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.
"""
writepovfile.py -- write a Part into a POV-Ray file
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 080917 split this out of graphics/rendering/fileIO.py.
For earlier history see that file's reposi... | NanoCAD-master | cad/src/graphics/rendering/povray/writepovfile.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
povheader.py
@author: Josh
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
#bruce 050413: moved povpoint from 4 other modules (identical copies) into this one.
# (I'd leave it in fileIO except that would cause... | NanoCAD-master | cad/src/graphics/rendering/povray/povheader.py |
NanoCAD-master | cad/src/graphics/rendering/povray/__init__.py | |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
povray.py - routines to support POV-Ray rendering in nE-1.
@author: Mark
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
History:
mark 060529 - Created file to support "View > Raytrace Scene".
bruce 060711 major... | NanoCAD-master | cad/src/graphics/rendering/povray/povray.py |
# Copyright 2004-2007 Nanorex, Inc. See LICENSE file for details.
"""
qutemol.py - provides routines to support QuteMolX as a plug-in.
@author: Mark
@version: $Id$
@copyright: 2004-2007 Nanorex, Inc. See LICENSE file for details.
History:
mark 2007-06-02
- Created file. Much of the plug-in checking code was copied... | NanoCAD-master | cad/src/graphics/rendering/qutemol/qutemol.py |
NanoCAD-master | cad/src/graphics/rendering/qutemol/__init__.py | |
# Copyright 2006-2009 Nanorex, Inc. See LICENSE file for details.
"""
displaymodes.py -- support for new modular display modes.
@author: Bruce
@version: $Id$
@copyright: 2006-2009 Nanorex, Inc. See LICENSE file for details.
Initially this only handles ChunkDisplayModes, which draw entire chunks (even if they are
hi... | NanoCAD-master | cad/src/graphics/display_styles/displaymodes.py |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
CylinderChunks.py -- define a new whole-chunk display mode,
which shows a chunk as a single opaque bounding cylinder of the chunk's color.
@author: Bruce
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
This is mai... | NanoCAD-master | cad/src/graphics/display_styles/CylinderChunks.py |
NanoCAD-master | cad/src/graphics/display_styles/__init__.py | |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
ProteinChunks.py -- defines I{Reduced Protein} display modes.
@author: Piotr
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
piotr 080623: First preliminary version of the protein display style.
piotr 0... | NanoCAD-master | cad/src/graphics/display_styles/ProteinChunks.py |
# Copyright 2008-2009 Nanorex, Inc. See LICENSE file for details.
"""
DnaCylinderChunks.py -- defines I{DNA Cylinder} display mode, which draws
axis chunks as a cylinder in the chunk's color.
@author: Mark, Piotr
@version: $Id$
@copyright: 2008-2009 Nanorex, Inc. See LICENSE file for details.
History:
Mark 2008-02... | NanoCAD-master | cad/src/graphics/display_styles/DnaCylinderChunks.py |
# Copyright 2006-2009 Nanorex, Inc. See LICENSE file for details.
"""
SurfaceChunks.py -- define a new whole-chunk display mode,
which uses Oleksandr's new code to display a chunk as a surface in the chunk's color.
@version: $Id$
@copyright: 2006-2009 Nanorex, Inc. See LICENSE file for details.
See also CylinderChu... | NanoCAD-master | cad/src/graphics/display_styles/SurfaceChunks.py |
# Copyright 2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_drawingset_methods.py -- DrawingSet/CSDL helpers for GLPane_minimal
@author: Bruce
@version: $Id$
@copyright: 2009 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 090219 refactored this out of yesterday's additions to
Part.after_dra... | NanoCAD-master | cad/src/graphics/widgets/GLPane_drawingset_methods.py |
# Copyright 2007-2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_image_methods.py
@author: Bruce
@version: $Id$
@copyright: 2007-2008 Nanorex, Inc. See LICENSE file for details.
