python_code stringlengths 0 992k | repo_name stringlengths 8 46 | file_path stringlengths 5 162 |
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# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
SimulatorParameters.py
Read the sim-params.txt file, and extract information needed on the
NE1 side. This currently consists of parameters controlling the
Yukawa non-bonded potential function for PAM3 and PAM5 DNA models.
NE1 generates the tables whic... | NanoCAD-master | cad/src/simulation/SimulatorParameters.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
SimSetup.py
Dialog for setting up to run the simulator.
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Created by Mark, under the name runSim.py.
Bruce 050324 changed some comments and did some co... | NanoCAD-master | cad/src/simulation/SimSetup.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
SimServer.py - hold attributes needed to connect to and run a SimJob.
(Appears to be specific to GAMESS in some ways.)
[bruce 071217 guess at description]
@author: Mark
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for detail... | NanoCAD-master | cad/src/simulation/SimServer.py |
NanoCAD-master | cad/src/simulation/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
PyrexSimulator.py - Wrapper around the pyrex/C ND-1 simulator code.
Responsible for maintaining references to strings which are passed
to the C code, and which end up referenced by variables defined in
src/sim/globals.c.
@version: $Id$
@copyright: ... | NanoCAD-master | cad/src/simulation/PyrexSimulator.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
runSim.py -- setting up and running the simulator, for Simulate or Minimize
(i.e. the same code that would change if the simulator interface changed),
and part of the implementation of user-visible commands for those operations.
@version: $Id$
@cop... | NanoCAD-master | cad/src/simulation/runSim.py |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'SimSetupDialog.ui'
#
# Created: Fri Jun 06 12:02:42 2008
# by: PyQt4 UI code generator 4.2
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_SimSetupDialog(object):
def setupUi(self,... | NanoCAD-master | cad/src/simulation/SimSetupDialog.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
GromacsLog.py
Parse the .log file output of the GROMACS mdrun program, specifically
during conjugate gradients minimization. Note the energy values for
various components as they change, and report their final values.
@author: Eric M
@version: $Id$
@... | NanoCAD-master | cad/src/simulation/GromacsLog.py |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
movie.py -- class Movie, used for simulation parameters and open movie files
@author: Mark
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
History:
Initially by Mark.
Some parts rewritten by Bruce circa 050427.
... | NanoCAD-master | cad/src/simulation/movie.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
sim_aspect.py -- represent a "simulatable aspect" (portion) of one Part,
and help with its simulation
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce, probably sometime in 2005, wrot... | NanoCAD-master | cad/src/simulation/sim_aspect.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
SimJob.py - The base class for a simulation job.
(Used only for GAMESS, but unclear whether the code is specific to GAMESS.)
@author: Mark
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
import time
import sys... | NanoCAD-master | cad/src/simulation/SimJob.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
sim_commandruns.py -- user-visible commands for running the simulator,
for simulate or minimize (aka Run Dynamics, Minimize, Adjust --
but I'm not sure it's used for all of those)
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. S... | NanoCAD-master | cad/src/simulation/sim_commandruns.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
YukawaPotential.py
Create an .xvg file suitable for passing as the argument to -table for
mdrun.
@author: Eric M
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
The table consists of 7 columns:
r f f'' g g'' h ... | NanoCAD-master | cad/src/simulation/YukawaPotential.py |
NanoCAD-master | cad/src/simulation/ROSETTA/__init__.py | |
"""
RosettaSimulationPopUpDialog.py
Qt Dialog for setting the arguments for a rosetta simulation
@author: Urmi
@version: $Id$
@copyright:2008 Nanorex, Inc. See LICENSE file for details.
"""
from PyQt4.Qt import SIGNAL, SLOT
from PyQt4.Qt import QSizePolicy
from PyQt4.QtGui import QDialog, QLineEdit, QPushButton, QLab... | NanoCAD-master | cad/src/simulation/ROSETTA/RosettaSimulationPopUpDialog.py |
"""
runRosetta.py -- setting up and running rosetta simulations
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
Urmi copied this file from runSim.py and then modified it.
