Author: bugman
Date: Fri Mar 15 17:09:02 2013
New Revision: 18833
URL: http://svn.gna.org/viewcvs/relax?rev=18833&view=rev
Log:
Started to remodel the frame_order.pdb_model user function.
The dist_file argument has been added for the creation of a special
distribution of models spanning
the frame order dynamics.
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=18833&r1=18832&r2=18833&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/frame_order.py (original)
+++ branches/frame_order_testing/specific_fns/frame_order.py Fri Mar 15
17:09:02 2013
@@ -975,19 +975,20 @@
return num
- def _pdb_model(self, size=30.0, file=None, dir=None, inc=36,
force=False):
+ def _pdb_model(self, file=None, dir=None, size=30.0, inc=36,
force=False):
"""Create a PDB file containing a geometric object representing the
Frame Order cone models.
- @param size: The size of the geometric object in Angstroms.
+ @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
- @param inc: The number of increments for the filling of the
cone objects.
+ @keyword inc: The number of increments for the filling of the
cone objects.
@type inc: int
- @param file: The name of the PDB file to create.
- @type file: str
- @param dir: The name of the directory to place the PDB file
into.
- @type dir: str
- @param force: Flag which if set to True will cause any
pre-existing file to be
- overwritten.
+ @keyword force: Flag which if set to True will cause any
pre-existing file to be overwritten.
@type force: bool
"""
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=18833&r1=18832&r2=18833&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/frame_order.py (original)
+++ branches/frame_order_testing/user_functions/frame_order.py Fri Mar 15
17:09:02 2013
@@ -124,8 +124,36 @@
# The frame_order.pdb_model user function.
uf = uf_info.add_uf('frame_order.pdb_model')
-uf.title = "Create a PDB file representing the Frame Order cone models."
-uf.title_short = "Cone model PDB creation."
+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",
+ 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.",
+ wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dist_file",
+ default = "frame_order_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.",
+ wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
+ wiz_filesel_style = FD_SAVE
+)
+uf.add_keyarg(
+ name = "dir",
+ py_type = "str",
+ arg_type = "dir",
+ desc_short = "directory name",
+ desc = "The directory where the file is to be located.",
+ can_be_none = True
+)
uf.add_keyarg(
name = "size",
default = 30.0,
@@ -142,29 +170,11 @@
wiz_element_type = "spin"
)
uf.add_keyarg(
- name = "file",
- default = "cone.pdb",
- py_type = "str",
- arg_type = "file sel",
- desc_short = "file name",
- desc = "The name of the PDB file to create.",
- wiz_filesel_wildcard = "PDB files (*.pdb)|*.pdb;*.PDB",
- wiz_filesel_style = FD_SAVE
-)
-uf.add_keyarg(
- name = "dir",
- py_type = "str",
- arg_type = "dir",
- desc_short = "directory name",
- desc = "The directory where the file is to be located.",
- can_be_none = True
-)
-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."
+ desc = "A flag which, if set to True, will overwrite the any
pre-existing files."
)
# Description.
uf.desc.append(Desc_container())
r18833 - in /branches/frame_order_testing: specific_fns/frame_order.py user_functions/frame_order.py