Author: bugman
Date: Sat Feb 14 10:54:43 2015
New Revision: 27642
URL: http://svn.gna.org/viewcvs/relax?rev=27642&view=rev
Log:
Created the front-end of the frame_order.distribute user function.
This is a copy and modification of the frame_order.simulate user function, as
the concepts are
similar.
Modified:
branches/frame_order_cleanup/user_functions/frame_order.py
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=27642&r1=27641&r2=27642&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Sat Feb 14
10:54:43 2015
@@ -38,7 +38,7 @@
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
-from user_functions.wildcards import WILDCARD_RELAX_SAVE
+from user_functions.wildcards import WILDCARD_RELAX_SAVE,
WILDCARD_STRUCT_PDB_ALL
# The user function class.
@@ -59,6 +59,68 @@
uf.menu_text = "&count_sobol_points"
uf.gui_icon = "oxygen.categories.applications-education"
uf.wizard_size = (800, 400)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
+
+
+# The frame_order.distribute user function.
+uf = uf_info.add_uf('frame_order.distribute')
+uf.title = "Structural distribution of the frame order motions."
+uf.title_short = "Frame order motional distribution."
+uf.add_keyarg(
+ name = "file",
+ default = "distribution.pdb.gz",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "distribution file",
+ desc = "The PDB file for storing the frame order motional distribution.
The compression is determined automatically by the file extensions '*.pdb',
'*.pdb.gz', and '*.pdb.bz2'.",
+ wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
+ wiz_filesel_style = FD_OPEN,
+ wiz_filesel_preview = False
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the files are to be located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "total",
+ default = 1000,
+ min = 1,
+ max = 1000000,
+ py_type = "int",
+ desc_short = "total number of structures",
+ desc = "The total number of structures to include in the uniform
distribution.",
+ wiz_element_type = "spin"
+)
+uf.add_keyarg(
+ name = "model",
+ default = 1,
+ min = 1,
+ py_type = "int",
+ desc_short = "original structural model",
+ desc = "Only one model from an analysed ensemble of structures can be used
for the distribution, as the distribution PDB file consists of one model per
state.",
+ wiz_element_type = "spin"
+)
+uf.add_keyarg(
+ name = "force",
+ default = False,
+ py_type = "bool",
+ desc_short = "force flag",
+ desc = "A flag which, if set to True, will overwrite the any pre-existing
file."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("To visualise the frame order motions, this user
function generates a distribution of structures randomly within the bounds of
the uniform distribution of the frame order model. The original structure is
rotated randomly and only accepted for the distribution if it is within the
bounds. This is a more faithful representation of the dynamics than the
pseudo-Brownian simulation user function.")
+uf.desc[-1].add_paragraph("Note that the RDC and PCS data does not contain
information about all parts of the real distribution of structures. Therefore
the structures in this distribution only represent the components of the
distribution present in the data, as modelled by the frame order models.")
+uf.desc[-1].add_paragraph("As the distribution consists of one model per
state, if an ensemble of structures has been analysed, only one model from the
ensemble can be used for the representation.")
+uf.backend = simulate
+uf.menu_text = "&distribute"
+uf.gui_icon = "oxygen.actions.document-save"
+uf.wizard_height_desc = 420
+uf.wizard_size = (900, 600)
uf.wizard_image = WIZARD_IMAGE_PATH + 'frame_order.png'
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