History:
bruce 070626 wrote some of these in GLPane.py
bruce 080919 split this into its own file, added new methods & callin... | NanoCAD-master | cad/src/graphics/widgets/GLPane_image_methods.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_mixin_for_DisplayListChunk.py
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
bruce 080910 split this out of class GLPane
"""
from OpenGL.GL import glGenLists
from OpenGL.GL import glNewList
from OpenGL.GL... | NanoCAD-master | cad/src/graphics/widgets/GLPane_mixin_for_DisplayListChunk.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_stereo_methods.py
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
piotr 080515 and 080529 wrote these in GLPane.py
bruce 080912 split this into its own file
"""
import foundation.env as env... | NanoCAD-master | cad/src/graphics/widgets/GLPane_stereo_methods.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_lighting_methods.py
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
bruce 080910 split this out of class GLPane
"""
from graphics.drawing.gl_lighting import glprefs_data_used_by_setup_standard_lights
from... | NanoCAD-master | cad/src/graphics/widgets/GLPane_lighting_methods.py |
# Copyright 2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_csdl_collector.py -- classes for use as a GLPane's csdl_collector
@author: Bruce
@version: $Id$
@copyright: 2009 Nanorex, Inc. See LICENSE file for details.
History:
Bruce 090218 wrote this as part of Part_drawing_frame,
then realized it belon... | NanoCAD-master | cad/src/graphics/widgets/GLPane_csdl_collector.py |
NanoCAD-master | cad/src/graphics/widgets/__init__.py | |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_view_change_methods.py
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
I think Mark wrote most or all of these, in GLPane.py.
bruce 080912 split this out of class GLPane
"""
import time
impo... | NanoCAD-master | cad/src/graphics/widgets/GLPane_view_change_methods.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
DynamicTip.py - supports dynamic, informative tooltips of highlighted objects in GLPane
History:
060817 Mark created dynamicTip class
060818 Ninad moved DynamicTip class into this file DynamicTip.py and added more
@author: Mark, Ninad
@version: $I... | NanoCAD-master | cad/src/graphics/widgets/DynamicTip.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_minimal.py -- common superclass for GLPane-like widgets.
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
History:
bruce 070914 made this to remind us that GLPane and ThumbView
need a common superclass (and... | NanoCAD-master | cad/src/graphics/widgets/GLPane_minimal.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_text_and_color_methods.py - methods for GLPane related to
text rendering or backgroundColor/backgroundGradient
(Maybe it should be renamed GLPane_text_and_background_methods?)
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE ... | NanoCAD-master | cad/src/graphics/widgets/GLPane_text_and_color_methods.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_event_methods.py
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
bruce 080910 split this out of class GLPane
"""
import time
from PyQt4.Qt import QEvent
from PyQt4.Qt import QMouseEvent
from PyQt4.Qt impo... | NanoCAD-master | cad/src/graphics/widgets/GLPane_event_methods.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane.py -- NE1's main model view. A subclass of Qt's OpenGL widget, QGLWidget.
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
NOTE: If you add code to class GLPane, please carefully consider
whether it belongs ... | NanoCAD-master | cad/src/graphics/widgets/GLPane.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
ThumbView.py - a simpler OpenGL widget, similar to GLPane
(which unfortunately has a lot of duplicated but partly modified
code copied from GLPane)
@author: Huaicai
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
"... | NanoCAD-master | cad/src/graphics/widgets/ThumbView.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_highlighting_methods.py - highlight drawing and hit-detection
@author: Bruce
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
bruce 080915 split this out of class GLPane_rendering_methods
Russ added some sh... | NanoCAD-master | cad/src/graphics/widgets/GLPane_highlighting_methods.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_rendering_methods.py
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
bruce 080913 split this out of class GLPane
"""
TEST_DRAWING = False # True ## Debug/test switch. Never check in a True value.
# A... | NanoCAD-master | cad/src/graphics/widgets/GLPane_rendering_methods.py |
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
GLPane_frustum_methods.py
@author: Piotr
@version: $Id$
@copyright: 2008 Nanorex, Inc. See LICENSE file for details.
History:
piotr circa 080331 wrote these in GLPane.py
bruce 080912 split this code into its own file
Explanation of code:
# The fol... | NanoCAD-master | cad/src/graphics/widgets/GLPane_frustum_methods.py |
"""
This directory is for startup code.
$Id$
Note: new startup functionality should be added
to an appropriate file herein, but if possible,
not to startup_before_most_imports.py.
