text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# Generated from STIXPattern.g4 by ANTLR 4.9.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .STIXPatternParser import STIXPatternParser
else:
from STIXPatternParser import STIXPatternParser
# This class defines a complete generic visitor for a parse tree produced by STIXPatternParser.... | oasis-open/cti-pattern-validator | stix2patterns/v20/grammars/STIXPatternVisitor.py | Python | bsd-3-clause | 6,635 | [
"VisIt"
] | 1109572dad5738860e0cdf12646d4276c0d1d28f6706cbeae563e7a55cbaeb49 |
from pyaccessories.TimeLog import Timer
import os
from RedmineAPI.RedmineAPI import RedmineInterface
from pyaccessories.SaveLoad import SaveLoad
from main import AutoSNVPhyl
import base64
import requests
# TODO documentation
class Run(object):
def main(self):
if self.first_run == 'yes':
choice... | OLC-LOC-Bioinformatics/auto-SNVPhyl | server_runner.py | Python | mit | 13,786 | [
"Galaxy"
] | 7367a748e96f02af3a5af29677d796adcc5832c109a85adc323620375a0f7076 |
"""
Acoustic echo cancellation in white background noise with NLMS.
Consider a scenario where two individuals, John and Emily, are talking over the
Internet. John is using his loudspeakers, which means Emily can hear herself
through John's microphone. The speech signal that Emily hears, is a distorted
version of her o... | Wramberg/adaptfilt | examples/echocancel.py | Python | mit | 4,018 | [
"ADF",
"Gaussian"
] | f951919280002e0565848b9cf2082edbd33f7e440ede530195d7ea9d6554909c |
import pytest
from django.contrib.auth.models import User
from django.contrib.messages import get_messages
from graphapi.tests.utils import populate_db
from openstates.data.models import Person
from profiles.models import Subscription, Notification
from profiles.views import PermissionException
from profiles.utils impo... | openstates/openstates.org | profiles/tests/test_views.py | Python | mit | 9,868 | [
"MOOSE"
] | bedd8865f64b8d010c0ed23affd566ff75c0308e28201e11e94d754df4d01a03 |
"""Plotting functions related to PDF plots."""
from __future__ import absolute_import, print_function
import os
import matplotlib.pyplot as plt
import numpy as np
from .config import FIGEXT, key2label
from .ssp import SSP
def unify_axlims(axs, bycolumn=True, x=True, y=False):
"""Set all axes limits to largest ... | philrosenfield/core_overshoot_clusters | core_overshoot_clusters/pdf_plots.py | Python | mit | 18,419 | [
"Gaussian"
] | 6fc8d4569e7bc9afa04f9fb3c6b44cf6611a6d0e0a21a987d6a02cb8ab5d2e3e |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/notifications/send-notification-with-badge/send-notification-with-badge.7.x.py | Python | mit | 748 | [
"VisIt"
] | 0ef4270abbe73f03b94ac9dbccf0d16da6990e48dcb9923ac849a47442fd625a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
freeseer - vga/presentation capture software
Copyright (C) 2013 Free and Open Source Software Learning Centre
http://fosslc.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
the ... | Freeseer/freeseer | src/freeseer/plugins/videoinput/videotestsrc/widget.py | Python | gpl-3.0 | 1,766 | [
"VisIt"
] | 438c18c6b6836ac46abd1a4c6a75f2db16832e5038f3e4d2b0bc6669839bb337 |
#! /usr/bin/env python
"""
Module with the MCMC (``emcee``) sampling for NEGFC parameter estimation.
"""
__author__ = 'O. Wertz, Carlos Alberto Gomez Gonzalez, V. Christiaens'
__all__ = ['mcmc_negfc_sampling',
'chain_zero_truncated',
'show_corner_plot',
'show_walk_plot',
'... | vortex-exoplanet/VIP | vip_hci/fm/negfc_mcmc.py | Python | mit | 57,611 | [
"Gaussian"
] | 0644727873e9dc4979aadb70271e4892d47f297a340f8eb0085c2d8bfe237c87 |
#!/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... | SuYiling/chrome_depot_tools | git_cl.py | Python | bsd-3-clause | 128,773 | [
"VisIt"
