text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# Copyright (C) 2012,2013,2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the te... | kkreis/espressopp | src/standard_system/LennardJones.py | Python | gpl-3.0 | 5,625 | [
"ESPResSo"
] | 705214160bc1c1ac5f5e4fd88b541f0b5c0e9816b014f82fc486ca9c4705b7c1 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/netcdf-cxx4/package.py | Python | lgpl-2.1 | 1,757 | [
"NetCDF"
] | ba0f37b6bb365d4ac41d1a760cf9803d347b4be73bcf44e16285f4c941da48b0 |
subway_data = [
{'lat':40.799494,'lng':-73.968308,'lines':'1', 'stop':'103rd St'},
{'lat':40.790697,'lng':-73.947472,'lines':'6', 'stop':'103rd St'},
{'lat':40.749804,'lng':-73.862436,'lines':'7', 'stop':'103rd St'},
{'lat':40.796185,'lng':-73.961448,'lines':'BC', 'stop':'103rd St'},
{'la... | MultiRRomero/manhattan-map | la-data/subway_data.py | Python | mit | 34,003 | [
"COLUMBUS"
] | bc2920e7652a6d9cf51c01152a4c34ff8abb103fc81bca9d3ed3531eac15df83 |
# $Id$
#
# Copyright (C) 2004-2005 Rational Discovery LLC
# All Rights Reserved
#
import os
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import ExplicitBitVect
from rdkit.ML.Data import DataUtils
from rdkit.ML.NaiveBayes import CrossValidate
from rdkit.ML.NaiveBayes.ClassificationModel import ... | ptosco/rdkit | rdkit/ML/NaiveBayes/UnitTestNB.py | Python | bsd-3-clause | 7,351 | [
"RDKit"
] | 51f7622a1343b5ba33b35af14ad6dac016c7b74522af04acb9b1bd74f5635853 |
# -*- coding: utf-8 -*-
#
# if_curve.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# ... | terhorstd/nest-simulator | pynest/examples/if_curve.py | Python | gpl-2.0 | 5,831 | [
"NEURON"
] | 344d82de68869450161210d216f339550147bf145df15f3615c05a75856dbcb0 |
# Copyright 2022 The Magenta Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | magenta/magenta | magenta/models/piano_genie/configs.py | Python | apache-2.0 | 11,722 | [
"Gaussian"
] | 11a3f5531b625b17e05926d0bff666f90c937c471c10bcda036aeae6415f6245 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import numpy as np
import itertools
from pymatgen.analysis.structure_matcher import StructureMatcher, \
ElementComparator, FrameworkComparator, OrderDisorderElementCo... | fraricci/pymatgen | pymatgen/analysis/tests/test_structure_matcher.py | Python | mit | 51,414 | [
"pymatgen"
] | 2e6ed9c1b7ac832a6006717d697f32ab3dfd365add6b3410260fee9145043ab3 |
# ------------------------------------------------------------------------------
# Copyright (c) 2010-2013, EVEthing team
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of... | cmptrgeekken/evething | thing/tasks/archive/assetlist.py | Python | bsd-2-clause | 8,895 | [
"VisIt"
] | 206c79d47d0038f1f35994defee81c9172ad40238fe0ee1b1a9bb5c1677d40b1 |
#
# ------------------------------------------------------------
# Copyright (c) All rights reserved
# SiLab, Institute of Physics, University of Bonn
# ------------------------------------------------------------
#
# E221 multiple spaces before operator
# flake8: noqa
import logging
from basil.HL.HardwareLayer imp... | SiLab-Bonn/basil | basil/HL/MIO_PLL.py | Python | bsd-3-clause | 8,539 | [
"CRYSTAL"
] | 89e4e5e38a022cb4a9bb72acae194e6b83d0a26f3beb967d2a25e99ebc4b8ac0 |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Generic functionality useful for all gene representations.
This module contains classes which can be used for all the different
types of patterns... | zjuchenyuan/BioWeb | Lib/Bio/NeuralNetwork/Gene/Pattern.py | Python | mit | 9,024 | [
"Biopython"
] | ba07b7792d4aec96a1b3db004078c798541a135fde459e242a26a774b6d80a3b |
#! /usr/bin/python
# Version info: $Id: NeuralNetwork3D.py 314 2011-07-11 08:50:50Z zunzun.com $
'''
# the pythonequations base is located up one directory from the top-level examples
# directory, go up one directory in the path from there for the import to work properly
import sys, os
if os.path.join(sys.path[0][:s... | JMoravec/unkRadnet | zunzunCode/pythonequations/Examples/SimpleExamples/NeuralNetwork3D.py | Python | bsd-3-clause | 2,824 | [
"NEURON"
] | d9a7c9999e8180ca735f96e4249235aa0bcf3a72b8cc223c50f24cb9a2ef497b |
# LAMMPS Documentation Utilities
#
# Copyright (C) 2015 Richard Berger
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | SGenheden/lammps | doc/utils/converters/tests/test_txt2rst.py | Python | gpl-2.0 | 17,407 | [
"LAMMPS"
] | 5587c2dead6d7c34833c3c748ca6f53d19eee7fb520451a70010c8c73479a085 |
from zds.forum.models import Forum
def get_authorized_forums(user):
"""
Find forums the user is allowed to visit.
:param user: concerned user.