"""
| NanoCAD-master | cad/src/ne1_startup/__init__.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
startup_misc.py - miscellaneous application startup functions
which are free to do whatever imports they need to.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
bruce 050902 made startup_funcs.py by mov... | NanoCAD-master | cad/src/ne1_startup/startup_misc.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
startup_before_most_imports.py - some application startup functions
which need to be run before most imports are done, and which therefore
need to be careful about doing imports themselves.
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LI... | NanoCAD-master | cad/src/ne1_startup/startup_before_most_imports.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
main_startup.py -- provides the startup_script function called by main.py
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
mostly unrecorded, except in cvs;
originally by Josh (under the name atom.py);
lo... | NanoCAD-master | cad/src/ne1_startup/main_startup.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
widgets.py - helpers related to widgets, and some simple custom widgets.
@author: Mark, Ninad, perhaps others
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
TODO:
Probably should be split into a few modules (e.g... | NanoCAD-master | cad/src/widgets/widget_helpers.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
Mixin class to help some of our widgets offer a debug menu.
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
Needs refactoring: [bruce 080104]
- to move the global variable (sim_params_set) elsewhere
(and maybe a... | NanoCAD-master | cad/src/widgets/DebugMenuMixin.py |
# Copyright 2006-2008 Nanorex, Inc. See LICENSE file for details.
"""
StatusBar.py - status bar widgets, AbortHandler, ProgressReporters
@author: Mark, EricM
@version: $Id$
@copyright: 2006-2008 Nanorex, Inc. See LICENSE file for details.
Module classification: [bruce 071228]
It appears to have no requirement of ... | NanoCAD-master | cad/src/widgets/StatusBar.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
menu_helpers.py - helpers for creating or modifying Qt menus
@author: Josh, Bruce
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
History:
Originally by Josh, as part of GLPane.py.
Bruce 050112 moved this code i... | NanoCAD-master | cad/src/widgets/menu_helpers.py |
# Copyright 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
simple_dialogs.py - simple dialogs, collected here for convenience.
TODO: merge some of them into one function.
@author: Bruce, based on code by others
@version: $Id$
@copyright: 2004-2009 Nanorex, Inc. See LICENSE file for details.
"""
from PyQ... | NanoCAD-master | cad/src/widgets/simple_dialogs.py |
"""
GlobalDisplayStylesComboBox.py - Provides a combo box with all the global display
styles.
@author: Mark
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE file for details.
To do (for Mark):
- Add tooltip and What's This text.
- Change "Default Display Style" in the preferences dialog (Mode page) to
... | NanoCAD-master | cad/src/widgets/GlobalDisplayStylesComboBox.py |
NanoCAD-master | cad/src/widgets/__init__.py | |
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
widget_controllers.py - miscellaneous widget-controller classes
@author: bruce
@version: $Id$
@copyright: 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
# a widget expr controller for a collapsible GroupBox
# (different default style ... | NanoCAD-master | cad/src/widgets/widget_controllers.py |
# Copyright 2004-2008 Nanorex, Inc. See LICENSE file for details.
"""
NE1_QToolBar.py - Main NE1 toolbar class, which subclasses Qt's QToolBar
class. All NE1 main window toolbars should use this class (except for the
Command Toolbar).
@author: Mark Sims
@version: $Id$
@copyright: 2004-2008 Nanorex, Inc. See LICENSE ... | NanoCAD-master | cad/src/widgets/NE1_QToolBar.py |
# Copyright 2005-2008 Nanorex, Inc. See LICENSE file for details.
"""
prefs_widgets.py -- Utilities related to both user preferences and Qt widgets.
Note: also includes some code related to "connect with state"
which should be refiled.
@author: Bruce
@version: $Id$
@copyright: 2005-2008 Nanorex, Inc. See LICENSE fil... | NanoCAD-master | cad/src/widgets/prefs_widgets.py |
# Copyright 2007 Nanorex, Inc. See LICENSE file for details.
"""
NE1ToolBar.py - Variant of QToolBar in which the toolbar border is not rendered
@author: Ninad
@version: $Id$
@copyright: 2007 Nanorex, Inc. All rights reserved.
