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# Copyright 2009 New England Biolabs <davisp@neb.com>
#
# This file is part of the BioNEB package released
# under the MIT license.
#
import re
import stream
class FastaRecord(object):
def __init__(self, headers, seq):
self.headers = headers
self.seq = seq
def __iter__(self):... | pombredanne/bioneb | bioneb/parsers/fasta.py | Python | mit | 2,564 | [
"BLAST"
] | c494318ab45e95c5cda9ebe03ac49f5bf72cbd248939713f1809ea6e46d6356c |
# -*- 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-dialogflow-cx | tests/unit/gapic/dialogflowcx_v3/test_pages.py | Python | apache-2.0 | 94,547 | [
"Octopus"
] | b4020b9abaa738293ba34589e9d618a88c520ee0dc92fc9df1f31e2bf6b1bb43 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2018, 2021, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | smarr/Truffle | vm/mx.vm/mx_vm.py | Python | gpl-2.0 | 19,478 | [
"ESPResSo",
"VisIt"
] | de62b4eb7801c274617c8f6be4c70476619330f9c733e26d82828c42bae7cff3 |
# Analyzing neural spiking data using Hopfield networks
# - Markov probability of window labels approach
# Felix Effenberger, Jan 2015
# This assumes that a Hopfield network has already been fitted to windowed
# spike train data and the denoised patterns have been computed and saved
# via the Patterns class (see file ... | team-hdnet/hdnet | examples/examine_pattern_sequence.py | Python | gpl-3.0 | 8,834 | [
"VisIt"
] | 40f81ed63d0de2f2400932b6b913ae393f96b713ba2ff721f36e8543c70ff866 |
""" A computing element class using singularity containers.
This computing element will start the job in the container set by
the "ContainerRoot" config option.
DIRAC will the re-installed within the container, extra flags can
be given to the dirac-install command with the "ContainerExtraOpts"
opt... | chaen/DIRAC | Resources/Computing/SingularityComputingElement.py | Python | gpl-3.0 | 11,852 | [
"DIRAC"
] | 17ae3d365b8a9127d76a82ec3364ceb2cf2df183e59d652cef04a50d0b996a85 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_zip_counties_api.py | Python | apache-2.0 | 10,219 | [
"VisIt"
] | 71351bd485f01996d0c0e8801338d205d00e855edaf4c5b329f9efee4fb8e6c2 |
""" This is the RFIO StorageClass
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import re
import os
import time
import six
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/RFIOStorage.py | Python | gpl-3.0 | 43,317 | [
"DIRAC"
] | e6a37fde11e6b467d05d3fbb86f2bd1cca2df2e665134b817bb8aa5cef15cb55 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/tests/test_reporter.py | Python | lgpl-2.1 | 7,441 | [
"MDTraj",
"OpenMM"
] | 97acec2556098ddb4e0f1ce2af1b47a0b755f156857afe921cd1b5818269550a |
# Generated from asparagram.g4 by ANTLR 4.5.1
from antlr4 import *
if __name__ is not None and "." in __name__:
from .asparagramParser import asparagramParser
else:
from asparagramParser import asparagramParser
# This class defines a complete generic visitor for a parse tree produced by asparagramParser.
clas... | Caian/Asparagus | asparagramVisitor.py | Python | gpl-2.0 | 3,513 | [
"VisIt"
] | 7c1913ef8fad7dc166efd26436e18c2b10999e0a6f2eecec6d54bf4e634dc554 |
import warnings
import matplotlib.pyplot as plt
import numpy as np
from sklearn.preprocessing import normalize
class RandomWalk2D:
''' Class for TD-lambda random walk '''
def __init__(self, grid_size=3, end_states=[(0,0)], rewards=[1], \
exploration=.1, move_cost=0, alpha=.3, gamma=.9, lmbda=.7):
... | rahulsrma26/code-gems | RL/randomWalk/TDLambda.py | Python | mit | 5,584 | [
"VisIt"
] | fe520187adf586f293331f816d898f9979aba11d3d80fc0b104726ae2fc0c956 |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | valtandor/easybuild-easyblocks | easybuild/easyblocks/n/nwchem.py | Python | gpl-2.0 | 24,264 | [
"Amber",
"NWChem"
] | f14145a4ade90d9a734a438fbe91312d887d2da1522efa8747638eccf4392e5c |
'''
Create PV-slices of the spectrally down-sampled HI cube.
