python_code stringlengths 0 992k | repo_name stringlengths 8 46 | file_path stringlengths 5 162 |
|---|---|---|
#!/usr/bin/python
# Copyright 2005, 2007 Nanorex, Inc. See LICENSE file for details.
"""Nanotube generation tool for nanoENGINEER-1
Usage:
nanotube.py <n> <m> <length>
where (n,m) is the chirality of the nanotube, and the length is in
nanometers. The resulting MMP file is written to standard output.
According to... | NanoCAD-master | cad/tests/nanotube.py |
# Copyright 2005, 2007 Nanorex, Inc. See LICENSE file for details.
import unittest
import chem
import assembly
from qt import QApplication, SIGNAL
import Utility
import os
#########################
import undo
undo._use_hcmi_hack = False
#########################
import MWsemantics
import startup_funcs
STILL_NEED... | NanoCAD-master | cad/tests/filetest.py |
import unittest
from VQT import angleBetween
from Numeric import array, alltrue
class GeometryFunctionsTestCase(unittest.TestCase):
"""Unit tests for the geometry functions defined in VQT.py"""
def setUp(self):
"""Sets up any objects needed by this test case."""
pass
def tearDown(self)... | NanoCAD-master | cad/tests/VQT_Test.py |
# Copyright 2005, 2007 Nanorex, Inc. See LICENSE file for details.
import unittest
import chem
import assembly
import Utility
import debug
from elements import PeriodicTable
Hydrogen = PeriodicTable.getElement(1)
Carbon = PeriodicTable.getElement(6)
Nitrogen = PeriodicTable.getElement(7)
Oxygen = PeriodicTable.getEle... | NanoCAD-master | cad/tests/chemtest.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
splitting_a_mode.py -- explanation/demo of how to split an old mode, while
maintaining temporary compatibility with non-split methods and subclass modes.
@author: Bruce
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
This ... | NanoCAD-master | cad/doc/splitting_a_mode.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
_import_roots.py - import all toplevel files in the import dependency hierarchy
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Note: most of the files we import here are for separate main programs,... | NanoCAD-master | cad/src/_import_roots.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
NE1_Build_Constants.py is intended to be a very small file which consists
of only the data that is likely to change for any given release, including
anything which might be changed (manually or automatically) during the
process of building a release itse... | NanoCAD-master | cad/src/NE1_Build_Constants.py |
#!/usr/bin/env python
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
ExecSubDir.py
This is an odd little utility that might appear to do absolutely nothing.
All it does is call execfile() on its first argument. It puts more
effort into validating that it has an argument than what it does to
that ... | NanoCAD-master | cad/src/ExecSubDir.py |
#! /usr/bin/python
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
main.py -- the initial startup file for NanoEngineer-1, treated specially
by the release-building process.
$Id$
This file should not be imported as the "main" module -- doing so
prints a warning [as of 050902] and doesn't run th... | NanoCAD-master | cad/src/main.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ElementChooser.py
@author: Mark Sims
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-08-03: Created.
"""
from PM.PM_MolecularModelingKit import PM_MolecularModelingKit
from PyQt4.Qt import SIGNAL, ... | NanoCAD-master | cad/src/PM/PM_ElementChooser.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ComboBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrComboBox out of PropMgrBaseClass.py into this file
and renamed it PM_ComboBox.
"""
from PyQt4.Qt import... | NanoCAD-master | cad/src/PM/PM_ComboBox.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_DoubleSpinBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrDoubleSpinBox out of PropMgrBaseClass.py into this file
and renamed it PM_DoubleSpinBox.
"""
from P... | NanoCAD-master | cad/src/PM/PM_DoubleSpinBox.py |
#Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_TreeView.py
The PM_TreeView class provides a partlib object (as a 'treeview' of any user
specified directory) to the client code.
The parts from the partlib can be pasted in the 3D Workspace.
@author: Bruce, Huaicai, Mark, Ninad
@version: $Id$
... | NanoCAD-master | cad/src/PM/PM_TreeView.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
TODO
- remove all self.command calls.