] | b68306c28eb233808eebf06cf59d0de4566519013acd27eeed090cd9266bb963 |
import os
import logging
import tempfile
import tensorflow as tf
from explainable_ai_sdk.metadata.tf.v2 import SavedModelMetadataBuilder
from tensorflow.python.framework import dtypes
from tensorflow_io.bigquery import BigQueryClient
from tensorflow_io.bigquery import BigQueryReadSession
# Model feature constants.
NU... | GoogleCloudPlatform/training-data-analyst | self-paced-labs/vertex-ai/vertex-ai-qwikstart/online-retail-clv-3M/trainer/model.py | Python | apache-2.0 | 5,562 | [
"NEURON"
] | 71601f2b9b0338e562a0e6d2b6f9c9bde45a59cf3cb038effcaa8235fcf965e0 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Concrete collection candidate management helper module."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ... | abadger/ansible | lib/ansible/galaxy/collection/concrete_artifact_manager.py | Python | gpl-3.0 | 24,294 | [
"Galaxy"
] | 540e51353cb49adbacf64b3c37ef6de6ca165e01030f944dc2c3af7b2af8ba8a |
#!/usr/bin/python
from biokbase.cdmi.client import CDMI_EntityAPI
from biokbase.probabilistic_annotation.DataExtractor import getFieldFromEntity, getFieldFromRelationship
# For the CDMI URL and other constants
from biokbase.probabilistic_annotation.PYTHON_GLOBALS import *
import os
import sys
try:
import json
ex... | kbase/probabilistic_annotation | internalScripts/MakeReactionProbabilityObject.py | Python | mit | 8,967 | [
"BLAST"
] | 6eaf015fdb7875776a235159f717a725563cce37af2d88b9d03594fded86d849 |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | Azure/azure-sdk-for-python | sdk/databoxedge/azure-mgmt-databoxedge/azure/mgmt/datab/models/_models_py3.py | Python | mit | 207,248 | [
"ASE"
] | de53d2e08125a6cd313af4fa4b829b0186cc6f6df3b4c5388d8b83464d07d34f |
""" Module for dealing with VOMS (Virtual Organization Membership Service)
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import stat
import tempfile
import shlex
import shutil
from DIRAC import S_OK, S_ERROR, gConfig, roo... | ic-hep/DIRAC | src/DIRAC/Core/Security/VOMS.py | Python | gpl-3.0 | 14,153 | [
"DIRAC"
] | 221cfa25c85ee2e2ddeae4dbaaff582ae26113160ee6b3c4acade9cacc91a15d |
"""
RequestOperation to create a tarball from a list of LFNs.
Download a list of files to local storage, then tars it and uploads it to a StorageElement
This operation requires the following arguments:
* ArchiveLFN: The LFN of the tarball
* SourceSE: Where the files to be archived are downloaded from
* TarballSE:... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/ArchiveFiles.py | Python | gpl-3.0 | 10,230 | [
"DIRAC"
] | 18db2b44e331477050c132e0c7ab4bcc8e36daa6a6d4ab778374a1f72d1f7a59 |
#!/usr/bin/env python
#
# texttable - module for creating simple ASCII tables
# Copyright (C) 2003-2011 Gerome Fournier <jef(at)foutaise.org>
#
# 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 Foundat... | golismero/golismero | thirdparty_libs/texttable.py | Python | gpl-2.0 | 20,745 | [
"Brian"
] | 96f7bff41f2c5505bcdd8a7ac862cdc6e7c98b85465e5ece3782f513fe24365a |
# -*- coding: utf-8 -*-
#
# PyZMQ documentation build configuration file, created by
# sphinx-quickstart on Sat Feb 20 23:31:19 2010.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | takluyver/pyzmq | docs/conf.py | Python | lgpl-3.0 | 6,614 | [
"Brian"
] | 03276064113696cde676a885cf61e8c4bd385527bbb35a35c21353037f357591 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2017, Marc Tschapek <marc.tschapek@itelligence.de>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview'],
'supp... | sgerhart/ansible | lib/ansible/modules/windows/win_disk_facts.py | Python | mit | 29,705 | [
"VisIt"
] | aec3753068b673ff4e8d2f63f3d2cb0ac7fcab6be2e1196c22c87a73aba5aa30 |
"""MPF plugin for an auditor which records switch events, high scores, shots,
etc."""
# auditor.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logg... | jabdoa2/mpf | mpf/plugins/auditor.py | Python | mit | 11,236 | [
"Brian"
] | e3f6104cc9ad08223daec2215bcf16f65863591dc7fdfa5067163b804cb75aaa |
# commands.py - command processing for mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2, incorporated herein by reference.
from node import hex, nullid, nullrev, short
from lock import rel... | dkrisman/Traipse | mercurial/commands.py | Python | gpl-2.0 | 132,320 | [
"VisIt"
] | f4d0be51f4da5c0883530bd827b2655d4ac1c382ca26053b87102c6db3d4684d |
#!/usr/bin/env python
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 COP... | Kleptobismol/scikit-bio | skbio/diversity/alpha/_ace.py | Python | bsd-3-clause | 3,694 | [
"scikit-bio"
] | 0ee9ac38caf6798e72047a264bbbf193aa601bf5d1971c5fd2624dee4c616e79 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-cpu-normalization
# Author : Ricardo Graciani
########################################################################
"""
Determine Normalization for current CPU
"""
__RCSID__ = "$Id$"
import DIRAC
f... | hgiemza/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-cpu-normalization.py | Python | gpl-3.0 | 2,623 | [
"DIRAC"
] | b013a89bf7cdd9bd3d1b667124528c5a467a152f3e6f30d6763171f5c451d8d4 |
#!/usr/bin/env python
'''
CREATED:2011-11-12 09:39:09 by Brian McFee <bmcfee@cs.ucsd.edu>
Spatial tree demo for dictionary-type data
Any object X which implements a mapping to vector data (X[key] -> numpy array)
may be used here.
