Author: bugman
Date: Wed Jul 2 14:53:21 2014
New Revision: 24410
URL: http://svn.gna.org/viewcvs/relax?rev=24410&view=rev
Log:
Redesign of the pymol.frame_order user function to match the redesign of
frame_order.pdb_model.
The file names are no longer given but rather the file root. Then all PDB
files matching that file
root in the given directory will be loaded into PyMOL.
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=24410&r1=24409&r2=24410&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Wed Jul 2
14:53:21 2014
@@ -30,7 +30,7 @@
import pymol
from math import pi
from numpy import float64, transpose, zeros
-from os import F_OK, access, pardir, sep
+from os import F_OK, access, getcwd, pardir, sep
PIPE, Popen = None, None
if dep_check.subprocess_module:
from subprocess import PIPE, Popen
@@ -41,6 +41,7 @@
from lib.errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError
from lib.geometry.rotations import euler_to_R_zyz, R_to_axis_angle
from lib.io import delete, file_root, get_file_path, open_read_file,
open_write_file, test_binary
+from lib.structure.files import find_pdb_files
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data
from pipe_control.result_files import add_result_file
@@ -316,87 +317,106 @@
return commands
-def frame_order(ave_pos_file="ave_pos.pdb", rep_file="frame_order.pdb",
dist_file="domain_distribution.pdb", dir=None):
+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).
- @keyword ave_pos_file: The name of the file for the average molecule
structure.
- @type ave_pos_file: str or None
- @keyword rep_file: The name of the file of the PDB representation
of the frame order dynamics to create.
- @type rep_file: str or None
- @keyword dist_file: The name of the file which will contain multiple
models spanning the full dynamics distribution of the frame order model.
- @type dist_file: str or None
- @keyword dir: The name of the directory to place the PDB file
into.
- @type dir: str or None
+ @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.
+ @type dir: str or None
"""
# The path.
- path = ''
+ path = getcwd()
if dir != None:
path = dir + sep
# Set up the respective objects.
- if ave_pos_file:
- frame_order_ave_pos(file=path+ave_pos_file)
- if rep_file:
- frame_order_geometric(file=path+rep_file)
- if dist_file:
- frame_order_distribution(file=path+dist_file)
-
-
-def frame_order_ave_pos(file=None):
+ if ave_pos:
+ 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)
+
+
+def frame_order_ave_pos(root=None, path=None):
"""Display the PDB structure for the frame order average domain position.
- @keyword file: The name of the PDB file containing the frame order
average structure.
- @type file: str
- """
-
- # Read in the PDB file.
- pymol_obj.exec_cmd("load " + file)
-
- # The object ID.
- id = file_root(file)
-
-
-def frame_order_distribution(file=None):
+ @keyword root: The file root of the PDB file containing the frame order
average structure.
+ @type root: str
+ """
+
+ # Find all PDB files.
+ pdb_files = find_pdb_files(path=path, file_root=root)
+
+ # Read in the PDB files.
+ print pdb_files
+ for file in pdb_files:
+ pymol_obj.exec_cmd("load " + file)
+
+ # The object ID.
+ id = file_root(file)
+
+
+def frame_order_distribution(root=None, path=None):
"""Display the PDB structure for the frame order distribution of domain
positions.
- @keyword file: The name of the PDB file containing the frame order
distribution of domain positions.
- @type file: str
- """
-
- # Read in the PDB file.
- pymol_obj.exec_cmd("load " + file)
-
-
-def frame_order_geometric(file=None):
+ @keyword root: The file root of the PDB file containing the frame order
distribution of domain positions.
+ @type root: str
+ """
+
+ # Find all PDB files.
+ pdb_files = find_pdb_files(path=path, file_root=root)
+
+ # Read in the PDB files.
+ for file in pdb_files:
+ pymol_obj.exec_cmd("load " + file)
+
+
+def frame_order_geometric(root=None, path=None):
"""Display the frame order geometric object.