History:
File created on 20070507. There could be more than one NE1Toolbar classes
(subc... | NanoCAD-master | cad/src/widgets/NE1ToolBar.py |
#!/usr/bin/python
# Copyright 2005-2006 Nanorex, Inc. See LICENSE file for details.
"""runtest.py description.test [--generate]
runs the described test and concatenates the results
to stdout (after removing lines which vary inconsequentially (e.g. dates)
if --generate is given, the results are written to $base.out,... | NanoCAD-master | sim/src/runtest.py |
#!/usr/bin/python
# Copyright 2006 Nanorex, Inc. See LICENSE file for details.
# usage:
#
# mergemmpxyz.py file.mmp file.xyz > merged.mmp
#
import sys
import re
if len(sys.argv) != 3:
print >>sys.stderr, "usage: mergemmpxyz.py file.mmp file.xyz > merged.mmp"
sys.exit(1)
atomLinePattern = re.compile(r"^(ato... | NanoCAD-master | sim/src/mergemmpxyz.py |
#!/usr/bin/python
# Copyright 2005-2006 Nanorex, Inc. See LICENSE file for details.
"""run regression tests
how to make a regression test:
Inside one of the directories listed below, you need to create three files.
I'm going to call them test_000X.* here. Just number them sequentially
although that doesn't really ... | NanoCAD-master | sim/src/regression.py |
#! /usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
from string import *
import re
import os
import sys
from math import sqrt
findBondNamePattern = re.compile(r"^(\S+)\s+(.*)$")
bondNamePattern = re.compile(r"(.*)([-=+@#])(.*)$")
parameterPattern = re.compile(r"^([^=]+)\s*\=\s*(\S+)\... | NanoCAD-master | sim/src/stretch.py |
# Copyright 2004-2006 Nanorex, Inc. See LICENSE file for details.
"""Vectors, Quaternions, and Trackballs
Vectors are a simplified interface to the Numeric arrays.
A relatively full implementation of Quaternions.
Trackball produces incremental quaternions using a mapping of the screen
onto a sphere, tracking the curs... | NanoCAD-master | sim/src/VQT.py |
# Copyright 2005-2006 Nanorex, Inc. See LICENSE file for details.
'''
setup.py (for sim code)
Distutils setup file -- tells distutils how to rebuild our custom extension modules.
NOTE: very similar to cad/src/setup.py in the cad cvs module.
Some comments and docstrings (more relevant to cad than to sim)
appear only ... | NanoCAD-master | sim/src/setup.py |
#! /usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
from string import *
import re
import os
import sys
from math import sqrt
findBondNamePattern = re.compile(r"^(\S+)\s+(.*)$")
bondNamePattern = re.compile(r"(.*)([-=+@#])(.*)([-=+@#])(.*)$")
parameterPattern = re.compile(r"^([^=]+)\... | NanoCAD-master | sim/src/bend.py |
#!/usr/bin/env python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
"""
Users place files into the INPUT directory and run batchsim.
After a while, results appear in the OUTPUT directory.
Each time batchsim is run, it scans the INPUT directory. Each .mmp
file it finds is moved into a consecu... | NanoCAD-master | sim/src/batchsim.py |
#!/usr/bin/python
# Copyright 2005-2006 Nanorex, Inc. See LICENSE file for details.
# usage:
#
# onetest.py <test_name> [args for tests.py]
#
# runs a single regression test by name
#
import sys
import tests
class Main(tests.Main):
def main(self, args):
self.theTest = args[0]
tests.Main.main(sel... | NanoCAD-master | sim/src/onetest.py |
#!/usr/bin/python
# Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
# usage:
#
# merge.parameters.py existingParameterFile newParameterFiles...
#
# creates existingParameterFile.new
#
import sys
import re
leadingWhitespacePattern = re.compile(r"^\s*")
trailingWhitespacePattern = re.compile(r"\s*$")
... | NanoCAD-master | sim/src/merge.parameters.py |
#!/usr/bin/python
# Copyright 2005-2006 Nanorex, Inc. See LICENSE file for details.
"""Regression and QA test script for the simulator
$Id$
Test cases will generally arrive as MMP files with QM-minimized atom
positions (or for QM dynamics simulations, sequences of atom
positions). These should be translated into *.... | NanoCAD-master | sim/src/tests.py |
# Copyright 2006 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, k, k... | NanoCAD-master | sim/src/distutils_compile_options.py |