'''
import numpy
from spatialtree import spatialtree
N = 5000
D = 20
# A random pr... | bmcfee/spatialtree | examples/dictionaryDemo.py | Python | gpl-3.0 | 1,745 | [
"Brian"
] | b66a2a6ff30946df18dfc8655457f34fb720425996707325cfcf7ea5dea50db8 |
# -*- coding: utf-8 -*-
# Copyright 2015 Spotify AB. All rights reserved.
#
# The contents of this file are 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/LICE... | spotify/napalm | test/junos/TestJunOSDriver.py | Python | apache-2.0 | 5,013 | [
"Firefly"
] | 4b0632b357fc10227663b62a6e5d53594f50f08e1f1cf8ea85df7fdaaa249400 |
#!/usr/bin/env python
#
# Inkscape extension making long continuous paths from shorter pieces.
# (C) 2015 juewei@fabmail.org
#
# code snippets visited to learn the extension 'effect' interface:
# - convert2dashes.py
# - http://github.com/jnweiger/inkscape-silhouette
# - http://github.com/jnweiger/inkscape-gears-dev
# -... | fablabnbg/inkscape-chain-paths | chain_paths.py | Python | gpl-2.0 | 13,520 | [
"VisIt"
] | eccbc3ab4da01e942dec8679f1b97039ec8608264097bcc7c1ad2b318f798999 |
import __future__
import os
import tempfile
import requests
from Bio import SeqIO
from Bio import SwissProt
from Bio.Blast.Applications import NcbiblastpCommandline
from Bio.Blast import NCBIXML
# sp: swiss-prot formatted text
def fetchSwissProt(spAcc):
url = 'http://www.uniprot.org/uniprot/%s.txt' % spAcc
r... | minzhangcheng/MPL | MPL/Bio/swissprot.py | Python | lgpl-3.0 | 3,786 | [
"BLAST"
] | ed429b0ebbd065f4c9db30570fd1baf94dcbbe2db440c6041a66918c6298c80f |
import itertools
import numpy as np
import mdtraj as md
import msmbuilder as msmb
n_traj = 735
tica = msmb.reduce.tICA.load("./tICAData.h5")
tics = []
for filename in ["./Trajectories/trj%d.h5" % i for i in range(n_traj)]:
print(filename)
trj = md.load(filename)
tics.append(tica.project(trajectory=trj, wh... | choderalab/MSMs | attic/src/code/tica/examine_tics.py | Python | gpl-2.0 | 339 | [
"MDTraj"
] | f823af236af65e997a5c51ae8f5709c34a7de8ba129d44088340d20a0e62daba |
#!/usr/bin/python
########################################################################
# 09 Oct 2014
# Patrick Lombard, Centre for Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import os, re, sys
i... | pdl30/rnaseq_misc | fake_gfold_counts.py | Python | gpl-2.0 | 2,789 | [
"HTSeq"
] | 608159f1d499f0e318d5a5985dfb25327c676c5f4a7d72ca93103c355e3d7037 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from itertools import product
import numpy as np
from pymatgen.analysis.elasticity.strain import Deformation
from pymatgen.core.surface import (SlabGenerator,
... | Bismarrck/pymatgen | pymatgen/analysis/substrate_analyzer.py | Python | mit | 17,299 | [
"pymatgen"
] | 3e10743142406f6a7f04a60b287317544cbcb24f37f082807a17a185f2ae4d07 |
"""This function rips through a BAM from simulated reads and bins reads into a three dimensional histogram.
The dimensions are:
Xd - alignment error
MQ - mapping quality
vlen - length of variant carried by read
The histogram is saved as a numpy array and different views of the histogram are plotted.
"""
from multi... | sbg/Mitty | mitty/benchmarking/xmv.py | Python | apache-2.0 | 14,303 | [
"pysam"
] | e1891ba95a682e4c1fffc9470e526ce53722b8346f2c58562b1a586ac5254abc |
"""
This module includes functions for generating various .rule files based on well-known automata
All code is released under the MIT License and is (C) copyright 2016 Jay Valentine
"""
global_paths = {
'rules':'rules/'
}
def elementary_rules():
"""
return lines to write for elementary rules
"""
elements = [
... | jayvalentine/CellularAutomata | setup_functions.py | Python | mit | 1,828 | [
"Brian"
] | f9486348e9f7d724e015d2647c8e4114a29737cdc45f671304a9fc01caa8d578 |
""" Encapsulate here the logic for matching jobs
Utilities and classes here are used by MatcherHandler
"""
__RCSID__ = "$Id"
import time
from DIRAC import gLogger
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.Core.Utilities.PrettyPrint import printDict
from DIRAC.Core.Security i... | petricm/DIRAC | WorkloadManagementSystem/Client/Matcher.py | Python | gpl-3.0 | 14,601 | [
"DIRAC"
] | 98d398e34be8703148ce9aa6df08adedefa2efc63a21c0bda7907ebc03b2f67e |
"""Validate dependencies."""