:return: authorized_forums
"""
forums_pub = Forum.objects.filter(groups__isnull=True).all()
if user and user.is_authenticated:
forums_priv... | ChantyTaguan/zds-site | zds/utils/templatetags/authorized_forums.py | Python | gpl-3.0 | 550 | [
"VisIt"
] | b27afb23f5588f293aaebe2ac63c58af3f5f2c753840a2e7dbae54fb6c8132ad |
# ******************************************************************************
# Copyright (c) 2015 UT-Battelle, LLC.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the Eclipse Public License v1.0
# which accompanies this distribution, and is available at
# ... | wo-amlangwang/ice | org.eclipse.ice.installer/Install_ICE.py | Python | epl-1.0 | 18,733 | [
"VisIt"
] | 9b5453bec654a1b3ed24b13a33ba8714b4ca33ceaa9453355c187b788d323b3c |
# -*-python-*-
#
# Copyright (C) 1999-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/vclib/ccvs/rcsparse/default.py | Python | agpl-3.0 | 4,757 | [
"VisIt"
] | 418237265c1b3261000f68de18c5c96a2d9d578cec770a0556c3aa612b1388a0 |
"""
Dist Plot Bokeh
===============
_thumb: .2, .8
"""
import bokeh.plotting as bkp
import numpy as np
from bokeh.layouts import row
import arviz as az
a = np.random.poisson(4, 1000)
b = np.random.normal(0, 1, 1000)
figure_kwargs = dict(height=500, width=500, output_backend="webgl")
ax_poisson = bkp.figure(**figure... | arviz-devs/arviz | examples/bokeh/bokeh_plot_dist.py | Python | apache-2.0 | 638 | [
"Gaussian"
] | b40b5992e47f77c7285c0a9bb51d40f8589411ff9750586db6acad3381e02b27 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/range/range.py | Python | lgpl-2.1 | 854 | [
"MOOSE"
] | 742a53beae7305989f03c3b1d9d9637e4891d00dcc8c48783bc1b34a00ddf09a |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | sillvan/hyperspy | hyperspy/gui/egerton_quantification.py | Python | gpl-3.0 | 17,981 | [
"Gaussian"
] | f46d22c78f81fbb604d267bca39d7895fb1599228921c5ffc28ea2243af6e771 |
import matplotlib.pyplot as plt
import matplotlib.gridspec as gs
import numpy as np
import matplotlib.patches as patches
import sys
from matplotlib import rc, cm
from matplotlib.colors import LinearSegmentedColormap
from astroML.density_estimation import XDGMM
#PARAMETROS
file1 = sys.argv[1] #Archivo con los PM
p... | astrofelipe/MP2015 | hess.py | Python | mit | 4,276 | [
"Gaussian"
] | 76b3f84067476de3f8454f9b801c8b633c1373defcdf2921ad32a01029b0ebb0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
logger = logging.getLogger(__name__)
import numpy as nm
from ruamel.yaml import YAML
import argparse
import sys
import numpy as np
import vtk
import vtk.vtkCommonDataModelPython
from scipy.interpolate import InterpolatedUnivariateSpline
from . import tree
... | mjirik/teigen | teigen/tb_vtk.py | Python | apache-2.0 | 42,829 | [
"VTK"
] | 130203bb9af32e642e8259edd16ae5cb11f4e50013ae1f79d6ea77d8b5beb46a |
print("Loading...")
import os
import io
import sys
import cmd
import types
import base64
import codecs
import random
import getpass
import textwrap
import readline
import argparse
import traceback
from functools import wraps,partial
from datetime import datetime,timedelta
import code
import importlib
try:
import lu... | Earthnuker/Universe | main.py | Python | mit | 48,981 | [
"VisIt"
] | 71af51392673d4535fee021acc86698b3e741e729c2f7ee8d2eb5dbdd79ce430 |
"""
===================================================
Segmenting the picture of a raccoon face in regions
===================================================
This example uses :ref:`spectral_clustering` on a graph created from
voxel-to-voxel difference on an image to break this image into multiple
partly-homogeneous... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/cluster/plot_face_segmentation.py | Python | mit | 2,838 | [
"Brian"
] | 5ea0d26f5a71708448ad694360965ca5bb9b46161c05ff351f28cc6f77a059f5 |
# mgui.py ---
#
# Filename: mgui.py
# Description:
# Author:
# Maintainer:
# Created: Mon Nov 12 09:38:09 2012 (+0530)
# Version:
# Last-Updated: Fri Oct 30 11:54:33 2015 (+0530)
# By: Harsha
# Update #: 1338
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# The gui driver
#
#
# Change log:
#
#
... | dilawar/moose-full | moose-gui/mgui.py | Python | gpl-2.0 | 55,653 | [
"MOOSE",
"NEURON"
] | ee9612c384181af01b926a74a656e33a48803f46dc3aff4df4c7d7dd61c26d6e |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | amjames/psi4 | psi4/share/psi4/scripts/ixyz2database.py | Python | lgpl-3.0 | 18,061 | [
"Psi4"
] | 15374413d580963b4250ceca5b24843537dbbf96219985591253abbbcb54ec30 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Development script to test the algorithms of all the model coordination environments
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "2.0"
__maintainer__ = "David... | vorwerkc/pymatgen | dev_scripts/chemenv/test_algos_all_geoms.py | Python | mit | 4,690 | [
"pymatgen"