# Copyright 2006 Nanorex, Inc. See LICENSE file for details.
__author__ = "Will"
import sys, os, Pyrex
def find_pyrexc():
if sys.platform == 'darwin':
# MacOS
x = os.path.dirname(Pyrex.__file__).split('/')
y = '/'.join(x[:-4] + ['bin', 'pyrexc'])
if os.path.exists(y):
... | NanoCAD-master | sim/src/findpyrex.py |
# Copyright 2006 Nanorex, Inc. See LICENSE file for details.
import sys
import time
import os.path
if sys.platform == "darwin":
extra_compile_args = [ "-O" ]
else:
extra_compile_args = [ ]
DISTUTILS_FLAGS = None
if sys.platform != "win32":
from distutils.core import setup
from distutils.extension im... | NanoCAD-master | sim/src/makehelp.py |
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
"""Physical units for calculations
Physical quantities are represented here as dictionaries. One key is
'coefficient', the other keys are metric units like 'm', 'sec', 'kg'.
The value for each dimension key is the power to which that unit is
raised. For ins... | NanoCAD-master | sim/src/experimental/units.py |
#!/usr/bin/python
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
# Refer to http://tinyurl.com/8zl86, the 22 Dec discussion about
# rotary motors.
from math import pi, cos, sin
import random
import units
import sys
DEBUG = False
DT = 1.e-16 * units.second
SPRING_STIFFNESS = 10 * units.newton / units.... | NanoCAD-master | sim/src/experimental/rotaryMotor.py |
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
"""Usage:
Type 'python interp.py c' to generate C code.
Type 'python interp.py gnuplot' to see graphs of the approximations.
Type 'python interp.py quadratic c' to generate C code for a
quadratic interpolator.
Type 'python interp.py linear c' to generate ... | NanoCAD-master | sim/src/experimental/interp.py |
# Copyright 2004-2005 Nanorex, Inc. See LICENSE file for details.
"""
VQT.py
Vectors, Quaternions, and Trackballs
Vectors are a simplified interface to the Numeric arrays.
A relatively full implementation of Quaternions.
Trackball produces incremental quaternions using a mapping of the screen
onto a sphere, tracking... | NanoCAD-master | sim/src/experimental/josh_dev/VQT.py |
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
from bondage import *
e,p,b = readmmp('ethane.mmp')
bondsetup(b)
dt=1e-16
massacc=array([dt*dt/elmass[x] for x in e])
n=p+massacc*force(p)
x= os.times()
## print 'running...',
## for i in xrange(100000):
## o=p
## p=n
## n=2*p-o+massacc*forc... | NanoCAD-master | sim/src/experimental/josh_dev/test.py |
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
from Numeric import *
from VQT import *
from string import *
import re
keypat = re.compile("(\S+)")
molpat = re.compile("mol \(.*\) (\S\S\S)")
atompat = re.compile("atom (\d+) \((\d+)\) \((-?\d+), (-?\d+), (-?\d+)\)")
def readmmp(fname):
pos = []
... | NanoCAD-master | sim/src/experimental/josh_dev/readmmp.py |
#! /usr/bin/python
# Copyright 2005 Nanorex, Inc. See LICENSE file for details.
from Numeric import *
from VQT import *
from string import *
import re
import os
import sys
keypat = re.compile("(\S+)")
molpat = re.compile("mol \(.*\) (\S\S\S)")
atompat = re.compile("atom (\d+) \((\d+)\) \((-?\d+), (-?\d+), (-?\d+)\)"... | NanoCAD-master | sim/src/experimental/josh_dev/bondage.py |
#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.c... | NanoCAD-master | sim/src/tests/heteroatom_organics/XyzFile.py |
#!/usr/bin/python
import os
import sys
import MmpFile
import XyzFile
damianFiles = map(lambda x: x.strip(),
open("damianFiles").readlines())
for df in damianFiles:
prefix = df[:df.index(".")]