from __future__ import annotations
import ast
from pathlib import Path
from homeassistant.requirements import DISCOVERY_INTEGRATIONS
from homeassistant.setup import BASE_PLATFORMS
from .model import Integration
class ImportCollector(ast.NodeVisitor):
"""Collect all integrations ref... | w1ll1am23/home-assistant | script/hassfest/dependencies.py | Python | apache-2.0 | 8,188 | [
"VisIt"
] | 3c9aa01b810e29eb7106fef811da5f939db78ec8a65d5910193b4e3fb89ed619 |
# Copyright 2015 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 a... | Eric-Gaudiello/tensorflow_dev | tensorflow_home/tensorflow_venv/lib/python3.4/site-packages/tensorflow/python/ops/gradients.py | Python | gpl-3.0 | 25,746 | [
"VisIt"
] | 4e7723ddf2b2d54827b58b228d4b3e74b41efc0a281f7b63fe3d1ddb6b9fcd62 |
# Copyright (c) 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 it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Software Founda... | smarr/Truffle | vm/benchmarks/interpreter/sieve.py | Python | gpl-2.0 | 1,625 | [
"VisIt"
] | 717aeceb1e2b8aad3fbfa9a0b4d6a2d41f132f343a2d3d764ed30d14f13152a8 |
# Copyright 2016 Massachusetts Open Cloud
#
# 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... | CCI-MOC/moc-openstack-tools | addusers.py | Python | apache-2.0 | 21,809 | [
"VisIt"
] | 1f6f2c77aa936d1f97a6a1d182f2ae226e9005230c2dc15b6ae5cf3594752f1f |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Installed collections management package."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import f... | jctanner/ansible | lib/ansible/galaxy/collection/__init__.py | Python | gpl-3.0 | 56,495 | [
"Galaxy"
] | a93ccee56213b9ba91ca11a7a6f0f9f82f280605087b8d3400d08fd8bddabb84 |
__author__ = 'stephen'
# ===============================================================================
# GLOBAL IMPORTS:
import os,sys
import numpy as np
import argparse
# ===============================================================================
# LOCAL IMPORTS:
HK_DataMiner_Path = os.path.relpath(os.pardir)
#... | stephenliu1989/HK_DataMiner | hkdataminer/scripts/test_mrdbscan_rmsd.py | Python | apache-2.0 | 8,623 | [
"MDTraj"
] | ab7a925ffd8797ba73b20d5fade2467f902e6a84cff3b15843921923cc1f54d1 |
##
## nw_rtparse
##
## Kenneth Lopata
## Last modified: 2013-05-01
##
## Python script for parsing NWChem real-time TDDFT output for various
## time-dependent quantities (e.g., dipole moment, electric field, etc)
##
## nw_rtparse --help
##
##
import sys
from optparse import OptionParser
from signal import signal, SIGP... | rangsimanketkaew/NWChem | contrib/parsers/nw_rtparse.py | Python | mit | 10,896 | [
"NWChem"
] | 93410f4fead9b5023d51bca19eca4c50cfc33902fd8a328e4264fb6a6b0442e6 |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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... | gforcada/jenkins-job-builder | jenkins_jobs/modules/scm.py | Python | apache-2.0 | 70,100 | [
"Octopus"
] | 882b32db821b345b70159e9dd77527109f96e9b61c7bb95389d0bd181ebd44f2 |
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0 fdm=marker fmr=#{,#}
"""
An RPC service using ZeroMQ as a transport.
Authors:
* Brian Granger
* Alexander Glyzov
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2012-2014. Brian Granger, Min Ragan-Kelley, Alexander... | srault95/netcall | netcall/tornado/service.py | Python | bsd-3-clause | 4,504 | [
"Brian"
] | 883c7d115183725660191024b1f74b525102c96cadb765e37e825662639a38d0 |
# 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 RGostats(RPackage):
"""Tools for manipulating GO and microarrays.
A set of tools f... | iulian787/spack | var/spack/repos/builtin/packages/r-gostats/package.py | Python | lgpl-2.1 | 1,721 | [
"Bioconductor"
] | 922a48398c18924beb56f6a81b11598ccbcd0fafee830bf0ac75a0b956d2e9d5 |
#!/usr/bin/env python
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of franklin.
