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from __future__ import print_function
"""
NBody in N^2 complexity
Note that we are using only Newtonian forces and do not consider relativity
Neither do we consider collisions between stars
Thus some of our stars will accelerate to speeds beyond c
This is done to keep the simulation simple enough for teaching purpose... | bh107/benchpress | benchpress/benchmarks/nbody/python_numpy/nbody.py | Python | apache-2.0 | 3,326 | [
"Galaxy",
"Gaussian"
] | 0d051e032f2518472143696916a8e5e637450556be135fbbb415fae44174967a |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | mlperf/training_results_v0.5 | v0.5.0/google/research_v3.32/gnmt-tpuv3-32/code/gnmt/model/t2t/tensor2tensor/models/mtf_transformer.py | Python | apache-2.0 | 43,327 | [
"MOE"
] | 10c12d9c3134d9b7342662e3c0d7893c6eed25f5cd5bc667405beb2df49f2d67 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# 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 option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/orca_platform.py | Python | gpl-3.0 | 1,404 | [
"ORCA"
] | 73daa779530d0f13bbf9084065b5c2360aabc759ec6b5a3c3ab52d94834ca346 |
"""
parser.http.movieParser module (imdb package).
This module provides the classes (and the instances), used to parse the
IMDb pages on the akas.imdb.com server about a movie.
E.g., for Brian De Palma's "The Untouchables", the referred
pages would be:
combined details: http://akas.imdb.com/title/tt0094226/combi... | p4u/hmdb | imdb/parser/http/movieParser.py | Python | agpl-3.0 | 79,826 | [
"Brian"
] | 92d0a4672da0212e6a33859d9ba3754f213369b1864658dffc4416835e8e4b63 |
# -*- coding: utf-8 -*-
# Copyright 2020 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... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_index_service.py | Python | apache-2.0 | 87,670 | [
"Octopus"
] | 0d9deebb00612f7c9dd17ad7195974483fb164760ced20279e06815446f9b6ed |
#!/usr/bin/env python
desc="""Heterozygous genome assembly pipeline. It consists of three steps:
reduction, scaffolding and gap closing.
More info at: http://bit.ly/Redundans
TBA:
- reduction
- split contigs on likely problems (fasta2qc.py)
- add exception if lastdb or lastal doesn't finish successfully
- pyScaf sh... | lpryszcz/redundans | redundans.py | Python | gpl-2.0 | 25,135 | [
"BWA"
] | 4c59b54d338a62e2ac23365d6e0995eecc27b92c31597eb14a191b8d15594e07 |
#!/usr/bin/env python
import sys
import subprocess
import shlex
if __name__ == '__main__':
failures = []
if len(sys.argv) < 4:
print 'Usage: %s <alexalist.csv> <top-x-sites> <iterations>' % sys.argv[0]
exit(1)
top_x_sites = int(sys.argv[2])
iterations = int(sys.argv[3])
success =... | cs-au-dk/Artemis | artemis-code/tests/alexa/run.py | Python | gpl-3.0 | 1,441 | [
"VisIt"
] | 28b82b255c2441edf5311f36b8011ade091374a96184b85f76af0d4d9d8da48c |
"""Stores properties associated with the class of an object (DEPRECATED).
This module is deprecated, and is expected to be removed in the next release.
If you use this module, please contact the Biopython developers via the
mailing lists.
"""
#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC
# Wou... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PropertyManager.py | Python | gpl-2.0 | 2,895 | [
"Biopython"
] | f6f12967522d86ac39dc4de436719808e2366ac6c5e54974d8fa9e6f3d835e14 |
#!/usr/bin/env python
"""
Read a maf and print the text as a fasta file.
"""
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
from galaxy.tools.util import maf_utilities
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
... | dbcls/dbcls-galaxy | tools/maf/maf_to_fasta_multiple_sets.py | Python | mit | 1,574 | [
"Galaxy"
] | 0ecbee092279720247f53c01febda8d75de9d928e5f5e26c46e3cb0a681fdbc0 |
"""
test_Record.py
This file is part of ANNarchy.
Copyright (C) 2013-2016 Joseph Gussev <joseph.gussev@s2012.tu-chemnitz.de>,
Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public L... | ANNarchy/ANNarchy | tests/Unittests/test_Record.py | Python | gpl-2.0 | 7,815 | [
"NEURON"
] | 49161febdcfb38b481547d9b5a41333ef325d5cd26df68a848961b43deba0c31 |
"""
Created on Apr 8, 2013
@author: briank
USB_driver.py - USB Driver module.
This will interface various PyHouse modules to a USB device.
This may be instanced as many times as there are USB devices to control.
This should also allow control of many different houses.
"""
__updated__ = '2019-10-08'
__author__ = '... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Drivers/Usb/Driver_Hid.py | Python | mit | 8,343 | [
"Brian"
] | e0b0a2f17bdff369cc8f7d3b1a00323f639d1e6745bd5b0509e5f78cb5462b7b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Example script for evaluation with the nc2map module
This script is part of the nc2map Python module, version 0.0b.
It's a quite advanced script showing you the main features in the (currently
implemented) fldmean and violin plot evaluation routines.