testPrefix = "test_" + prefix
damianMmp = MmpFile.MmpFile()
damianMmp.read(df)
# Gener... | NanoCAD-master | sim/src/tests/heteroatom_organics/CreateTests.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/heteroatom_organics/MmpFile.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H... | NanoCAD-master | sim/src/tests/heteroatom_organics/Atom.py |
#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.c... | NanoCAD-master | sim/src/tests/amino_acids/XyzFile.py |
#!/usr/bin/python
import os
import sys
import MmpFile
import XyzFile
damianFiles = ("ala_l_aminoacid.mmp",
"arg_l_aminoacid.mmp",
"asn_l_aminoacid.mmp",
"asp_l_aminoacid.mmp",
"cys_l_aminoacid.mmp",
"gln_l_aminoacid.mmp",
"glu_l... | NanoCAD-master | sim/src/tests/amino_acids/CreateTests.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/amino_acids/MmpFile.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H... | NanoCAD-master | sim/src/tests/amino_acids/Atom.py |
#!/usr/bin/python
"""This script merges an MMP file with an XYZ file, by replacing the
MMP file's atom positions with the positions from the XYZ file,
producing a new MMP file with the XYZ positions. The merged MMP file
is written to standard output.
Usage:
xyzmerge.py input1.mmp input2.xyz > output.mmp
$Id$
"""... | NanoCAD-master | sim/src/tests/scripts/xyzmerge.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import os
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def... | NanoCAD-master | sim/src/tests/scripts/XyzFile.py |
#!/usr/bin/python
"""This script examines the structure in an MMP file to enumerate all
the bond length terms and bond angle terms for the structure. If an
XYZ file is given, use the position information from the XYZ file,
otherwise use position information from the MMP file. Bond lengths are
in angstroms, bond angles... | NanoCAD-master | sim/src/tests/scripts/findterms.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/scripts/MmpFile.py |
#!/usr/bin/python
"""This script translates an MMP file to an XYZ file.
Usage:
mmp2xyz.py input.mmp > output.xyz
$Id$
"""
__author__ = "Will"
import sys
from MmpFile import MmpFile
from XyzFile import XyzFile
import Atom
try:
mmpInputFile = sys.argv[1]
xyz = XyzFile()
mmp = MmpFile()
mmp.read... | NanoCAD-master | sim/src/tests/scripts/mmp2xyz.py |
#!/usr/bin/python
"""A common Atom definition to be shared by the classes for various
molecule file formats including MMP and XYZ. This will make it easy to
move information back and forth between formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
... | NanoCAD-master | sim/src/tests/scripts/Atom.py |
#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.c... | NanoCAD-master | sim/src/tests/floppy_organics/XyzFile.py |
#!/usr/bin/python
import os
import sys
import MmpFile
import XyzFile
damianFiles = filter(lambda x: x,
os.popen("ls C*.mmp").read().split("\n"))
for df in damianFiles:
prefix = df[:df.index(".")]
testPrefix = "test_" + prefix
damianMmp = MmpFile.MmpFile()
damianMmp.read(df)
... | NanoCAD-master | sim/src/tests/floppy_organics/CreateTests.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/floppy_organics/MmpFile.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H... | NanoCAD-master | sim/src/tests/floppy_organics/Atom.py |
#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.c... | NanoCAD-master | sim/src/tests/rigid_organics/XyzFile.py |
#!/usr/bin/python
import os
import sys
import MmpFile
import XyzFile
damianFiles = filter(lambda x: x,
os.popen("ls C*.mmp").read().split("\n"))
for df in damianFiles:
prefix = df[:df.index(".")]
testPrefix = "test_" + prefix
damianMmp = MmpFile.MmpFile()
damianMmp.read(df)
... | NanoCAD-master | sim/src/tests/rigid_organics/CreateTests.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/rigid_organics/MmpFile.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H... | NanoCAD-master | sim/src/tests/rigid_organics/Atom.py |
#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.c... | NanoCAD-master | sim/src/tests/singlebond_stretch/XyzFile.py |
#!/usr/bin/python
import os
import sys
import MmpFile
import XyzFile
damianFiles = map(lambda x: x.strip(),
open("damianFiles").readlines())
for df in damianFiles:
prefix = df[:df.index(".")]
