summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMark Sims <mark@nanorex.com>2008-12-22 02:18:57 +0000
committerMark Sims <mark@nanorex.com>2008-12-22 02:18:57 +0000
commit33bddf0891338973556f01abe91ee2e678f77e3d (patch)
tree7cc9570b08f0d00e8c69ea67a7147fb15fd450ad
parentdcd7bc35fafd8987d1754bdcc88316cc6f78d26a (diff)
downloadnanoengineer-theirix-33bddf0891338973556f01abe91ee2e678f77e3d.tar.gz
nanoengineer-theirix-33bddf0891338973556f01abe91ee2e678f77e3d.zip
Diffstat
-rw-r--r--cad/src/commandSequencer/builtin_command_loaders.py4
-rwxr-xr-xcad/src/ne1_ui/MWsemantics.py10
-rw-r--r--cad/src/ne1_ui/ToolTipText_for_CommandToolbars.py2
-rw-r--r--cad/src/ne1_ui/WhatsThisText_for_CommandToolbars.py8
-rw-r--r--cad/src/ne1_ui/toolbars/Ui_ProteinFlyout.py28
-rw-r--r--cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py4
-rw-r--r--cad/src/protein/commands/EditProtein/EditProtein_Command.py (renamed from cad/src/protein/commands/EditRotamers/EditRotamers_Command.py)18
-rw-r--r--cad/src/protein/commands/EditProtein/EditProtein_PropertyManager.py (renamed from cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py)25
-rw-r--r--cad/src/protein/commands/EditProtein/__init__.py (renamed from cad/src/protein/commands/EditRotamers/__init__.py)0
-rw-r--r--cad/src/protein/model/Protein.py6
-rw-r--r--cad/src/protein/model/Residue.py2
-rw-r--r--cad/src/ui/actions/Command Toolbar/BuildProtein/EditProtein.pngbin0 -> 333 bytes
12 files changed, 55 insertions, 52 deletions
diff --git a/cad/src/commandSequencer/builtin_command_loaders.py b/cad/src/commandSequencer/builtin_command_loaders.py
index 6ba93a48f..b894c4596 100644
--- a/cad/src/commandSequencer/builtin_command_loaders.py
+++ b/cad/src/commandSequencer/builtin_command_loaders.py
@@ -82,7 +82,7 @@ from dna.commands.ConvertDna.ConvertDna_Command import ConvertDna_Command
# Protein commands
from protein.commands.InsertPeptide.InsertPeptide_EditCommand import InsertPeptide_EditCommand
from protein.commands.ProteinDisplayStyle.ProteinDisplayStyle_Command import ProteinDisplayStyle_Command
-from protein.commands.EditRotamers.EditRotamers_Command import EditRotamers_Command
+from protein.commands.EditProtein.EditProtein_Command import EditProtein_Command
from protein.commands.EditResidues.EditResidues_Command import EditResidues_Command
from protein.commands.CompareProteins.CompareProteins_Command import CompareProteins_Command
@@ -171,7 +171,7 @@ def preloaded_command_classes():
InsertPeptide_EditCommand,
ProteinDisplayStyle_Command,
LightingScheme_Command,
- EditRotamers_Command,
+ EditProtein_Command,
EditResidues_Command,
CompareProteins_Command,
ModelProtein_Command,
diff --git a/cad/src/ne1_ui/MWsemantics.py b/cad/src/ne1_ui/MWsemantics.py
index 34529f67e..1633bd870 100755
--- a/cad/src/ne1_ui/MWsemantics.py
+++ b/cad/src/ne1_ui/MWsemantics.py
@@ -1414,7 +1414,7 @@ class MWsemantics(QMainWindow,
"""
protein = ""
if self.commandSequencer.currentCommand.commandName == 'BUILD_PROTEIN' or \
- self.commandSequencer.currentCommand.commandName == 'EDIT_ROTAMERS' or \
+ self.commandSequencer.currentCommand.commandName == 'EDIT_PROTEIN' or \
self.commandSequencer.currentCommand.commandName == 'EDIT_RESIDUES':
protein = self.commandSequencer.currentCommand.propMgr.current_protein
@@ -1662,15 +1662,15 @@ class MWsemantics(QMainWindow,
self.enterOrExitTemporaryCommand('EDIT_PROTEIN_DISPLAY_STYLE')
- def enterEditRotamersCommand(self, isChecked = False):
+ def enterEditProteinCommand(self, isChecked = False):
"""
Enter edit rotamers command
- @param isChecked: If enterEditRotamersCommand button in the
+ @param isChecked: If enterEditProteinCommand button in the
Protein Flyout toolbar is
- checked, enter enterEditRotamersMode.