This file is very different from runSim.py, partly because rosetta simulation
is quite different from gromacs... | NanoCAD-master | cad/src/simulation/ROSETTA/runRosetta.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
rosetta_commandruns.py -- user-visible commands for running the rosetta simulator,
@author: Urmi
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
Copied from sim_commandruns.py and then modified to suit rosetta... | NanoCAD-master | cad/src/simulation/ROSETTA/rosetta_commandruns.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
RosettaSetup.py
Dialog for setting up to run the simulator.
@author: Urmi
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Copied and then modified from SimSetup.py
"""
from simulation.movie import Movie
_stickyParams... | NanoCAD-master | cad/src/simulation/ROSETTA/RosettaSetup.py |
NanoCAD-master | cad/src/simulation/GROMACS/__init__.py | |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
GROMACS.py - defines class GROMACS, for a temporary demo of
atomic-level-DNA GROMACS simulation
@author: Brian
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
Encapsulates the running of energy minimizations and molecular d... | NanoCAD-master | cad/src/simulation/GROMACS/GROMACS.py |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
changes.py - utilities for tracking changes, usage, nested events, etc.
@author: Bruce
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
History:
original features were stubs and have mostly been removed.
bruce 05... | NanoCAD-master | cad/src/foundation/changes.py |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
env.py - for global variables and functions treated as "part of the
environment".
@author: Bruce
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
This module is for various global or "dynamic" variables,
which can ... | NanoCAD-master | cad/src/foundation/env.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
state_constants.py -- definitions needed by state_utils and its client code,
including constants for declaring attributes' roles in
holding state or referring to objects that hold state. (Also some
names for the available kinds of specialcase treatm... | NanoCAD-master | cad/src/foundation/state_constants.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
wiki_help.py -- associate webpages (typically in a wiki) with program features,
and provide access to them. Pages typically contain feature-specific help info,
FAQ, forum, etc.
@author: Will, Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc.... | NanoCAD-master | cad/src/foundation/wiki_help.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
Utility.py -- class Node (superclass for all model-tree objects),
Group [now defined in Group.py, no longer imported here],
and a few related classes or functions, defining a uniform
API to permit all Node subclasses to be shown in the model tree,
a... | NanoCAD-master | cad/src/foundation/Utility.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
LeafLikeGroup.py - abstract superclass for groups that appear as leaves
in the MT, e.g. DnaStrandOrSegment, NanotubeSegment, PeptideSegment.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
... | NanoCAD-master | cad/src/foundation/LeafLikeGroup.py |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
preferences.py -- Preferences system.
@author: Bruce
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
Module classification: [bruce 071215]
At least foundation, due to integral use of "from changes import UsageTr... | NanoCAD-master | cad/src/foundation/preferences.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
changedicts.py - utilities related to dictionaries of changed objects
@author: Bruce
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
History:
bruce 071106 split this out of changes.py
Current status:
This code ... | NanoCAD-master | cad/src/foundation/changedicts.py |
NanoCAD-master | cad/src/foundation/__init__.py | |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
state_utils.py - general state-related utilities, and undo-related uses of them.
@author: Bruce
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
Note: same_vals was moved from here into a new file, utilities/Compar... | NanoCAD-master | cad/src/foundation/state_utils.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
FeatureDescriptor.py - descriptor objects for program features
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
# == constants
_KLUGE_PERMIT_INHERITED_CLASSNAMES = (
"Command",
"basicMod... | NanoCAD-master | cad/src/foundation/FeatureDescriptor.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
node_indices.py
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
Utilities for finding node indices in a tree,
and using them to help move the nodes around.
(And other things useful for fixing bug 2... | NanoCAD-master | cad/src/foundation/node_indices.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
whatsthis_utilities.py
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
from PyQt4.Qt import QAction
from PyQt4.Qt import QWidget
from PyQt4.Qt import QMenu
from PyQt4.Qt import QMenuBar
import ... | NanoCAD-master | cad/src/foundation/whatsthis_utilities.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
undo_internals.py - wrap our Qt slot methods with Undo checkpoints.