"""
from PM.PM_SelectionListWidget import PM_SelectionListWidget
from utilities.constants import lightred_1, ligh... | NanoCAD-master | cad/src/PM/PM_ObjectChooser.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_SpinBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrSpinBox out of PropMgrBaseClass.py into this file
and renamed it PM_SpinBox.
"""
from PyQt4.Qt import QLa... | NanoCAD-master | cad/src/PM/PM_SpinBox.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_Dial.py
@author: Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. All rights reserved.
History:
piotr 2008-07-29: Created this file.
"""
from PyQt4.Qt import QDial
from PyQt4.Qt import QLabel
from PyQt4.Qt import QWidget
from widgets.prefs_wi... | NanoCAD-master | cad/src/PM/PM_Dial.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_PreviewGroupBox.py
The PM_PreviewGroupBox widget provides a preview pane for previewing
elements , clipboard items , library parts etc. from the element chooser
or list provided in the property manager. (The object being previewed can
then be deposit... | NanoCAD-master | cad/src/PM/PM_PreviewGroupBox.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_LineEdit.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrLineEdit out of PropMgrBaseClass.py into this
file and renamed it PM_LineEdit.
"""
from PyQt4.Qt import ... | NanoCAD-master | cad/src/PM/PM_LineEdit.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_Dialog.py
@author: Mark
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrBaseClass out of PropMgrBaseClass.py into this
file and renamed it PM_Dialog.
"""
import foundation.env a... | NanoCAD-master | cad/src/PM/PM_Dialog.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_LabelGrid.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-14: Created.
"""
from PyQt4.Qt import QFont
from PM.PM_WidgetGrid import PM_WidgetGrid
class PM_LabelGrid( PM_Widget... | NanoCAD-master | cad/src/PM/PM_LabelGrid.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_Utilities.py
$Id$
"""
from PyQt4.QtGui import QSizePolicy
# Special Qt debugging functions written by Mark. 2007-05-24 ############
def getSizePolicyName(sizepolicy):
"""Returns the formal name of <sizepolicy>, a QSizePolicy.
FYI:
... | NanoCAD-master | cad/src/PM/PM_Utilities.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_Clipboard.py
The PM_Clipboard class provides a groupbox containing a list of clipboard
items that can be pasted in the 3D Workspace. The selected item in this
list is shown by its elementViewer (an instance of L{PM_PreviewGroupBox})
The object being ... | NanoCAD-master | cad/src/PM/PM_Clipboard.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_FontComboBox.py
@author: Derrick
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
"""
from PyQt4.Qt import QFontComboBox
from PyQt4.Qt import QLabel
from PyQt4.Qt import QWidget
class PM_FontComboBox( QFontComboBox ):... | NanoCAD-master | cad/src/PM/PM_FontComboBox.py |
"""
The Property Manager (PM) module provides classes for creating NE1 property
manager dialogs.
The main class in the PM module is L{PM_Dialog}, which is a base class. It can
contain one or more group boxes (L{PM_GroupBox}) that can contain one or more
PM widgets.
IMAGE(http://www.nanoengineer-1.net/mediawiki/images... | NanoCAD-master | cad/src/PM/__init__.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_StackedWidget.py
@author: Mark
@version: $Id$
@copyright: 2008 Nanorex, Inc. All rights reserved.
History:
Mark 2008-05-07: Written for L{DnaDisplayStyle_PropertyManager} to deal with
the UI requirements imposed by adding all the DNA display ... | NanoCAD-master | cad/src/PM/PM_StackedWidget.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_TableWidget.py
Simple wrapper over Qt QtableWidget class.
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. All rights reserved.
History:
piotr 2008-07-15: Created this file.
"""
from PyQt4.Qt import Qt
from PyQt4.Qt import QTableWid... | NanoCAD-master | cad/src/PM/PM_TableWidget.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_DockWidget.py
@author: Ninad
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
Ninad 2007-11-20: Created to implement DnaSequenceEditor
TODO:
- Add more documentation
NOTE: methods addPmWidget and getPmW... | NanoCAD-master | cad/src/PM/PM_DockWidget.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_MessageGroupBox.py
The PM_MessageGroupBox widget provides a message group box with a
collapse/expand button and a title.