# franklin is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either ve... | JoseBlanca/franklin | scripts/snv/run_bwa.py | Python | agpl-3.0 | 4,175 | [
"BWA"
] | c70dd7f3f2d64f8cca09c26757afa417aa75983d5a37847227a48e7fea3968ff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import time
from powers import moog, utils
"""
This code is used to estimate the projected rotation speed of a star given a
spectral line, correction factors and an initial guess. You need to have all
the necessary input files for MOOG (atmosphere model... | RogueAstro/PoWeRS | powers/estimate.py | Python | gpl-2.0 | 15,253 | [
"Gaussian"
] | 5b898822a3109826d53022da877040c9eb057b599b843d59caa90550a60095ef |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/contrib/distributions/python/ops/mvn_tril.py | Python | apache-2.0 | 8,007 | [
"Gaussian"
] | ad99217ea411a047c1f32e0b84cc78c83b6d2a0bedc78430d42b4eae441933fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Authors and copyright:
# © 2012-2013, John Lehmann (first last at geemail dotcom or @jplehmann)
# © 2012-2020, Rogério Theodoro de Brito
# © 2013, Jonas De Taeye (first dt at fastmail fm)
#
# Contributions are welcome, but please add new unit tests to test yo... | coursera-dl/coursera-dl | coursera/coursera_dl.py | Python | lgpl-3.0 | 9,648 | [
"VisIt"
] | 4a7e8b16af73a0b8d04d5357e39d79ca76fc3c6fb79e0b5b65fb87ef6331c8a6 |
#!/usr/bin/env python
""" update local cfg
"""
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s [option|cfgFile]' % Script.scriptName] ) )
Script.registerSwitch( 'F:', ... | Andrew-McNab-UK/DIRAC | tests/Jenkins/dirac-cfg-update.py | Python | gpl-3.0 | 2,661 | [
"DIRAC"
] | 7876583c22fdaedad42f29c4a066ea7a505cf43e6305418a8c26e915750d1655 |
"""
Beta diversity measures (:mod:`skbio.diversity.beta`)
=====================================================
.. currentmodule:: skbio.diversity.beta
This package provides implementations of beta diversity measures for computing
sample dissimilarity. Users of this package should also explore
``scipy.spatial.distanc... | anderspitman/scikit-bio | skbio/diversity/beta/__init__.py | Python | bsd-3-clause | 1,097 | [
"scikit-bio"
] | cfe7ef98bae643156d4cf39b954bc461a7919fc160b74155df96db553b82d930 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# coding=utf-8
# Copyright 2019 The SGNMT 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... | ucam-smt/sgnmt | cam/sgnmt/decode.py | Python | apache-2.0 | 4,398 | [
"VisIt"
] | 821ec75d9a5381c4193dc630a931737ef9334fd81c28de7e0ffc7f40de1a74f9 |
import pytest
import logging
import asyncio
from deathstar.kybercrystals import KyberCrystals
class MockDeathStar:
pass
@pytest.fixture
def kyber_crystals(empire):
dt = MockDeathStar()
dt.empire = empire
k = KyberCrystals(dt)
return k
@pytest.mark.asyncio
async def test_kyber_crystallization(... | byt3bl33d3r/DeathStar | tests/test_kyber_crystals.py | Python | gpl-3.0 | 823 | [
"CRYSTAL"
] | 0007b293fdbb33cdda923a0e319c7abeba25bca052b5b5622812fe85786f0552 |
# Copyright (C) 2012,2013
# 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 t... | BackupTheBerlios/espressopp | src/analysis/__init__.py | Python | gpl-3.0 | 2,575 | [
"ESPResSo"
] | d7a12cd58605cc725f27420a0ebe4eae9d15dd63174073605054385c0c83d67e |
import time
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from django.urls import reverse
from splinter import Browser
class TestBaseViews(StaticLiveServerTestCase):
"""Integration test suite for testing the views in the app: base.
Test the url for home and the basefiles like robots... | tosp/Leyes.io | base/test_views.py | Python | mit | 1,828 | [
"VisIt"
] | 097061875a4e57719a87c1a12af3e98011474397f923e4f38900ddd9e36cdfa5 |
"""
.. _step_methods:
============
Step Methods
============
In PySMC we define a few step methods for the Metropolis-Hastings algorithm
that extend the capabilities of PyMC.
Here is a list of what we offer:
"""
__all__ = ['RandomWalk', 'LognormalRandomWalk', 'DiscreteRandomWalk',
'GaussianMixtureStep... | PredictiveScienceLab/pysmc | pysmc/_step_methods.py | Python | lgpl-3.0 | 16,020 | [
"Gaussian"
] | a5b9f15496b7181d9e5cbff4cf1a9bd5e789b7a30065c104af8bea6f4950aa4c |
# CaPool.py ---
#
# Filename: capool.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Wed Apr 22 22:21:11 2009 (+0530)
# Version:
# Last-Updated: Sat Dec 8 15:46:00 2012 (+0530)
# By: subha
# Update #: 189
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Implements ... | BhallaLab/moose-examples | traub_2005/py/capool.py | Python | gpl-2.0 | 971 | [