It creates the outp... | Chilipp/nc2map | demo/evaluators_demo.py | Python | gpl-2.0 | 4,806 | [
"NetCDF"
] | 33b0023a14b0a323ccc8d998ec491f65fd4ef8018b20a7322d5eacff69267903 |
from __future__ import (absolute_import, division, print_function)
import os
import numpy as np
from mantid import config, mtd, logger
from mantid.kernel import StringListValidator, Direction
from mantid.api import PythonAlgorithm, MultipleFileProperty, FileProperty, \
WorkspaceGroupProperty, FileAction, Progress
... | ScreamingUdder/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLEnergyTransfer.py | Python | gpl-3.0 | 17,107 | [
"CRYSTAL"
] | f0c5dcc7ee5769d3b6e63accef87362fa966b6d5208c97baa38b68b0caaee89a |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/tree_view.py | Python | gpl-3.0 | 1,393 | [
"Brian"
] | c2b172e75a097f04ed6290ea682e833e5e13c226dd60c6f589c5ddc9c7ff08f0 |
# -*- coding: utf-8 -*-
"""
===================================================================
Determining and plotting the altitude/azimuth of a celestial object
===================================================================
This example demonstrates coordinate transformations and the creation of
visibility cur... | stargaser/astropy | examples/coordinates/plot_obs-planning.py | Python | bsd-3-clause | 6,298 | [
"VisIt"
] | c70e746177c9963a5fbaf04e61d0f2d02b990385eaf2c901d6857a53b6358b57 |
#!/usr/bin/env python3
import sys
import argparse
import numpy as np
from mapTools import *
from utilities import filesFromList, writeLog
from plotTools import addImagePlot
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@helsinki.fi
University of Helsinki &
... | mjsauvinen/P4UL | pyRaster/rasterTileSuperposition.py | Python | mit | 5,276 | [
"Gaussian"
] | 0bbd6f161028550ca7e5ceb9e4cec3c9e1bb38457934ce6c7e239f22df336830 |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# 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 Licens... | tuffy/python-audio-tools | audiotools/vorbiscomment.py | Python | gpl-2.0 | 25,399 | [
"Brian"
] | f7cf3e929d28677311bdef3ee4dc11ad3fabfa5f9cc97ed159022402dd357172 |
"""Support for Ecobee Thermostats."""
import collections
from typing import Optional
import voluptuous as vol
from homeassistant.components.climate import ClimateDevice
from homeassistant.components.climate.const import (
HVAC_MODE_COOL,
HVAC_MODE_HEAT,
HVAC_MODE_AUTO,
HVAC_MODE_OFF,
ATTR_TARGET_T... | joopert/home-assistant | homeassistant/components/ecobee/climate.py | Python | apache-2.0 | 24,128 | [
"VisIt"
] | 230c18f5a01891850327d7077baddfa5dc7ad2fdbbab40d5d7071be887d8dd27 |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_global_operations.py | Python | apache-2.0 | 87,954 | [
"Octopus"
] | cef7c48cb303b4065119b7c5c942fc6f6e0c8cd5e2a35d9a4aaf480f3874450d |
"""
The B{0install add-feed} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import SafeException, _
from zeroinstall.support import tasks, raw_input
from zeroinstall.cmd import Us... | rammstein/0install | zeroinstall/cmd/add_feed.py | Python | lgpl-2.1 | 3,489 | [
"VisIt"
] | a4ffbd3b63d7fc10f3e402cd83b04c078a08781f3ff731cd00ae7ba4f7715123 |
""" This is a test of the chain
ReqClient -> ReqManagerHandler -> ReqDB
It supposes that the DB is present, and that the service is running
"""
# pylint: disable=invalid-name,wrong-import-position
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import unittest
import sys
from DIRAC i... | andresailer/DIRAC | tests/Integration/RequestManagementSystem/Test_Client_Req.py | Python | gpl-3.0 | 12,304 | [
"DIRAC"
] | 87814d071aaad2ffe26c345318ef6166b1e5ccaf1a88a21be9e8fae2e83e150c |
import psi4
import re
import os
import inputparser
import math
import warnings
from driver import *
from wrappers import *
from molutil import *
import p4util
from psiexceptions import *
def run_fvno(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
fvno can be called via ... | lothian/fvno | pymodule.py | Python | lgpl-3.0 | 1,180 | [
"Psi4"
] | d1b1cc5cc341185f6aa1d647d62eea5e349889c73b70306c9af83315b2775432 |
"""
gpo.py - optimization using Gaussian process regression.
Marcus Frean.
usage: python gpo.py [datafile]
Reads a initial set of input vectors (x) from the file. Output (y)
values for these (and any future) x are given by one of the functions
in testFunctions.py
The task is then to choose where to sample next.
E... | garibaldu/ego-demo | safe-demo-gpo.py | Python | gpl-2.0 | 7,832 | [
"Gaussian"
] | fcdc6de0731d7946a57331b304ed34f21bc26297502d466b1513895148c3e7df |
# $HeadURL$
"""
Collection of DIRAC useful network related modules
by default on Error they return None
getAllInterfaces and getAddressFromInterface do not work in MAC
"""
__RCSID__ = "$Id$"
import socket
import urlparse
import struct
import array
import os
import fcntl
import platform
from DIRAC.Core.Utilit... | Sbalbp/DIRAC | Core/Utilities/Network.py | Python | gpl-3.0 | 3,982 | [
"DIRAC"
] | 06b021f9bfa466c0a6c6143c1976a3e200b8149e2085df6a4a32a25ef9330e33 |
from ase.transport.calculators import TransportCalculator
import numpy as np
#Aux. function to write data to a text file.