'''
from spectral_cube import SpectralCube, Projection
import pvextractor as pv
from astropy.utils.console import ProgressBar
from astropy.io import fits
from astropy import units as u
import numpy as np
import matplotlib.pyplot as plt
from paths import fo... | e-koch/VLA_Lband | 14B-088/HI/analysis/HI_pvslices.py | Python | mit | 5,875 | [
"Galaxy"
] | 02f3b313dbf5356d402286c56a897622522cc72cc540c31daec632fbdaff8537 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyHtseq(PythonPackage):
"""HTSeq is a Python package that provides infrastructure to proce... | rspavel/spack | var/spack/repos/builtin/packages/py-htseq/package.py | Python | lgpl-2.1 | 1,029 | [
"HTSeq",
"pysam"
] | d6052413ecd1191bba5b062a008e22300f2acfe7a8282aeed2fada7ca7eb4d85 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/cube.py | Python | gpl-3.0 | 158,449 | [
"NetCDF"
] | a31b4f2d2091b9de6967feed63655f9d565aea8d974678cdc134d4930baea977 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/gaussian.py | Python | gpl-3.0 | 17,417 | [
"Gaussian"
] | 610605213ff613c7d06822fd7c0fd32b1b321856da99fe0b2d2eeed048185bba |
from brian2 import *
from data_utils import *
set_device('cpp_standalone', build_on_run=False)
# neuronal parameters
N = 12500 # total number of neurons
NE = 10000 # number of excitatory neurons
vth = 20*mV # threshold potential
vr = 10*mV # reset potential
tau = 20*ms # membrane time constant
eqs_neurons='''
inp : ... | h-mayorquin/camp_india_2016 | tutorials/EI networks/STEP3_ExcInhNet_Brunel2000_brian2.py | Python | mit | 2,316 | [
"NEURON"
] | d1618bda437cef9bfebb20ed465c842940c77e79e8b5a395c00358699a83e25a |
#
# Copyright 2014-2015, 2017, 2020-2021 Lars Pastewka (U. Freiburg)
# 2018-2021 Jan Griesser (U. Freiburg)
# 2020 Jonas Oldenstaedt (U. Freiburg)
# 2015 Adrien Gola (KIT)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https:/... | libAtoms/matscipy | matscipy/calculators/manybody/explicit_forms/__init__.py | Python | lgpl-2.1 | 1,181 | [
"Matscipy"
] | 591e8df1b22e592dcd19ca40cdd3c7443f15cb981e712c07a54f97bf2a7d726b |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | titanium-forks/appcelerator-modules.ti.touchid | ios/build.py | Python | apache-2.0 | 8,826 | [
"VisIt"
] | 93bf4defa9c2a57d32ad31d86cc9754e1c395b14e2f270e87e204963643b17c2 |
import unittest
from keras2pmml import keras2pmml
from sklearn.datasets import load_iris
import numpy as np
import theano
from keras.utils import np_utils
from keras.models import Sequential
from keras.layers.core import Dense
class GenericFieldsTestCase(unittest.TestCase):
def setUp(self):
iris = load_i... | vaclavcadek/keras2pmml | tests/sequential.py | Python | mit | 4,863 | [
"NEURON"
] | 03c8d8ffab446f3e7a1776145e9032e5ae01afea5065ddba9632497520601538 |
#!/usr/bin/env python
#
# Copyright (c) 2009- Facebook
# Distributed under the Thrift Software License
#
# See accompanying file LICENSE or visit the Thrift site at:
# http://developers.facebook.com/thrift/
#
"""
This script can be used to make the output from
facebook::thrift::profile_print_info() more human-readable.... | uber/fbthrift | thrift/contrib/parse_profiling.py | Python | apache-2.0 | 9,945 | [
"VisIt"
] | 4677203a7786469940a86d86aef0f755922a53df76ae5f23bb6beab948d812b4 |
# Copyright (C) 2015, 2016, 2017, 2018 Francisco Favela
# This file is part of isonav
# isonav 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 optio... | ffavela/isonav | isonavBase.py | Python | gpl-3.0 | 46,355 | [
"Avogadro"
] | b4236adb7ceb5b344af3cc04cbefafa22e921cf2562ec06012019ff67c16861c |
# Copyright 2013 Google Inc. 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 applicable law or ... | gdgjodhpur/appengine-opencv-sudoku-python | sudoku_image_parser.py | Python | apache-2.0 | 11,664 | [
"Gaussian"
] | 9fee3947ce0c1c4ffa4ed12b5b25fd77a0065d870eeb94c3fff1385c61987a62 |
#!/usr/bin/python
# Copyright 2008 Marcus D. Hanwell <marcus@cryos.org>
# Distributed under the terms of the GNU General Public License v2 or later
#
# Taken from commit 40304a05323c68d0297a8ade123d27c6e0c78d8c at
# http://github.com/cryos/avogadro/blob/master/scripts/gitlog2changelog.py
import string, re, os
# Execu... | Beirdo/beirdobot | scripts/gitlog2changelog.py | Python | lgpl-2.1 | 4,359 | [
"Avogadro"
] | d1e15a079860e5b4bf6143ed3326ff4a555ef9f2b4e49ae2f315e6e61a6e0861 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyBrian(PythonPackage):
"""A clock-driven simulator for spiking neural networks"""
ho... | iulian787/spack | var/spack/repos/builtin/packages/py-brian/package.py | Python | lgpl-2.1 | 724 | [
"Brian"
] | 702a144240ad96ddd60a10799980eb747b7e39857588b7e4f36adc072fc404ca |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""K-point/spin combination-descriptors
This module contains classes for defining combinations of two indices:
* Index k for irreducible kpoints in the 1st Brillouin zone.
