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
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