"MOOSE"
] | a7d0c43f5c4e6c7587f7138ce1d33f8b7c47f7a8979d9b64eae47aabd7d364f3 |
"""This file contains
License: The MIT License (MIT)
Copyright (c) 2015 Brian Eujin Kim (http://briank.im)
Dependencies:
Must have BeautifulSoup4 installed
For use with Python 2.7 (untested in Python 3)
"""
import urllib2
from bs4 import BeautifulSoup
import string
from datetime import datetime
import re
import pickl... | briamkin/BoxOfficeMojoScrape | BoxOfficeMojoScrape.py | Python | mit | 6,431 | [
"Brian"
] | 86a12b53a0b03c1bdbb02a8edf1a6de12827a414236ab91e410f62c1ca46f06f |
r"""
FASTQ format (:mod:`skbio.io.fastq`)
====================================
.. currentmodule:: skbio.io.fastq
The FASTQ file format (``fastq``) stores biological (e.g., nucleotide)
sequences and their quality scores in a simple plain text format that is both
human-readable and easy to parse. The file format was in... | Achuth17/scikit-bio | skbio/io/fastq.py | Python | bsd-3-clause | 22,914 | [
"BioPerl",
"Biopython",
"scikit-bio"
] | 61833f9b5754ee3a502191479ec48ec6c4f078ad70b066b2d6796cfd32ba2b46 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/misc/imfit.py | Python | agpl-3.0 | 12,412 | [
"Gaussian"
] | 980dbf372462efd502b92e0d1a82115e283f13a6fa6ee951199760081e894015 |
# (C) British Crown Copyright 2010 - 2013, 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... | kwilliams-mo/iris | lib/iris/fileformats/cf.py | Python | gpl-3.0 | 34,967 | [
"NetCDF"
] | 6a18fd76842df42ffd4e62f01b9d6a52303eb48c289ec42e9e20f294c5656cbd |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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... | KonradBreitsprecher/espresso | testsuite/nsquare.py | Python | gpl-3.0 | 1,950 | [
"ESPResSo"
] | 7943d15eee7fde67158a48af8059c31e266ec8473b8278685965afab14ef4c77 |
import serial
import inspect
import time
import itertools
from util import two_byte_iter_to_str, to_two_bytes, str_to_two_byte_iter, two_byte_iter_to_str
ARDUINOIDALL = 0x21
# Message command bytes - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE = 0xE0 # send... | sauloal/arduino | control/firmata/pyfirmata/pyfirmata/pyfirmata.py | Python | mit | 22,564 | [
"CRYSTAL"
] | ee5ac4e9e7398968faddab34ec5231b989215b020234bca327f875c65b2e0fd7 |
#!/usr/bin/env python
# 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 in the hope that ... | dmnfarrell/smallrnaseq | smallrnaseq/utils.py | Python | gpl-3.0 | 25,700 | [
"BLAST",
"HTSeq",
"pysam"
] | 3b54a1569394e96c340198c155fd0529b7b9830ae3a470b824ed64b6a17c7b41 |
from jaspyx.visitor import BaseVisitor
class Delete(BaseVisitor):
def visit_Delete(self, node):
for target in node.targets:
self.indent()
self.output('delete ')
self.visit(target)
self.finish()
| iksteen/jaspyx | jaspyx/visitor/delete.py | Python | mit | 256 | [
"VisIt"
] | 8ea44e00c481b2d7a07dd96b43290f78b4a2727edae18795112452b2fd9b7e4f |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/lo/ibo.py | Python | apache-2.0 | 16,558 | [
"CRYSTAL",
"PySCF"
] | f4ce622772453339c0f361ccd05c5b1c44ad57733f7d6edccf41f637dbb90b04 |
#!/usr/bin/env python
#
# 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 require... | anthrotype/nototools | nototools/test_vertical_extents.py | Python | apache-2.0 | 5,500 | [
"xTB"
] | 0b08486e563413af824cee70c2456e24777b30ff67668c7d1d615862d5e8682f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 17 16:26:48 2017
@author: lamahamadeh
"""
#First: Python-based implementation
#------------------------------------
'''
source:
-------
Video 2.4.2: Examples Involving Randomness
Week 2 Overview/Python Libraries and Concepts Used in Research
Using... | LamaHamadeh/Harvard-PH526x | Week2-Python-Libraries-and-Concepts-Used-in-Research/Dice_Probability.py | Python | mit | 3,903 | [
"Gaussian"
] | 6a01ea1cdbcba11764894326c29a8d38f4dbb0e7158c40e96d92a18588ef5e3c |
#! /usr/bin/env python3.4
########################################################################
# #
# This script will take a file output by abinit of a band structure #
# and pull out the k points and the energy of the bands at those #
#... | thompcinnamon/Format-Band-Struct-Data | Format-Band-Struct-Data-Print.py | Python | apache-2.0 | 6,266 | [
"ABINIT"
] | d1cdd23ad69637c1262a2f7ea91c1663044c2a851b964580b99fa1626e4436bb |
"""Tools for handling ion mutation."""
