python_code stringlengths 0 992k | repo_name stringlengths 8 46 | file_path stringlengths 5 162 |
|---|---|---|
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
builtin_command_loaders.py -- loaders for NE1 builtin commands, used in order.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Module classification: [bruce 080209]
For now, part of Command Sequencer package, sin... | NanoCAD-master | cad/src/commandSequencer/builtin_command_loaders.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
CommandSequencer.py - class for sequencing commands and maintaining command stack.
Each Assembly owns one of these.
@author: Bruce (partly based on older code by Josh)
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details... | NanoCAD-master | cad/src/commandSequencer/CommandSequencer.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
command_levels.py - utilities for interpreting and using command_level values,
including the rules for how commands can nest on the command stack
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
# fixed_pa... | NanoCAD-master | cad/src/commandSequencer/command_levels.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
TreeModel_api.py - API class for a TreeModel needed by ModelTreeGui
@author: Will, Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
from modelTree.Api import Api
from operations.ops_select import topmost... | NanoCAD-master | cad/src/modelTree/TreeModel_api.py |
NanoCAD-master | cad/src/modelTree/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
TreeModel.py - tree of nodes and rules for its appearance and behavior,
for use in NE1 model tree
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
For earlier history, see ModelTree.py.
Bruce 081216 is d... | NanoCAD-master | cad/src/modelTree/TreeModel.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
Api.py - superclass for testing API compliance
Note: this is used in NE1 if certain private debug flags are set,
but has not been tested or maintained for a long time (as of 081216).
If it is ever verified to work and be useful, it can be moved int... | NanoCAD-master | cad/src/modelTree/Api.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
ModelTreeGUI_api.py - API class for ModelTreeGui
@author: Will, Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
from modelTree.Api import Api
# old comments by Will from his refactoring circa 2006:
# T... | NanoCAD-master | cad/src/modelTree/ModelTreeGUI_api.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
Node_as_MT_DND_Target.py -- controller for a Node as a Model Tree DND target
@author: Bruce
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 071025 moved these methods from class Node
and class Clip... | NanoCAD-master | cad/src/modelTree/Node_as_MT_DND_Target.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
modelTreeGui.py - provide a Qt4-compatible Model Tree widget,
inherited by modelTree.py to provide NE1's Model Tree of Nodes.
@author: Will, Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
Goals (of Will's r... | NanoCAD-master | cad/src/modelTree/modelTreeGui.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ModelTree.py -- owner and external interface to the NE1 model tree
(which is implemented as several objects by the modules in this
modelTree package)
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
model... | NanoCAD-master | cad/src/modelTree/ModelTree.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
Node_api.py - API of Nodes, as assumed by modelTree code
Note: not used (so far, 081216) except as documentation and in test code;
probably not complete
@author: Will, Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for ... | NanoCAD-master | cad/src/modelTree/Node_api.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
mt_statistics.py - count types of nodes, when making MT context menu commands
@author: Bruce
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce wrote these long ago within the model tree code
Bruce 0... | NanoCAD-master | cad/src/modelTree/mt_statistics.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
Plugins.py - a collection of general plugin helper functions for the purpose of
checking and/or verifying that a plugin is enabled and that the path pointed
to by its pref_key is the plugin.
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See L... | NanoCAD-master | cad/src/processes/Plugins.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
ServerManager.py - persistent db and UI for list of servers & current server.
Unclear whether or not this is GAMESS-specific.
[bruce 071217 guess at description]
@author: Huaicai
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file ... | NanoCAD-master | cad/src/processes/ServerManager.py |
# -*- coding: utf-8 -*-
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
# Form implementation generated from reading ui file 'ServerManagerDialog.ui'
#
# Created: Wed Sep 20 09:07:05 2006
# by: PyQt4 UI code generator 4.0.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 im... | NanoCAD-master | cad/src/processes/ServerManagerDialog.py |
NanoCAD-master | cad/src/processes/__init__.py | |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
Process.py
Provides class Process, a QProcess subclass which is more convenient to use,
and a convenience function run_command() for using it to run external commands.