* Index s for spin up/down if spin-polarized (othe... | qsnake/gpaw | gpaw/kpt_descriptor.py | Python | gpl-3.0 | 17,804 | [
"ASE",
"GPAW"
] | 1ec134d6a5b25e24d59987e3d0dd12f4f9c343bdf61925df828a64a014c7ab3e |
#!/usr/bin/env python
import os.path, sys
from fityk import Fityk
class GaussianFitter(Fityk):
def __init__(self, filename):
Fityk.__init__(self)
if not os.path.isfile(filename):
raise ValueError("File `%s' not found." % filename)
self.filename = filename
self.execute("... | wojdyr/fityk | samples/hello.py | Python | gpl-2.0 | 1,092 | [
"Gaussian"
] | e7f7ab53b455315b406a355f2ff3d33d3f14e0bf1506d7978cf054ebb3f7f37b |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.7 on 2016-08-05 00:09
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('visit', '0116_auto_20160803_1607'),
]
operations = [
migrations.AddField(
... | koebbe/homeworks | visit/migrations/0117_auto_20160804_1909.py | Python | mit | 719 | [
"VisIt"
] | 6164b324b4e4bf1485be680a5fe8ce7deaea7ad855ae483cf04fd467b5c46de7 |
import copy
import os
import datetime
import inspect
import hashlib
import re
import os.path
import random
import glob
from GangaCore.GPIDev.Base.Proxy import stripProxy, isType, getName
from GangaCore.GPIDev.Lib.GangaList.GangaList import GangaList
from GangaCore.GPIDev.Schema import Schema, Version, SimpleItem, Compo... | ganga-devs/ganga | ganga/GangaDirac/Lib/Files/DiracFile.py | Python | gpl-3.0 | 39,137 | [
"DIRAC"
] | b0c26460a6989291cd8c90f6997ea32faecc25c13b2a49f0b51d8c2379cb571e |
import numpy as np
from scipy import sparse
from . import Mapper, _savecache
from . import samplers
class LineMapper(Mapper):
@classmethod
def _cache(cls, filename, subject, xfmname, **kwargs):
from .. import db
masks = []
xfm = db.get_xfm(subject, xfmname, xfmtype='coord')
pia... | CVML/pycortex | cortex/mapper/line.py | Python | bsd-2-clause | 1,505 | [
"Gaussian"
] | bb67b0f3a6b9807e6e9851f88c5f25ea7fb0561b1873dbed48190a6dcbe8e754 |
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013,2014,2015
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & F... | kkreis/espressopp | src/interaction/Tabulated.py | Python | gpl-3.0 | 44,792 | [
"ESPResSo"
] | 74ef8f8b45d1134baf4b2239f22854bda2c312b0322ed1dec9d586b65a8ccce0 |
# Orca
#
# Copyright 2016 Igalia, S.L.
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your opt... | GNOME/orca | src/orca/scripts/terminal/script.py | Python | lgpl-2.1 | 5,468 | [
"ORCA"
] | e104f1a4804ee92a06573e2ad5be2b031d3ad8b6490f8f1c2afa84387fd5b7f9 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed ... | JWDebelius/scikit-bio | skbio/tree/_nj.py | Python | bsd-3-clause | 10,840 | [
"scikit-bio"
] | 9723b37db240477c8a76c5484ec1e50fc0dba1bfe0ad9fbb646a9ee2240f53ec |
import shutil
import jinja2 as j2
import pytoml
from pathlib import Path
from core import Model, ModelType
from core.ModelValidator import ModelValidator
folders = {
"F-IND": "F-IND",
}
mfDict = {
# 'pairwise-linear': ,
'triangle': 'TRI_MF',
'trapezoid': 'TRAP_MF',
# 'gaussi... | lab-robotics-unipv/pyFUZZYgenerator | core/fuzzyCreator.py | Python | lgpl-3.0 | 4,604 | [
"Gaussian"
] | fa1fb85df9562641448a888e2b522c76499aa31c13b365860ed37de506f6c029 |
####################################################################################################
# Copyright 2013 John Crawford
#
# This file is part of PatchCorral.
#
# PatchCorral is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the ... | psychobaka/PatchCorral | src/data/synthesizers/generalmidi/GM.py | Python | gpl-3.0 | 7,553 | [
"CRYSTAL"
] | 4406add65fe239f7481e9b289612b722b20d6043c7f96a5bd9a1adc27e3f2681 |
"""Command line interface module"""
import sys
import logging
from pathlib import Path
from argparse import ArgumentParser
import helper
import helper.main
import helper.device
LOGGER = logging.getLogger(__name__)
PARSER = ArgumentParser(
prog="helper", description="CLI utility for interfacing with Android devic... | rmmbear/Android-QA-Helper | helper/cli.py | Python | gpl-3.0 | 18,327 | [
"Galaxy"
] | bda2dc66376dd41ede28047aa709a805689b11bc14ccd7e3e7522337949fc62b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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 redistribute it and/or modify
#... | jturney/psi4 | psi4/driver/p4util/spectrum.py | Python | lgpl-3.0 | 13,818 | [
"Avogadro",
"Gaussian",
"Psi4"
] | 07fb4c1b9714feef5de615531a982d1d76855e367786ad10738888093717b14d |
#!/usr/bin/env python
# Pyctools-pal - PAL coding and decoding with Pyctools.
# http://github.com/jim-easterbrook/pyctools-pal
# Copyright (C) 2014-20 Jim Easterbrook jim@jim-easterbrook.me.uk
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public ... | jim-easterbrook/pyctools-pal | src/pyctools/components/pal/coder.py | Python | gpl-3.0 | 7,608 | [
"Gaussian"
] | 36a1a8792e18a7ddc2e50222ef899160fc749e39f512b56f2d199e15f3e9bdbd |
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
from itertools import chain
from itertools import cycle
import pytest
import requests
TEST_HOSTNAME = 'localhost'
TEST_PORT = 4301
ANDROID_PHONE_UA = [
# Samsung Galaxy S6
'Mozilla/5.0 (Linux; Android 6.0.1; SM-G920V Build/MMB29K) Ap... | ajacksified/reddit-mobile | test/test_vcl.py | Python | mit | 8,795 | [
"Galaxy"
] | 34517ae805d25b544fea7d67abb81859c521ffbaf184724510637bc082321d4f |
import os
from os.path import join
import numpy as n
def writeScript(rootName, plate):
f=open(rootName+".sh",'w')
f.write("#!/bin/bash \n")
f.write("#PBS -l walltime=260:00:00 \n")
f.write("#PBS -o "+plate+".o.$PBS_JOBID \n")
f.write("#PBS -e "+plate+".e$PBS_JOBID \n")
f.write("#PBS -M comparat@mpe.mpg.de \n")
f... | JohanComparat/pySU | spm/bin/write_run_scripts_dr14_chabrier.py | Python | cc0-1.0 | 973 | [
"Galaxy"
] | 3faf701da6819b246152b8a2a8f8ab5ba249c43eddfbc891ea2df800df7e3f2d |
"""
Utilities for handling the Graphic Unit Interface.