] | 67ec80c0912fce197c75754c26a38755db87c2ad20052f5aedf138047538f203 |
import peel
import pymolecule
# The purpose of this test case is to show the versatility of the string-input scoring functions.
# Users can use functions from the numpy package to construct score components.
# Please note that these functions are meant to show the versatility of the software
# and do not have any act... | j-wags/POVME | binana/tests/algebra_func_input/funcInputTest.py | Python | gpl-3.0 | 1,937 | [
"VMD"
] | a54c1425c11ab765a51ebc706beb92abff4b55145adb6f576d86ba93175f4c46 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/apps/annotate.py | Python | bsd-3-clause | 3,185 | [
"NEURON"
] | 39755ce6921cfaf50a6e34f837acf5d951e9797b845d84c2051b94798f7ad7f7 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/util/tty/__init__.py | Python | gpl-2.0 | 4,269 | [
"Psi4"
] | 1ffe8ae3c5677d158903d5d5fd24d7bdebd7408a7f3ae729fc4dc1ac5a098cbb |
# -*- coding: utf-8 -*-
from __future__ import print_function, unicode_literals
import json
import logging
import numbers
import phonenumbers
import regex
import time
import urllib2
import re
import six
from collections import OrderedDict, defaultdict
from datetime import timedelta
from decimal import Decimal
from dj... | tsotetsi/textily-web | temba/flows/models.py | Python | agpl-3.0 | 259,436 | [
"VisIt"
] | bdf9294ef6db98d39b92fb0aa21b799b591e3808ddd84b75c736ce2af678824f |
"""Utility functions for plotting M/EEG data."""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | teonlamont/mne-python | mne/viz/utils.py | Python | bsd-3-clause | 104,908 | [
"Mayavi"
] | afc65b29ed18b5e36c49de15cd398f9db5a51579da69706157fad046f9c4ecb1 |
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exc import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
import sys, logging
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
log = lo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0020_library_upload_job.py | Python | gpl-3.0 | 5,184 | [
"Galaxy"
] | 680e768e4b73bb4631cfc7af806c777c70d19c650b4358a95a8b30afa30fb488 |
# COPYRIGHT 2007 BY BBN TECHNOLOGIES CORP.
# BY USING THIS SOFTWARE THE USER EXPRESSLY AGREES: (1) TO BE BOUND BY
# THE TERMS OF THIS AGREEMENT; (2) THAT YOU ARE AUTHORIZED TO AGREE TO
# THESE TERMS ON BEHALF OF YOURSELF AND YOUR ORGANIZATION; (3) IF YOU OR
# YOUR ORGANIZATION DO NOT AGREE WITH THE TERMS OF THIS AGRE... | Juicechuan/AMR_graph | camr_conversion/on/corpora/proposition.py | Python | mit | 116,017 | [
"ASE"
] | 9b5fcdf419db04f774030059e443ef53d00a256dd5fbf4b7a8c5595ed36bac5d |
#!/usr/bin/env python2
# This file is part of the OpenMV project.
#
# Copyright (c) 2013-2021 Ibrahim Abdelkader <iabdalkader@openmv.io>
# Copyright (c) 2013-2021 Kwabena W. Agyeman <kwagyeman@openmv.io>
#
# This work is licensed under the MIT license, see the file LICENSE for details.
#
# This script augments an image... | kwagyeman/openmv | tools/augment_images.py | Python | mit | 3,289 | [
"Gaussian"
] | ed90793826d1599e8019b812744831b3ccbbc911c28a4c488d05a9a7486a0d97 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_sellablepricedialog.py | Python | gpl-2.0 | 2,262 | [
"VisIt"
] | 537fa4040e922aa7b44375131b3af1050638337a9cf4ecbf129f66562b7dc37f |
#-------------------------------------------------------------------------------
# . File : GenerateComponent.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#-------------------------------------------... | mfx9/MolarisTools | examples/AminoComponentFromPDB/GenerateComponent.py | Python | gpl-3.0 | 1,028 | [
"Avogadro"
] | 13fc7f6a10324ae2445357abb800bca0ffbf90a5bf79f6ef51696c5189476ff5 |
# -*- coding: utf-8 -*-
"""
sphinx.pycode
~~~~~~~~~~~~~
Utilities parsing and analyzing Python code.
:copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import sys
from os import path
from sphinx import package_dir
from sphinx.errors impor... | havard024/prego | venv/lib/python2.7/site-packages/sphinx/pycode/__init__.py | Python | mit | 13,077 | [
"VisIt"
] | ef4bb68c67c93c835e849082f1b0b76448e1c284331e686999ff030a93a73122 |
# coding: utf-8
# <img src="images/JHI_STRAP_Web.png" style="width: 150px; float: right;">
# # 03b - An Example Reproducible Document
# ## Table of Contents
#
# 1. [Introduction](#introduction)
# 2. [Python Imports/Startup](#python_imports)
# 3. [Biological Motivation](#motivation)
# 4. [Load Sequence](#load_sequen... | widdowquinn/Teaching-SfAM-ECS | workshop/data/reproducible/example_output/example.py | Python | mit | 18,537 | [
"BLAST",
"Biopython"
] | 5fd33d8df69a61bbe5c7bba53964e33339cdde440c011fa6d1b26ec96e85e83f |
#!/usr/bin/env python
# $ vtkpython TestImagePlaneWidget.py --help
# provides more details on other options.
import os
import os.path
import vtk
from vtk.test import Testing
class TestImagePlaneWidget(Testing.vtkTest):
def testBug(self):
# Uncomment the next line if you want to run this via
# `gd... | ashray/VTK-EVM | Interaction/Widgets/Testing/Python/TestImagePlaneWidget.py | Python | bsd-3-clause | 5,226 | [
"VTK"
] | d2338f20feaf24a17adb39b79bba70cdf20aaa361da0b96c353b1952b6c6a306 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module provides classes to create phase diagrams.