See also: undo_archive.py, undo_manager.py, undo_UI.py,
def wrap_callable_for_undo, and perhaps some undo-related
code in env.py, changes.py, HistoryWidget.py.
@author: Bruce
@ver... | NanoCAD-master | cad/src/foundation/undo_internals.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
undo_archive.py - Collect and organize a set
of checkpoints of model state and diffs between them,
providing undo/redo ops which apply those diffs to the model state.
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE fi... | NanoCAD-master | cad/src/foundation/undo_archive.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
Group.py -- Class (or superclass) for all non-leaf nodes in the
internal model tree of Nodes.
@author: Josh
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
Originally by Josh; gradually has been greatly ... | NanoCAD-master | cad/src/foundation/Group.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
NodeWithAtomContents.py -- abstract class for Node subclasses which
can contain Atoms.
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 080305 added some abstract classes between Node and Group... | NanoCAD-master | cad/src/foundation/NodeWithAtomContents.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
inval.py -- simple invalidation/update system for attributes within an object
@author: Bruce
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
bruce 050513 replaced some == with 'is' and != with 'is not', to avoid _... | NanoCAD-master | cad/src/foundation/inval.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
undo_manager.py - own and manage an UndoArchive, feeding it info about
user-command events (such as when to make checkpoints and how to describe
the diffs generated by user commands), and package the undo/redo ops it offers
into a reasonable form fo... | NanoCAD-master | cad/src/foundation/undo_manager.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
Assembly_API.py -- API for class assembly, also useful for isinstance tests
Note: the API is not filled in yet, but the isinstance usage is
relied on to remove some import cycles.
@author: bruce
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENS... | NanoCAD-master | cad/src/foundation/Assembly_API.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
test_connectWithState_constants.py -- constants for use in
test_connectWithState command and its PM.
This file can be merged into the command class, once it's possible
for the PM code to get these values directly from the staterefs
(an intended improvem... | NanoCAD-master | cad/src/prototype/test_connectWithState_constants.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
example_expr_command.py -- example of how to use an interactive graphics
expr in a command (unfinished, so partly scratch code); command and PM
are each variants of ExampleCommand1's command and PM classes
@author: Bruce
@version: $Id$
@copyright: ... | NanoCAD-master | cad/src/prototype/example_expr_command.py |
NanoCAD-master | cad/src/prototype/__init__.py | |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
test_drawing.py -- replaces or augments GLPane.paintGL() to try various
OpenGL rendering models, determine whether the performance bottleneck is
in OpenGL, Qt, or somewhere else, and find a better alternative.
@author: Russ
@version: $Id$
@copyrigh... | NanoCAD-master | cad/src/prototype/test_drawing.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
test_connectWithState.py -- test the connectWithState features.
Also serves as scratch code for their improvement.
@author: Bruce
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc. See LICENSE file for details.
History:
070830 bruce split this o... | NanoCAD-master | cad/src/prototype/test_connectWithState.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
test_connectWithState_PM.py -- Property Manager for test_connectWithState command.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
070830 bruce split this out of test_command_PMs.py
"""
#... | NanoCAD-master | cad/src/prototype/test_connectWithState_PM.py |
# Copyright 2007-2009 Nanorex, Inc. See LICENSE file for details.
"""
test_commands.py -- try out using mode classes as command classes for a command stack;
find out the minimal needs for a command with PM (and improve them);
prototype a command stack
@author: Bruce
@version: $Id$
@copyright: 2007-2009 Nanorex, Inc... | NanoCAD-master | cad/src/prototype/test_commands.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
test_command_PMs.py - property manager classes for test_commands.py.
See that file for more info.
