Author: bugman
Date: Tue Dec 16 09:10:28 2014
New Revision: 27113
URL: http://svn.gna.org/viewcvs/relax?rev=27113&view=rev
Log:
Changed the paragraph ordering in the documentation of a number of the
structure user functions.
This includes the structure.align, structure.displacement, and
structure.find_pivot user functions.
Modified:
trunk/user_functions/structure.py
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27113&r1=27112&r2=27113&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Tue Dec 16 09:10:28 2014
@@ -234,10 +234,10 @@
uf.desc[-1].add_paragraph("This allows a set of related structures to be
superimposed to each other. The current algorithm will only use atoms with
the same residue name and number and atom name in the superimposition, hence
this is not a true sequence alignment. Just as with the
structure.superimpose user function two methods are currently supported:")
uf.desc[-1].add_item_list_element("'fit to mean'", "All models are fit to
the mean structure. This is the default and most accurate method for an
ensemble description. It is an iterative method which first calculates a
mean structure and then fits each model to the mean structure using the
Kabsch algorithm. This is repeated until convergence.")
uf.desc[-1].add_item_list_element("'fit to first'", "This is quicker but is
not as accurate for an ensemble description. The Kabsch algorithm is used to
rotate and translate each model to be superimposed onto the first model of
the first data pipe.")
-uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the superimposition. The allows, for example, the superimposition
about a pivot point.")
uf.desc[-1].add_paragraph(paragraph_multi_struct)
uf.desc[-1].add_paragraph(paragraph_atom_id)
uf.desc[-1].add_paragraph(paragraph_displace_id)
+uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the superimposition. The allows, for example, the superimposition
about a pivot point.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To superimpose all sets of models, exactly as in
the structure.superimpose user function, type one of:")
@@ -655,9 +655,9 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This user function allows the rotational and
translational displacement between different models or molecules to be
calculated. The information will be printed out in various formats and held
in the relax data store. This is directional, so there is a starting and
ending position for each displacement. Therefore the displacements in all
directions between all models and molecules will be calculated.")
-uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the motion. The allows, for example, a pivot of a rotational domain
motion to be specified. This is not a formally correct algorithm, all
translations will be zero, but does give an indication to the amplitude of
the pivoting angle.")
uf.desc[-1].add_paragraph(paragraph_multi_struct)
uf.desc[-1].add_paragraph(paragraph_atom_id)
+uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the motion. The allows, for example, a pivot of a rotational domain
motion to be specified. This is not a formally correct algorithm, all
translations will be zero, but does give an indication to the amplitude of
the pivoting angle.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To determine the rotational and translational
displacements between all sets of models, type:")
@@ -727,9 +727,9 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This is used to find pivot point of motion
between a set of structural models. If the list of models is not supplied,
then all models will be used.")
-uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the superimposition. The allows, for example, the superimposition
about a pivot point.")
uf.desc[-1].add_paragraph(paragraph_multi_struct)
uf.desc[-1].add_paragraph(paragraph_atom_id)
+uf.desc[-1].add_paragraph("By supplying the position of the centroid, an
alternative position than the standard rigid body centre is used as the focal
point of the superimposition. The allows, for example, the superimposition
about a pivot point.")
uf.backend = pipe_control.structure.main.find_pivot
uf.menu_text = "&find_pivot"
uf.wizard_height_desc = 450
r27113 - /trunk/user_functions/structure.py