def write(fname,xs,ys):
fd = open(fname,'w')
for x,y in zip(xs,ys):
print >> fd, x, y
fd.close()
H_lead = np.zeros([4,4])
# On-site energies are zero
for i in range(4):
H_... | freephys/python_ase | ase/transport/test_transport_calulator.py | Python | gpl-3.0 | 2,194 | [
"ASE"
] | 50976375eb87447f755c0a5077971bf1d4808d813302dfb5bada3aacef3c010e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import warnings
import numpy
from monty.serialization import loadfn
from pymatgen.core.lattice import Lattice
from pymatgen.electronic_structure.bandstructure import (
BandStructure... | materialsproject/pymatgen | pymatgen/electronic_structure/tests/test_bandstructure.py | Python | mit | 24,824 | [
"VASP",
"pymatgen"
] | 04c48a4a98376dc2845af2e37d3cc509614bf866facd86ef59ef76c986c2bfbc |
from rdkit import RDConfig, rdBase, Chem
from io import StringIO, BytesIO
from rdkit.Chem import PandasTools
import numpy
import unittest
import tempfile
import shutil
import os
import gzip
import doctest
if (getattr(doctest, 'ELLIPSIS_MARKER')):
doctest.ELLIPSIS_MARKER = '*...*'
try:
import IPython
except ImportE... | bp-kelley/rdkit | rdkit/Chem/UnitTestPandasTools.py | Python | bsd-3-clause | 13,642 | [
"RDKit"
] | 431297f49fbb6c8103ab5dd395c737f09283a8ae5d3e981dd76db502b55be44f |
#!/usr/bin/env python2
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import re, th... | drxaero/calibre | src/calibre/ebooks/metadata/sources/base.py | Python | gpl-3.0 | 22,345 | [
"VisIt"
] | 3f91795d0dc27d7e3ee2f2473c57d551f49b0548687e6b8290fa1793ae3828b2 |
def makemask(snpath, color):
from config import datb, prog, path
import numarray, pyfits, os
id = readcat(snpath,color)
rawim = pyfits.open(path + snpath + "/" + color + "/reg" + color + "seg.fits")
imageseg = rawim[0].data
mask = replacewithzero(... | deapplegate/wtgpipeline | mstatlib.py | Python | mit | 32,305 | [
"Galaxy"
] | 64d79a55259bfe5cea1154051ca259fac808c7181023d401ce2009f4ebc1c111 |
from django.shortcuts import get_object_or_404, render, redirect
from django.core.urlresolvers import reverse
from django.http import HttpResponse, HttpResponseRedirect
from django.core.serializers import serialize
from django.db.models import Count, Max
from django.contrib.auth import logout
from django.contrib.aut... | mattblair/pdx-trees-django | trees/views.py | Python | mit | 10,663 | [
"VisIt"
] | 0a56d9f5d07064442df145b8ad00f472199d90828218e8ba0cd322d2eb215196 |
'''
This file contains input output code that runs against the large .tsv files.
author: David Thaler
date: July 2015
'''
import csv
import os
import pdb
import cPickle
import datetime
import re
import features
BASE = '/Users/davidthaler/Documents/Kaggle/avito2'
DATA = os.path.join(BASE, 'data')
PROCESSED = os.path.j... | davidthaler/Kaggle_Avito-2015 | avito2_io.py | Python | mit | 14,081 | [
"VisIt"
] | fe0ae26f8c8512165517a02a131058f1f9f49edc461e5481eee445097fa1a873 |
from __future__ import print_function
import eventlet
eventlet.monkey_patch()
import logging
import oslo_messaging
import time
from pyconejo import core
from oslo_config import cfg
LOG = logging.getLogger('pyconejo.oslo_rpc_server')
def setup_options(argv=None):
parser = core.common_options_server(description=... | freyes/pyconejo | pyconejo/oslo_rpc_server.py | Python | gpl-3.0 | 3,016 | [
"exciting"
] | b7382aad8b4e2d6882692deb8a818659c186fac453db641a38fc4cf259dca6f6 |
# -*- coding: utf-8 -*-
import datetime
import random
import string
from lxml.html import parse
from urllib import urlencode
from urllib2 import urlopen
from urlparse import urljoin
from urlparse import urlparse
from openerp import models, fields, api, _
def VALIDATE_URL(url):
if urlparse(url).scheme not in ('h... | OpusVL/odoo | addons/website_links/models/website_links.py | Python | agpl-3.0 | 9,130 | [
"VisIt"
] | 2382f143dab8a2c70916e2312454f05ae04342ec2e86258ed457100371afc096 |
"""
Copyright (c) 2011-2015 Nathan Boley
This file is part of GRIT.
GRIT 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.
GRIT is distribut... | nboley/grit | grit/files/reads.py | Python | gpl-3.0 | 41,726 | [
"pysam"
] | 47db80ba016df5a0dc5513487ff68188767fe088e0d8fff085c644bb57bd0d88 |
#!/usr/bin/env python
#%%
import ca_source_extraction as cse
import glob
from ipyparallel import Client
import matplotlib as mpl
mpl.use('TKAgg')
from matplotlib import pyplot as plt
import numpy as np
import os
import psutil
import pylab as pl
from scipy.sparse import coo_matrix
import shutil
import subprocess
import... | simonsfoundation/CaImAn | SLURM/demo_slurm.py | Python | gpl-2.0 | 4,379 | [
"NEURON"
] | 95fa33963e8aa33a8e5150b37db922b836f0c075beaec086aaf56457d6c85d15 |
"""
enerpy
gaussian error propagation with arbitrary precision, using the decimal module
"""
from enum import Enum
from decimal import Decimal as D
from decimal import getcontext
FUNCTIONS1 = ["Add", "Sub", "Mul", "Div", "Pwr", "Root", "Exp", "Log"]
# Importing enerpy with "from enerpy import *" will only include... | decathorpe/enerpy | enerpy/__init__.py | Python | gpl-2.0 | 12,599 | [
"Gaussian"