@version: $Id$
"""
from PM.PM_Dialog import PM_Dialog
from PM.PM_GroupBox import PM_GroupBox
from PM.PM_DoubleSpinBox import PM_DoubleSpi... | NanoCAD-master | cad/src/prototype/test_command_PMs.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
test_commands_init.py -- make the commands in test_commands available in the UI.
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
How to run these test commands: see test_commands.py docstring.
This... | NanoCAD-master | cad/src/prototype/test_commands_init.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
CommandToolbar.py - controls the main hierarchical toolbar for giving commands
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
Module classification: [bruce 071228]
This mainly contains control logic (espec... | NanoCAD-master | cad/src/commandToolbar/CommandToolbar.py |
NanoCAD-master | cad/src/commandToolbar/__init__.py | |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
CommandToolbar_Constants.py
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. See LICENSE file for details.
Module classification: [bruce 071228]
This is used only in Ui_CommandToolbar, slated for "ne1_ui" package.
But when we refactor Ui... | NanoCAD-master | cad/src/commandToolbar/CommandToolbar_Constants.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
move_atoms_and_normalize_bondpoints.py -- post-simulation helper function
@author: Josh, Bruce
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
090112 renamed from move_alist_and_snuggle, moved into new f... | NanoCAD-master | cad/src/operations/move_atoms_and_normalize_bondpoints.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
ops_select.py -- operations and internal methods for changing what's selected
and maintaining other selection-related state. (Not well-organized.)
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
bruce 05... | NanoCAD-master | cad/src/operations/ops_select.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
op_select_doubly.py -- workhorse function for the Select Doubly operation.
Needs some comment-cleanup. And some potential optimizations described herein
are worth doing if this op's speed ever matters. And it should now be allowed
to coexist with t... | NanoCAD-master | cad/src/operations/op_select_doubly.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_modify.py provides modifySlotsMixin for MWsemantics,
with modify slot methods and related helper methods.
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: many ops_*.py files provide mixin c... | NanoCAD-master | cad/src/operations/ops_modify.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_display.py provides displaySlotsMixin for MWsemantics,
with display slot methods and related helper methods.
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: most other ops_*.py files provid... | NanoCAD-master | cad/src/operations/ops_display.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_view.py provides viewSlotsMixin for MWsemantics,
with view slot methods and related helper methods.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: most other ops_*.py files provide mixin classes for Par... | NanoCAD-master | cad/src/operations/ops_view.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
bond_chains.py -- helper functions related to chains of bonds
(See also: pi_bond_sp_chain.py)
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
from model.bond_constants import DIRBOND_CHAIN_MIDD... | NanoCAD-master | cad/src/operations/bond_chains.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
bond_utils.py -- helper functions for bond-related UI code and its operations
(should be renamed, maybe to bond_menu_helpers.py)
@author: bruce
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
History:
created by... | NanoCAD-master | cad/src/operations/bond_utils.py |
NanoCAD-master | cad/src/operations/__init__.py | |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
ops_motion.py -- various ways of moving or spatially distorting
selected atoms or chunks (and someday, attached jigs).
These operations don't create or destroy atoms or bonds.
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for... | NanoCAD-master | cad/src/operations/ops_motion.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
jigmakers_Mixin.py -- provides a mixin class to be inherited by class Part,
for providing operations for making specific kinds of Jigs, and associated
public helper functions.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for... | NanoCAD-master | cad/src/operations/jigmakers_Mixin.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
chem_patterns.py -- finding simple patterns of bonded atoms
see also ND-1's pattern matching facility, which is faster and more general
@author: Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
Todo later:
-... | NanoCAD-master | cad/src/operations/chem_patterns.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_files.py - provides fileSlotsMixin for MWsemantics,
with file slot methods and related helper methods.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: most other ops_*.py files provide mixin classes for ... | NanoCAD-master | cad/src/operations/ops_files.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
update_select_mode.py - change currentCommand or assy.selwhat or selection
to make them consistent
@author: Bruce
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
Note: this can still have an effect, but ought to b... | NanoCAD-master | cad/src/operations/update_select_mode.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
reposition_baggage.py -- help reposition baggage atoms after real neighbor
atoms have moved
@author: Bruce
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
import math
from utilities import debug_flags
from ge... | NanoCAD-master | cad/src/operations/reposition_baggage.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
ops_atoms.py -- operations on the atoms and/or bonds inside a Part.