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split Pr... | NanoCAD-master | cad/src/PM/PM_MessageGroupBox.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ToolButtonGrid.py
@author: Mark Sims
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-08-02: Created.
ninad 2007-08-14: New superclass PM_WidgetGrid. Related refactoring and cleanup.
"""
import sys
... | NanoCAD-master | cad/src/PM/PM_ToolButtonGrid.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_WidgetsDemoPropertyManager.py - Displays all the PM module widgets in a PM.
$Id$
"""
from PyQt4.Qt import Qt, SIGNAL
from PM.PM_Dialog import PM_Dialog
from PM.PM_GroupBox import PM_GroupBox
from PM.PM_CheckBox import PM_Che... | NanoCAD-master | cad/src/PM/PM_WidgetsDemoPropertyManager.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ToolButtonRow.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-07: Created.
ninad 2007-08-14: Changes due to the new superclass of PM_ToolButtonGrid.
"""
from PM.PM_ToolButtonGri... | NanoCAD-master | cad/src/PM/PM_ToolButtonRow.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
This class provides a table widget to display search results for a DnaStrand or
DnaSegment. It displays node name in one column and number of nucleotides
in the other.
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version... | NanoCAD-master | cad/src/PM/PM_DnaSearchResultTable.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_TextEdit.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrTextEdit out of PropMgrBaseClass.py into this
file and renamed it PM_TextEdit.
"""
from PM.PM_Constants ... | NanoCAD-master | cad/src/PM/PM_TextEdit.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
GroupButtonMixin.py
$Id$
History and status:
Written by Will in GeneratorBaseClass.py, but no longer used there
or by anything that uses it.
bruce 070619 moved this from GeneratorBaseClass.py to its own file. It is deprecated;
its uses should be... | NanoCAD-master | cad/src/PM/GroupButtonMixin.py |
#Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_PartLib.py
The PM_PartLib class provides a groupbox that contains the partlib (any user
specified directory). The parts from the partlib can be pasted into the 3D
workspace. The selected item in this list is shown by its elementViewer
(an instanc... | NanoCAD-master | cad/src/PM/PM_PartLib.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_Colors.py -- Property Manager color theme functions and constants..
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Created initially for PM_Dialog as part of the code cleanup
... | NanoCAD-master | cad/src/PM/PM_Colors.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_PAM3_AtomChooser.py
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. All rights reserved.
"""
from PM.PM_MolecularModelingKit import PM_MolecularModelingKit
from utilities.constants import diBALL
from utilities.GlobalPreferenc... | NanoCAD-master | cad/src/PM/PM_PAM3_AtomChooser.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_CoordinateSpinBoxes.py
The PM_CoordinateSpinBoxes class provides a groupbox containing the three
coordinate spinboxes.
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
@TODO: Need to implement connectWidge... | NanoCAD-master | cad/src/PM/PM_CoordinateSpinBoxes.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ToolButton.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrToolButton out of PropMgrBaseClass.py into this
file and renamed it PM_ToolButton.
"""
import os
from ... | NanoCAD-master | cad/src/PM/PM_ToolButton.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_PAM5_AtomChooser.py
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. All rights reserved.
"""
from PM.PM_MolecularModelingKit import PM_MolecularModelingKit
from utilities.constants import diBALL
from utilities.GlobalPreferenc... | NanoCAD-master | cad/src/PM/PM_PAM5_AtomChooser.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_LabelRow.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-14: Created.
"""
from PM.PM_LabelGrid import PM_LabelGrid
class PM_LabelRow( PM_LabelGrid ):
"""
The PM_LabelRo... | NanoCAD-master | cad/src/PM/PM_LabelRow.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ColorComboBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
To do:
- Override addItem() and insertItem() methods.
"""
from PM.PM_ComboBox import PM_ComboBox
from PyQt4.Qt import QPixmap, QIcon, QCo... | NanoCAD-master | cad/src/PM/PM_ColorComboBox.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_GroupBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrGroupBox out of PropMgrBaseClass.py into this
file and renamed it PM_GroupBox.
