Author: bugman
Date: Wed Dec 3 09:34:46 2014
New Revision: 26908
URL: http://svn.gna.org/viewcvs/relax?rev=26908&view=rev
Log:
Redesign of the pymol.frame_order user function.
This user function was still fitting to the old design in the relax trunk. It
has been updated for
the frame_order_cleanup branch whereby the frame_order.pdb_model user function
has been split up and
the positional distribution has been replaced by the Brownian simulation user
function
frame_order.simulate.
Modified:
branches/frame_order_cleanup/pipe_control/pymol_control.py
branches/frame_order_cleanup/user_functions/pymol_control.py
Modified: branches/frame_order_cleanup/pipe_control/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pymol_control.py?rev=26908&r1=26907&r2=26908&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Wed Dec 3
09:34:46 2014
@@ -321,16 +321,16 @@
return commands
-def frame_order(ave_pos="ave_pos", rep="frame_order",
dist="domain_distribution", dir=None):
- """Display the frame order results (the geometric object, average position
and distribution).
+def frame_order(ave_pos="ave_pos", rep="frame_order", sim="simulation.pdb.gz",
dir=None):
+ """Display the frame order results (geometric object, average position and
Brownian simulation).
@keyword ave_pos: The file root of the average molecule structure.
@type ave_pos: str or None
@keyword rep: The file root of the PDB representation of the frame
order dynamics to create.
@type rep: str or None
- @keyword dist: The file root which will contain multiple models
spanning the full dynamics distribution of the frame order model.
- @type dist: str or None
- @keyword dir: The name of the directory to place the PDB file into.
+ @keyword sim: The full Brownian diffusion file name.
+ @type sim: str or None
+ @keyword dir: The name of the directory where the files are located.
@type dir: str or None
"""
@@ -347,8 +347,8 @@
frame_order_ave_pos(root=ave_pos, path=path)
if rep:
frame_order_geometric(root=rep, path=path)
- if dist:
- frame_order_distribution(root=dist, path=path)
+ if sim:
+ frame_order_sim(file=sim, path=path)
# Centre all objects and zoom.
pymol_obj.exec_cmd("center animate=3")
@@ -377,15 +377,15 @@
pymol_obj.exec_cmd("disable %s_sim" % root)
-def frame_order_distribution(root=None, path=None):
- """Display the PDB structure for the frame order distribution of domain
positions.
-
- @keyword root: The file root of the PDB file containing the frame order
distribution of domain positions.
+def frame_order_sim(file=None, path=None):
+ """Display the PDB structure for the frame order Brownian simulation.
+
+ @keyword root: The full Brownian diffusion file name.
@type root: str
"""
# Find all PDB files.
- pdb_files = find_pdb_files(path=path, file_root=root)
+ pdb_files = find_pdb_files(path=path, file_root=file)
# Read in the PDB files.
for file in pdb_files:
Modified: branches/frame_order_cleanup/user_functions/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/pymol_control.py?rev=26908&r1=26907&r2=26908&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/pymol_control.py
(original)
+++ branches/frame_order_cleanup/user_functions/pymol_control.py Wed Dec
3 09:34:46 2014
@@ -146,7 +146,7 @@
# The pymol.frame_order user function.
uf = uf_info.add_uf('pymol.frame_order')
-uf.title = "Display the frame order results from the frame_order.pdb_model
user function."
+uf.title = "Display the frame order results from the frame_order.pdb_model and
frame_order.simulate user functions."
uf.title_short = "Frame order results display."
