifted
to the correct average position is essential for understanding the dynamics
as this information is the major contributor to the RDC and PCS. The
motional eigenframe (spherical or Euler angles) and ordering (via order
parameters, cone angles or torsion angles) come second, and are therefore
severely distorted by an incorrect average domain position.")
+uf.desc[-1].add_paragraph("There are two pieces of information affecting
this average position - a rotation and translation. For the rotation, a
pivot point is required. Note that this pivot is not related to the pivot of
the motions. However if you believe that your starting structure lies within
the uniform distribution of positions of the domain motions, then the two
pivots can be linked by setting the average position pivot to the motional
pivot. The default however is to set the pivot to the centre of mass (CoM)
of the moving domain.")
+uf.desc[-1].add_paragraph("The second option allows the average domain
position to translate during optimisation. By default, only a rotation of
the initial structure of the domain is rotated to the average position. But
if the rotation is not sufficient to shift the domain to the average
position, then a translation will be required. This option will be ignored
if no PDC data is present, as RDCs do not contain information about the
translation of the domain.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To use the centre of mass as the rotational pivot
and to allow translation of the average domain position during optimisation,
type one of:")
+uf.desc[-1].add_prompt("relax> frame_order.translate('com', True)")
+uf.desc[-1].add_prompt("relax> frame_order.translate(translation=True)")
+uf.desc[-1].add_prompt("relax> frame_order.translate(pivot='com',
translation=True)")
+uf.desc[-1].add_paragraph("To use the motional pivot as the average domain
rotational pivot while disallowing translation of, type one of:")
+uf.desc[-1].add_prompt("relax> frame_order.translate('motional')")
+uf.desc[-1].add_prompt("relax> frame_order.translate('motional', False)")
+uf.desc[-1].add_prompt("relax> frame_order.translate(pivot='motional',
translation=False)")
+uf.backend = frame_order_obj._average_position
+uf.menu_text = "&average_position"
+uf.wizard_height_desc = 450
+uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
# The frame_order.cone_pdb user function.
@@ -297,27 +347,3 @@
uf.wizard_size = (1000, 750)
uf.wizard_apply_button = False
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
-
-
-# The frame_order.ave_pos_translate user function.
-uf = uf_info.add_uf('frame_order.ave_pos_translate')
-uf.title = "Allow the average domain position to translate."
-uf.title_short = "Average position translation."
-uf.add_keyarg(
- name = "flag",
- default = True,
- py_type = "bool",
- desc_short = "translation flag",
- desc = "A flag specifying if the average domain position should be
allowed to translate during optimisation. If False, then translation can be
disabled."
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This allows the average domain position to
translate during optimisation. By default, only a rotation of the initial
structure of the domain is rotated to the average position. This option will
be ignored if no PDC data is present, as RDCs contain zero information about
the translation of the domain.")
-# Prompt examples.
-uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To allow translation of the average domain
position during optimisation, type one of:")
-uf.desc[-1].add_prompt("relax> frame_order.translate(True)")
-uf.desc[-1].add_prompt("relax> frame_order.translate(flat=True)")
-uf.backend = frame_order_obj._ave_pos_translation
-uf.menu_text = "&translate"
-uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
r18627 - in /branches/frame_order_testing: specific_fns/frame_order.py user_functions/frame_order.py