summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPiotr Rotkiewicz <piotr@pirx.com>2008-08-13 22:50:37 +0000
committerPiotr Rotkiewicz <piotr@pirx.com>2008-08-13 22:50:37 +0000
commitd6084f06bcd79effd99b90e7473b9ace3e5182c5 (patch)
tree9feab6d0b6e4d54e449440c931a9680bba29d920
parent78f2b16038c03bcfcb2c48dd10aa3a43e06712e9 (diff)
downloadnanoengineer-d6084f06bcd79effd99b90e7473b9ace3e5182c5.tar.gz
nanoengineer-d6084f06bcd79effd99b90e7473b9ace3e5182c5.zip
=Refactoring of the code that uses modelAndSimulateProteins global constant.
Diffstat
-rwxr-xr-xcad/src/ne1_ui/MWsemantics.py4
-rw-r--r--cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py11
-rw-r--r--cad/src/protein/commands/CompareProteins/CompareProteins_Command.py8
-rw-r--r--cad/src/protein/commands/EditResidues/EditResidues_Command.py8
-rw-r--r--cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py4
-rw-r--r--cad/src/protein/commands/EditRotamers/EditRotamers_Command.py8
-rw-r--r--cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py10
-rw-r--r--cad/src/protein/commands/ModelAndSimulateProtein/ModelAndSimulateProtein_Command.py4
-rw-r--r--cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py4
-rw-r--r--cad/src/protein/model/Protein.py4
-rw-r--r--cad/src/simulation/ROSETTA/runRosetta.py4
-rw-r--r--cad/src/utilities/GlobalPreferences.py4
12 files changed, 38 insertions, 35 deletions
diff --git a/cad/src/ne1_ui/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py
index 319d0778a..8021ca1dd 100755
--- a/cad/src/ne1_ui/MWsemantics.py
+++ b/cad/src/ne1_ui/MWsemantics.py
@@ -1760,8 +1760,8 @@ class MWsemantics(QMainWindow,
Activates the Protein toolbar.
"""
commandSequencer = self.commandSequencer
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
commandSequencer.userEnterCommand('MODEL_AND_SIMULATE_PROTEIN')
#assert commandSequencer.currentCommand.commandName == 'MODEL_AND_SIMULATE_PROTEIN'
#commandSequencer.currentCommand.runCommand()
diff --git a/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py b/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py
index 470b28802..b3db852ed 100644
--- a/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py
+++ b/cad/src/protein/commands/BuildPeptide/Peptide_EditCommand.py
@@ -17,7 +17,7 @@ from protein.commands.BuildPeptide.PeptideGenerator import PeptideGenerator
from utilities.constants import gensym
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from protein.temporary_commands.PeptideLineMode import PeptideLine_GM
-from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
+from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
from utilities.debug import print_compact_stack, print_compact_traceback
from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import ModelAndSimulateProtein_Command
@@ -35,7 +35,7 @@ class Peptide_EditCommand(EditCommand):
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_PROTEIN'
- if modelAndSimulateProteins:
+ if MODEL_AND_SIMULATE_PROTEINS:
command_parent = 'MODEL_AND_SIMULATE_PROTEIN'
create_name_from_prefix = True
@@ -83,7 +83,7 @@ class Peptide_EditCommand(EditCommand):
#Clear the segmentList as it may still be maintaining a list of segments
#from the previous run of the command.
self._segmentList = []
- if modelAndSimulateProteins:
+ if MODEL_AND_SIMULATE_PROTEINS:
self._init_gui_flyout_action( 'buildPeptideAction', 'MODEL_AND_SIMULATE_PROTEIN' )
else:
self._init_gui_flyout_action( 'buildPeptideAction')
@@ -309,6 +309,7 @@ class Peptide_EditCommand(EditCommand):
This is used in isinstance test.