testPrefix = "test_" + prefix
damianMmp = MmpFile.MmpFile()
damianMmp.read(df)
# Gener... | NanoCAD-master | sim/src/tests/singlebond_stretch/CreateTests.py |
#!/usr/bin/python
"""Grab one of Damian's minimized MMP files, perturb each atom's
position by some fraction of an angstrom, write out the result as
another MMP file, which becomes an input file for the test.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import Atom
class MmpFile:
"... | NanoCAD-master | sim/src/tests/singlebond_stretch/MmpFile.py |
#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H... | NanoCAD-master | sim/src/tests/singlebond_stretch/Atom.py |
#! /usr/bin/python
import os
import sys
import re
from Numeric import *
from LinearAlgebra import *
nampat = re.compile("([A-Z][a-z]?[+=-][A-Z][a-z]?[+=-][A-Z][a-z]?)\.1\.log")
thetapat = re.compile(" INPUT CARD\> *theta *= *([\d\.-]+)")
engpat = re.compile(" FINAL U-B3LYP ENERGY IS +([\d\.-]+)")
hobond = re.compile(... | NanoCAD-master | sim/src/parameters/collang.py |
#! /usr/bin/python
from Numeric import *
from VQT import *
from LinearAlgebra import *
from string import *
import re
import os
import sys
from struct import pack
from stat import *
datapat = re.compile("\ \$DATA")
gradpat = re.compile("\ \$GRAD")
hesspat = re.compile(" \$HESS")
vecpat = re.compile(" \$VEC")
endpat =... | NanoCAD-master | sim/src/parameters/minimize.py |
# Copyright (c) 2004 Nanorex, Inc. All rights reserved.
"""
VQT.py
Vectors, Quaternions, and Trackballs
Vectors are a simplified interface to the Numeric arrays.
A relatively full implementation of Quaternions.
Trackball produces incremental quaternions using a mapping of the screen
onto a sphere, tracking the curso... | NanoCAD-master | sim/src/parameters/VQT.py |
#! /usr/bin/python
from string import *
import re
import os
import sys
from math import sqrt
parmpat = re.compile("([A-Z][a-z]?)([\+=\-@#])([A-Z][a-z]?) +Ks= *([\d\.]+) +R0= *([\d\.]+) +De= *([\d\.]+)")
commpat = re.compile("#")
elmnts=[("H", 1, 1.6737),
("He", 2, 6.646),
("Li", 3, 11.525),... | NanoCAD-master | sim/src/parameters/parmlist.py |
#! /usr/bin/python
from Numeric import *
import sys
import re
recpat = re.compile(" *([\d\.E+-]+) +([\d\.E+-]+) +([\d\.E+-]+)")
f=open(sys.argv[1])
card = f.readline()
m=recpat.match(card)
v=array(map(float,(m.group(1),m.group(2), m.group(3))))
while 1:
card = f.readline()
if len(card)<3: break
m=recpat... | NanoCAD-master | sim/src/parameters/dx.py |
#! /usr/bin/python
from math import *
r0=1
De=1
ks=100
beta = sqrt(ks/(2*De))
def morse(r):
return De*(1-exp(-sqrt(ks/(2*De))*(r-r0)))**2
def lipp(r):
return De*(1-exp(-ks*r0*(r-r0)**2/(2*De*r)))
def lippmor(r):
if r<r0: return morse(r) - De
else: return lipp(r) - De
def flp(x):
k1 ... | NanoCAD-master | sim/src/parameters/lippmor.py |
#! /usr/bin/python
from Numeric import *
from VQT import *
from LinearAlgebra import *
from string import *
import re
import os
import sys
from struct import pack
from stat import *
datapat = re.compile("\ \$DATA")
gradpat = re.compile("\ \$GRAD")
hesspat = re.compile(" \$HESS")
vecpat = re.compile(" \$VEC")
endpat =... | NanoCAD-master | sim/src/parameters/morgames.py |
#! /usr/bin/python
import os
import sys
import re
from string import *
from math import sqrt
leftpat=re.compile('([A-Z][a-z]?)([=+#@-])\.moi$')
rightpat=re.compile('([=+#@-])([A-Z][a-z]?)\.moi$')
centerpat=re.compile('([=+#@-])([A-Z][a-z]?)([=+#@-])\.moi$')
thetapat=re.compile(" *theta *= *([\d\.]+)")
parmpat = re.... | NanoCAD-master | sim/src/parameters/genang.py |
#!/usr/bin/env python3
import argparse
import random
import os
import numpy as np
import torch
from habitat import logger
from habitat_baselines.common.baseline_registry import baseline_registry
import habitat_extensions # noqa: F401
import vlnce_baselines # noqa: F401
from vlnce_baselines.config.default import get... | InternVideo-main | Downstream/Visual-Language-Navigation/run.py |
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