"""
from six.moves import filter
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "2.0"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue... | rousseab/pymatgen | pymatgen/phasediagram/pdmaker.py | Python | mit | 18,349 | [
"pymatgen"
] | 9b2bcc962b526726dd2582e063caabb0b9dd721e513cd4945de74fac87d9ebdd |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | Chuban/moose | python/MooseDocs/tests/app_syntax/test_app_syntax.py | Python | lgpl-2.1 | 9,411 | [
"MOOSE"
] | 19a73e64ef15393c8d8e18708610f2c3f5cd768a99a43bc5094c0c48d7beece1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrapper for netCDF readers."""
import os.path
import warnings
import numpy as np
from collections import OrderedDict
from monty.dev import requires
from monty.collections import AttrDict
from monty.functool... | dongsenfo/pymatgen | pymatgen/io/abinit/netcdf.py | Python | mit | 17,189 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 0de83135f75a11074eb3cd343b7338660b95702508b98da5c1fc8b5f2351f807 |
import os
from ase.test import NotAvailable
try:
elk_species_path = os.getenv('ELK_SPECIES_PATH')
if elk_species_path == None:
raise NotAvailable('ELK_SPECIES_PATH not defined')
except NotAvailable:
raise NotAvailable('ELK required')
import numpy as np
from ase.tasks.main import run
atoms, task... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/elk/elk_cmdline.py | Python | gpl-2.0 | 450 | [
"ASE",
"Elk"
] | e9b0eec66235f1261aede5d6d72e1f39047b89ee25a4490aea7857cd60419398 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.molecular_orbitals import MolecularOrbitals
test_case = MolecularOrbitals('NaCl')
class MolecularOrbitalTestCase(PymatgenTes... | dongsenfo/pymatgen | pymatgen/core/tests/test_molecular_orbitals.py | Python | mit | 1,431 | [
"pymatgen"
] | 211d2fa86dccb2b043bc90c9ea73c098d286eafa82356a2f1b7f1addcc584ee0 |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
end = my_traj.find('.pdb')
fout_angle = my_traj[0:end] + '_betafloor_glob_angle.dat'
c = u.selectAtoms("(segid A and resid 4:77) or (segid B and resid ... | demharters/git_scripts | angle_betafloor_glob_mhcii.py | Python | apache-2.0 | 932 | [
"MDAnalysis"
] | 8135aa184c6a0a244f04abaa141044d03329f1a2089a90fee6595ec2db350e34 |
from ase import *
from gpaw.utilities import equal
import numpy as np
from gpaw import GPAW
from gpaw.poisson import PoissonSolver
a = 2.7
bulk = Atoms('Li', pbc=True, cell=(a, a, a))
k = 4
g = 8
calc = GPAW(gpts=(g, g, g), kpts=(k, k, k), nbands=2,
poissonsolver=PoissonSolver(relax='GS'),
... | qsnake/gpaw | oldtest/average_potential.py | Python | gpl-3.0 | 764 | [
"ASE",
"GPAW"
] | cea3dc8ebfe112375896f67b6b71d6c80f59856fde480e0f27c6d123be3d037e |
"""
Test the enterprise support utils.
"""
import json
import uuid
from unittest import mock
import ddt
from completion.models import BlockCompletion
from completion.test_utils import CompletionWaffleTestMixin
from completion.waffle import ENABLE_COMPLETION_TRACKING_SWITCH
from django.conf import settings
from django... | eduNEXT/edx-platform | openedx/features/enterprise_support/tests/test_utils.py | Python | agpl-3.0 | 29,558 | [
"VisIt"
] | 65af531226176d8ffeb68c57a9b90de53e316b60c8c9b9360100a37b8498d6a5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at you... | LFPy/LFPy | LFPy/test/test_misc.py | Python | gpl-3.0 | 5,884 | [
"NEURON"
] | 5b76cdeda66f883cb58c6b327dcb5012fd4414ed4bbf098192868f26c7e66f00 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/scf/test/test_ghf.py | Python | apache-2.0 | 12,638 | [
"PySCF"
] | 5639972fec665b62c6b215f09d6f6605b827f1627fa18da18ade87fe0dacabf0 |
import os
import subprocess
def Create_scf(i):
with open('graphene.scf%d.in'%i, 'w') as f:
a = 2.4623 + (i-5)*0.01
s = "\
&CONTROL\n\
calculation = 'scf',\n\
restart_mode = 'from_scratch',\n\
pseudo_dir = './',\n\
outdir = './',\n\
prefix = 'graphene',\n\
/\n\
&SYSTEM\... | slek120/phys534 | HW3/graphene.py | Python | gpl-3.0 | 1,430 | [
"CRYSTAL",
"ESPResSo"
] | 7c11500a9b0d6f84fc12270ae0f1d002f86ac5dab51a74a9ed014892a3dfc57d |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Permission to use, modify, and distrib... | gfyoung/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 9,592 | [
"Gaussian"
] | 43ad2eeb0e98d8d501a1c0fcc43e99a9f1e6e45766267cfec4fbf7ff599df1ba |
##########################################################################
#
# This file is part of OCEMR.
#
# OCEMR is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License,... | ph1l/ocemr | ocemr/views/patient.py | Python | gpl-3.0 | 19,163 | [
"VisIt"
] | 32bf8df303249a7f35da6c01c694ea955991905a4a05be52da7b8572ab60ad49 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/test_match_seq.py | Python | apache-2.0 | 6,401 | [
"VisIt"
] | 398bcd7031dc47380f00e364fee99f01e92ae2e7838857e3754b24a36814b291 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This python program intends to look for localized MO near to atoms based on the
center of charges in order to perform later incremental calculations as stated
in H. Stoll, Chem. Phys. Lett., 1992, 19.