+ checked, enter enterEditProteinMode.
@type isChecked: bool
"""
- self.enterOrExitTemporaryCommand('EDIT_ROTAMERS')
+ self.enterOrExitTemporaryCommand('EDIT_PROTEIN')
def enterEditResiduesCommand(self, isChecked = False):
diff --git a/cad/src/ne1_ui/ToolTipText_for_CommandToolbars.py b/cad/src/ne1_ui/ToolTipText_for_CommandToolbars.py
index def794aa5..fd2c27ff5 100644
--- a/cad/src/ne1_ui/ToolTipText_for_CommandToolbars.py
+++ b/cad/src/ne1_ui/ToolTipText_for_CommandToolbars.py
@@ -45,7 +45,7 @@ def toolTipTextForProteinCommandToolbar(commandToolbar):
commandToolbar.simulateProteinAction.setToolTip("Simulate Protein using Rosetta")
commandToolbar.buildPeptideAction.setToolTip("Insert Peptide")
- commandToolbar.editRotamersAction.setToolTip("Edit Rotamers")
+ commandToolbar.editProteinAction.setToolTip("Edit Protein")
commandToolbar.compareProteinsAction.setToolTip("Compare Proteins")
commandToolbar.displayProteinStyleAction.setToolTip("Edit Protein Display Style")
diff --git a/cad/src/ne1_ui/WhatsThisText_for_CommandToolbars.py b/cad/src/ne1_ui/WhatsThisText_for_CommandToolbars.py
index c4ec7bde7..34e88785b 100644
--- a/cad/src/ne1_ui/WhatsThisText_for_CommandToolbars.py
+++ b/cad/src/ne1_ui/WhatsThisText_for_CommandToolbars.py
@@ -266,11 +266,11 @@ def whatsThisTextForProteinCommandToolbar(commandToolbar):
in the <a href=Property_Manager>property manager</a>.
</p>""")
- commandToolbar.editRotamersAction.setWhatsThis(
- """<b>Edit Rotamers</b>
+ commandToolbar.editProteinAction.setWhatsThis(
+ """<b>Edit Protein</b>
<p>
- <img source=\"ui/actions/Command Toolbar/BuildProtein/Rotamers.png\"><br>
- Edit rotamers in a peptide chain.
+ <img source=\"ui/actions/Command Toolbar/BuildProtein/EditProtein.png\"><br>
+ Edit the selected protein.