.. todo::
Switch to Ttk instead of Tk for a better look of the GUI
"""
import Tkinter
from tkFileDialog import askopenfilename
import pygem as pg
import sys
import os
import webbrowser
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
from matplot... | fsalmoir/PyGeM | pygem/gui.py | Python | mit | 8,725 | [
"VTK"
] | a084582cc605a066b771b5d75ecdac97b908f95538d33ab9287703ea826ddcac |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# License: BSD
from collections import Sequence
import numpy as np
import scipy.sparse as sp
from .utils import check_arrays, array2d
from .utils import wa... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sklearn/preprocessing.py | Python | agpl-3.0 | 29,089 | [
"Gaussian"
] | 20228e7a9e46f5f4990f6ad0b560cefe7702cd506357796c9ea22b4f0eaf0ccb |
import pysam
from readtagger.cluster import evidence_for
TEST_BAM = 'improve_counting_support.bam'
GOOD_BREAKPOINT = [13813889, 13813894]
WRONG_BREAKPOINT = 13813890
WRONG_BREAKPOINT_SEQS = {'ATATA', 'ATATA'}
GOOD_BREAKPOINT_SEQS = {'TAAGT', 'GTAAC'}
def test_evidence_for(datadir_copy): # noqa: D103
three_p_qn... | bardin-lab/readtagger | tests/test_evidence.py | Python | mit | 1,650 | [
"pysam"
] | 548043c2fa77e00cd5621b25ca313b122fc62a463a3bddd4b870fe7d17264f3a |
# Copyright (C) 2007 Google Inc.
#
# 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 writ... | zarnold/transitfeed | tests/transitfeed/testschedule_write.py | Python | apache-2.0 | 23,071 | [
"CASINO"
] | 89db0e4ae6d34c9aa072d5eb7f7d9d4d5a26361e9b06f6b3b5b52f0305096893 |
#!/usr/bin/python
"""
gene_server v0.01
- a xmlrpc server providing a storage/query service for the GA trade system
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License... | stahn/ga-bitbot | gene_server.py | Python | gpl-3.0 | 23,193 | [
"Brian"
] | 73121898ae09e867f0d6f554de90486ea6a56456d0ea150f76380291ce73942b |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import copy
urlBase="http://eutils.ncbi... | rdkit/rdkit-orig | rdkit/Dbase/Pubmed/QueryParams.py | Python | bsd-3-clause | 1,462 | [
"RDKit"
] | 2934936b45b422247a7a2685c352b9e72f043d0bb35bf6b4643edee42eb8601a |
#!/usr/bin/env python
import os
import numpy as np
import matplotlib.pyplot as plt
compare = True # flag to plot the comparison plot between Lammps dump file and values computed by sim using the Lammps traj
doPairWrite = True # flag to plot comparison between sim and Lammps pair_write
doParseLog = True # fla... | tanmoy7989/Lammps_Local_Density | plot_potentials.py | Python | gpl-2.0 | 9,007 | [
"LAMMPS"
] | 6e87699a20aada13a91b43a0fce58fde298ffde629b1ac4aceb1ceb45f6abc43 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/zeoio.py | Python | mit | 574 | [
"pymatgen"
] | 692f938cf720ee8854a87ea1e5fe76a9c1f8596991ee003d052baad775e4a98b |
#!/usr/bin/python2
from distutils.core import setup
import os
import sys
# config file
data_files = [("/etc/lorax", ["etc/lorax.conf"]),
("/etc/lorax", ["etc/composer.conf"]),
("/usr/lib/systemd/system", ["systemd/lorax-composer.service",
"system... | wgwoods/lorax | setup.py | Python | gpl-2.0 | 1,887 | [
"Brian"
] | e958979124d5041506b9bafe23e4af5713f4beccbbd2ed4e5a419455b8158672 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
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
... | thica/ORCA-Remote | src/ORCA/utils/Platform/android/android_GetMACAddress.py | Python | gpl-3.0 | 1,979 | [
"ORCA"
] | 4d7d61309a01d64aaa17be6ffdc1e5fb477f1c2a9b7906031884764655753ec5 |
"""Helper classes for doing jellium calculations."""
from math import pi
import numpy as np
from ase import Atoms
from ase.units import Bohr
from gpaw.poisson import PoissonSolver
class JelliumPoissonSolver(PoissonSolver):
"""Jellium Poisson solver."""