__author__ = "Muammar El Khatib"
__copyright__ = "Copyright 2014, Mu... | muammar/centerfinder | centers.py | Python | gpl-3.0 | 16,933 | [
"Molpro"
] | 2a1a52d06ae1604bf051c3bb01c8653fc5f518286651ec6c7cdfddccc3e56782 |
import sys
import csv
import numpy as np
from numpy import array
import argparse
from collections import OrderedDict
import HTSeq
def presence (d2):
d2c=np.copy(d2)
#genelist= d2[:1,1:]
for item in d2c:
print len(item)
genomeslist= d2c[1:,:1]
d2c = d2c[1:,1:-1]
row=0
while row<d2c.shape[0]:
column=... | mickaelsilva/pythonscripts | AlleleCalling/GetCleanLoci4Phyloviz.py | Python | gpl-2.0 | 6,692 | [
"HTSeq"
] | 2efe1a490cbf58f28cb764fa766fa45084d8f40f7ee2818d388494223367ba1e |
def VtkLoadNodes(setName, nmbContndr):
nmbContndr= vtk.vtkPoints() # Define the point set to be drawn
nSet= preprocessor.getSets.getSet(setName)
nSet.numerate()
print "nombre set: ",nSet.nombre
print "num. nodes: ",nSet.getNumNodes
nodes= nSet.getNodes
for n in nodes:
nmbContndr.InsertPoint(n.getIdx,c... | lcpt/xc | python_modules/postprocess/xcVtk/FE_model/vtk_load_nodes.py | Python | gpl-3.0 | 377 | [
"VTK"
] | f35fde9de3421ddf0e7b2cb3c0e92defc9b4ea7b31c94d5a867cb8543961d368 |
"""
Useful functions for manipulating parameters in a Parmed CharmmParameterSet.
"""
__author__ = 'Chaya D. Stern'
from parmed.topologyobjects import DihedralType
from torsionfit.utils import logger
from copy import copy as _copy
import warnings
def add_missing(param_list, param, sample_n5=False):
"""
Upda... | ChayaSt/Torsions | torsionfit/parameters.py | Python | gpl-2.0 | 9,987 | [
"CHARMM",
"OpenMM"
] | e76115291ef3ba735d0ecb215383df1d8a5ff355b98c9e08aa2e48240adeec28 |
#!/usr/bin/env python
"""Test program for a function in the module tools: filter_sam_file
"""
import os
import shutil
import subprocess
from pycits.tools import NotExecutableError
import pysam
import gzip
from nose.tools import nottest, assert_equal
from pycits.tools import filter_sam_file
# INPUT DATA LOCATION
IND... | widdowquinn/THAPBI-pycits | tests/test_tool_filter_sam_file.py | Python | mit | 1,611 | [
"pysam"
] | 895ab1fcc20b840629f8b32c1576592c3ec657658b001610c0ee73d419c722f5 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | Karaage-Cluster/karaage | karaage/plugins/kgapplications/conf/settings.py | Python | gpl-3.0 | 993 | [
"Brian"
] | 533e5f669eb1fade330b1d73eb363985f9b500f3bdad49d332b6d6981afad557 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Factory functions producing ABINIT Works.
Works are packed together in a flow. A flow can be ran using abirun (abipy)
Entry points for client code (high-level interface)
"""
from __future__ import unicode_li... | aykol/pymatgen | pymatgen/io/abinit/calculations.py | Python | mit | 17,910 | [
"ABINIT",
"pymatgen"
] | 8448d92d80f0358f704b56c330b414e62958ba524c73f7dfc08b0df0ba7bd252 |
#!/usr/bin/env python
# Scatter - A python tool to plot and output atomic scattering factors
# Copyright (C) 2018 Stef Smeets
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; ei... | stefsmeets/scatter | scatter/scatter.py | Python | gpl-2.0 | 18,840 | [
"Gaussian"
] | 8be881ab3bb85f303d2a000bc98bddaf74ea39eb3556d6325f97a735972dadf4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | mkurnikov/remote_job_aggregator | config/urls.py | Python | bsd-3-clause | 1,291 | [
"VisIt"
] | 929439068123e9a37207e28688dd3ed4461b1492ed478fcbcc63da101d3a34e0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from collections import OrderedDict
from aston.resources import tr
import aston.peaks.Integrators as ami
import aston.peaks.PeakFinding as ampf
peak_finders = OrderedDict()
peak_finders[tr('Simple')] = ampf.simple_peak_find
peak_finders[tr('StatSlope')] ... | jayansenaratne/aston | aston/qtgui/MenuOptions.py | Python | gpl-3.0 | 1,573 | [
"Gaussian"
] | 5203764d1241a9bbe731a9c0052b732453bea0240da9fb73eb67a050c9eb2f3b |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_hu.py | Python | gpl-2.0 | 10,871 | [
"Brian"
] | 8eb14e6b3aef7861438b8ff9ade12c5831783a88015075aa668dc8262dfaece8 |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from collections import OrderedDict
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | edxnercel/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 61,151 | [
"VisIt"
] | d5accd6b793af32fe7df7cf12e2aa242d2a872057d2c98c3735b7dfe2844c63b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from flask import Blueprint, render_template, request, jsonify, redirect, url_for, abort, current_app
from ..models import Slider, Category, Post, Label, Advertisement
from ..extensions import db
from ..helpers import get_client_ip
home = Blueprint('hom... | whypro/IBATI | ibati/views/home.py | Python | mpl-2.0 | 2,655 | [
"VisIt"
] | fe8eba3304f179ec8591308776bbe5253a3a8590af22d11fe3495d0c7cb4bad8 |
#!/usr/bin/env python
"""
Copyright 2017 Matt Settles
Created June 8, 2017
"""
from optparse import OptionParser
import os
import sys
import time
import traceback
import signal
from subprocess import Popen
from subprocess import PIPE
def sp_bwa_index(ref, overwrite=False):
if os.path.isfile(ref):
if os.p... | ucdavis-bioinformatics/proc10xG | process_mapping.py | Python | apache-2.0 | 16,762 | [
"BWA"
] | 407429b07b8ea61f9d518e51611f5fa618d452d9e7d7798031d1638158803a9d |
"""Copyright (c) 2010-2012 David Rio Vierra
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WA... | OniOniOn-/MCEdit-Unified | mcplatform.py | Python | isc | 14,166 | [
"Jaguar"