@see: EditCommand._getStructureType() (overridden here)
"""
+
return self.win.assy.Chunk
# Things needed for CntLine_GraphicsMode (NanotubeLine_GM) ======================
@@ -371,8 +372,10 @@ class Peptide_EditCommand(EditCommand):
Returns a string that gives the length of the Nanotube for the cursor
text
"""
- self.secondary, self.phi, self.psi, aa_type = self._gatherParameters()
+ # This should be moved to more appropriate place. piotr 081308
+ self.secondary, self.phi, self.psi, aa_type = self._gatherParameters()
+
peptideLengthString = ''
lengthUnitString = 'AA'
diff --git a/cad/src/protein/commands/CompareProteins/CompareProteins_Command.py b/cad/src/protein/commands/CompareProteins/CompareProteins_Command.py
index b3cbb42c0..631ac63b4 100644
--- a/cad/src/protein/commands/CompareProteins/CompareProteins_Command.py
+++ b/cad/src/protein/commands/CompareProteins/CompareProteins_Command.py
@@ -35,8 +35,8 @@ class CompareProteins_Command(EditCommand):
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_PROTEIN'
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
command_parent = 'MODEL_PROTEIN'
GraphicsMode_class = CompareProteins_GraphicsMode
@@ -52,8 +52,8 @@ class CompareProteins_Command(EditCommand):
"""
Initialize GUI for this mode
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
self._init_gui_flyout_action( 'compareProteinsAction', 'MODEL_AND_SIMULATE_PROTEIN' )
else:
self._init_gui_flyout_action( 'compareProteinsAction')
diff --git a/cad/src/protein/commands/EditResidues/EditResidues_Command.py b/cad/src/protein/commands/EditResidues/EditResidues_Command.py
index d80091429..15036771b 100644
--- a/cad/src/protein/commands/EditResidues/EditResidues_Command.py
+++ b/cad/src/protein/commands/EditResidues/EditResidues_Command.py
@@ -35,8 +35,8 @@ class EditResidues_Command(EditCommand):
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_PROTEIN'
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
command_parent = 'SIMULATE_PROTEIN'
GraphicsMode_class = EditResidues_GraphicsMode
@@ -52,8 +52,8 @@ class EditResidues_Command(EditCommand):
"""
Initialize GUI for this mode
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
self._init_gui_flyout_action( 'editResiduesAction', 'MODEL_AND_SIMULATE_PROTEIN' )
else:
self._init_gui_flyout_action( 'editResiduesAction')
diff --git a/cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py b/cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py
index 176401d1b..0517ba8b6 100644
--- a/cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py
+++ b/cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py
@@ -233,8 +233,8 @@ class EditResidues_PropertyManager( PM_Dialog, DebugMenuMixin ):
#"current protein" in this mode.
self.current_protein = ""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
previousCommand = self.command.find_parent_command_named('MODEL_AND_SIMULATE_PROTEIN')
else:
previousCommand = self.command.find_parent_command_named('BUILD_PROTEIN')
diff --git a/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py b/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py
index 8dd300877..04fdf766e 100644
--- a/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py
+++ b/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py
@@ -35,8 +35,8 @@ class EditRotamers_Command(EditCommand):
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_PROTEIN'
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
command_parent = 'MODEL_PROTEIN'
GraphicsMode_class = EditRotamers_GraphicsMode
@@ -52,8 +52,8 @@ class EditRotamers_Command(EditCommand):
"""
Initialize GUI for this mode
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
self._init_gui_flyout_action( 'editRotamersAction', 'MODEL_AND_SIMULATE_PROTEIN' )
else:
self._init_gui_flyout_action( 'editRotamersAction')
diff --git a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py b/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
index 788b08066..7528ee2dc 100644
--- a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
+++ b/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
@@ -157,8 +157,8 @@ class EditRotamers_PropertyManager( PM_Dialog, DebugMenuMixin ):
#Urmi 20080728: Update the residue combo box with amino acids for the
#currently selected protein in build protein mode
self.current_protein = ""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