mask_g = None # where to put the jellium
rs ... | robwarm/gpaw-symm | gpaw/jellium.py | Python | gpl-3.0 | 2,044 | [
"ASE",
"GPAW"
] | c2f754eae5fdd8936bf361baadc7767671160679523c2b956dd14f74e151659a |
""" simple hello world job
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.DataManagementSystem.Utilities.DMSHelpers import DMSHelpers
j = Job()
j.setName(... | yujikato/DIRAC | src/DIRAC/tests/Workflow/Regression/helloWorld.py | Python | gpl-3.0 | 618 | [
"DIRAC"
] | 54ad18ad1772d677a8ddb63d8613a2c90e5740745bf173344d14b0ebab2dadad |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components... | avedaee/DIRAC | WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 87,548 | [
"DIRAC"
] | 2879ce0191e15d8e8190696068a49147d3baea9e79dda41deea124644d86360f |
from OpenGL.GLUT import *
from OpenGL.GLU import *
from OpenGL.GL import *
import sys
import random
import threading
import time
import Tank as DewTank
name = 'Galaxy War'
#Up Down Left Right
xMin = 400 - 50
yMin = 300 - 50
xMax = 400 + 50
yMax = 300 + 50
def main():
print "main hi"
tmpRen = RenderPls()... | dewtx29/python_ann | python/myGame/main.py | Python | gpl-3.0 | 3,743 | [
"Galaxy"
] | da69594623428bc2f3d39c51635f6cdbfbf4202b2e3060bd6b6c4a948cbe18a2 |
###############
# Brian Burns
# MATH 238
# ay'' + by' + cy = 0
# secondOrder.py
###############
import sys
import math
def main():
# make sure we have enough arguments
if len(sys.argv) != 4:
print("Usage: \"python secondOrder.py [a] [b] [c]\"")
sys.exit(0)
# grab the arguments
a = fl... | brnbrns/DifferentialEquations | secondOrder.py | Python | gpl-2.0 | 1,287 | [
"Brian"
] | e26edd8df316417522d8e90665c3e4758836bb4f5aae40a414f5303765ba51d3 |
#
# Copyright 2008, 2009 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 t... | dursobr/Pythics | pythics/instruments/applied_motion_stepper.py | Python | gpl-3.0 | 20,942 | [
"Brian"
] | 50da430a364f4e5a4701cd071af0d8233786ca55a57d0e1b27b6529d22997cba |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# 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.o... | coufon/neon-distributed | tests/test_recurrent.py | Python | apache-2.0 | 10,970 | [
"Gaussian"
] | 90c022c8436e40ad2702c9740053ca958afc7718b04cedd1f904f89f5623387c |
#***********************************************************************
# This code is part of CMPL
#
# Copyright (C) 2007, 2008, 2009, 2010, 2011
# Thomas Schleiff - Halle(Saale), Germany and
# Mike Steglich - Technical University of Applied Sciences
# Wildau, Germany
#
# CMPL is a project of the Techn... | Mangara/ArboralExplorer | lib/Cmpl/bin/gurobiCmpl.py | Python | apache-2.0 | 3,962 | [
"VisIt"
] | df1209634e0194b45b01181aebd7161354a1f46142273f47fc4ba9f1783da729 |
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from StringIO import StringIO
import copy
import numpy
import unittest
import datasets
# Loc... | liulion/mayavi | mayavi/tests/test_contour.py | Python | bsd-3-clause | 6,068 | [
"Mayavi"
] | a87ccdf9bee0cf419f0707c2f99884bc863d68b51151b9f959c926996f1519b3 |
"""
Provides factory methods to assemble the Galaxy web application
"""
import logging, atexit
import os, os.path, sys
from inspect import isclass
from paste.request import parse_formvars
from paste.util import import_string
from paste import httpexceptions
import pkg_resources
from galaxy.util import asbool
impo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/reports/buildapp.py | Python | gpl-3.0 | 7,937 | [
"Galaxy"
] | 07f44dea496b623512f3860c4473fb173d017c456beb7ac7a1eadf1f6238cd9e |
# Copyright 2014 Google Inc. 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 applicable law or ag... | Sorsly/subtle | google-cloud-sdk/lib/surface/test/android/run.py | Python | mit | 10,247 | [
"ESPResSo"
] | 9e315540bb2aadaa47025b049f01ea2e30000bf349dcdb06ef5f91ec32774a16 |
#!/usr/bin/env python
extras = {}
try:
from setuptools import setup
extras['zip_safe'] = False
except ImportError:
from distutils.core import setup
setup(name='futures',
version='3.0.3',
description='Backport of the concurrent.futures package from Python 3.2',
author='Brian Quinlan',
... | harlowja/pythonfutures | setup.py | Python | bsd-2-clause | 969 | [
"Brian"
] | f1e9b0c2c783d4a7668ec7d060e9dc71980fa8706fb9358db39033c7299d2afc |
"""Unit test for roman82.py
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/05 21:57:20 $"
__copyr... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage8/romantest82.py | Python | mit | 5,848 | [
"VisIt"
] | d8a6b407f465400370d88a14d5e2ee064fac83c4d15cf3184b5b83e3a159f29d |
"""
Newick format (:mod:`skbio.io.newick`)
======================================
.. currentmodule:: skbio.io.newick
Newick format (``newick``) stores spanning-trees with weighted edges and node
names in a minimal file format [1]_. This is useful for representing
phylogenetic trees and taxonomies. Newick was created ... | Kleptobismol/scikit-bio | skbio/io/newick.py | Python | bsd-3-clause | 20,610 | [
"scikit-bio"
] | f525f7f889f34408657098302e67626d59b014c68f11d10c5d3cfe6779d1d21e |
# -*- coding: utf-8 -*-
import json
import magic
import copy
import re
import pytz
import hashlib
from sqlalchemy import or_
from mock import Mock, PropertyMock
from nose.tools import (
assert_raises,
assert_equal,
assert_not_equal,
assert_true)
from jsonschema.exceptions import ValidationError
from dat... | mostlygeek/splice | tests/test_ingest.py | Python | mpl-2.0 | 62,667 | [
"VisIt"
] | 0c682eecf19a0077d1d985d78ebd0be052712c17ae9962c332a320ea963c9a15 |
# -*- coding: utf-8 -*-
#
# Collection of functions related to BAM and SAM files
#
# pysam uses 0-based coordinates
from collections import namedtuple
import os
import re
import sys
import pysam
from .chain import ChainFile
from .exceptions import G2GCigarFormatError, G2GBAMError, G2GValueError
from .g2g_utils imp... | everestial/g2gtools | g2gtools/bamsam.py | Python | gpl-3.0 | 41,096 | [
"pysam"
] | 114bf5bee3b6a23008de3699c0e7758f486a5d92ced2ed5ba48c5dd33f1e0ffb |
#Cancer Sim
from numpy import *
import scipy as sp
import pylab as py
import math
import matplotlib.cm as cm
import matplotlib.colors as colors
import matplotlib.colorbar as cb
import matplotlib.pyplot as plt
import cPickle as pickle
from scipy.spatial.distance import euclidean
from math import pow
from scipy.spat... | alexalemi/cancersim | code/cancer.py | Python | mit | 39,321 | [
"ASE",
"VMD"
] | 603caa6559b7876a06c99a04a3c4c1651095bc2a17f89a454ae8345175d6a4ad |
"""
Tests for the pipeline_info.py module
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Prabhu Ramachandran Enthought, Inc.