] | 0afb431803a4fb7e4ccce44cba61abcfbcfd0a342954116070dc204fdbe1e7d6 |
#!/usr/bin/env python
################################################################################
# site-alerter-daemon.py
#
#
# Created by Brian Baughman on 3/7/13.
# Copyright 2013 Brian Baughman. All rights reserved.
################################################################################
try:
im... | bbaugh/gcn-parser | site-alerter-daemon.py | Python | gpl-2.0 | 4,784 | [
"Brian"
] | 1297867d3ec14a33baeb1ed7d8e72f14899eca5120bf81a03ce5e2ba2141a0c0 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Danelle Cline'
__copyright__ = '2017'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON September season activities in 2017
Mike McCann, Duane Edgington, Danelle Cline
MBARI 18 September 2017
@var __da... | duane-edgington/stoqs | stoqs/loaders/CANON/loadCANON_september2017.py | Python | gpl-3.0 | 12,477 | [
"NetCDF"
] | d54d923ca13c8f27312ad00cf73ebcc2de72f738828b27aad5377ecff9ae88a9 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
class Freshness(object):
__slots__ = ['time', 'text']
def __init__(self, time, text):
self.time = time
self.text = text
def __str__(self):
return self.text
freshness_levels = [
... | afb/0install | zeroinstall/gui/freshness.py | Python | lgpl-2.1 | 675 | [
"VisIt"
] | 30a75825c2430fa75a0178aa4c7d7cc564458a355f7a5cc5eaa98a11171b8d91 |
"""
Solve the unique lowest-cost assignment problem using the
Hungarian algorithm (also known as Munkres algorithm).
"""
# From scikit-learn:sklearn/utils/linear_assignment_.py
# Based on original code by Brain Clapper, adapted to NumPy by Gael Varoquaux.
# Heavily refactored by Lars Buitinck.
# Copyright (c) 2008 Br... | jamesxia4/neleval | neleval/munkres.py | Python | apache-2.0 | 9,404 | [
"Brian"
] | 8f5db28ecaf0ae35fe42c2f6156d187d008aeb9115a43981a8c20c9fa73fabb1 |
#!/usr/bin/env python
#Written by Nick Loman
#Part of the ZiBRA pipeline (zibraproject.org)
import pysam
import sys
from copy import copy
from vcftagprimersites import read_bed_file
from collections import defaultdict
def check_still_matching_bases(s):
for flag, length in s.cigartuples:
if flag == 0:
... | zibraproject/zika-pipeline | scripts/align_trim.py | Python | mit | 6,039 | [
"pysam"
] | e30c4d46c8c6bde8507e50825a46acdf642f4d0cc14af5d8238a712e28b8f22e |
######################################
#
# Nikolai Rozanov (C) 2017-Present
#
# nikolai.rozanov@gmail.com
#
#####################################
from Data.synthetic1 import blobs, gaussian, circle
from Utils.plotting import plot2D, plot2,plotfunc
from NP.Kernels.Kernels import GAUSSIAN_KERNEL
from NP.TESTS.HSIC ... | Kolyan-1/MSc-Thesis-Code | dev_profiling2.py | Python | bsd-3-clause | 1,055 | [
"Gaussian"
] | 9b07e9cc5d8f09513eaadbf994d651e75420f0ab62d4ff3a58004e9b20935fe4 |
# coding=utf-8
"""
Tests for the course home page.
"""
from datetime import datetime, timedelta
import ddt
import mock
import six
from django.conf import settings
from django.http import QueryDict
from django.urls import reverse
from django.utils.http import urlquote_plus
from django.utils.timezone import now
from p... | msegado/edx-platform | openedx/features/course_experience/tests/views/test_course_home.py | Python | agpl-3.0 | 47,421 | [
"VisIt"
] | cdea02701c1c340a3a4d79c67e1a96888eec27d971367cb257848e23b34158e8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from Tkinter import Frame, Tk, BOTH, Text, Menu, END, Button,RIGHT,LEFT,TOP,BOTTOM,RAISED,SUNKEN,RIDGE,Y,X,FLAT,INSERT,Entry,Label,LabelFrame,StringVar,OptionMenu,Radiobutton,Checkbutton,IntVar,Listbox
from numpy import *
import tkFileDialog
import matplotlib
import matplotli... | CBRUhelsinki/CENTplatform | CENTExtra/IAF Calculator Python Standalone/iafcalc.py | Python | gpl-2.0 | 18,565 | [
"Gaussian"
] | 3afd89b10bcbb765a4e5487ce551e8e86f6bb893c75302cb11fa3eaa90940568 |
############################################################
#Example 3: Saving the coordinates as an xyz file
############################################################
import numpy as np
import pele.potentials.lj as lj
import pele.basinhopping as bh
from pele.takestep import displace
from pele.storage.savenlowest i... | js850/pele | examples/basinhopping_no_system_class/3_savelowest.py | Python | gpl-3.0 | 1,324 | [
"PyMOL"
] | 1f5d1a23f270f53a45c5c39d9699302edb72a3c3f72a2ccae8edd5176c71d28c |
"""
Tests BSE curation functions
"""
import os
import pytest
from basis_set_exchange import api, readers, curate, manip, sort
from .common_testvars import bs_names_sample
# NOTE: CFour reader does not currently support ECP
roundtrip_formats = ['turbomole', 'gaussian94', 'nwchem']
@pytest.mark.parametrize('basis', ... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/tests/test_curate_roundtrip.py | Python | bsd-3-clause | 1,680 | [
"CFOUR",
"NWChem",
"TURBOMOLE"
] | 8a15d0935e393b27097ab1bf069e09932964f039ce2f8a1765b8ca3c32be8282 |
#!/usr/bin/env python
'''
Steve Biller, Dec 2010 - Oct 2011, Feb 2012
Usage: RNAseq_parser_gff.py -i <input SAM-formatted alignment file> -o <output> -d <dir with gff files> -p <tells it to print out intergenics)
IMPORTANT: Script requires a tab-delimited file of annotated genome regions for each reference genome wit... | cuttlefishh/papers | cyanophage-light-dark-transcriptomics/code/RNAseq_parser_gff_directional.py | Python | mit | 14,303 | [
"BWA",
"pysam"
] | 8f6aed01311a766d3ed7f422b20d1172598b838699983e930c7b5a31e5f82d96 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# -----------------------------------------------------------------------------