@author: Bruce, EricM
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See L... | NanoCAD-master | cad/src/processes/Process.py |
# -*- coding: utf-8 -*-
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
# Form implementation generated from reading ui file 'LinearMotorPropDialog.ui'
#
# Created: Wed Sep 20 10:14:34 2006
# by: PyQt4 UI code generator 4.0.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 ... | NanoCAD-master | cad/src/outtakes/LinearMotorPropDialog.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PropertyManagerMixin.py
@author: Ninad
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad20061215: created this mixin class to provide helper methods in various
Property managers
ninad20070206: added ma... | NanoCAD-master | cad/src/outtakes/PropertyManagerMixin.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
depositMode.py -- Build Atoms mode.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
TODO: As of 2007-01-04
- Items listed in BuildAtoms_GraphicsMode
- Items listed in Select_GraphicsMode.py
History:
depositMode.p... | NanoCAD-master | cad/src/outtakes/depositMode.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
test_modelTreeGui.py - test code for modelTreeGui.py (non-working)
@author: Will
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
update, bruce 081215:
This test code has not worked for a long time.
To run it at a... | NanoCAD-master | cad/src/outtakes/test_modelTreeGui.py |
def selection_changed(self): #bruce 070925 [not used outside this file as of 080731, except in docstrings/comments]
return
def selobj_changed(self): #bruce 071116 [not mentioned outside this file as of 080731] 8
return
def view_changed(self): #bruce 071116 [not mentioned outside this file ... | NanoCAD-master | cad/src/outtakes/model_changed-outtakes.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
TreeView.py -- NO LONGER USED IN Qt4 NE1
-- display and update, for a tree widget based on QTreeView,
and meant to display Nodes (with interface and semantics as in Utility.py).
Assumes each node is shown in at most one place in the widget.
This ... | NanoCAD-master | cad/src/outtakes/TreeView.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
prefsTree.py -- experimental code related to showing
user preferences in the model tree
(not presently used as of 050612, but works; very incomplete)
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
... | NanoCAD-master | cad/src/outtakes/prefsTree.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaDuplexGenerator.py
@author: Mark Sims
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2007-10-18:
- Created. Major rewrite of DnaGenerator.py.
"""
from foundation.Group import Group
from utiliti... | NanoCAD-master | cad/src/outtakes/DnaDuplexGenerator.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
old_extrude_widgets.py - these were used in the original Extrude Mode dashboard.
@author: Bruce
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
from PyQt4.Qt import QGroupBox, QSpinBox, QCheckBox
from PyQt4.Qt... | NanoCAD-master | cad/src/outtakes/old_extrude_widgets.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
MMKitDialog.py
THIS FILE HAS BEEN DEPRECATED.
SEE NEW IMPLEMETATION IN --
Ui_BuildAtomsPropertyManager.py,
BuildAtomsPropertyManager.py,
Ui_PartLibPropertyManager.py,
PartLibPropertyManager.py,
Ui_PastePropertyManager.py
PastePropertyManager.py
$... | NanoCAD-master | cad/src/outtakes/MMKitDialog.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
modelTreePrototype.py
$Id$
This is a prototype for a Qt 4 compatible Model Tree. It is a standalone test program, not part of NE1 proper.
Usage: on some sysems, this can be run from the command line using
% pythonw `pwd`/modelTreePrototype.py
... | NanoCAD-master | cad/src/outtakes/modelTreePrototype.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
NanotubeGroup.py - ...
@author: Bruce, Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.Group import Group
from utilities.constants import gensym
from utilities.icon_utilities import imag... | NanoCAD-master | cad/src/outtakes/NanotubeGroup.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PeptideSegment.py - ...
WARNING: this class is reportedly not used and will soon be moved to outtakes.
@author: Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Note: related to DnaStrandOrSegment, from which... | NanoCAD-master | cad/src/outtakes/PeptideSegment.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
RotaryMotorGenerator.py
$Id$
History:
Mark 2007-05-27: Created.
"""
__author__ = "Mark"
from utilities.Log import greenmsg
from PyQt4.Qt import QDialog
from RotaryMotorGeneratorDialog import RotaryMotorPropMgr
from command_support.GeneratorBas... | NanoCAD-master | cad/src/outtakes/RotaryMotorGenerator.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
test_polyline_drag.py
@author: Bruce
@version: $Id$
Simple test/example code for making a polyline.