These operations generally create or destroy atoms, bondpoints, or real bonds.
Operations specific to single modes (Build, Crystal, Extrude) are not included here.
@version: $Id$
@... | NanoCAD-master | cad/src/operations/ops_atoms.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_copy.py -- general cut/copy/delete operations on selections
containing all kinds of model tree nodes.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
bruce 050507 made this by collecting appropriate ... | NanoCAD-master | cad/src/operations/ops_copy.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_rechunk.py -- operations for changing the way atoms are divided
into chunks, without altering the atoms or bonds themselves.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
bruce 050507 made this by ... | NanoCAD-master | cad/src/operations/ops_rechunk.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
pastables.py -- identifying and using nodes that can be pasted
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
History:
Bruce circa 050121 split these out of existing code in depositMode,
probably by Josh, and ge... | NanoCAD-master | cad/src/operations/pastables.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
undo_UI.py - Undo-related main menu commands other than Undo/Redo themselves
@author: bruce
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
History:
bruce 071025 split this out of undo_manager.py
to rationalize i... | NanoCAD-master | cad/src/operations/undo_UI.py |
# Copyright 2005-2007 Nanorex, Inc. See LICENSE file for details.
"""
bonds_from_atoms.py -- experimental code for inferring bonds from
atom positions and elements alone
@author: Dr. K. Eric Drexler
@version: $Id$
@copyright: 2005-2007 Nanorex, Inc. See LICENSE file for details.
History:
bruce 050906 translated in... | NanoCAD-master | cad/src/operations/bonds_from_atoms.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
ops_debug.py -- various operations/commands for debugging
@author: Bruce
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
import sys, os
import utilities.EndUser as EndUser
from utilities.constants import CAD_SRC_PATH
f... | NanoCAD-master | cad/src/operations/ops_debug.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
ops_connected.py -- operations on the connectivity of bond networks.
@author: Josh, Bruce
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
History:
bruce 050507 made this by collecting appropriate methods (by Josh... | NanoCAD-master | cad/src/operations/ops_connected.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Sponsors.py - sponsors system, exporting PermissionDialog and SponsorableMixin
@author: Will
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
Motivation and design rationale:
We want to recoup some of the costs of... | NanoCAD-master | cad/src/sponsors/Sponsors.py |
NanoCAD-master | cad/src/sponsors/__init__.py | |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
version.py -- provide version information for NanoEngineer-1,
including author list, program name, release info, etc.
@author: Will, Mark
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
NOTE: this is copied and im... | NanoCAD-master | cad/src/utilities/version.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
EndUser.py
Some program features are intended specifically for developers, and
are best left disabled for end users. Examples might be debugging
prints, and the ability to reload a changed module. Such code is
wrapped with a test which calls enab... | NanoCAD-master | cad/src/utilities/EndUser.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
debug_flags.py -- provide the atom_debug developer debugging flag,
and other debugging flags which might be changed at runtime.
TODO: rename atom_debug, and perhaps change some of its uses
into more specific debugging flags.
@author: Bruce
@versio... | NanoCAD-master | cad/src/utilities/debug_flags.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
Initialize.py
Routines for supporting initialization functions.
An initialization function should look like this::
def initialize():
if (Initialize.startInitialization(__name__)):
return
... initialization code here ...
... | NanoCAD-master | cad/src/utilities/Initialize.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
utilities/Log.py -- utility functions related to message logging
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mark wrote these in HistoryWidget.py.
Bruce added quote_html and graymsg.
... | NanoCAD-master | cad/src/utilities/Log.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
constants.py -- constants and trivial functions used in multiple modules.