import itertools
import json
import os
import re
from copy import deepcopy
from operator import itemgetter
from typing import Callable, Generator, Optional, Tuple
import numpy as np
import pandas as pd
import pymatgen.analysis.structure_prediction as pymatgen_sp
fro... | WMD-group/SMACT | smact/structure_prediction/mutation.py | Python | mit | 14,352 | [
"pymatgen"
] | 882c61a33909ae68f271023367c35c1ede7c1ca8c7d0a79f4b8fc85716b3bbc3 |
import unittest
from test.asserting.ast import get_fixture_path
from vint.ast.parsing import Parser
from vint.ast.node_type import NodeType
from vint.ast.traversing import traverse, SKIP_CHILDREN
FIXTURE_FILE = get_fixture_path('fixture_to_traverse.vim')
class TestTraverse(unittest.TestCase):
def setUp(self):
... | RianFuro/vint | test/unit/vint/ast/test_traversing.py | Python | mit | 4,526 | [
"VisIt"
] | 5b079cb82ca0bd5d833251d164b1c711dfea3877a8659ffc5f4045698584c10d |
#!/usr/bin/env python
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors as Des
from rdkit.Chem import Draw
from rdkit.Chem import RWMol
from random import randint
import topomod
import filtermod as fm
###################################################
# Subroutines
# generate ... | jmargraf/indra | graph_gen.py | Python | mit | 3,757 | [
"RDKit"
] | b71e0e5d7b721d1137300bd93a653b68619086ea89f36fa932252156a095b701 |
##
# Copyright 2009-2016 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://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcleuven/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 16,547 | [
"NetCDF"
] | 7cd8c41f7ae148b1b6d1ad3ec5099b2790255b879a8e52da426f0b36f0da2005 |
# CREATED:2013-11-30 14:22:33 by Brian McFee <brm2132@columbia.edu>
#
# Restricted FDA
# only compute between-class scatter within each song
import itertools
import numpy as np
import scipy.linalg
from sklearn.base import BaseEstimator, TransformerMixin
class RFDA(BaseEstimator, TransformerMixin):
def __init__... | guiquanz/msaf | msaf/algorithms/olda/RFDA.py | Python | mit | 3,699 | [
"Brian"
] | e0c0b013a2e860e3aa7e1c6e5bded8c7dbc461f5492443d311ff1241fb8a8b8e |
tests = [
("python", "UnitTestMatcher.py", {}),
("python", "UnitTestSignature.py", {}),
#("python","UnitTestLazyGenerator.py",{}),
("python", "UnitTestUtils.py", {}),
("python", "UnitTestGobbi.py", {}),
("python", "Utils.py", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit impor... | jandom/rdkit | rdkit/Chem/Pharm2D/test_list.py | Python | bsd-3-clause | 418 | [
"RDKit"
] | e09be242b33371be2182138e6ae775046bb159d901940b776be996fcbcd694a6 |
#!/usr/bin/python
#-*- coding: utf-8 -*-
# Copyright (C) 2015, Nikolai Chernikov <nikolai.chernikov.ru@gmail.com>
#
# "convert2ugrid" is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License v3+. "convert2ugrid" is distributed in the
# hope that it will be use... | cdd1969/convert2ugrid | lib/ui.py | Python | gpl-3.0 | 11,135 | [
"NetCDF"
] | b0b65ea73e5fc1ad1360d1d2d6e8d1aead8e15f20d04937251e33b8534249940 |
#!/usr/bin/env python
from __future__ import division
from builtins import zip
from builtins import map
from builtins import range
from past.utils import old_div
import numpy
from numpy import *
x = r_[ 9., 35., -13., 10., 23., 0.]
y = r_[ 34., 10., 6., -14., 27., -10.]
#x = x / max(x)
#y = y / max(y)
# t... | lfairchild/PmagPy | SPD/lib/lib_curvature.py | Python | bsd-3-clause | 12,671 | [
"ADF"
] | 911a1c9963e85271889b31a5d8e34b29c68c5082affe9940bdcfc7dbbdb6870a |
from ase import *
from espresso import espresso
from ase.lattice import bulk
import matplotlib
matplotlib.use('Agg') #turn off screen output so we can plot from the cluster
import matplotlib.pyplot as plt
import numpy as np
metal = 'Pt'
metal2 = None # if you have an alloy, specify the second metal
name = metal
if... | CBE544/CBE544.github.io | ASE/Getting_Started/run_sp.py | Python | gpl-2.0 | 2,085 | [
"ASE",
"CRYSTAL",
"ESPResSo"
] | 675f431d56c55f5a7c54a21c5cc39b4c8252830d9387f86106d2bf0cb2957f41 |
import numpy as np, pandas as pd
from copy import deepcopy
__author__ = "alex han"
""" ---------------------------------------
<<<< statistical analysis >>>>
--------------------------------------- """
""" for arrays representing probability densities """
def normalize(input):
""" <numpy array>: normali... | chaohan/code-samples | toolbox/toolbox.py | Python | mit | 7,311 | [
"Gaussian"
] | 176bff80f1013d4087c55dfab9c9bc2ef428229de2fea963d6c69d2cf23dbc8c |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import Editor
import SimpleITK as sitk
import sitkUtils as su
import math
from Resources.atlasSmallIslandCleanup import DustCleanup
#
# LabelAtlasEditor
#
class LabelAtlasEditor(ScriptedLoadableModule):
"... | BRAINSia/LabelAtlasEditor | LabelAtlasEditor/LabelAtlasEditor.py | Python | mit | 51,513 | [
"VTK"
] | f7f3f0a2922a6a82409d9859f074957c64ba47b60fac7bd9421ccc977d1996c1 |
# -*- coding: utf-8 -*-
from __future__ import print_function
try:
from setuptools import setup, find_packages, Extension
except ImportError:
from distutils.core import setup, Extension
def find_packages():
return ['treeCl', 'treeCl.interfacing', 'treeCl.tasks', 'treeCl.utils']
from Cython.Distut... | kgori/treeCl | setup.py | Python | mit | 3,873 | [
"Biopython"
] | aab22712458a4692e11f708174e840d6c0047652b3b32d1de25e4079430108e4 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 38,977 | [
"VisIt"
] | eacc06acf7431240ab693252e34df7bb59454b0ef569df912e9b4411a6c9674b |
# pylint: disable=too-many-branches,too-many-locals, invalid-name
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid.kernel import *
from mantid.api import *
from scipy.io import netcdf
import numpy as np
import re
import time
class AngularAutoCorrelationsSi... | wdzhou/mantid | Framework/PythonInterface/plugins/algorithms/AngularAutoCorrelationsSingleAxis.py | Python | gpl-3.0 | 12,238 | [
"NetCDF"
] | 4bfa23fabef33db6f00b4c13e16396dde6458cb1f70244ef46b0c17b6d75abfd |
"""Test the dirac-transformation-replication script and helper"""
import unittest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.TransformationSystem.Utilities.ReplicationTransformation import createDataTransformation
from DIRAC.TransformationSystem.Utilities.ReplicationCLIPara... | petricm/DIRAC | TransformationSystem/test/Test_replicationTransformation.py | Python | gpl-3.0 | 10,097 | [
"DIRAC"
] | 085b6bee960e10b3c6fa62e50d89f234128c9fd022ef5655ed9b118ec699e3f4 |
#!/usr/bin/python
# Guillermo Torres MSc,
# ggtorrese@unal.edu.co, guigotoe@gmail.com
# Bioinformatic Research Group
# Biotechnology Institute of National University of Colombia
# last update: November 2013
# **HISS integrates: Comparison + Section processes
# This is written as part of IN SILCO MICROARRAY pipeline, bu... | guigotoe/HISS | scripts/HISS.py | Python | gpl-3.0 | 9,626 | [
"BLAST",
"Biopython"
] | 5489da773f84441c624d5b4f6799248296e1a0114c18c9d2d29ab6f143aee63d |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
A "grab bag" of relatively small general-purpose utilities that don't have
a clear module/package to live in.