Goal is just to demonstrate intercepting mouse events
to change the usual meaning of a click,
detecting GLPane enter/leave, etc.
Not yet suitable for us... | NanoCAD-master | cad/src/outtakes/test_polyline_drag.py |
"""
the main code will replace __class__ of Atom or Bond with related classes,
since Python supports this. This is done in dna_updater_utils.replace_atom_class().
If Python ever stops supporting this,
here is some unfinished code which indicates the sort of thing we'd have to do.
The hard part is replacing one atom wi... | NanoCAD-master | cad/src/outtakes/Atom_replace_class.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
TreeWidget.py -- NO LONGER USED IN Qt4 NE1
-- adds event handling and standard event bindings to TreeView.py.
$Id$
History: modelTree.py was originally written by some combination of
Huaicai, Josh, and Mark. Bruce (Jan 2005) reorganized its inte... | NanoCAD-master | cad/src/outtakes/TreeWidget.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
MMKit.py
THIS FILE HAS BEEN DEPRECATED.
SEE NEW IMPLEMETATION IN --
Ui_BuildAtomsPropertyManager.py,
BuildAtomsPropertyManager.py,
Ui_PartLibPropertyManager.py,
PartLibPropertyManager.py,
Ui_PastePropertyManager.py
PastePropertyManager.py
$Id$
... | NanoCAD-master | cad/src/outtakes/MMKit.py |
"""
$Id$
"""
# debug/test functions (in other submenu of debug menu) which won't be kept around.
# [moved out of undo.py by bruce 071004]
# not all of these are needed, perhaps:
from cPickle import dump, load, HIGHEST_PROTOCOL
import foundation.env as env
from utilities.debug import register_debug_menu_command, regis... | NanoCAD-master | cad/src/outtakes/undo_related_timing_tests.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PeptideGroup.py - ...
@author: Bruce, Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from foundation.Group import Group
from utilities.constants import gensym
from utilities.icon_utilities import image... | NanoCAD-master | cad/src/outtakes/PeptideGroup.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
RotaryMotorProp.py
$Id$
"""
from PyQt4.Qt import QDialog
from PyQt4.Qt import QWidget
from PyQt4.Qt import SIGNAL
from PyQt4.Qt import QColorDialog
from RotaryMotorPropDialog import Ui_RotaryMotorPropDialog
from widgets.widget_helpers import RGBf... | NanoCAD-master | cad/src/outtakes/RotaryMotorProp.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
'''
widget_hacks.py
Miscellaneous widget-related code (such as experimental code or
temporary bug workarounds) which needs cleanup before being suitable
for widgets.py.
$Id$
History:
Bruce 050809 moved the "Mac OS X 10.4 Tiger QToolButton bug workar... | NanoCAD-master | cad/src/outtakes/widget_hacks.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""\
<p>This is an attempt to implement Mark's \"Starting NE-1\" slideshow
ideas. This is just a little prototype, and is meant to be tweaked as
we discuss things and reach a consensus about what kind of UI behavior
we want.</p>
<p>T... | NanoCAD-master | cad/src/outtakes/uiPrototype.py |
# -*- coding: utf-8 -*-
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
# Form implementation generated from reading ui file 'RotaryMotorPropDialog.ui'
#
# Created: Wed Sep 20 10:35:36 2006
# by: PyQt4 UI code generator 4.0.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 ... | NanoCAD-master | cad/src/outtakes/RotaryMotorPropDialog.py |
def describe_leftDown_action(self, selatom): # bruce 050124
# [bruce 050124 new feature, to mitigate current lack of model tree highlighting of pastable;
# this copies a lot of logic from leftDown, which is bad, should be merged somehow --
# maybe as one routine to come up with a command o... | NanoCAD-master | cad/src/outtakes/describe_leftDown_action.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
Peptide.py -- Peptide generator helper classes, based on empirical data.