previousCommand = self.command.find_parent_command_named('MODEL_AND_SIMULATE_PROTEIN')
else:
previousCommand = self.command.find_parent_command_named('BUILD_PROTEIN')
@@ -247,8 +247,8 @@ class EditRotamers_PropertyManager( PM_Dialog, DebugMenuMixin ):
self.current_protein = ""
#Urmi 20080728: fill up the combo box with amino acids belonging to the
# current protein in build protein mode
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
previousCommand = self.command.find_parent_command_named('MODEL_AND_SIMULATE_PROTEIN')
else:
previousCommand = self.command.find_parent_command_named('BUILD_PROTEIN')
@@ -529,7 +529,7 @@ class EditRotamers_PropertyManager( PM_Dialog, DebugMenuMixin ):
current_aa = chunk.protein.get_current_amino_acid()
if current_aa:
chunk.protein.expand_rotamer(current_aa)
- current_aa.set_chi_angle(chi, angle, lock=self.lockEditedCheckBox.isChecked())
+ current_aa.set_chi_angle(chi, angle)
self.win.glpane.gl_update()
return
diff --git a/cad/src/protein/commands/ModelAndSimulateProtein/ModelAndSimulateProtein_Command.py b/cad/src/protein/commands/ModelAndSimulateProtein/ModelAndSimulateProtein_Command.py
index cd8f3710b..6dab8d824 100644
--- a/cad/src/protein/commands/ModelAndSimulateProtein/ModelAndSimulateProtein_Command.py
+++ b/cad/src/protein/commands/ModelAndSimulateProtein/ModelAndSimulateProtein_Command.py
@@ -13,10 +13,6 @@ from utilities.constants import gensym
from ne1_ui.toolbars.Ui_ProteinFlyout_v2 import ProteinFlyout_v2
from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_PropertyManager import ModelAndSimulateProtein_PropertyManager
from utilities.debug_prefs import debug_pref, Choice_boolean_False
-modelAndSimulateProteins = debug_pref("Enable model and simulate protein flyout? (next session)",
- Choice_boolean_False,
- non_debug = True,
- prefs_key = True)
_superclass = EditCommand
class ModelAndSimulateProtein_Command(EditCommand):
diff --git a/cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py b/cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py
index 8b6fa17e9..fa6c48f49 100644
--- a/cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py
+++ b/cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py
@@ -52,8 +52,8 @@ class ProteinDisplayStyle_Command(EditCommand):
"""
Initialize GUI for this mode
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
self._init_gui_flyout_action( 'displayProteinStyleAction' ,
'MODEL_AND_SIMULATE_PROTEIN')
else:
diff --git a/cad/src/protein/model/Protein.py b/cad/src/protein/model/Protein.py
index e30fa3116..b6fb9e3ec 100644
--- a/cad/src/protein/model/Protein.py
+++ b/cad/src/protein/model/Protein.py
@@ -1053,8 +1053,8 @@ class Protein:
model. May be we'll take care of that when we move to the new model
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
win.commandSequencer.userEnterCommand('MODEL_AND_SIMULATE_PROTEIN')
else:
win.commandSequencer.userEnterTemporaryCommand('BUILD_PROTEIN')
diff --git a/cad/src/simulation/ROSETTA/runRosetta.py b/cad/src/simulation/ROSETTA/runRosetta.py
index 777619acd..cc6ee3dbf 100644
--- a/cad/src/simulation/ROSETTA/runRosetta.py
+++ b/cad/src/simulation/ROSETTA/runRosetta.py
@@ -1107,8 +1107,8 @@ class RosettaRunner:
@type outProtein: L{Chunk}
"""
- from protein.commands.ModelAndSimulateProtein.ModelAndSimulateProtein_Command import modelAndSimulateProteins
- if modelAndSimulateProteins:
+ from utilities.GlobalPreferences import MODEL_AND_SIMULATE_PROTEINS
+ if MODEL_AND_SIMULATE_PROTEINS:
command = self.win.commandSequencer.find_innermost_command_named('MODEL_AND_SIMULATE_PROTEIN')
else:
command = self.win.commandSequencer.find_innermost_command_named('BUILD_PROTEIN')
diff --git a/cad/src/utilities/GlobalPreferences.py b/cad/src/utilities/GlobalPreferences.py
index 57fd71815..e6367fd4f 100644
--- a/cad/src/utilities/GlobalPreferences.py
+++ b/cad/src/utilities/GlobalPreferences.py
@@ -484,6 +484,10 @@ enableProteins = debug_pref("Enable Proteins? (next session)",
prefs_key = True
)
+MODEL_AND_SIMULATE_PROTEINS = debug_pref("Enable model and simulate protein flyout? (next session)",
+ Choice_boolean_False,
+ non_debug = True,
+ prefs_key = True)
def _debug_pref_keep_signals_always_connected(): #Ninad 2008-08-13
#-The current code always connects signals while shown a PM and
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-30 21:02:07 +0000