] | 572e8e77b1aa9bc6721b3fc193640c54fd8eeba75eef1548a3200e15b1c21d54 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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, or
# (at your... | pmghalvorsen/gramps_branch | gramps/gen/proxy/living.py | Python | gpl-2.0 | 15,357 | [
"Brian"
] | e51cd71014bc2e7eb0dbba240543eb07bfea93b32399d136f59c6bc7094d1b04 |
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Shape(_BaseLayoutHierarchyType):
# class properties
# --------------------
_parent_path_str = "layout"
_path_str = "layout.shape"
_valid_props = {
"editable",
"fillcolor... | plotly/python-api | packages/python/plotly/plotly/graph_objs/layout/_shape.py | Python | mit | 38,072 | [
"VisIt"
] | 105ca6a1e1753afd29463ebe7224c765450859759e0f212db7ffc9b2ffea78bc |
from django.conf.urls import url
from crystal_dashboard.dashboards.crystal.policies.policies import views
urlpatterns = [
url(r'^create_static_policy/$', views.CreateStaticPolicyView.as_view(), name='create_static_policy'),
url(r'^create_dynamic_policy/$', views.CreateDynamicPolicyView.as_view(), name='create_... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/policies/policies/urls.py | Python | gpl-3.0 | 764 | [
"CRYSTAL"
] | 2218ba3b2ab53fc525cb389ba72971e3b419ae8e1f4d112b1b3e06c5293dfabf |
# Copyright (C) 2012,2013,2016
# 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 terms of ... | espressopp/espressopp | src/analysis/Configurations.py | Python | gpl-3.0 | 3,525 | [
"ESPResSo"
] | 23742104579df4c777a4f7ed6903f2c277115d6f186c491072021fd8758b712b |
#!/usr/bin/env python
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Can... | adamcandy/QGIS-Meshing | plugins/mesh_surface/scripts/NcTools.py | Python | lgpl-2.1 | 6,588 | [
"NetCDF"
] | 89b68f08e78baf2fb840396c4dbfe981550d80d9d0cd5e3732fc8239bba60fc4 |
import vigra
from vigra import graphs
# parameter:
filepath = '12003.jpg' # input image path
sigmaGradMag = 2.0 # sigma Gaussian gradient
superpixelDiameter = 10 # super-pixel size
slicWeight = 10.0 # SLIC color - spatial weight
gamma = 0.15 # exp(-gamma * edgeIndicator)
edgeThreshold = 2.5... | timoMa/vigra | vigranumpy/examples/graph_smoothing.py | Python | mit | 626 | [
"Gaussian"
] | ad6a0e0b6056248a1884dd2ee864d9a9f58d6ee0baa9f224d70d7db472e44fc9 |
# Copyright 2008-2010 by Peter Cock. All rights reserved.
#
# 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.
"""
Bio.AlignIO support for the "nexus" file format.
You are expected to use this module v... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/AlignIO/NexusIO.py | Python | gpl-2.0 | 7,161 | [
"Biopython"
] | 95ced07a6dd4b6acdf9bc60f82ae4c5c168d64c5a93b2fa4f548165263a365c2 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import analytics
import waffle
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.storage import staticfiles_storage
from django.core.mail import se... | miptliot/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 48,374 | [
"VisIt"
] | ea0e64cc0853a9b951871b3fa882eb7a08a07bcb1387e63eceb88b2764f0ba78 |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""This module contains functions related to various energy components."""
import sys
import numpy as np
from collections import OrderedDict
class Energy(object):
"""This class handles all energy related functions."""
def __init__(self, job):
"""Initiali... | jdcapa/MolecularToolbox | moleculartoolbox/energy.py | Python | gpl-3.0 | 3,931 | [
"CFOUR",
"ORCA"
] | 5f44f17c7627da89850bf37a4aae04c5e4a60b784a25767efe2000d1a3804dc8 |
########################################################################
# $HeadURL $
# File: OperationHandlerBaseTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 08:09:08
########################################################################
""" :mod: OperationHandlerBaseTests
==============... | andresailer/DIRAC | RequestManagementSystem/Service/test/OperationHandlerBaseTests.py | Python | gpl-3.0 | 2,527 | [
"DIRAC"
] | bf7782d8e1541ebf4cf9534758014b4df4a42419bf3f00ca04ee15d4ace09bae |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 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 ... | kannon92/psi4 | psi4/driver/qcdb/libmintsmolecule.py | Python | gpl-2.0 | 124,679 | [
"Elk",
"Psi4"
] | 5232ff546d7fb9a2ed54563595414fc612d0d85209004a1ba2eb9cf4a181d9da |
"""
Forcefield.py
This module takes a pdblist as input and replaces the occupancy and
tempfactor fields with charge and radius fields, with values as defined
by a particular forcefield. The forcefield structure is modeled off of
the structures.py file, where each forcefield is considered a chain o... | MonZop/BioBlender | bin/pdb2pqr-1.6/src/forcefield.py | Python | bsd-2-clause | 34,641 | [
"Amber",
"CHARMM"
] | 3eb4f04f79c393ce1b925db9544a53f006ac1bf0abfb3361c4c4b13b1f922a7b |
"""
Two electron integral evaluation using Rys polynomials.
References:
ABD: Augspurger, Bernholdt, and Dykstra. 'Concise, Open-Ended
Implementation of Rys Polynomial Evaluation of Two-Electron
Integrals.' J. Comp. Chem. 11 (8), 972-977 (1990).