@author: Mark Sims
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2008-03-09:
- Created (incorporating some code from Will's... | NanoCAD-master | cad/src/outtakes/Peptide.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = 'Will'
import sys
from distutils.core import setup
from distutils.extension import Extension
if (__name__ == '__main__'):
try:
from Pyrex.Distutils import build_ext
except:
print "Problem importing Pyrex. You nee... | NanoCAD-master | cad/src/outtakes/setup2.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
LinearMotorProp.py
$Id$
"""
from PyQt4.Qt import QDialog
from PyQt4.Qt import QWidget
from PyQt4.Qt import SIGNAL
from PyQt4.Qt import QColorDialog
from LinearMotorPropDialog import Ui_LinearMotorPropDialog
from widgets.widget_helpers import RGBf... | NanoCAD-master | cad/src/outtakes/LinearMotorProp.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version $Id$
piotr 080713: Added editRotamers action.
"""
import foundation.env as env
from PyQt4 import QtCore, QtGui
from PyQt4.Qt import Qt
from PyQt4.Qt import SIGNA... | NanoCAD-master | cad/src/outtakes/Ui_ProteinFlyout.py |
class unused_methods_in_class_MT_View: #removed from it, bruce 081216
def repaint_some_nodes_NOT_YET_USED(self, nodes): #bruce 080507 experimental, for cross-highlighting; maybe not used; rename?
"""
For each node in nodes, repaint that node, if it was painted the last
time we repainted sel... | NanoCAD-master | cad/src/outtakes/MT_View_outtakes.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PropMgrBaseClass.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-05-20: Split PropMgrBaseClass out of PropertyManagerMixin into
this file.
mark 2007-05-23: New PropMgrBa... | NanoCAD-master | cad/src/outtakes/PropMgrBaseClass.py |
see also model/prefsTree.py
since then moved to outtakes
=====
from modelTree/TreeModel.py:
_DEBUG_PREFTREE = False # bruce 050602 experiment; do not commit with True
from end of get_topnodes in TreeModel
if _DEBUG_PREFTREE: #bruce 050602
try:
from foundation.Utility import... | NanoCAD-master | cad/src/outtakes/prefsTree-in-other-files.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
BuildProtein_EditCommand.py
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from command_support.EditCommand import EditCommand
from utilities.Log import greenmsg
from ne1_ui.toolbars.Ui_ProteinFlyout imp... | NanoCAD-master | cad/src/outtakes/BuildProtein/BuildProtein_EditCommand.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
BuildProtein_PropertyManager.py
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History: Urmi initially copied from BuildDna_PropertyManager.py but this version
used for proteins is much more simp... | NanoCAD-master | cad/src/outtakes/BuildProtein/BuildProtein_PropertyManager.py |
NanoCAD-master | cad/src/outtakes/BuildProtein/__init__.py | |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
$Id$
History:
Mark 2007-05-18: Implemented Nanotube generator dialog using PropMgrBaseClass.
Mark 2007-08-06: Renamed NanotubeGeneratorDialog to NanotubeGeneratorPropertyManager.
"""
import math
from PyQt4 import QtCore, QtGui
from PyQt4.Qt impo... | NanoCAD-master | cad/src/outtakes/InsertNanotube/NanotubeGeneratorPropertyManager.py |
NanoCAD-master | cad/src/outtakes/InsertNanotube/__init__.py | |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
NanotubeGenerator.py
@author: Will
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
@see http://www.nanoengineer-1.net/mediawiki/index.php?title=Nanotube_generator_dialog
for notes about what's going on here.
"""
... | NanoCAD-master | cad/src/outtakes/InsertNanotube/NanotubeGenerator.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaGenerator.py
WARNING: this file has been mostly superseded by DnaDuplexGenerator.py.
@author: Will Ware
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
History:
Jeff 2007-06-13:
- Moved Dna class (and subclas... | NanoCAD-master | cad/src/outtakes/BuildDuplex_old/DnaGenerator.py |
NanoCAD-master | cad/src/outtakes/BuildDuplex_old/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
DnaGenHelper.py -- DNA generator helper classes, based on empirical data.
WARNING: this file has been mostly superseded by DnaDuplex.py.
It is used only in DnaGenerator.py, also superseded.