# Copyright (c) 2018 The Regents of the University of California
#
# This file is part of kevlar (http://github.com/dib-lab/kevlar) and is
# licensed under the MIT license: see LICENSE.
# ----... | dib-lab/kevlar | kevlar/cli/localize.py | Python | mit | 2,806 | [
"BWA"
] | 9d19843da15027814d6283ab66e6b59342bf5856f8f2bf4174916ef4e0f630e6 |
# -*- coding: utf-8 -*-
"""Quadratic DeepOBS dataset."""
import numpy as np
import tensorflow as tf
from . import dataset
class quadratic(dataset.DataSet):
"""DeepOBS data set class to create an n dimensional stochastic quadratic\
testproblem.
This toy data set consists of a fixed number (``train_size``... | fsschneider/DeepOBS | deepobs/tensorflow/datasets/quadratic.py | Python | mit | 4,855 | [
"Gaussian"
] | d22c31fdcdc154d46b0988220a4f2356857c12dbd91b268b73f9d692d1792884 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-containeranalysis | tests/unit/gapic/containeranalysis_v1/test_container_analysis.py | Python | apache-2.0 | 83,961 | [
"Octopus"
] | 8766815c83a77fc8b75e805c37d4a7e14dd6cd04cb894cd948a5cced3f987fd1 |
#!/usr/bin/env python
# Generates a phantom from an atlas of tracts
# Saves the phantom to a niftii image afterwards
## Import common Python libraries
# import os
# import getopt
# import sys
# import time
import glob
# import re
#Modif outside toolobx
import sct_utils as sct
#import sct_utilsc as sct
import numpy as... | neuropoly/spinalcordtoolbox | dev/atlas/validate_atlas/generate_phantom.py | Python | mit | 6,988 | [
"Gaussian"
] | 8293e49c8dc1485aa0fdb2502fc6d319bbd53d56eefad0eaf06791bdce0959e9 |
# being a bit too dynamic
# pylint: disable=E1101
from __future__ import division
import warnings
import re
from collections import namedtuple
from distutils.version import LooseVersion
import numpy as np
from pandas.util._decorators import cache_readonly
import pandas.core.common as com
from pandas.core.base import... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/pandas/plotting/_core.py | Python | mit | 126,105 | [
"Gaussian"
] | c86b24689baedecb41c350dd3079b21c580929deb0c776e6f753e283f8a9bc23 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | xzturn/tensorflow | tensorflow/python/autograph/pyct/static_analysis/activity.py | Python | apache-2.0 | 20,994 | [
"VisIt"
] | 09408dba8a1d5710cfd87d90b257656cbcc17d704294637808ff7407473f9111 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pytest
import numpy
import pandas
import dendropy
import Bio.Alphabet
from Bio.AlignIO import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from pandas.util.testing import (
assert_categorical_equal,
assert_dict_equal,
... | jmenglund/pandas-charm | test_pandascharm.py | Python | mit | 7,631 | [
"Biopython"
] | 6b022b508372a85db2e813ef8bc395391ddae33080a733df68065e82028dbf03 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/peacock_app/check_vectorpostprocessor/test_check_vectorpostprocessor.py | Python | lgpl-2.1 | 1,791 | [
"MOOSE"
] | f9d62d9d533b75c884f3597a1b559925493e9711ebd922fc8c28964c1a98c87c |
#
# basic run through the PDB with ray-tracing
#
from glob import glob
import threading
import time
from pymol import cmd
import sys, os, os.path
import random
import traceback
ent_dir = "pdb"
def load():
r = 0
rep = [ "lines","sticks","spheres","dots","ribbon","cartoon" ]
list = glob("pdb/*/*... | gratefulfrog/lib | python/pymol/pymol_path/test/inp/B02.py | Python | gpl-2.0 | 1,767 | [
"PyMOL"
] | be53317075d2685826a3438c4f7010fc38e00dee1587ee91fd76161202e59ead |
#!/usr/bin/python
import numpy as np
import mayavi.mlab as mylab
# temp vis for debug
def view_lsegs(slabels):
for k in range(slabels.shape[2]):
for j in range(slabels.shape[1]):
for i in range(slabels.shape[0]):
if slabels[i][j][k]['xyzlabel'][0] != "" :
mylab.plot3d([i,i+1], [j,j], [k,... | jrugis/cell_mesh | vis.py | Python | gpl-3.0 | 820 | [
"Mayavi"
] | 6afb9f3933584e71f5cb9e46310594853ed3d06ec7f302db60a079d60199d306 |
from __future__ import absolute_import
from __future__ import unicode_literals
from compose.config.errors import DependencyError
def get_service_name_from_network_mode(network_mode):
return get_source_name_from_network_mode(network_mode, 'service')
def get_container_name_from_network_mode(network_mode):
re... | shakamunyi/fig | compose/config/sort_services.py | Python | apache-2.0 | 2,486 | [
"VisIt"
] | f5d888c0c2a028019935a4dd303bfa058d2b5e3064912456f7d8896e30d02f03 |
import numpy as np
import pdb
import math
import scipy.special
from . import ModelObjs, Utils
"""
This module contains definitions for Stochs with standard probability
distributions that are used regularly when defining models, such as Gaussian,
Uniform, and Gamma. Additional Stoch definitions can be trivially added.