"""
import sys
from utili... | NanoCAD-master | cad/src/PM/PM_GroupBox.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_MolecularModelingKit.py - Atom Chooser widget
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
"""
from model.elements import PeriodicTable
from PyQt4.Qt import SIGNAL
from PM.PM_GroupBox import PM_GroupBox
from PM.PM_... | NanoCAD-master | cad/src/PM/PM_MolecularModelingKit.py |
# Copyright 2006-2009 Nanorex, Inc. See LICENSE file for details.
"""
PM_ColorChooser.py
@author: Mark
@version: $Id$
@copyright: 2006-2009 Nanorex, Inc. All rights reserved.
History:
"""
from PyQt4.Qt import QLabel
from PyQt4.Qt import QFrame
from PyQt4.Qt import QToolButton
from PyQt4.Qt import QHBoxLayout
from... | NanoCAD-master | cad/src/PM/PM_ColorChooser.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_PrefsCheckBoxes.py
PM_PrefsCheckBoxes class provides a way to insert a groupbox within
a Property Manager, that contains a bunch of check boxes connected
to the User Preference via preference keys.
@author: Ninad
@copyright: 2008 Nanorex, Inc. See... | NanoCAD-master | cad/src/PM/PM_PrefsCheckBoxes.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_RadioButton.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrRadioButton out of PropMgrBaseClass.py into this
file and renamed it PM_RadioButton.
"""
from PyQt4.Q... | NanoCAD-master | cad/src/PM/PM_RadioButton.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_Constants.py -- Property Manager constants.
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Created initially for PM_Dialog as part of the code cleanup
and revie... | NanoCAD-master | cad/src/PM/PM_Constants.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_WidgetGrid.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-14: Created.
"""
from PyQt4.Qt import QSizePolicy
from PyQt4.Qt import QSpacerItem
from PyQt4.Qt import QSize
from Py... | NanoCAD-master | cad/src/PM/PM_WidgetGrid.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_SelectionListWidget.py
@author: Ninad
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. All rights reserved.
TODO:
- Probably need to revise the tag instructions. At the moment it is confusing.
If a list widget item is selected from that wi... | NanoCAD-master | cad/src/PM/PM_SelectionListWidget.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_ListWidget.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrListWidget out of PropMgrBaseClass.py into this
file and renamed it PM_ListWidget.
"""
from PyQt4.Qt i... | NanoCAD-master | cad/src/PM/PM_ListWidget.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_PushButton.py
@author: Mark
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrPushButton out of PropMgrBaseClass.py into this
file and renamed it PM_PushButton.
"""
from PyQt4.Qt i... | NanoCAD-master | cad/src/PM/PM_PushButton.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_Slider.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-21: Created.
"""
from PyQt4.Qt import Qt
from PyQt4.Qt import QSlider
from PyQt4.Qt import QLabel
from PyQt4.Qt import QWi... | NanoCAD-master | cad/src/PM/PM_Slider.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
@author: Ninad
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
@version:$Id$
History:
2008-08-12 created.
TODO 2008-08-12:
- This uses global pref keys (hardcoded) because the preference is supposed
to remain in all commands. Other optio... | NanoCAD-master | cad/src/PM/PM_DnaBaseNumberLabelsGroupBox.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
PM_CheckBox.py
@author: Mark
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
History:
mark 2007-07-22: Split PropMgrCheckBox out of PropMgrBaseClass.py into this file
and renamed it PM_CheckBox.
"""
from PyQt4.Qt import... | NanoCAD-master | cad/src/PM/PM_CheckBox.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_RadioButtonList.py
@author: Mark Sims
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. All rights reserved.
History:
mark 2007-08-05: Created.
"""
from PyQt4.Qt import QButtonGroup
from PyQt4.Qt import QRadioButton
from PM.PM_GroupBox imp... | NanoCAD-master | cad/src/PM/PM_RadioButtonList.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_FileChooser.py
@author: Mark
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. All rights reserved.