@author: Will Ware
@version: $Id$
@copyright: 2004-2008 N... | NanoCAD-master | cad/src/outtakes/BuildDuplex_old/DnaGenHelper.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
DnaGeneratorPropertyManager.py
WARNING: this file has been mostly superseded by DnaDuplexPropertyManager.py.
@author: Will Ware
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
History:
Ninad (Nov2006 and later):... | NanoCAD-master | cad/src/outtakes/BuildDuplex_old/DnaGeneratorPropertyManager.py |
NanoCAD-master | cad/src/protein/__init__.py | |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
Ui_ProteinSequenceEditor.py
@author: Urmi
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
Urmi copied this from Ui_DnaSequenceEditor.py and modified it to suit the
requirements of a protein sequence editor
TODO:
- ... | NanoCAD-master | cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
ProteinSequenceEditor.py
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version: $Id$
@author: Urmi
History:
Urmi copied this from DnaSequenceEditor.py and modified it to suit the
requirements of a protein sequence editor.
"""
import f... | NanoCAD-master | cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py |
NanoCAD-master | cad/src/protein/ProteinSequenceEditor/__init__.py | |
NanoCAD-master | cad/src/protein/model/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
Residue.py -- Residue class implementation.
Residue class stores information on individual amino acids of a protein
chain.
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
piotr 082708: Re-factored... | NanoCAD-master | cad/src/protein/model/Residue.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
Protein.py -- Protein class implementation.
The Protein class stores protein-related information and provides several
methods used by Protein display style and Rosetta simulations.
Currently, the protein objects can be created by reading a protein
str... | NanoCAD-master | cad/src/protein/model/Protein.py |
NanoCAD-master | cad/src/protein/commands/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComma... | NanoCAD-master | cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
ProteinDisplayStyle_PropertyManager.py
The ProteinDisplayStyle_PropertyManager class provides a Property Manager
for the B{Display Style} command on the flyout toolbar in the
Build > Protein mode.
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, ... | NanoCAD-master | cad/src/protein/commands/ProteinDisplayStyle/ProteinDisplayStyle_PropertyManager.py |
NanoCAD-master | cad/src/protein/commands/ProteinDisplayStyle/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
EditResidues_PropertyManager.py
B{Edit Residues} is a front-end for
The EditResidues_PropertyManager class provides a Property Manager
for the B{Edit Residues} command on the flyout toolbar in the
Build > Protein mode.
@author: Piotr
@version: $Id$
@c... | NanoCAD-master | cad/src/protein/commands/EditResidues/EditResidues_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComm... | NanoCAD-master | cad/src/protein/commands/EditResidues/EditResidues_Command.py |
NanoCAD-master | cad/src/protein/commands/EditResidues/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Piotr, Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version: $Id$
History:
2008-07-24: Created
"""
from utilities.Log import greenmsg
from command_support.EditCommand import EditCommand
from protein.commands.InsertPe... | NanoCAD-master | cad/src/protein/commands/InsertPeptide/InsertPeptide_EditCommand.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
This is a Property Manager dialog for the "Insert Peptide" command.
@author: Piotr, Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
Piotr 2008-01-11: Implemented Peptide Generator dialog using PropMgrBaseCla... | NanoCAD-master | cad/src/protein/commands/InsertPeptide/InsertPeptide_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
PeptideGenerator.py
Peptide Generator can generate short polypeptide chains of arbitrarily choosen
sequence and secondary structure.
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@see http://www.nanoengine... | NanoCAD-master | cad/src/protein/commands/InsertPeptide/PeptideGenerator.py |
NanoCAD-master | cad/src/protein/commands/InsertPeptide/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
BuildProtein_Command.py
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from command_support.EditCommand import EditCommand
from utilities.Log import greenmsg
from ne1_ui.toolbars.Ui_ProteinFlyout import ... | NanoCAD-master | cad/src/protein/commands/BuildProtein/BuildProtein_Command.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
BuildProtein_PropertyManager.py
@author: Urmi, Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
Mark 20081212: Heavily rewritten, modeled after BuildDna_PropertyManager.py.