# License: BSD Style.
import unittest
from tvtk.api import tvtk
from mayavi.core import pipeline_info
class TestPipelineInfoTest(unittest.TestCase):
def... | dmsurti/mayavi | mayavi/tests/test_pipeline_info.py | Python | bsd-3-clause | 1,524 | [
"Mayavi"
] | 260d4e4224de5be1f9d29a00b019db59342ff3e74ede643ad2a6835077575932 |
# pylint: disable=R0913,R0914,W0201,W0622,C0302,R0902,R0903,W1001,W0612,W0613
"""Useful functions and objects used more or less everywhere."""
from __future__ import print_function
from builtins import zip
from builtins import str
from builtins import range
from builtins import object
__author__ = "Lorenzo Bolla"
i... | lbolla/EMpy | EMpy/utils.py | Python | mit | 42,390 | [
"CRYSTAL"
] | cb05930542d973a2367943c7ffc13c12eb7074a08f95d685418ef20f9b785c40 |
# -*- coding: utf-8 -*-
#LICENCE
#
# This File is part of the Webbouqueteditor plugin
# and licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
# License if not stated otherwise in a files head. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc-sa/3.0... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/BouquetEditor.py | Python | gpl-2.0 | 26,057 | [
"VisIt"
] | 6d26bbadb32a49693eb4948b1127e6d7261afa805437ba2b2ef6c7797fc94760 |
import blockbuster.bb_logging as log
import blockbuster.bb_dbconnector_factory
from blockbuster.messaging import bb_sms_handler
def go(smsrequest):
instance_name = smsrequest.instancename
blockbuster.bb_dbconnector_factory.DBConnectorInterfaceFactory().create()\
.add_analytics_record("Count", "Comma... | mattstibbs/blockbuster-server | blockbuster/workflows/command_start.py | Python | mit | 3,306 | [
"VisIt"
] | 1e82be6a04a31f39e5e642f8c9f3133a6e762877081584403d1f4cf4b34cddec |
""" The input data resolution module is a plugin that
allows to define VO input data policy in a simple way using existing
utilities in DIRAC or extension code supplied by the VO.
The arguments dictionary from the Job Wrapper includes the file catalogue
result and in principle has all the necessary inf... | rajanandakumar/DIRAC | WorkloadManagementSystem/Client/InputDataResolution.py | Python | gpl-3.0 | 6,629 | [
"DIRAC"
] | 89d450ba9079dcb09c8ee6b8bf97d8246432b942138394b360cdb399b7ce58f6 |
# GLOBAL IMPORTS
#import pysam # from pysam 0.8.1
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
class Interval(object):
"""
@class Reference
@brief Object oriented class containing informations of genomic interval
"""
#~~~~~~~~~~~~~~~~~~~~~~~~~~~... | a-slide/Find_overlap_reads | Find_overlap_read_src/Interval.py | Python | gpl-2.0 | 3,643 | [
"pysam"
] | 0e9bd3463fe1bff38903dc5cd0dfcb0b1a44a4035cdcd14fa3be1caa16cb2774 |
#! /usr/bin/env python
#
# Author: Sergey Savchenko (savchenko.s.s@gmail.com)
#
from threading import Thread
import subprocess
from math import hypot, log10, sqrt
from time import time, sleep
import urllib.request
import urllib
import sys
import os
import glob
import shutil
import argparse
import bz2
import numpy a... | latrop/sdss_downloader | sdss_downloader.py | Python | gpl-3.0 | 22,627 | [
"Galaxy"
] | dc4da2409a7cb493bc364dce9a57a6270c84382a63dd495d1daedda2b688df09 |
from typing import List, Tuple
import numpy as np
from deepchem.utils.typing import RDKitAtom, RDKitBond, RDKitMol
from deepchem.feat.graph_data import GraphData
from deepchem.feat.base_classes import MolecularFeaturizer
from deepchem.utils.molecule_feature_utils import get_atom_type_one_hot
from deepchem.utils.molecu... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/mol_graph_conv_featurizer.py | Python | mit | 8,431 | [
"RDKit"