- @keyword file: The name of the PDB file containing the frame order
geometric object.
- @type file: str
- """
-
- # Read in the PDB file.
- pymol_obj.exec_cmd("load " + file)
-
- # The object ID.
- id = file_root(file)
-
- # First hide everything.
- pymol_obj.exec_cmd("select %s" % id)
- pymol_obj.exec_cmd("hide ('sele')")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
- # Set up the pivot points.
- represent_pivots(id=id)
-
- # Set up the rotor objects.
- represent_rotor_object(id=id)
-
- # Set up the cone axis.
- represent_cone_axis(id=id)
-
- # Set up the cone object.
- represent_cone_object(id=id)
+ @keyword root: The file root of the PDB file containing the frame order
geometric object.
+ @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=root+'_pos')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_neg')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim_pos')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim_neg')
+
+ # Read in the PDB files.
+ for file in pdb_files:
+ # Read in the PDB file.
+ pymol_obj.exec_cmd("load " + file)
+
+ # The object ID.
+ id = file_root(file)
+
+ # First hide everything.
+ pymol_obj.exec_cmd("select %s" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Set up the pivot points.
+ represent_pivots(id=id)
+
+ # Set up the rotor objects.
+ represent_rotor_object(id=id)
+
+ # Set up the cone axis.
+ represent_cone_axis(id=id)
+
+ # Set up the cone object.
+ represent_cone_object(id=id)
def macro_apply(data_type=None, style="classic", colour_start_name=None,
colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None,
colour_list=None):
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=24410&r1=24409&r2=24410&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/pymol_control.py
(original)
+++ branches/frame_order_cleanup/user_functions/pymol_control.py Wed
Jul 2 14:53:21 2014
@@ -149,36 +149,33 @@
uf.title = "Display the frame order results from the frame_order.pdb_model
user function."
uf.title_short = "Frame order results display."
uf.add_keyarg(
- name = "ave_pos_file",
- default = "ave_pos.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "average structure file name",
- desc = "The name of the 3D structure PDB file for the molecular
structure with the moving domains shifted to the average position.",
+ name = "ave_pos",
+ default = "ave_pos",
+ py_type = "str",
+ 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,
- wiz_filesel_style = FD_OPEN,
- can_be_none = True
-)
-uf.add_keyarg(
- name = "rep_file",
- default = "frame_order.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "PDB representation file name",
- desc = "The name of the PDB file for the geometric object representation
of the frame order dynamics.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "rep",
+ default = "frame_order",
+ py_type = "str",
+ 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.",
wiz_filesel_wildcard = WILDCARD_STRUCT_PDB_ALL,
- wiz_filesel_style = FD_OPEN,
- can_be_none = True
-)
-uf.add_keyarg(
- name = "dist_file",
- default = "domain_distribution.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "distribution file name",
- desc = "The name of the file which will contain multiple models spanning
the full dynamics distribution of the frame order model.",
+ 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,
can_be_none = True
)
uf.add_keyarg(
@@ -191,7 +188,8 @@
)
# 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
files created by frame_order.pdb_model - the molecular structure with the
averaged domain positions, the frame order dynamics representation file, and
the moving domain distribution file - and display them in PyMOL. Rather than
loading the three files into PyMOL manually, this user function will change
the representation to significantly improve the visualisation.")
+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 representation files,if the
file root is left to the default of 'frame_order' then all of the following
files will be loaded: 'frame_order.pdb', 'frame_order_pos.pdb',
'frame_order_neg.pdb', 'frame_order_sim.pdb', 'frame_order_sim_pos.pdb',
'frame_order_sim_neg.pdb'. 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.")
uf.backend = pymol_control.frame_order
uf.menu_text = "&frame_order"
uf.gui_icon = "relax.frame_order"
r24410 - in /branches/frame_order_cleanup: pipe_control/pymol_control.py user_functions/pymol_control.py