Author: bugman
Date: Fri Jul 4 10:47:05 2014
New Revision: 24450
URL: http://svn.gna.org/viewcvs/relax?rev=24450&view=rev
Log:
Changed the alternative representation names for the frame order geometric
objects.
The aim is to put both representations on a more equal footing, as they are
identical solutions.
Hence the inverted representation might be the correct representation of the
domain motions. So
instead of calling these 'positive' and 'negative', the 'A' and 'B' notation
will be used.
This affects the names of the files produced by the frame_order.pdb_model
user function as well as
the internal titles. Instead of ending the files with "*_pos.*" and
""*_neg.*", these have been
changed to "*_A.*" and ""*_B.*". The atoms used for the titles have also
been renamed, and the
pymol.frame_order user function now labels the titles using the 'A' and 'B'
notation.
Modified:
branches/frame_order_cleanup/pipe_control/pymol_control.py
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.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=24450&r1=24449&r2=24450&view=diff
==============================================================================
--- branches/frame_order_cleanup/pipe_control/pymol_control.py (original)
+++ branches/frame_order_cleanup/pipe_control/pymol_control.py Fri Jul 4
10:47:05 2014
@@ -397,11 +397,11 @@
# 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+'_A')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_B')
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')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim_A')
+ pdb_files += find_pdb_files(path=path, file_root=root+'_sim_B')
# Read in the PDB files.
for file in pdb_files:
@@ -433,8 +433,8 @@
# Disable the MC simulation representation - the user can find this out
for themselves.
pymol_obj.exec_cmd("disable %s_sim" % root)
- pymol_obj.exec_cmd("disable %s_sim_pos" % root)
- pymol_obj.exec_cmd("disable %s_sim_neg" % root)
+ pymol_obj.exec_cmd("disable %s_sim_A" % root)
+ pymol_obj.exec_cmd("disable %s_sim_B" % root)
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):
@@ -699,16 +699,16 @@
if id == None:
raise RelaxError("The PyMOL object ID must be supplied.")
- # Frame order positive representation.
- pymol_obj.exec_cmd("select (%s & resn TLE & name p)" % id)
- pymol_obj.exec_cmd("hide ('sele')")
- pymol_obj.exec_cmd("label 'sele', 'Positive representation'")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
- # Frame order negative representation.
- pymol_obj.exec_cmd("select (%s & resn TLE & name n)" % id)
- pymol_obj.exec_cmd("hide ('sele')")
- pymol_obj.exec_cmd("label 'sele', 'Negative representation'")
+ # Frame order representation A.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name a)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Representation A'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order representation B.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name b)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'Representation B'")
pymol_obj.exec_cmd("cmd.delete('sele')")
# Frame order MC sim representation.
@@ -717,16 +717,16 @@
pymol_obj.exec_cmd("label 'sele', 'MC sim representation'")
pymol_obj.exec_cmd("cmd.delete('sele')")
- # Frame order MC sim positive representation.
- pymol_obj.exec_cmd("select (%s & resn TLE & name p-mc)" % id)
- pymol_obj.exec_cmd("hide ('sele')")
- pymol_obj.exec_cmd("label 'sele', 'Positive MC sim representation'")
- pymol_obj.exec_cmd("cmd.delete('sele')")
-
- # Frame order MC sim negative representation.
- pymol_obj.exec_cmd("select (%s & resn TLE & name n-mc)" % id)
- pymol_obj.exec_cmd("hide ('sele')")
- pymol_obj.exec_cmd("label 'sele', 'Negative MC sim representation'")
+ # Frame order MC sim representation A.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name mc-a)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'MC sim representation A'")
+ pymol_obj.exec_cmd("cmd.delete('sele')")
+
+ # Frame order MC sim representation B.
+ pymol_obj.exec_cmd("select (%s & resn TLE & name mc-b)" % id)
+ pymol_obj.exec_cmd("hide ('sele')")
+ pymol_obj.exec_cmd("label 'sele', 'MC sim representation B'")
pymol_obj.exec_cmd("cmd.delete('sele')")
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py?rev=24450&r1=24449&r2=24450&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Fri Jul 4 10:47:05 2014
@@ -48,7 +48,7 @@
@keyword structure: The internal structural object to add the
rotor objects to.
@type structure: lib.structure.internal.object.Internal
instance
- @keyword representation: The representation to create. If this is
set to None or 'pos', the standard representation will be created. If set to
'neg', the axis system will be inverted.