History:
"""
import os
from PyQt4.Qt import QLabel
from PyQt4.Qt import QLineEdit
from PyQt4.Qt import QToolButton
from PyQt4.Qt import QHBo... | NanoCAD-master | cad/src/PM/PM_FileChooser.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
PM_WidgetRow.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
History:
ninad 2007-08-09: Created.
@attention: This file is subject to heavy modifications.
"""
from PM.PM_WidgetGrid import PM_WidgetGrid
f... | NanoCAD-master | cad/src/PM/PM_WidgetRow.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
bond_updater.py
Recompute structural bond orders when necessary.
@author: Bruce
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
This is needed for bonds between atoms whose atomtypes make p orbitals
available for... | NanoCAD-master | cad/src/model_updater/bond_updater.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
master_model_updater.py - do the post-event (or pre-checkpoint) updates
necessary for all of NE1's model types, in an appropriate order (which may
involve recursively running some lower-level updates to completion after
higher-level ones change thin... | NanoCAD-master | cad/src/model_updater/master_model_updater.py |
NanoCAD-master | cad/src/model_updater/__init__.py | |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""This addresses bug 1167, where if the BROWSER environment variable
is not set, nE-1 may not be able to find the web browser to do wiki
help. Let's see if we can resolve that issue without putting \"export
BROWSER\" in the .bashrc o... | NanoCAD-master | cad/src/experimental/browserHack.py |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'PreferencesDialog.ui'
#
# Created: Wed Aug 27 16:00:53 2008
# by: PyQt4 UI code generator 4.3.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_PreferencesDialog(object):
def setup... | NanoCAD-master | cad/src/experimental/prefs/Ui_PreferencesDialog.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
WhatsThisText_for_PreferencesDialog.py
This file provides functions for setting the "What's This" and tooltip text
for widgets in the NE1 Preferences dialog only.
Edit WhatsThisText_for_MainWindow.py to set "What's This" and tooltip text
for widgets in... | NanoCAD-master | cad/src/experimental/prefs/WhatsThisText_for_PreferencesDialog.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
Preferences.py
@author: Mark
@version: $Id: Preferences.py 14197 2008-09-11 04:52:29Z brucesmith $
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
History:
-Mark 2008-05-20: Created by Mark from a copy of UserPrefs.py
"""
impor... | NanoCAD-master | cad/src/experimental/prefs/Preferences.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
PreferencesDialog.py
This is experimental.
To run, type:
python PreferencesDialog.py
"""
import sys, os
from PyQt4.Qt import *
from PyQt4 import QtCore, QtGui
from Ui_PreferencesDialog import Ui_PreferencesDialog
# imports for testing
from PM.P... | NanoCAD-master | cad/src/experimental/prefs/PreferencesDialog.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
extensions.py
Note: for now, this is intentionally not imported (even indirectly or
conditionally) by main.py; see comment below for why. But it should
remain in this directory. [bruce 071005].
Someday: handle all our custom extension modules.
Fo... | NanoCAD-master | cad/src/experimental/pyrex_test/extensions.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
setup.py
Distutils setup file -- tells distutils how to rebuild our custom extension modules.
$Id$
This file is NOT meant to be imported directly by nE-1.
One way to run it might be "make extensions"; see Makefile in this directory.
A more direc... | NanoCAD-master | cad/src/experimental/pyrex_test/setup.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1 simulation-related API.
"""
| NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_Simulation/__init__.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Encapsulates all the particulars of a simulation.
The L{SimSpecification} class is essentially a hierarchical parameter set that
describes a cross-package compatible simulation specification.
All reusable configuration is captured here including mo... | NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_Simulation/SimSpecification.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Encapsulates the information necessary for viewing and editing single parameters
via some GUI.
The following is the object model of the Parameter module:
IMAGE_2
"""
class Parameter:
"""
A GUI editable key/value pair. When newly construc... | NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_Simulation/Parameter.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Adjusts the positions of the given atoms so as to minimize the structure's total
energy.
"""
from NE1_Simulation.Parameter import Parameter
class EnergyMinimizer:
"""
Adjusts the positions of the given atoms so as to minimize the structu... | NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/EnergyMinimizer.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Plugin APIs that interface directly with the NE1 core.