uf.add_keyarg(
name = "ave_pos",
@@ -155,7 +155,6 @@
arg_type = "str",
desc_short = "average structure file root",
desc = "The file root of the 3D structure PDB file for the molecular
structure with the moving domains shifted to the average position.",
- wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
can_be_none = True
)
uf.add_keyarg(
@@ -165,17 +164,18 @@
arg_type = "str",
desc_short = "PDB representation file root",
desc = "The file root of the PDB file for the geometric object
representation of the frame order dynamics.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sim",
+ default = "simulation.pdb.gz",
+ py_type = "str",
+ arg_type = "file sel",
+ desc_short = "Brownian simulation file",
+ desc = "The full name the Brownian simulation PDB file.",
wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
- can_be_none = True
-)
-uf.add_keyarg(
- name = "dist",
- default = "domain_distribution",
- py_type = "str",
- arg_type = "str",
- desc_short = "distribution file root",
- desc = "The file root of the file which will contain multiple models
spanning the full dynamics distribution of the frame order model.",
- wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
+ wiz_filesel_style = FD_OPEN,
+ wiz_filesel_preview = False,
can_be_none = True
)
uf.add_keyarg(
@@ -183,21 +183,22 @@
py_type = "str",
arg_type = "dir",
desc_short = "directory name",
- desc = "The directory where the file is to be located.",
- can_be_none = True
-)
-# Description.
-uf.desc.append(Desc_container())
-uf.desc[-1].add_paragraph("This user function is designed to be combined with
the frame_order.pdb_model user function. It will take the three PDB
representations created by frame_order.pdb_model - the molecular structure with
the averaged domain positions, the frame order dynamics representation files,
and the moving domain distribution file - and display them in PyMOL. Rather
than loading the three representations into PyMOL manually, this user function
will change the representation to significantly improve the visualisation.")
-uf.desc[-1].add_paragraph("For the frame order position files, if the file
roots are left to the defaults then the following files will be loaded:")
-uf.desc[-1].add_list_element("The file root 'ave_pos' will load the
'ave_pos.pdb' and 'ave_pos_sim.pdb' files.")
-uf.desc[-1].add_list_element("The file root 'frame_order' will load the
'frame_order.pdb', 'frame_order_pos.pdb', 'frame_order_neg.pdb',
'frame_order_sim.pdb', 'frame_order_sim_pos.pdb' and 'frame_order_sim_neg.pdb'
files.")
-uf.desc[-1].add_list_element("The file root 'dist' will load the 'dist.pdb'
file.")
-uf.desc[-1].add_paragraph("The user function will not only search for these
files, but also all *.gz and *.bz2 versions of these files. This is to support
all output files from the frame_order.pdb_model user function.")
+ desc = "The directory where the files are located.",
+ can_be_none = True
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This user function is designed to be combined with
the frame_order.pdb_model and frame_order.simulate user functions. It will
take the two PDB representations created by frame_order.pdb_model, the
molecular structure with the averaged domain positions and the frame order
dynamics representation files, and the Brownian simulation PDB file and display
them in PyMOL. Rather than loading the three representations into PyMOL
manually, this user function will change the representation to improve
visualisation.")
+uf.desc[-1].add_paragraph("For the PDB files, if the file roots are left to
the defaults then the following files will be loaded:")
+uf.desc[-1].add_item_list_element("Average position", "The default is to load
the 'ave_pos.pdb' and 'ave_pos_sim.pdb' files.")
+uf.desc[-1].add_item_list_element("Frame order motional representation", "The
is to load the 'frame_order.pdb', 'frame_order_A.pdb', 'frame_order_B.pdb',
'frame_order_sim.pdb', 'frame_order_sim_A.pdb' and 'frame_order_sim_B.pdb'
files, if present.")
+uf.desc[-1].add_item_list_element("Brownian simulation", "The default is to
load the 'simulation.pdb.gz' file.")
+uf.desc[-1].add_paragraph("The user function will not only search for these
files, but also all *.gz and *.bz2 versions of the average position and frame
order representations. This is to support all output files from the
frame_order.pdb_model user function.")
uf.backend = pymol_control.frame_order
uf.menu_text = "&frame_order"
uf.gui_icon = "relax.frame_order"
-uf.wizard_size = (900, 600)
+uf.wizard_height_desc = 400
+uf.wizard_size = (1000, 700)
uf.wizard_apply_button = False
uf.wizard_image = WIZARD_IMAGE_PATH + 'pymol' + sep + 'pymol.png'
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