+ @keyword representation: The representation to create. If this is
set to None or 'A', the standard representation will be created. If set to
'B', the axis system will be inverted.
@type representation: None or str
@keyword size: The size of the geometric object in
Angstroms.
@type size: float
@@ -61,7 +61,7 @@
structure.add_molecule(name=mol_name)
# The transformation matrix (identity matrix or inversion matrix).
- if representation == 'neg':
+ if representation == 'B':
T = -eye(3)
else:
T = eye(3)
@@ -149,7 +149,7 @@
@keyword structure: The internal structural object to add the
rotor objects to.
@type structure: lib.structure.internal.object.Internal
instance
- @keyword representation: The representation to create. If this is
set to None or 'pos', the standard representation will be created. If set to
'neg', the axis system will be inverted.
+ @keyword representation: The representation to create. If this is
set to None or 'A', the standard representation will be created. If set to
'B', the axis system will be inverted.
@type representation: str
@keyword size: The size of the geometric object in
Angstroms.
@type size: float
@@ -163,7 +163,7 @@
structure.add_molecule(name='cones')
# The transformation matrix (identity matrix or inversion matrix).
- if representation == 'neg':
+ if representation == 'B':
T = -eye(3)
else:
T = eye(3)
@@ -301,7 +301,7 @@
@keyword structure: The internal structural object to add the
rotor objects to.
@type structure: lib.structure.internal.object.Internal
instance
- @keyword representation: The representation to create. If this is
set to None or 'pos', the standard representation will be created. If set to
'neg', the axis system will be inverted.
+ @keyword representation: The representation to title.
@type representation: None or str
@keyword displacement: The distance away from the pivot point, in
Angstrom, to place the title. The simulation title will be shifted by a few
extra Angstrom to avoid clashes.
@type displacement: float
@@ -313,16 +313,16 @@
atom_name = None
if representation == None and sims:
atom_name = 'mc'
- elif representation == 'pos':
+ elif representation == 'A':
if sims:
- atom_name = 'p-mc'
+ atom_name = 'mc-a'
else:
- atom_name = 'p'
- elif representation == 'neg':
+ atom_name = 'a'
+ elif representation == 'B':
if sims:
- atom_name = 'n-mc'
+ atom_name = 'mc-b'
else:
- atom_name = 'n'
+ atom_name = 'b'
# Nothing to do.
if atom_name == None:
@@ -337,7 +337,7 @@
structure.add_molecule(name=mol_name)
# The transformation matrix (identity matrix or inversion matrix).
- if representation == 'neg':
+ if representation == 'B':
T = -eye(3)
else:
T = eye(3)
@@ -656,43 +656,43 @@
if cdp.model in ['rotor', 'free rotor', 'double rotor']:
sym = False
- # The positive representation.
- titles.append("positive representation")
+ # The standard representation.
+ titles.append("Representation A")
structures.append(Internal())
if sym:
- representation.append('pos')
- file_root.append("%s_pos" % file)
+ representation.append('A')
+ file_root.append("%s_A" % file)
else:
representation.append(None)
file_root.append(file)
sims.append(False)
- # The negative (inverted) representation.
+ # The inverted representation.
if sym:
- titles.append("negative representation")
+ titles.append("Representation A")
structures.append(Internal())
- representation.append('neg')
- file_root.append("%s_neg" % file)
+ representation.append('B')
+ file_root.append("%s_B" % file)
sims.append(False)
- # The positive MC simulation representation.
+ # The standard MC simulation representation.
if hasattr(cdp, 'sim_number'):
- titles.append("positive MC simulation representation")
+ titles.append("MC simulation representation A")
structures.append(Internal())
if sym:
- representation.append('pos')
- file_root.append("%s_sim_pos" % file)
+ representation.append('A')
+ file_root.append("%s_sim_A" % file)
else:
representation.append(None)
file_root.append("%s_sim" % file)
sims.append(True)
- # The negative MC simulation representation.
+ # The inverted MC simulation representation.
if hasattr(cdp, 'sim_number') and sym:
- titles.append("negative MC simulation representation")
+ titles.append("MC simulation representation B")
structures.append(Internal())
- representation.append('neg')
- file_root.append("%s_sim_neg" % file)
+ representation.append('B')
+ file_root.append("%s_sim_B" % file)
sims.append(True)
# Loop over each structure and add the contents.
r24450 - in /branches/frame_order_cleanup: pipe_control/pymol_control.py specific_analyses/frame_order/geometric.py