] | 7a5083f9a02ff1ce94f69c1f353afb0a360b6866fca595f444e688a5fc25cebd |
#!/usr/bin/env python
# NOTE: multiprocessing import required for issues with nose tests.
# See: http://bugs.python.org/issue15881#msg170215
import multiprocessing
from setuptools import setup
setup(
name='reference_genome_maker',
version='0.1',
author='Church Lab',
author_email='gleb@mit.edu',
m... | churchlab/reference_genome_maker | setup.py | Python | mit | 624 | [
"Biopython"
] | 8ee618dc982f4109d146048076b99971df8300dc262bbf91afbeaa667a29cb88 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | wonderfly/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 32,431 | [
"CDK"
] | 7181a15e73d57b8ed5438e4e394aea229d5689bb0fb03103d08f5eb18164c509 |
from jasp import *
import uuid
import textwrap
# http://cms.mpi.univie.ac.at/vasp/vasp/Files_used_VASP.html
vaspfiles = ['INCAR', 'STOPCAR', 'stout', 'POTCAR',
'OUTCAR', 'vasprun.xml',
'KPOINTS', 'IBZKPT', 'POSCAR', 'CONTCAR',
'EXHCAR', 'CHGCAR', 'CHG', 'WAVECAR',
'T... | prtkm/jasp | jasp/jasp_extensions.py | Python | gpl-2.0 | 56,254 | [
"ASE",
"VASP"
] | 4604d3a9a61c85abbb7fc0d984bf871f317b9aad72da2f00f4826c492c90a288 |
# -*- 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
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | sztosz/invoices | config/urls.py | Python | bsd-3-clause | 1,230 | [
"VisIt"
] | 21db073c04536ab15980e1bec9b5a6c4884f3f2e25100e21a9cac507b907fc61 |
from rest_framework import serializers
from qmpy.analysis.vasp import Calculation
class CalculationSerializer(serializers.ModelSerializer):
class Meta:
model = Calculation
fields = (
"id",
"entry",
"composition",
"path",
"label",
... | wolverton-research-group/qmpy | qmpy/web/serializers/calculation.py | Python | mit | 544 | [
"VASP"
] | 8ab832468693f4516296a719f9e10fd6703ea7c64bf04179be4c92087352cef5 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | ankurankan/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 41,106 | [
"Gaussian"
] | 9d12d4c3849871bc76b9ce3cf3cb306efb30340ca97c4955cab29eb3a17a1468 |
# coding=utf-8
# Copyright (c) 2014 Merck KGaA
from __future__ import print_function
import os,re,gzip,json,requests,sys, optparse,csv
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import SDWriter
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
from scipy ... | soerendip42/rdkit | Contrib/pzc/p_con.py | Python | bsd-3-clause | 48,985 | [
"ASE",
"RDKit"
] | 9522915bb86d4f8384aeb825c37beef196473656d4a423bd5073c4cf6698c963 |
# Zulip Settings intended to be set by a system administrator.
#
# See http://zulip.readthedocs.io/en/latest/settings.html for
# detailed technical documentation on the Zulip settings system.
#
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development environment,
# sensible default values w... | Diptanshu8/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 16,999 | [
"VisIt"
] | b69917858bc18c9ed2b93059c7136cb972ce23e00726f3ecd42e3b49d4a22b1f |
from django.core.urlresolvers import reverse_lazy
from django.utils.translation import ugettext_lazy as _
from django.core.urlresolvers import reverse
from horizon import exceptions
from horizon import forms
import json
from crystal_dashboard.dashboards.crystal.controllers.instances import forms as instances_forms
from... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/controllers/instances/views.py | Python | gpl-3.0 | 2,229 | [
"CRYSTAL"
] | 15297b558f05ac0b24d5e55afbbbe13a9b65454365b676dd2d6ec481e8a6aeb9 |
# Copyright (C) 2007-2010 www.stani.be
#
# 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.
#
# This program is distributed... | Cobinja/Cinnamon | files/usr/share/cinnamon/cinnamon-settings/bin/imtools.py | Python | gpl-2.0 | 40,072 | [
"Gaussian"
] | 9277dea7c3d650f5fc230000313265ce899f8205bb4f88a9d174f3670032ad20 |
from pymol.wizard import Wizard
from pymol import cmd
import pymol
import types
import string
class Renaming(Wizard):
def __init__(self,old_name,mode='object',_self=cmd):
Wizard.__init__(self,_self)
self.prefix = 'Renaming \\999%s\\--- to: \\999'%old_name
self.old_name = old_name... | gratefulfrog/lib | python/pymol/wizard/renaming.py | Python | gpl-2.0 | 1,544 | [
"PyMOL"
] | ccdb97ab7209ee2b2ae190abaa5e8bec734e73ec84272c2dc831d43d12831820 |
# -*- 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 Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/lib/test/test_xlsexporter.py | Python | gpl-2.0 | 1,981 | [
"VisIt"
] | f71c0f9cfca8765778b307420eecbc95cb4836e03be9b52efa1d230032caea8a |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | aurofable/medhack-server | venv/lib/python2.7/os.py | Python | mit | 26,300 | [
"VisIt"
] | 1516262162cb0023c1b944fd8259cbd2b75a6fe6616c3e5df19d35d577f0d72f |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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.