Special thanks to Cliff Dykstra for providing a working v... | berquist/PyQuante | PyQuante/rys.py | Python | bsd-3-clause | 82,427 | [
"GAMESS"
] | 036120787dd0ccf43ca02c8f4111435236db43dbe79b70c0eb5c85d1ec192c28 |
# -*- coding: utf-8 -*-
import moose
import re
def fixPath(path):
path = re.sub(r'/+', '/', path)
return path
paths = [ '/a'
, '//a'
, '/a/b'
, '/a/b/'
, '//a//b/////'
, '/a/./b'
, '///a/././b'
]
expectedPath = set([fixPath(p) for p in paths])
expectedC... | upibhalla/moose-core | tests/python/test_moose_paths.py | Python | gpl-3.0 | 679 | [
"MOOSE"
] | e772e3f0b43e87c27de3719a7f01444b9699dd4fa6ab6c4499ca6a909a36d7c4 |
##
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
#
# Copyright:: Copyright 2013-2019 CaSToRC, The Cyprus Institute
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
# $Id$
#
##
"""
Easybuild support for building NAMD, implemented as an easyblock
@autho... | pescobar/easybuild-easyblocks | easybuild/easyblocks/n/namd.py | Python | gpl-2.0 | 9,061 | [
"NAMD"
] | cb2a393cc0f9b1b9c2bf10587e10d79601d06afef8fc612c0992a32dfa1245d9 |
def listNames():
names = [
'Aaron',
'Aaron',
'Abbey',
'Abbie',
'Abby',
'Abdul',
'Abe',
'Abel',
'Abigail',
'Abraham',
'Abram',
'Ada',
'Adah',
'Adalberto',
'Adaline',
'Adam',
'Adam',
'Adan',
'Addie',
'Adela',
'Adelaida',
'Adelaide... | dalmoz/CAPLex | heads/lists.py | Python | gpl-3.0 | 79,657 | [
"Amber",
"Brian",
"COLUMBUS",
"CRYSTAL",
"Dalton",
"Desmond"
] | a3f5a70848ae93f2b82b8c11e3c736a3bd9683226d1f3b1999e21172130f7ad3 |
from django.db import models
from django.core.urlresolvers import reverse
from edc.subject.registration.models import RegisteredSubject
from edc_base.model.models import BaseUuidModel
from lis.specimen.lab_aliquot.managers import AliquotManager
from lis.specimen.lab_aliquot.models import BaseAliquot
from .aliquot_co... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_lab/models/aliquot.py | Python | gpl-2.0 | 3,573 | [
"VisIt"
] | 4630121c803ac0661e6b524b793d9d675dbf1588b1a7155eaee4de17f31daa17 |
"""
focus field (psf) calulcations for a single beam originating from objectives
with ring like (gaussian) and annulus (bessel ) pupil functions
via the Debye Wolf integral
see e.g.
Foreman, M. R., & Toeroek, P. (2011). Computational methods in vectorial imaging.
Journal of Modern Optics, 58(5-6)
"""
from __futu... | maweigert/biobeam | biobeam/core/focus_field_beam.py | Python | bsd-3-clause | 9,427 | [
"Gaussian"
] | 061d7cec35a84ea6be2d67bfeee9d7e469d5286bfadd55163a9832cd1b039f6c |
# This file is part of the Manycore Form Compiler.
#
# The Manycore Form Compiler 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.
#
# T... | gmarkall/manycore_form_compiler | mcfc/expression.py | Python | gpl-3.0 | 12,564 | [
"VisIt"
] | dbbef23dc9e6819c9f5c27ec6f6c158985e66f91ac017ff1a97278bbfdfc4d4b |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=invalid-name
from __future__... | mganeva/mantid | scripts/Interface/reduction_gui/widgets/inelastic/dgs_pd_sc_conversion.py | Python | gpl-3.0 | 5,097 | [
"CRYSTAL"
] | 112b3dd723e93b09f570393aef7cbb97d5328aa389a0c34d8af2dfc5a9d06da4 |
#########################################################################################
# $HeadURL$
# SLURM.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" SLURM.py is a DIRAC independent class representing SLURM batch system.
SLURM obj... | miloszz/DIRAC | Resources/Computing/BatchSystems/SLURM.py | Python | gpl-3.0 | 6,551 | [
"DIRAC"
] | ae6a8e58839ca82d6c18ea707557b25e79f6c74ac81c427613f4b3e512a5e882 |
import numpy as np
import tensorflow as tf
import tensorflow.contrib.slim as slim
from tensorflow.contrib.layers.python import layers as tf_layers
from models.conv_lstm import basic_conv_lstm_cell, conv_lstm_cell_no_input
# Amount to use when lower bounding tensors
RELU_SHIFT = 1e-12
FC_LAYER_SIZE = 1000
FC_LSTM_LAYE... | jonasrothfuss/DeepEpisodicMemory | models/model_zoo/model_conv5_fc_lstm2_1000_deep_64.py | Python | mit | 11,709 | [
"Gaussian"
] | e0c1a18476bac30c4ac08aaea35b5cce3209caf8f37044ad0a058cf1eefdf06d |
""" ResourceStatusClient
Client to interact with the ResourceStatus service and from it with the DB.
"""
# pylint: disable=unused-argument
from DIRAC import S_OK
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.FrameworkSy... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Client/ResourceStatusClient.py | Python | gpl-3.0 | 18,357 | [
"DIRAC"
] | 2d54bdab8f07a44407980a4a2e8ec1553af9477645edb49e7c9a654e296b9084 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
from builtins import object
import numpy as np
from scipy import optimize, special
class _baseFunctionFit(object):
"""Not needed by most users except as a superclass for developing
your own functio... | hoechenberger/psychopy | psychopy/data/fit.py | Python | gpl-3.0 | 8,441 | [
"Gaussian"
] | 869d4a714425ebc3167248efc140755c421ee630156b146b36522a4a1679e597 |
from setuptools import setup, find_packages
def parse_requirements(filename):
""" load requirements from a pip requirements file """
lineiter = (line.strip() for line in open(filename))
return [line for line in lineiter if line and not line.startswith("#")]
version = '0.9.2'
LONG_DESCRIPTION = """
======... | capless/kev | setup.py | Python | gpl-3.0 | 1,402 | [
"Brian"
] | eb60b35a58e35608facddbf40d91b3693474493d2848d3caf06333d708ff5330 |
#! /usr/bin/python3.9
import sys
import os
import rdkit
from rdkit import Chem
from rdkit.Chem import Descriptors, inchi
from rdkit.Chem.rdMolDescriptors import CalcMolFormula
from pubchempy import get_compounds, Compound
import json
import db_preprocessor
from collections import Counter
from chemicals import serializ... | CalebBell/chemical-metadata | scifinder-inorganic/generate_db.py | Python | mit | 7,165 | [
"RDKit"