</p>""")
commandToolbar.compareProteinsAction.setWhatsThis(
diff --git a/cad/src/ne1_ui/toolbars/Ui_ProteinFlyout.py b/cad/src/ne1_ui/toolbars/Ui_ProteinFlyout.py
index fc498924d..74f75e03b 100644
--- a/cad/src/ne1_ui/toolbars/Ui_ProteinFlyout.py
+++ b/cad/src/ne1_ui/toolbars/Ui_ProteinFlyout.py
@@ -86,7 +86,7 @@ class ProteinFlyout(Ui_AbstractFlyout):
#Command list for the subcontrol area button 'Model Proteins Tool'
modelProteinsCmdLst = []
modelProteinsCmdLst.append(self.buildPeptideAction)
- modelProteinsCmdLst.append(self.editRotamersAction)
+ modelProteinsCmdLst.append(self.editProteinAction)
modelProteinsCmdLst.append(self.compareProteinsAction)
modelProteinsCmdLst.append(self.displayProteinStyleAction)
commandActionLists[2].extend(modelProteinsCmdLst)
@@ -103,7 +103,7 @@ class ProteinFlyout(Ui_AbstractFlyout):
else:
modelProteinsCmdLst = []
modelProteinsCmdLst.append(self.buildPeptideAction)
- modelProteinsCmdLst.append(self.editRotamersAction)
+ modelProteinsCmdLst.append(self.editProteinAction)
modelProteinsCmdLst.append(self.compareProteinsAction)
modelProteinsCmdLst.append(self.displayProteinStyleAction)
commandActionLists[0].extend(modelProteinsCmdLst)
@@ -191,12 +191,12 @@ class ProteinFlyout(Ui_AbstractFlyout):
self.buildPeptideAction.setIcon(
geticon("ui/actions/Command Toolbar/BuildProtein/InsertPeptide.png"))
- self.editRotamersAction = \
+ self.editProteinAction = \
NE1_QWidgetAction(self.subControlActionGroupForModelProtein, win = self.win)
- self.editRotamersAction.setText("Rotamers")
- self.editRotamersAction.setCheckable(True)
- self.editRotamersAction.setIcon(
- geticon("ui/actions/Command Toolbar/BuildProtein/EditRotamers.png"))
+ self.editProteinAction.setText("Protein")
+ self.editProteinAction.setCheckable(True)
+ self.editProteinAction.setIcon(
+ geticon("ui/actions/Command Toolbar/BuildProtein/EditProtein.png"))
self.compareProteinsAction = \
NE1_QWidgetAction(self.subControlActionGroupForModelProtein, win = self.win)
@@ -215,7 +215,7 @@ class ProteinFlyout(Ui_AbstractFlyout):
self.subControlActionGroupForModelProtein.addAction(self.buildPeptideAction)
self.subControlActionGroupForModelProtein.addAction(self.displayProteinStyleAction)
self.subControlActionGroupForModelProtein.addAction(self.compareProteinsAction)
- self.subControlActionGroupForModelProtein.addAction(self.editRotamersAction)
+ self.subControlActionGroupForModelProtein.addAction(self.editProteinAction)
return
def _createSimulateProteinsActions(self, parentWidget):
@@ -313,9 +313,9 @@ class ProteinFlyout(Ui_AbstractFlyout):
SIGNAL("triggered(bool)"),
self.activateInsertPeptide_EditCommand)
- change_connect(self.editRotamersAction,
+ change_connect(self.editProteinAction,
SIGNAL("triggered(bool)"),
- self.activateEditRotamers_EditCommand)
+ self.activateEditProtein_EditCommand)
change_connect(self.editResiduesAction,
SIGNAL("triggered(bool)"),
self.activateEditResidues_EditCommand)
@@ -412,15 +412,15 @@ class ProteinFlyout(Ui_AbstractFlyout):
if action is not self.buildPeptideAction and action.isChecked():
action.setChecked(False)
- def activateEditRotamers_EditCommand(self, isChecked):
+ def activateEditProtein_EditCommand(self, isChecked):
"""
- Slot for B{EditRotamers} action.
+ Slot for B{EditProtein} action.