import os
import os.path
from _paml import Paml, PamlError, _relpath
import _parse_codeml
... | asherkhb/coge | bin/last_wrapper/Bio/Phylo/PAML/codeml.py | Python | bsd-2-clause | 9,214 | [
"Biopython"
] | fc10069f0e654f20f1d4157f949e8ff62a0757f09feb9b81dee41eee19645a29 |
#
# @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 file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/diatomic.py | Python | lgpl-3.0 | 10,978 | [
"Psi4"
] | f83cf68e0eaa722564f91828ecc276bcc1330f0a695f4df0ce52be6545fced64 |
import re
from distutils.core import setup
def get_version_string():
version_file = "vqsr_cnn/_version.py"
version_str_line = open(version_file, "rt").read()
version_regexp = r"^__version__ = ['\"]([^'\"]*)['\"]"
re_out = re.search(version_regexp, version_str_line, re.M)
if re_out is not None:
... | magicDGS/gatk | src/main/python/org/broadinstitute/hellbender/setup_vqsr_cnn.py | Python | bsd-3-clause | 999 | [
"Biopython",
"pysam"
] | a39c152f5ff0d22d436b0190b240f2bfb35ea54b994f62fafc9ddcc72af28590 |
from build.management.commands.base_build import Command as BaseBuild
from django.conf import settings
from protein.models import Protein, ProteinSegment, ProteinConformation, ProteinState
from structure.models import Structure, Rotamer
from structure.functions import BlastSearch
from Bio.Blast import NCBIXML, NCBIWWW
... | protwis/protwis | protein/management/commands/pairwise.py | Python | apache-2.0 | 1,185 | [
"BLAST"
] | a230c68e510d232084d142b54608603e76480b48e4ab475b9f6e473c77b7bdc4 |
import android, sys, threading, time
def set_parse_options():
parser = OptionParser()
parser.add_option("-a", "--adb_lport", dest="adb_lport", type="int",
help="local port that adb will forward too")
parser.add_option("-b", "--adb_rport", dest="adb_rport", type="int",
help... | deeso/python_scrirpts | convert_android_result_to_gpgll.py | Python | apache-2.0 | 3,598 | [
"ASE"
] | bafcfd43fe86764babf655f2169c01bb5ccf80ff620a8c4bb67ff4333db48414 |
# AUTHOR: Diego Paris drp2121@columbia.edu
import os
from Bio.Blast import NCBIXML as xmlparse
# searchSpecies must be a string, the name of the species being searched for as reported by the classifier
# xmls must be an array of absolute file paths to .xmls
# speciesDict must be the output of the xmls having been run... | blt2114/gen_snacks | Assignment_2/question3_pt1/confusionMat.py | Python | gpl-2.0 | 2,828 | [
"BLAST"
] | 23c9e9b97bb1da846f1e2e57826542cc50c7d4db82071ffd0a83255d6793771c |
import logging
from ray.rllib.agents.trainer import with_common_config
from ray.rllib.agents.dqn.dqn import GenericOffPolicyTrainer
from ray.rllib.agents.ddpg.ddpg_tf_policy import DDPGTFPolicy
logger = logging.getLogger(__name__)
# yapf: disable
# __sphinx_doc_begin__
DEFAULT_CONFIG = with_common_config({
# ===... | richardliaw/ray | rllib/agents/ddpg/ddpg.py | Python | apache-2.0 | 7,642 | [
"Gaussian"
] | e7127c5702a063c17797469bfa6787ac144a1c250497f918de878df0269e771c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module implements various transmuter classes.
Transmuters are essentially classes that generate TransformedStructures from
various data sources. They enable the... | Bismarrck/pymatgen | pymatgen/alchemy/transmuters.py | Python | mit | 16,738 | [
"VASP",
"pymatgen"
] | 1959a6bee3428b29125609a03ec3910d3a6c5921e20bac4443a45f33e319e9b7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Airscript-ng - A script to conduct simple WiFi audits with ease.
# Copyright (C) 2018 Yudhajit N. (Sh3llcod3)
#
# 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
# t... | Sh3llcod3/Aircrack-ng | airscript-ng.py | Python | gpl-3.0 | 27,707 | [
"VisIt"
] | ca8400709c4c3bc3d2c23e1a28a1018d59a1570154e9971013a96ff45646c6c6 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
from distutils.vers... | Midrya/chromium | git_cl.py | Python | bsd-3-clause | 133,721 | [
"VisIt"
] | 7205429025983a82faf9602b425c787a3ab8e15990a0ba7558b8e75bdb49154b |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['Aperture', 'Aperture_Watchpoint', 'Watchpoint']
for el_name in names:
... | mkeilman/sirepo | tests/template/srw_generate_data/tabulated-undulator-example.py | Python | apache-2.0 | 22,553 | [
"Gaussian"
] | 2f3e8e700695fab650dc0965fb5e77275c5b2da75bb3fcb436967c0887d2aa0d |
# Copyright (c) 2000-2010 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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 2 of the License, o... | dbbhattacharya/kitsune | vendor/packages/pylint/pyreverse/diadefslib.py | Python | bsd-3-clause | 8,190 | [
"VisIt"
] | 03fd1753a0f0648fecbc5c49116e892ebe699b4b8ac1ecf0a6b6cb7391674992 |
"""
[2015-03-13] Challenge #205 [Hard] DNA and Protein Sequence Alignment
https://www.reddit.com/r/dailyprogrammer/comments/2yx8b8/20150313_challenge_205_hard_dna_and_protein/
#Description
If you are studying a particular pair of genes or proteins, an important question is to what extent the two sequences
are similar... | DayGitH/Python-Challenges | DailyProgrammer/DP20150313C.py | Python | mit | 3,971 | [
"BLAST"
] | 2532a2960f88066980a566ad2658762d1031c107fb6f52b2cf2d9b6aa7d7939a |
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