Everything defined here must require no imports except from builtin
modules or PyQt, and use names that we don't mind reserving throughout NE1.
(At the moment there are some e... | NanoCAD-master | cad/src/utilities/constants.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
parse_utils.py -- utilities for general parsing, and for parsing streams of python tokens.
Also a prototype "description class" which can be used to represent results of parsing a "description".
Also an example grammar, which can be used for parsing... | NanoCAD-master | cad/src/utilities/parse_utils.py |
NanoCAD-master | cad/src/utilities/__init__.py | |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
exception_classes.py -- exception classes for general use
@author: Will
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
Note:
This module can't be called exceptions.py, since that confuses
some other modules whic... | NanoCAD-master | cad/src/utilities/exception_classes.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
GlobalPreferences.py
Routines that test for various global user preferences.
Note: this module is likely to be imported early, and should be
considered a low level support module. As such, importing it should
not drag in much else. As of 2007/09... | NanoCAD-master | cad/src/utilities/GlobalPreferences.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
prefs_constants.py
Constants and utilities related to user preferences,
which need to be defined immediately upon startup.
@author: Mark, Bruce, Ninad
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE file for details.
History:
Mar... | NanoCAD-master | cad/src/utilities/prefs_constants.py |
# Copyright 2005-2009 Nanorex, Inc. See LICENSE file for details.
"""
utilities/Comparison.py - provides same_vals, for correct equality comparison.
See also state_utils.py, which contains the closely related copy_val.
@author: Bruce
@version: $Id$
@copyright: 2005-2009 Nanorex, Inc. See LICENSE file for details.
H... | NanoCAD-master | cad/src/utilities/Comparison.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
qt4transition.py - Useful markers and messages for Qt 4 transition work.
@author: Will
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
import sys
import traceback
import types
import utilities.debug_prefs as ... | NanoCAD-master | cad/src/utilities/qt4transition.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
objectBrowse.py
@author: Will
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
History:
Will wrote this and used it for debugging.
Bruce 071107 split it out of debug.py.
(It has an undefined reference, but presum... | NanoCAD-master | cad/src/utilities/objectBrowse.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
debug.py -- various debugging utilities and debug-related UI code
TODO: split into several modules in a debug package.
(Some of the functions here should logically be moved into ops_debug.py.)
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. Se... | NanoCAD-master | cad/src/utilities/debug.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
icon_utilities.py - helper functions for finding icon and pixmap files
in standard places, and caching them, and handling errors when they're
not found.
$Id$
History: developed by several authors; moved out of Utility.py
by bruce 070831.
WARNING:... | NanoCAD-master | cad/src/utilities/icon_utilities.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
utilities/TimeUtilities.py Stuff related to processing time values.
Not called utilities/time.py because of the python time package.
@author: EricM
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
"""
from datetime import... | NanoCAD-master | cad/src/utilities/TimeUtilities.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
debug_prefs.py -- user-settable flags to help with debugging;
serves as a prototype of general first-class-preference-variables system.
Also contains some general color/icon/pixmap utilities which should be refiled.
@author: Bruce
@version: $Id$
@... | NanoCAD-master | cad/src/utilities/debug_prefs.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
Utilities for formatting various data types as strings.
@author: Eric Messick
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
@license: GPL
"""
def Vector3ToString(v):
"""
Print a 3-vector surround... | NanoCAD-master | cad/src/utilities/Printing.py |
NanoCAD-master | cad/src/cnt/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
NanotubeParameters.py -- Generates Nanotube from parameters.
@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 older file ... | NanoCAD-master | cad/src/cnt/model/NanotubeParameters.py |
NanoCAD-master | cad/src/cnt/model/__init__.py | |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
NanotubeSegment.py - ...
@author: Mark
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
Note: related to DnaStrandOrSegment, from which it was copied and modified.
"""
import foundation.env as env
from utilities.... | NanoCAD-master | cad/src/cnt/model/NanotubeSegment.py |
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