Author: bugman
Date: Mon Mar 18 16:52:00 2013
New Revision: 18863
URL: http://svn.gna.org/viewcvs/relax?rev=18863&view=rev
Log:
More changes to the frame_order.pdb_model user function.
The idea is that a 3D structure file of the domains moved to the average
position will be created
using the new 'ave_pos_file' argument. The 'file' argument has been renamed
to 'rep_file' as this
will simply contain the geometric object representation.
Modified:
branches/frame_order_testing/specific_fns/frame_order.py
branches/frame_order_testing/user_functions/frame_order.py
Modified: branches/frame_order_testing/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/frame_order.py?rev=18863&r1=18862&r2=18863&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Mon Mar 18
16:52:00 2013
@@ -946,23 +946,25 @@
return num
- def _pdb_model(self, file=None, dist_file=None, dir=None, size=30.0,
inc=36, force=False, neg_cone=True):
+ def _pdb_model(self, ave_pos_file="ave_pos.pdb",
rep_file="frame_order.pdb", dist_file="domain_distribution.pdb", dir=None,
size=30.0, inc=36, force=False, neg_cone=True):
"""Create a PDB file containing a geometric object representing the
Frame Order cone models.
- @keyword file: The name of the file of the PDB representation
of the frame order dynamics to create.
- @type file: str
- @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
- @keyword dir: The name of the directory to place the PDB file
into.
- @type dir: str
- @keyword size: The size of the geometric object in Angstroms.
- @type size: float
- @keyword inc: The number of increments for the filling of the
cone objects.
- @type inc: int
- @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
- @type force: bool
- @keyword neg_cone: A flag which if True will cause the negative
cone to be added to the representation.
- @type neg_cone: bool
+ @keyword ave_pos_file: The name of the file for the average
molecule structure.
+ @type ave_pos_file: str
+ @keyword rep_file: The name of the file of the PDB
representation of the frame order dynamics to create.
+ @type rep_file: str
+ @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
+ @keyword dir: The name of the directory to place the PDB
file into.
+ @type dir: str
+ @keyword size: The size of the geometric object in
Angstroms.
+ @type size: float
+ @keyword inc: The number of increments for the filling of
the cone objects.
+ @type inc: int
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
+ @type force: bool
+ @keyword neg_cone: A flag which if True will cause the negative
cone to be added to the representation.
+ @type neg_cone: bool
"""
# Test if the current data pipe exists.
Modified: branches/frame_order_testing/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/frame_order.py?rev=18863&r1=18862&r2=18863&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/frame_order.py (original)
+++ branches/frame_order_testing/user_functions/frame_order.py Mon Mar 18
16:52:00 2013
@@ -98,18 +98,28 @@
uf.title = "Create a PDB file representation of the frame order dynamics."
uf.title_short = "Frame order dynamics PDB representation."
uf.add_keyarg(
- name = "file",
- default = "frame_order.pdb",
+ name = "ave_pos_file",
+ default = "ave_pos.pdb",
py_type = "str",
arg_type = "file sel",
- desc_short = "file name",
- desc = "The name of the file of the PDB representation of the frame
order dynamics to create.",
+ 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.",
wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
wiz_filesel_style = FD_SAVE
)
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.",
+ wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
name = "dist_file",
- default = "frame_order_distribution.pdb",
+ default = "domain_distribution.pdb",
py_type = "str",
arg_type = "file sel",
desc_short = "distribution file name",
r18863 - in /branches/frame_order_testing: specific_fns/frame_order.py user_functions/frame_order.py