] | 97283dc7c6323e1db73c05a3cd539a792079658524cafb550c04e09e96f595b9 |
# $Id$
#
# Copyright (C) 2003-2008 greg Landrum and 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.
#
"""unit testing code ... | AlexanderSavelyev/rdkit | rdkit/ML/UnitTestScreenComposite.py | Python | bsd-3-clause | 10,507 | [
"RDKit"
] | 75d50dfc877a1e0e7a29d51c6d0bffb381919ed304f1e70ef3cadf219a3a8626 |
#!/usr/bin/env python
import sys
import numpy as nmp
from os import system
from netCDF4 import Dataset
from string import replace
if len(sys.argv) != 2:
print 'Usage: '+sys.argv[0]+' <nemo_bathy.nc>'
sys.exit(0)
cf_old = sys.argv[1]
cf_new = replace(cf_old, '.nc', '_new.nc')
cv_bathy = 'Bathymetry'
... | plesager/barakuda | python/exec/.old/orcaX_edit_bathy.py | Python | gpl-2.0 | 740 | [
"NetCDF"
] | b6276f2e1572a8119388fe618e8909d55ddec79f54b94db2aa2b489dfc6e8018 |
import atmPy.atmos.water as water
class TestWater(object):
def __init__(self):
self.T = range(-40, 40, 20)
self.RH = range(25, 100, 25)
# Dewpoint caluclations are from Brian McNoldy's dewpoint calcuator at
# http://andrew.rsmas.miami.edu/bmcnoldy/Humidity.html
... | mtat76/atm-py | atmPy/atmos/tests/test_water.py | Python | mit | 1,133 | [
"Brian"
] | b4a81cac7ae220b78e4153b1395480996e046dca5a95706cd2d03cf2415bec5d |
#!/usr/bin/env python
# Copyright (C) 2011-2014 Swift Navigation Inc.
# Contact: Fergus Noble <fergus@swift-nav.com>
#
# This source is subject to the license found in the file 'LICENSE' which must
# be be distributed together with this source. All other rights reserved.
#
# THIS CODE AND INFORMATION IS PROVIDED "AS IS... | mfine/piksi_firmware | scripts/acq_plot.py | Python | gpl-3.0 | 967 | [
"Mayavi"
] | 385f7e08a571582b67d18ab68277c62d4e45dd50a171249172c85c07fcb83f5f |
from gromacs.fileformats import TOP
import numpy as np
import math
import copy, argparse
def scale_angles(mol, angles):
new_angles = {}
for dh in mol.angles:
atypes = dh.atom1.get_atomtype(), dh.atom2.get_atomtype(), dh.atom3.get_atomtype()
atypes = [a.replace("_", "").replace("=","") for a in atypes]
for is... | pslacerda/GromacsWrapper | scripts/gw-forcefield.py | Python | gpl-3.0 | 4,538 | [
"Gromacs"
] | be2bd556a3df93d91ec0bf9b062e70dcd2ca8182a060896c4b639c8d544e0a37 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 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... | andrebellafronte/stoq | tests/__init__.py | Python | gpl-2.0 | 966 | [
"VisIt"
] | edaab89d1e5a2609c5222b91bb101268a12f1b131c5d84ac298bd031d23ae6b4 |
import signal_processing as sig_proc
import pickle
from matplotlib import pyplot as plt
import copy
import random as rnd
import math
import numpy as np
def plot_spikes_classified_mod(spikes_values, spike_count, threshold_template, template, extra_text=''):
if spike_count > spikes_values.shape[0]:
spike_cou... | scauglog/brain_record_toolbox | script_r415_spike_classifier.py | Python | mit | 4,416 | [
"NEURON"
] | 4629645844770d97a952b0c0e9a143c4f92ddc9e6e037b5389d2791db8e1c627 |
# -*- coding: UTF-8 -*-
# -----------------------------------------------------------------------------
# xierpa server
# Copyright (c) 2014+ buro@petr.com, www.petr.com, www.xierpa.com
#
# X I E R P A 3
# Distribution by the MIT License.
#
# ---------------------------------------------------------------... | petrvanblokland/Xierpa3 | xierpa3/contributions/filibuster/content/geography.py | Python | mit | 16,029 | [
"COLUMBUS"
] | 09e1e2cb252bd1adb0933c4a46428a414ad181049ee8c4c43573bec48ecb8bae |
# ========================== Start Copyright Notice ========================== #
# #
# Copyright 2014 F.D.I.S. #
# This file is part of Kinetic Gunner: Gunner of Angst ... | CertainlyUncertain/Kinetic-Gunner-Gunner-of-Angst | gameMgr.py | Python | gpl-3.0 | 12,110 | [
"VisIt"
] | 3757656f47b5177da899020bdf4543444a215ebefbf4ecb5ff28a53940e91afe |
from Module import AbstractModule
class Module(AbstractModule):
def __init__(self):
AbstractModule.__init__(self)
def run(
self, network, antecedents, out_attributes, user_options, num_cores,
out_path):
import os
from genomicode import parallel
from genomicode i... | jefftc/changlab | Betsy/Betsy/modules/align_with_bowtie1.py | Python | mit | 2,900 | [
"Bowtie"
] | 41e53f493b31408f8486023a0ee55b344e85f9082c5ac702685d3a0008c8cb8d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# SpectralClustering.py
#
# Copyright 2014 Carlos "casep" Sepulveda <casep@alumnos.inf.utfsm.cl>
#
# 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 Fo... | creyesp/RF_Estimation | Clustering/clustering/SpectralClustering.py | Python | gpl-2.0 | 6,225 | [
"Gaussian"
] | db5347cb9baaa7458eb940042b1d50f7624454a3ff2bc13a482935b6920c2f24 |