"""
- self.win.enterEditRotamersCommand(isChecked)
+ self.win.enterEditProteinCommand(isChecked)
for action in self.subControlActionGroupForModelProtein.actions():
- if action is not self.editRotamersAction and action.isChecked():
+ if action is not self.editProteinAction and action.isChecked():
action.setChecked(False)
def activateEditResidues_EditCommand(self, isChecked):
diff --git a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
index 7a6c91d44..068813554 100644
--- a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
+++ b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
@@ -612,14 +612,14 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
# Provide amino acid info as cursor position changes
env.history.statusbar_msg("")
current_command = self.win.commandSequencer.currentCommand
- commandSet = ('EDIT_ROTAMERS', 'EDIT_RESIDUES')
+ commandSet = ('EDIT_PROTEIN', 'EDIT_RESIDUES')
if current_command.commandName not in commandSet:
return
aa_index = min(cursorPos, self.getSequenceLength() - 1)
- if current_command.commandName == 'EDIT_ROTAMERS':
+ if current_command.commandName == 'EDIT_PROTEIN':
current_command.propMgr.setCurrentAminoAcid(aa_index)
if current_command.commandName == 'EDIT_RESIDUES':
current_command.propMgr._sequenceTableCellChanged(aa_index, 0)
diff --git a/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py b/cad/src/protein/commands/EditProtein/EditProtein_Command.py
index 18552f053..a0763a8d5 100644
--- a/cad/src/protein/commands/EditRotamers/EditRotamers_Command.py
+++ b/cad/src/protein/commands/EditProtein/EditProtein_Command.py
@@ -9,31 +9,31 @@ import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditCommand import EditCommand
from utilities.constants import red
-from protein.commands.EditRotamers.EditRotamers_PropertyManager import EditRotamers_PropertyManager
+from protein.commands.EditProtein.EditProtein_PropertyManager import EditProtein_PropertyManager
# == GraphicsMode part
_superclass_for_GM = SelectChunks_GraphicsMode
-class EditRotamers_GraphicsMode(SelectChunks_GraphicsMode ):
+class EditProtein_GraphicsMode(SelectChunks_GraphicsMode ):
"""
- Graphics mode for Edit Rotamers command.
+ Graphics mode for Edit Protein command.
"""
pass
# == Command part
-class EditRotamers_Command(EditCommand):
+class EditProtein_Command(EditCommand):
"""
"""
# class constants
- GraphicsMode_class = EditRotamers_GraphicsMode
+ GraphicsMode_class = EditProtein_GraphicsMode
- PM_class = EditRotamers_PropertyManager
+ PM_class = EditProtein_PropertyManager
- commandName = 'EDIT_ROTAMERS'
- featurename = "Edit Rotamers"
+ commandName = 'EDIT_PROTEIN'
+ featurename = "Edit Protein"
from utilities.constants import CL_SUBCOMMAND
command_level = CL_SUBCOMMAND
command_parent = 'BUILD_PROTEIN'
@@ -48,7 +48,7 @@ class EditRotamers_Command(EditCommand):
See superclass for documentation.
@see: self.command_update_flyout()
"""
- flyoutActionToCheck = 'editRotamersAction'
+ flyoutActionToCheck = 'editProteinAction'
parentCommandName = 'BUILD_PROTEIN'
return flyoutActionToCheck, parentCommandName
diff --git a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py b/cad/src/protein/commands/EditProtein/EditProtein_PropertyManager.py
index ce5a69b5f..0e3fc4e98 100644
--- a/cad/src/protein/commands/EditRotamers/EditRotamers_PropertyManager.py
+++ b/cad/src/protein/commands/EditProtein/EditProtein_PropertyManager.py
@@ -1,9 +1,9 @@
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
-EditRotamers_PropertyManager.py
+EditProtein_PropertyManager.py
-The EditRotamers_PropertyManager class provides a Property Manager
-for the B{Edit Rotamers} command on the flyout toolbar in the
+The EditProtein_PropertyManager class provides a Property Manager
+for the B{Edit Protein} command on the flyout toolbar in the
Build > Protein mode.
@author: Piotr, Mark
@@ -11,20 +11,23 @@ Build > Protein mode.
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
TODO:
-- Rename "Edit Rotamers" to "Edit Proteins".
- Better messages, especially when selecting different peptides.
- Need to implement a validator for the Name line edit field.
NICETOHAVE:
-- Dim everything in the current protein except the atoms in the current aa.
+- Some way of showing the current rotamer when all rotamers are displayed.
+ Ideas include:
+ - Dim all rotamers in the current protein except the atoms in the current rotamer.
+ - Highlight atoms in current rotamer for 1 second (when switching rotamers).
- Include "Show entire model" checkbox in PM (checked by default).
- Show residue label in GA of current residue, including AA and # (i.e. SER[14]).
+- "Show adjacent rotamers" checkbox.
REFACTORING:
Things to discuss with Bruce include an asterisk:
- Should current_protein be renamed to command.struct everywhere? *
-- Move some methods to EditRotamers_Command or EditCommand class. *
- - add setStructureName(name) in EditRotamers_Command or in superclass EditCommand?
