Author: bugman
Date: Thu Dec 11 13:40:41 2014
New Revision: 27090
URL: http://svn.gna.org/viewcvs/relax?rev=27090&view=rev
Log:
Refactored the descriptions of a number of structure user functions.
This includes the structure.align, structure.displacement,
structure.find_pivot, structure.rmsd and
structure.superimpose user functions. The paragraph_multi_struct and
paragraph_atom_id module
strings have been created and are shared as two paragraphs for each of these
user function
descriptions. This standardises the pipe/model/molecule/atom_id descriptions.
The user function
wizard page sizes have been updated for these changes.
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=27090&r1=27089&r2=27090&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Thu Dec 11 13:40:41 2014
@@ -43,6 +43,11 @@
from user_functions.wildcards import WILDCARD_STRUCT_GAUSSIAN_ALL,
WILDCARD_STRUCT_PDB_ALL, WILDCARD_STRUCT_XYZ_ALL
+# Text for the multi-structure paragraph.
+paragraph_multi_struct = "Support for multiple structures is provided by the
data pipes, model numbers and molecule names arguments. Each data pipe, model
and molecule combination will be treated as a separate structure. As only
atomic coordinates with the same residue name and number and atom name will be
assembled, structures with slightly different atomic structures can be
compared. If the list of models is not supplied, then all models of all data
pipes will be used. If the optional molecules list is supplied, each molecule
in the list will be considered as a separate structure for comparison between
each other."
+paragraph_atom_id = "The atom ID string, which uses the same notation as the
spin ID, can be used to restrict the coordinates compared to a subset of
molecules, residues, or atoms. For example to only use backbone heavy atoms in
a protein, set the atom ID to '@N,C,CA,O', assuming those are the names of the
atoms in the 3D structural file."
+
+
# The user function class.
uf_class = uf_info.add_class('structure')
uf_class.title = "Class containing the structural related functions."
@@ -221,9 +226,9 @@
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("If the list of models is not supplied, then all
models of all data pipes will be superimposed.")
-uf.desc[-1].add_paragraph("The atom ID, which uses the same notation as the
spin ID strings, can be used to restrict the superimpose calculation to certain
molecules, residues, or atoms. For example to only superimpose backbone heavy
atoms in a protein, use the atom ID of '@N,C,CA,O', assuming those are the
names of the atoms from the structural file.")
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)
# 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:")
@@ -240,7 +245,7 @@
uf.backend = pipe_control.structure.main.align
uf.menu_text = "&align"
uf.wizard_apply_button = False
-uf.wizard_height_desc = 450
+uf.wizard_height_desc = 400
uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
@@ -641,17 +646,17 @@
# 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("The atom ID, which uses the same notation as the
spin ID strings, can be used to restrict the displacement calculation to
certain molecules, residues, or atoms. This is useful if studying domain
motions, secondary structure rearrangements, amino acid side chain rotations,
etc.")
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("If the optional molecules list is supplied, then
the displacements will be calculated between the molecules in the list rather
than the models. Therefore no models are allowed to be present in the current
data pipe.")
+uf.desc[-1].add_paragraph(paragraph_multi_struct)
+uf.desc[-1].add_paragraph(paragraph_atom_id)
# 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:")
uf.desc[-1].add_prompt("relax> structure.displacement()")
uf.backend = pipe_control.structure.main.displacement
uf.menu_text = "displace&ment"
-uf.wizard_height_desc = 400
-uf.wizard_size = (900, 700)
+uf.wizard_height_desc = 450
+uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
@@ -713,13 +718,13 @@
# 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("The atom ID, which uses the same notation as the
spin ID strings, can be used to restrict the search to certain molecules,
residues, or atoms. For example to only use backbone heavy atoms in a protein,
use the atom ID of '@N,C,CA,O', assuming those are the names of the atoms from
the structural file.")
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("If the optional molecules list is supplied, then
the optimisation will be performed on molecules in the list rather than the
models. Therefore no models are allowed to be present in the current data
pipe.")
+uf.desc[-1].add_paragraph(paragraph_multi_struct)
+uf.desc[-1].add_paragraph(paragraph_atom_id)
uf.backend = pipe_control.structure.main.find_pivot
uf.menu_text = "&find_pivot"
-uf.wizard_height_desc = 400
-uf.wizard_size = (900, 700)
+uf.wizard_height_desc = 450
+uf.wizard_size = (1000, 750)
uf.wizard_apply_button = False
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
@@ -1087,15 +1092,16 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This allows the root mean squared deviation (RMSD)
between all models to be calculated.")
-uf.desc[-1].add_paragraph("The atom ID, which uses the same notation as the
spin ID strings, can be used to restrict the RMSD calculation to certain
molecules, residues, or atoms.")
-uf.desc[-1].add_paragraph("If the optional molecules list is supplied, then
the RMSD calculation will be between the molecules in the list.")
+uf.desc[-1].add_paragraph(paragraph_multi_struct)
+uf.desc[-1].add_paragraph(paragraph_atom_id)
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To determine the RMSD of all models in the current
data pipe, simply type:")
uf.desc[-1].add_prompt("relax> structure.rmsd()")
uf.backend = pipe_control.structure.main.rmsd
uf.menu_text = "&rmsd"
-uf.wizard_size = (800, 600)
+uf.wizard_height_desc = 400
+uf.wizard_size = (900, 700)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
@@ -1194,7 +1200,7 @@
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.")
uf.desc[-1].add_paragraph("If the list of models is not supplied, then all
models will be superimposed.")
-uf.desc[-1].add_paragraph("The atom ID, which uses the same notation as the
spin ID strings, can be used to restrict the superimpose calculation to certain
molecules, residues, or atoms. For example to only superimpose backbone heavy
atoms in a protein, use the atom ID of '@N,C,CA,O', assuming those are the
names of the atoms from the structural file.")
+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.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
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