Author: bugman
Date: Wed Oct 1 19:44:10 2014
New Revision: 26105
URL: http://svn.gna.org/viewcvs/relax?rev=26105&view=rev
Log:
Created the frontend of the structure.align user function.
This is almost the same as that of the structure.superimpose user function
except that the pipes
argument has been added and the titles and description changed to indicate the
differences.
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=26105&r1=26104&r2=26105&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Wed Oct 1 19:44:10 2014
@@ -34,6 +34,7 @@
# relax module imports.
from graphics import WIZARD_IMAGE_PATH
+from pipe_control.pipes import pipe_names
import pipe_control.structure.geometric
import pipe_control.structure.main
from user_functions.data import Uf_info; uf_info = Uf_info()
@@ -144,6 +145,90 @@
uf.menu_text = "&add_model"
uf.gui_icon = "oxygen.actions.list-add-relax-blue"
uf.wizard_size = (700, 400)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
+
+
+# The structure.align user function.
+uf = uf_info.add_uf('structure.align')
+uf.title = "Align and superimpose different structures."
+uf.title_short = "Structural alignment and superimposition."
+uf.add_keyarg(
+ name = "pipes",
+ py_type = "str_list",
+ desc_short = "data pipes",
+ desc = "The data pipes to include in the alignment and superimposition.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = pipe_names,
+ wiz_read_only = True,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "models",
+ py_type = "int_list_of_lists",
+ desc_short = "model list",
+ desc = "The list of models for each data pipe to superimpose. The number
of elements must match the pipes argument.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "method",
+ default = "fit to mean",
+ py_type = "str",
+ desc_short = "superimposition method",
+ desc = "The superimposition method.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["fit to mean", "fit to first"],
+ wiz_read_only = True
+)
+uf.add_keyarg(
+ name = "atom_id",
+ py_type = "str",
+ desc_short = "atom ID string",
+ desc = "The atom identification string.",
+ 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",
+ desc = "The alternative position of the centroid.",
+ can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+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.")
+# 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:")
+uf.desc[-1].add_prompt("relax> structure.align()")
+uf.desc[-1].add_prompt("relax> structure.align(method='fit to mean')")
+uf.desc[-1].add_paragraph("To superimpose the models 1, 2, 3, 5 onto model 4,
type:")
+uf.desc[-1].add_prompt("relax> structure.align(models=[4, 1, 2, 3, 5],
method='fit to first')")
+uf.desc[-1].add_paragraph("To superimpose an ensemble of protein structures
using only the backbone heavy atoms, type one of:")
+uf.desc[-1].add_prompt("relax> structure.align(atom_id='@N,C,CA,O')")
+uf.desc[-1].add_prompt("relax> structure.align(method='fit to mean',
atom_id='@N,C,CA,O')")
+uf.desc[-1].add_paragraph("To superimpose the structures in the 'A' data pipe
onto the structures of the 'B' data pipe using backbone heavy atoms, type one
of:")
+uf.desc[-1].add_prompt("relax> structure.align(['B', 'A'], None, 'fit to
first', '@N,C,CA,O')")
+uf.desc[-1].add_prompt("relax> structure.align(pipes=['B', 'A'], method='fit
to first', atom_id='@N,C,CA,O')")
+uf.backend = pipe_control.structure.main.align
+uf.menu_text = "&align"
+uf.wizard_apply_button = False
+uf.wizard_height_desc = 450
+uf.wizard_size = (1000, 750)
uf.wizard_image = WIZARD_IMAGE_PATH + 'structure' + sep + '2JK4.png'
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