##############################################################################
# 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... | TheTimmy/spack | var/spack/repos/builtin/packages/r-genefilter/package.py | Python | lgpl-2.1 | 1,800 | [
"Bioconductor"
] | 54d35a88e2d421008d318be4268a4b8d938fda33558c259fc390c6bf6776a153 |
# Copyright 2015 datawire. 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 agr... | datawire/quark | quarkc/ast.py | Python | apache-2.0 | 23,567 | [
"VisIt"
] | 369dab4a5cfe62a81293f9dc779f01b26937db38c7b1d0bc6f33848dac84a98d |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | WangWenjun559/Weiss | summary/sumy/sklearn/covariance/robust_covariance.py | Python | apache-2.0 | 29,735 | [
"Gaussian"
] | 3b24027b071af0aa86bca7294e7042051acdd43f02da8fde8470dc888977329b |
# -*- coding: utf-8 -*-
#
# tsodyks_depressing.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 Lice... | stinebuu/nest-simulator | pynest/examples/tsodyks_depressing.py | Python | gpl-2.0 | 5,611 | [
"NEURON"
] | c1a474520fa616c2db5a0a0feae55e4eb17efb75609e31902ce4eee59a3593e0 |
from __future__ import division
# Local RGZ modules
import collinearity
from load_contours import get_contours,make_pathdict
# Default packages
import datetime
import operator
from collections import Counter
import cStringIO
import urllib
import json
import os.path
import time
import shutil
# Other packages
impor... | willettk/rgz-analysis | python/test_consensus.py | Python | mit | 15,556 | [
"Galaxy"
] | e124941312285d52c8b1f00a5391a92a6d100543d69b35fdba805a4793fc0b14 |
#---------------------------------------------------------------------------------
# Concentric Maclaurin Spheroids gravity calculator
#
# Author: Naor Movshovitz (nmovshov at gee mail dot com)
#---------------------------------------------------------------------------------
from __future__ import division
import sys... | nmovshov/CMS-planet | cms.py | Python | gpl-3.0 | 18,335 | [
"Brian",
"Gaussian"
] | 6a2b63a2245e849e47773294964928cbcfaab068c4682ccf4cbf6ff6c90cfde6 |
from datetime import timedelta
import pytest
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession
from virtool.blast.data import BLASTData
from virtool.blast.models import NuVsBlast
from virtool.tasks.models import Task
@pytest.fixture
async def blast_data(dbi, pg, static_time,... | igboyes/virtool | tests/blast/test_data.py | Python | mit | 2,791 | [
"BLAST"
] | 2ddf652be0d4cae617b367ff70da1f317696b57e45d52994f21bee07c48a0660 |
import numpy as np
import tensorflow as tf
import math
import func
#import matplotlib.pyplot as plt
#import matplotlib.patches as patches
from skimage.measure import block_reduce
import input_data
def transform_data(image, img_size, d, noise_var):
mnist_size = 28
image = np.reshape(image, [28, 28])
# do... | amrit110/deepLearThesis | tensorflow/mnist_transform.py | Python | mit | 4,319 | [
"Gaussian"
] | abd69a85b426a97dd61386f08afbc0713b1a4c2240f1a8532ee68e8e0ec18a7e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/pca.py | Python | gpl-2.0 | 14,859 | [
"MDAnalysis"
] | b1d1a26a904c37f00e913ff46ce96455666b8b8db0fad2c1360f964ecd682602 |
# -*- coding: utf-8 -*-
from collections import defaultdict, OrderedDict
from itertools import permutations
import math
import pytest
try:
import numpy as np
except ImportError:
np = None
from chempy import Equilibrium, Reaction, ReactionSystem, Substance
from chempy.thermodynamics.expressions import MassA... | bjodah/chempy | chempy/kinetics/tests/test_ode.py | Python | bsd-2-clause | 41,283 | [
"ChemPy"
] | a22a7536a1e7d503fc3be3fb876b87f0c1002a7d278286b5f4f06c331717237c |
# coding: utf-8
"""
jinja2schema.visitors.util
~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
import jinja2.nodes
from ..mergers import merge
from ..model import Dictionary, Scalar, Unknown
def visit(node, macroses, config, predicted_struct_cls=Scalar, return_struct_cls=Unknown):
if isinstance(node, jinja2.nodes.Stmt):
... | aromanovich/jinja2schema | jinja2schema/visitors/util.py | Python | bsd-3-clause | 1,720 | [
"VisIt"
] | c9aa3e2806ac92a84dc86fcc9a9b8c2ec914222a1b9f01c2821ab6372b8eadd7 |
#!/usr/bin/env python
# Run most of AmberTools serial tests
''' Require: AMBERHOME
You need to call amber.setup_test_folders first (only do once)
amber.setup_test_folders
Then run test (anywhere)
amber.run_tests
Adjust the test by updating env TEST_TASK (please lookt at the code)
'''
from time import tim... | Amber-MD/ambertools-conda-build | outdated/devtools/ci/ci_test.py | Python | mit | 6,062 | [
"Amber"
] | 4493b686ef2b8b4b2330e26d3680d0518c054e0bc41e09b0615255dd18b73007 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@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.