To do list:
- Add "Edit Properties" menu... | NanoCAD-master | cad/src/protein/commands/BuildProtein/BuildProtein_PropertyManager.py |
NanoCAD-master | cad/src/protein/commands/BuildProtein/__init__.py | |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
BuildProtein_GraphicsMode.py
@author: Mark
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from commands.Select.Select_Grap... | NanoCAD-master | cad/src/protein/commands/BuildProtein/BuildProtein_GraphicsMode.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
"""
from utilities.debug import print_compact_stack, print_compact_traceback
from protein.commands.BuildProtein.BuildProtein_Command import BuildProtein_Command
... | NanoCAD-master | cad/src/protein/commands/BuildProtein/ModelProtein_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
"""
from utilities.debug import print_compact_stack, print_compact_traceback
from protein.commands.BuildProtein.BuildProtein_Command import BuildProtein_Command
... | NanoCAD-master | cad/src/protein/commands/BuildProtein/SimulateProtein_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComma... | NanoCAD-master | cad/src/protein/commands/FixedBBProteinSim/FixedBBProteinSim_Command.py |
NanoCAD-master | cad/src/protein/commands/FixedBBProteinSim/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
FixedBBProteinSim_PropertyManager.py
The FixedBBProteinSim_PropertyManager class provides a Property Manager
for the B{Fixed Backbone protein sequence design} command on the flyout toolbar in the
Build > Protein mode.
@author: Urmi
@version: $Id$
@copy... | NanoCAD-master | cad/src/protein/commands/FixedBBProteinSim/FixedBBProteinSim_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
BackrubProteinSim_PropertyManager.py
The BackrubProteinSim_PropertyManager class provides a Property Manager
for the B{Backrub protein sequence design} command on the flyout toolbar in the
Build > Protein > Simulate mode.
@author: Urmi
@version: $Id$
@... | NanoCAD-master | cad/src/protein/commands/BackrubProteinSim/BackrubProteinSim_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComm... | NanoCAD-master | cad/src/protein/commands/BackrubProteinSim/BackrubProteinSim_Command.py |
NanoCAD-master | cad/src/protein/commands/BackrubProteinSim/__init__.py | |
NanoCAD-master | cad/src/protein/commands/EditProtein/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
EditProtein_PropertyManager.py
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
@version: $Id$
@copyright: 2008 Nanorex, Inc. See L... | NanoCAD-master | cad/src/protein/commands/EditProtein/EditProtein_PropertyManager.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComm... | NanoCAD-master | cad/src/protein/commands/EditProtein/EditProtein_Command.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
CompareProteins_PropertyManager.py
The CompareProteins_PropertyManager class provides a Property Manager
for the B{Compare Proteins} command on the flyout toolbar in the
Build > Protein mode.
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc.... | NanoCAD-master | cad/src/protein/commands/CompareProteins/CompareProteins_PropertyManager.py |
NanoCAD-master | cad/src/protein/commands/CompareProteins/__init__.py | |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import foundation.changes as changes
from commands.SelectChunks.SelectChunks_GraphicsMode import SelectChunks_GraphicsMode
from command_support.EditComm... | NanoCAD-master | cad/src/protein/commands/CompareProteins/CompareProteins_Command.py |
NanoCAD-master | cad/src/protein/temporary_commands/__init__.py | |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
@author: Urmi, Mark
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc. See LICENSE file for details.
@license: GPL
"""
from utilities.constants import gray, black, darkred, blue, white
from graphics.drawing.drawPeptideTrace import drawPept... | NanoCAD-master | cad/src/protein/temporary_commands/PeptideLine_GraphicsMode.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
Python atoms, atom sets, diff factories, diff objects (tests)
http://tinyurl.com/rv7fx
May need changes to work in this location. Used to be in cad/src.
Probably depends on atombasehelp.c, which will likely move as the
cad/src directory is clean... | NanoCAD-master | cad/src/tests/atombasetests.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: EricM
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import unittest
from samevals import same_vals, setArrayType
import Numeric
class SameValsTests(unittest.TestCase):
def test_simple(self):
... | NanoCAD-master | cad/src/tests/samevalstests.py |
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