... | tomevans/pyhm | pyhm/BuiltinStochastics.py | Python | gpl-2.0 | 5,281 | [
"Gaussian"
] | 975c74cc740c18d6e109092995299b9d2a774a5eb0aec671dd676a276f690bbc |
"""This file contains code for use with "Think Stats",
by Allen B. Downey, available from greenteapress.com
Copyright 2010 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function
import math
import sys
import pandas
import numpy as np
import thinkstats2
impo... | wavelets/ThinkStats2 | code/brfss.py | Python | gpl-3.0 | 4,718 | [
"Gaussian"
] | 169ab2b273b8220b09f2461ad8d5d6696dadcd6035a5c087612fb7210f05acef |
'''
Created on Apr 29, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version ... | tectronics/chimerascan | chimerascan/deprecated/estimate_fragment_length_distribution.py | Python | gpl-3.0 | 6,774 | [
"pysam"
] | f592792f675d2401136aa51ce118055d21fb1e862bce2af0e9d50a2f8b9b3c96 |
"""
Numba-specific errors and warnings.
"""
import abc
import contextlib
import os
import sys
import warnings
import numba.core.config
import numpy as np
from collections import defaultdict
from numba.core.utils import chain_exception
from functools import wraps
from abc import abstractmethod
# Filled at the end
__a... | cpcloud/numba | numba/core/errors.py | Python | bsd-2-clause | 23,534 | [
"VisIt"
] | 4d44cb1f5c68a27af70f4fbbce7e98c173d205dfccc06e133662235cd4e5fc32 |
# $HeadURL$
__RCSID__ = "$Id$"
import time
import copy
import os.path
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities.Network import checkHostsMatch
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Security import Locations
from DIRAC.Core.Security.X50... | vmendez/DIRAC | Core/DISET/private/Transports/SSL/SocketInfo.py | Python | gpl-3.0 | 13,338 | [
"DIRAC"
] | 1c2579563dc16ca4b7cf1a8dc6a7fa1c943a40aa99a6036f4f5364d252510c39 |
import string
import EMR_utilities
import re
import datetime
import decimal
def format_address(somedictionary):
"""parameter is a dictionary with appropriate keys for an address"""
somedictionary['phonenumber'] = phone_format(somedictionary['phonenumber'])
address = """%(firstname)s %(lastname)s
%(address)s
%(cit... | barronmo/gecko_emr | EMR_formats.py | Python | gpl-2.0 | 5,956 | [
"VisIt"
] | b75869dacec4109370d4e27723563b09e8dec30f9c862be2676c0a670e3a87ba |
import wx, application, speech, os, random, time, pygame.mixer, webbrowser
pygame.mixer.init(frequency = 44100) # Get the mixer ready for sounds.
class MyTextCtrl(wx.TextCtrl):
"""This class is used so that every time tehe value gets set, the cursor is jumped to the end, instead of the beginning (which is the wx defa... | chrisnorman7/typingtutor | main.py | Python | gpl-2.0 | 8,802 | [
"VisIt"
] | 096f4322d16f8eec01144ae5e2b8acf5beda994e6e10efff6a0c7767ef797e98 |
# -*- coding: utf-8 -*-
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the a... | jochym/spglib | python/test/vasp.py | Python | bsd-3-clause | 5,507 | [
"phonopy"
] | 5d490fb690774837c5b2a32a26080181c2902a558124bd47034c2098f76a2d4a |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | doc/examples/nest_network.py | Python | gpl-3.0 | 2,891 | [
"Gaussian"
] | 5d46999c662e5fcec1747433807660c78bb4a71a5b3f521f38e7ce17d9a66a13 |
#!usr/bin/python
# Copyright 2016, Rohan Dandage <rraadd_8@hotmail.com,rohan@igib.in>
# This program is distributed under General Public License v. 3.
"""
================================
``io_data_files``
================================
"""
import sys
import pandas as pd
from os.path import exists,basename,abspat... | rraadd88/dms2dfe | dms2dfe/lib/io_data_files.py | Python | gpl-3.0 | 14,758 | [
"Bowtie"
] | 03b223ab44561cf4284204211a3afc0ffb39fa1f7a2ff39c73352fdecf4b7bfd |
# Run a Splunk Search on the Selected Index
# For use with Munk - Maltego for Splunk
# Author: Brian Warehime @nulltr0n
# 9/6/2014
# Importing various modules
from MaltegoTransform import *
import sys
import webbrowser
import ConfigParser
import os
# Configuration Parser to grab necessary options.
def getLocalConfP... | brianwarehime/munk | transforms/splunkindexsearch.py | Python | gpl-2.0 | 1,331 | [
"Brian"
] | 104a6615cc90646993d25dc5492adb4bbee66fd4f91d331477943a88372398d8 |
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