"""PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Phylo/PhyloXMLIO.py | Python | gpl-2.0 | 33,376 | [
"Biopython"
] | 34bf30d8c4b697b9deb208e6a57811d1b4cdc4e2022a7e9120ea217838260af1 |
from __future__ import print_function
from pybrain.structure import FeedForwardNetwork
from pybrain.structure import LinearLayer, SigmoidLayer
from pybrain.structure import BiasUnit,TanhLayer
from pybrain.structure import FullConnection
from pybrain.datasets import SupervisedDa... | affordablewindurbines/jarvisproject | pybrain/examples/supervised/test_network_read_write/jpq2layersWriter.py | Python | gpl-3.0 | 3,987 | [
"NEURON"
] | 9e8dddcbc8406a707de0116552d1fecd09b4f60f459b8cd7fdca1c01a5fa2824 |
#
# Copyright (c) 2017 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... | yashdsaraf/scancode-toolkit | src/plugincode/output.py | Python | apache-2.0 | 3,189 | [
"VisIt"
] | 3d19bed62aff86c5f331779084c193402140c5172cce4781d058892db20dbb38 |
model = """# Generated by PySCeS 0.7.2 (2010-08-10 13:12)
# Keywords
Description: Dimerisation model (003), variant 04
Modelname: Dimerisation04
Output_In_Conc: True
Species_In_Conc: False
# GlobalUnitDefinitions
UnitVolume: litre, 1.0, 0, 1
UnitLength: metre, 1.0, 0, 1
UnitSubstance: item, 1.0, 0, 1
UnitArea: met... | SystemsBioinformatics/stochpy | stochpy/pscmodels/dsmts_003_04.py | Python | gpl-3.0 | 3,700 | [
"PySCeS"
] | e3664b4c9bfc9c2aa8a239f6317326f37cc67f83317dd0ef2cd278169cdd9291 |
from math import log
from argparse import ArgumentParser
# Multiple Polynomial Quadratic Sieve
def mpqs(n, verbose=False):
if verbose:
time1 = clock()
root_n = isqrt(n)
root_2n = isqrt(n+n)
# formula chosen by experimentation
# seems to be close to optimal for n < 10^50
bound = int(5 * log(n, 10)**2)... | rezaqes/MadeLineProtoForHost | vendor/danog/primemodule/lib/danog/prime.py | Python | agpl-3.0 | 12,105 | [
"Gaussian"
] | ac1fc7496d3c43779d3e7d5a3a461930d6c9d442b2604119bbafafe26814464e |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | tests/galaxy_props.py | Python | bsd-3-clause | 7,161 | [
"Galaxy"
] | 16a5172e37cd5884fe02eba7dc7c9a8ecb0c4902abd6b4b34fd85055fcca1c76 |
#-*. coding: utf-8 -*-
## Copyright (c) 2011, Noel O'Boyle; 2012, Adrià Cereto-Massagué
## All rights reserved.
##
## This file is part of Cinfony.
## The contents are covered by the terms of the GPL v3 license
## which is included in the file LICENSE_GPLv3.txt.
"""
indy - A Cinfony module for accessing Indigo fro... | cinfony/cinfony | cinfony/indy.py | Python | bsd-2-clause | 22,495 | [
"RDKit"
] | 1b32a20e6e5cdc5aec6e5c29292d39c5b9fc9e145e1c53c34755fb1ee90aaaf6 |
from __future__ import print_function
from rdkit.SimDivFilters import rdSimDivPickers as rdsimdiv
import numpy
from rdkit import RDRandom
RDRandom.seed(23)
pkr = rdsimdiv.MaxMinPicker()
n = 1000
m = 80
dataPts = []
for i in range(n) :
pt = numpy.zeros(2, 'd')
pt[0] = 10.*RDRandom.random()
pt[1] = 10.*RDR... | adalke/rdkit | Code/SimDivPickers/Wrap/testMaxMin.py | Python | bsd-3-clause | 827 | [
"RDKit"
] | 18c3ee4b4300c42c8211a11111a9a4542292135d6672a425c782551ae8740b54 |
#
# This is the configuration file for the RPi environd
#
### Presentation - General
# All datetime stamps use typical strftime codes: https://docs.python.org/2/library/datetime.html#strftime-strptime-behavior
# The date/time stamp of the last (most current) reading.
present_lastread_stamp = "%I:%M %p on %A, %b %d"
... | modalexii/RPi-Environd | config.py | Python | mpl-2.0 | 2,371 | [
"TINKER"
] | 74f37c9984f6f97fd7ab9d74a04755bbe17f581bcb75fbbfe30c40bd1a70add9 |
#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
from astropy import table, units as u
import cjam
# read in the positions from the example and add appropriate units
pos = table.QTable.read("xy.dat", format="ascii", names=["x","y"])
pos["x"].unit = u.arcsec
pos["y"].unit = u.arcsec
# read in ... | lauralwatkins/cjam | example/example.py | Python | bsd-2-clause | 4,606 | [
"Gaussian"
] | 64c66ec228b2a3060c061bedb94d36f73a95834fb5aa0fa1b971469983299054 |
"""
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. module:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univariate distribution is an insta... | vhaasteren/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 8,414 | [
"Gaussian"
] | fb5e44b517b9cd6fa98b552c8d70741feec473291d5f69b69e4bd05db04ecf08 |
from __future__ import print_function, division
import os
import platform
import socket
import copy
import numpy as np
from datetime import datetime
import time
# globals
FILLVALUE = -99999.9
ITMUNI = {0: "undefined", 1: "seconds", 2: "minutes", 3: "hours", 4: "days",
5: "years"}
LENUNI = {0: "u... | bdestombe/flopy-1 | flopy/export/netcdf.py | Python | bsd-3-clause | 38,500 | [
"NetCDF"
] | c3c00de9600bb6d141673722a90b875ca7f6f0edee8b8e369836b206acd9b38e |
""" Test_RSS_Policy_Configurations
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id: $'
import unittest
import DIRAC.ResourceStatusSystem.Policy.Configurations as moduleTested
#########################################################... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/test/Test_RSS_Policy_Configurations.py | Python | gpl-3.0 | 1,612 | [
"DIRAC"
] | 2316c57ce96d608b6be112318940d493b83d521d17ccc73b7cd1cdde40acc210 |
import pytest
from merakicommons.container import SearchError, searchable, SearchableList, SearchableSet, SearchableDictionary, LazyList, SearchableLazyList
VALUE_COUNT = 100
# Seriously where is this in the std lib...
GENERATOR_CLASS = (None for _ in range(0)).__class__
@searchable({str: "strings"})
class Inner(o... | sserrot/champion_relationships | venv/Lib/site-packages/tests/test_container.py | Python | mit | 18,183 | [
"MOE"
] | 9a13025e041edebed49eb50e6eaf8196bdc7f58f915e7912a86615759427cf2a |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | poem/core/models.py | Python | apache-2.0 | 25,344 | [
"Gaussian"
] | d7d383deed491c5ff5f5f65463b978630c98a3217afce122523437ca048452f4 |
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