"""
| NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_CorePlugins/__init__.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1 core-library-related API.
"""
| NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_Lib/__init__.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1 core-library-related API.
"""
class NE1_Lib:
"""
Core NE1 methods (to support the NH1 wizard.) This API is just to give an
idea - still needs to be thought through.
The premise of the getXxxUI() methods is that NE1 shall prov... | NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_Lib/NE1_Lib.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
A job that the NE1 Job Manager schedules and monitors.
"""
class NE1_Job:
"""
A job that the NE1 Job Manager schedules and monitors. Subclasses know how
to run themselves and can be polled.
This is an abstract/interface class and... | NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/NE1_Job.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1 job-management-related API.
"""
| NanoCAD-master | cad/src/experimental/NH1_Integration/lib/NE1_JobManagement/__init__.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
Encapsulates a simulation results data store.
The main class in this module is L{SimResultsDataStore}. The L{SimResultsBond}
class is really just a container for bond information.
"""
class SimResultsBond:
"""
A chemical bond. See L{SimResults... | NanoCAD-master | cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/SimResultsDataStore.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1 simulation-related API.
"""
| NanoCAD-master | cad/src/experimental/NH1_Integration/HDF5_SimResults/lib/NE1_Simulation/__init__.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import os, sys
seq = 'gattaca'
n = len(seq)
strands = 2
# NAMOT seems broken for one strand? Am I using it wrong?
#########################################################
#
# We will need to ask Paul R to help us understand these distortions.
# I can... | NanoCAD-master | cad/src/experimental/namot/hack.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import sys
import distutils.sysconfig
import distutils.ccompiler
class FakeCompiler:
def __init__(self):
self.compiler_type = distutils.ccompiler.get_default_compiler()
def set_executables(self, **kw):
for k in kw: setattr(self,... | NanoCAD-master | cad/src/experimental/pyrex-example/distutils_compile_options.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = "Will"
import sys, os, Pyrex
def find_pyrexc():
if sys.platform == 'darwin':
x = os.path.dirname(Pyrex.__file__).split('/')
return '/'.join(x[:-4] + ['bin', 'pyrexc'])
elif sys.platform == 'linux2':
if os.... | NanoCAD-master | cad/src/experimental/pyrex-example/findpyrex.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = 'oleksandr'
from Interval import *
from Triple import *
"""box representation"""
class Box:
def __init__(self, *args):
"""box constructor"""
self.x = Interval()
self.y = Interval()
self.z = Interval(... | NanoCAD-master | cad/src/experimental/oleksandr/Box.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = 'oleksandr'
"""interval representation"""
class Interval:
def __init__(self, *args):
"""interval constructor"""
self.min = 0
self.max = 0
if len(args) == 0:
pass
if len(args) == 2:... | NanoCAD-master | cad/src/experimental/oleksandr/Interval.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import sys
import distutils.sysconfig
import distutils.ccompiler
class FakeCompiler:
def __init__(self):
self.compiler_type = distutils.ccompiler.get_default_compiler()
def set_executables(self, **kw):
for k in kw: setattr(self,... | NanoCAD-master | cad/src/experimental/oleksandr/distutils_compile_options.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = 'oleksandr'
import types, operator, math
"""3D vector representation"""
class Triple:
def __init__(self, *args):
"""vector constructor"""
self.x = 0
self.y = 0
self.z = 0
if len(args) == 0:
... | NanoCAD-master | cad/src/experimental/oleksandr/Triple.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = "Will"
import sys, os, Pyrex
def find_pyrexc():
if sys.platform == 'darwin':
x = os.path.dirname(Pyrex.__file__).split('/')
return '/'.join(x[:-4] + ['bin', 'pyrexc'])
elif sys.platform == 'linux2':
if os.... | NanoCAD-master | cad/src/experimental/oleksandr/findpyrex.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
>... anything I'm doing wrong?
Not overriding QGLWidget's necessary methods that draw things,
paintGL, resizeGL, maybe an init method. GLPane shows the way,
so does the smaller ThumbView.