+- Move some methods to EditProtein_Command or EditCommand class. *
+ - add setStructureName(name) in EditProtein_Command or in superclass EditCommand?
- other methods that edit the current protein.
"""
import os, time, fnmatch, string
@@ -63,10 +66,10 @@ from PyQt4.Qt import QTextCursor
from command_support.Command_PropertyManager import Command_PropertyManager
_superclass = Command_PropertyManager
-class EditRotamers_PropertyManager(Command_PropertyManager):
+class EditProtein_PropertyManager(Command_PropertyManager):
"""
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
- for the B{Edit Rotamers} command on the Build Protein command toolbar.
+ for the B{Edit Protein} command on the Build Protein command toolbar.
The selected peptide/protein is displayed in the protein reduced display
style. The user can select individual rotamers and edit their chi angles.
@@ -85,9 +88,9 @@ class EditRotamers_PropertyManager(Command_PropertyManager):
@type iconPath: str
"""
- title = "Edit Rotamers"
+ title = "Edit Protein"
pmName = title
- iconPath = "ui/actions/Command Toolbar/BuildProtein/EditRotamers.png"
+ iconPath = "ui/actions/Command Toolbar/BuildProtein/EditProtein.png"
current_protein = None # The currently selected peptide.
previous_protein = None # The last peptide selected.
diff --git a/cad/src/protein/commands/EditRotamers/__init__.py b/cad/src/protein/commands/EditProtein/__init__.py
index e69de29bb..e69de29bb 100644
--- a/cad/src/protein/commands/EditRotamers/__init__.py
+++ b/cad/src/protein/commands/EditProtein/__init__.py
diff --git a/cad/src/protein/model/Protein.py b/cad/src/protein/model/Protein.py
index 245d1017c..eade6919a 100644
--- a/cad/src/protein/model/Protein.py
+++ b/cad/src/protein/model/Protein.py
@@ -106,7 +106,7 @@ class Protein:
# in the following format: "1abc"
self.pdbId = ""
- # Index of "current" amino acid (used by Edit Rotamers command).
+ # Index of "current" amino acid (used by Edit Protein command).
self.current_aa_idx = 0
# Display list for expanded rotamers, used by ProteinChunk.draw_realtime
@@ -537,7 +537,7 @@ class Protein:
# General comment regarding the "current residue" mechanism. The purpose
# of the "current_aa_idx" attribute is to have a mechanism for selecting
# and focusing on an individual amino acid. Currently, this mechanism
- # is only used by "Edit Rotamers" command and probably the "Edit Rotamers"
+ # is only used by "Edit Protein" command and probably the "Edit Protein"
# command should keep track of the current residue. It would be
# better if this attribute was removed from the Protein class.
# -- piotr 080902
@@ -635,7 +635,7 @@ class Protein:
the actual model. Maybe we'll take care of that when we move to the
new model
"""
- win.commandSequencer.userEnterCommand('EDIT_ROTAMERS')
+ win.commandSequencer.userEnterCommand('EDIT_PROTEIN')
return
pass # end of class Protein
diff --git a/cad/src/protein/model/Residue.py b/cad/src/protein/model/Residue.py
index e8694c3a2..f754701df 100644
--- a/cad/src/protein/model/Residue.py
+++ b/cad/src/protein/model/Residue.py
@@ -438,7 +438,7 @@ class Residue:
# protein display style.
self.expanded = False
- # Rotamer color, used by "Edit Rotamers" command.
+ # Rotamer color, used by "Edit Protein" command.
self.color = None
# These Rosetta-related attributes should be probably moved from this
diff --git a/cad/src/ui/actions/Command Toolbar/BuildProtein/EditProtein.png b/cad/src/ui/actions/Command Toolbar/BuildProtein/EditProtein.png
new file mode 100644
index 000000000..ab62409b9
--- /dev/null
+++ b/cad/src/ui/actions/Command Toolbar/BuildProtein/EditProtein.png
Binary files differ
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-14 04:23:16 +0000