But it's easier and more relevant to NE1... | NanoCAD-master | cad/src/experimental/LearningOpenGL/Cruft.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""Try to do all the OpenGL stuff in Python, on the theory that
C extensions are hard to debug.
"""
import CruftDialog
from qt import *
from qtcanvas import *
from qtgl import *
from OpenGL.GL import *
import Numeric
import sys
impor... | NanoCAD-master | cad/src/experimental/LearningOpenGL/Craft.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import sys
import distutils.sysconfig
import distutils.ccompiler
class FakeCompiler:
def __init__(self):
self.compiler_type = distutils.ccompiler.get_default_compiler()
def set_executables(self, **kw):
for k in kw: setattr(self,... | NanoCAD-master | cad/src/experimental/LearningOpenGL/distutils_compile_options.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
from jelloGui import *
import sys
import random
import time
import types
import string
from math import cos, sin, sqrt
PROFILING = True
if PROFILING:
import hotshot, hotshot.stats
GOT_PYREX = False
try:
import comp
GOT_P... | NanoCAD-master | cad/src/experimental/finite-element/jello.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import sys
import distutils.sysconfig
import distutils.ccompiler
class FakeCompiler:
def __init__(self):
self.compiler_type = distutils.ccompiler.get_default_compiler()
def set_executables(self, **kw):
for k in kw: setattr(self,... | NanoCAD-master | cad/src/experimental/finite-element/distutils_compile_options.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
__author__ = "Will"
import sys, os, Pyrex
def find_pyrexc():
if sys.platform == 'darwin':
x = os.path.dirname(Pyrex.__file__).split('/')
return '/'.join(x[:-4] + ['bin', 'pyrexc'])
elif sys.platform == 'linux2':
if os.... | NanoCAD-master | cad/src/experimental/finite-element/findpyrex.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
units.py - physical units for calculations
$Id$
When quantities are multiplied or divided, the powers of units are
correctly maintained. If one unit ends up being raised to a zeroth
power, that unit is discarded in the product or ratio. If there are
no... | NanoCAD-master | cad/src/experimental/units/units.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""Convert CoNTub's PDB output to an MMP file
Typical usage:
python pdb2mmp.py < hetero.pdb > hetero.mmp
"""
import sys, string
class Atom:
def __init__(self, index, elem, xyz):
self.index = index
self.elem = elem
self... | NanoCAD-master | cad/src/experimental/graphene/pdb2mmp.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import os, sys, string
from math import *
sys.path.append("/home/wware/polosims/cad/src")
from geometry.VQT import A, V, vlen
class AtomType:
def __init__(self, symbol, number, rcovalent):
self.symbol = symbol
s... | NanoCAD-master | cad/src/experimental/bdna-bases/prepare.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""Arbitrary 2D surfaces in 3D space can be represented as:
f(v) = 0
where f takes a 3D vector v and returns a scalar. For a
sphere, where f(x,y,z) = x**2 + y**2 + z**2 - R**2.
By convention, the points where f(v) < 0 are the i... | NanoCAD-master | cad/src/experimental/tiling/shapes.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""Arbitrary 2D surfaces in 3D space can be represented as:
f(v) = 0
where f takes a 3D vector v and returns a scalar. For a
sphere, where f(x,y,z) = x**2 + y**2 + z**2 - R**2.
We would like to take these arbitrary surfaces and... | NanoCAD-master | cad/src/experimental/tiling/foo.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
# Think about the set sizes for which this scheme is memory efficient.
import time
import unittest
import Numeric
stuff = None
#stuff = [ ]
N = 10**4
#N = 1000
## Verifying Bruce's suspicion that the 9/9/9/5 scheme was a memory
## h... | NanoCAD-master | cad/src/experimental/pyrex-atoms-bonds/smallerFootprint.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
import time
import unittest
import random
import Numeric
from bases import *
N = int(10**6)
#N = int(10**6)
class PerformanceLog:
def __init__(self):
self.records = [ ]
def __setitem__(self, name, time):
self.records.append("%s... | NanoCAD-master | cad/src/experimental/pyrex-atoms-bonds/tryit.py |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.