"""
import abc
import contextlib
import difflib
import inspect
import json
import os
import signal
import sys
import ... | mhvk/astropy | astropy/utils/misc.py | Python | bsd-3-clause | 30,389 | [
"ESPResSo"
] | 11df7356a4966420846daabe845499f1d55085243e9381f2b2368bca21e4e993 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS that utilize the
progress page.
"""
from contextlib import contextmanager
from six.moves import range
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.logout import LogoutPage
from ...pages.lms.courseware import CoursewareP... | stvstnfrd/edx-platform | common/test/acceptance/tests/lms/test_progress_page.py | Python | agpl-3.0 | 10,717 | [
"VisIt"
] | 1446f19c1338bf318ac6e57bc0f668ba673cd23481f24fc16ffa970d8522d9fa |
#!/usr/bin/env python3
###############################################################
# Copyright 2014 Lawrence Livermore National Security, LLC
# (c.f. AUTHORS, NOTICE.LLNS, COPYING)
#
# This file is part of the Flux resource manager framework.
# For details, see https://github.com/flux-framework.
#
# SPDX-License-I... | grondo/flux-core | t/python/t0010-job.py | Python | lgpl-3.0 | 23,184 | [
"NEURON"
] | 6f9c4c684aac58142f9227cce985a671ab493a687e415a56c3a25e9da7fda1ac |
from django.contrib import admin
from leaflet.admin import LeafletGeoAdmin
from django.contrib import admin
from let_me_app.models import (InternalMessage, Peeper, PrivateComment,
Changelog, Site, Court, Occasion, BookingPolicy, Invoice, InventoryList,
Event, Equipment, Inventory, Proposal, Application, Rece... | oleg-chubin/let_me_play | let_me_app/admin.py | Python | apache-2.0 | 1,138 | [
"VisIt"
] | 7263410155ad733ccc1484b9f365de716d631856aabfd6f7c1487586600d5612 |
"""
Module containing a compartmental cell class
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import super
from builtins import next
from builtins import zip
from builtins import range
from buil... | Neurosim-lab/netpyne | netpyne/cell/compartCell.py | Python | mit | 73,140 | [
"NEURON"
] | 51a5f2d2ffbc55829f657087666e19f871ae7ed5e595adede66d6791bc1cbdf3 |
from base import find_root
from gaussian import truncated_gaussian
from chi import truncated_chi, truncated_chi2
from T import truncated_T
from F import truncated_F
| stefanv/selective-inference | selection/truncated/__init__.py | Python | bsd-3-clause | 166 | [
"Gaussian"
] | fc0a837be3ae0cf6f7a9b5afb9200b1d66712903f657694bf414da040c8b9d10 |
"""This module defines an ASE interface to GROMACS.
http://www.gromacs.org/
It is VERY SLOW compared to standard Gromacs
(due to slow formatted io required here).
Mainly intended to be the MM part in the ase QM/MM
Markus.Kaukonen@iki.fi
To be done:
1) change the documentation for the new file-io-calculator (test wo... | askhl/ase | ase/calculators/gromacs.py | Python | gpl-2.0 | 17,801 | [
"ASE",
"GROMOS",
"Gromacs"
] | 63070d793a37dd3d0f1dcb9398d982ac7f2c62320b6911ab1cd1aef1ffb03e6d |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 option) any later ver... | spring01/libPSI | lib/python/qcdb/vecutil.py | Python | gpl-2.0 | 9,914 | [
"Psi4"
] | bd2f526b2da6bce315ca712acc2a639f4f99abe48f27ba2e702ebdabd4587c7e |
# Generate AMBER parameters for an input file
import os, sys
startdir = os.getcwd()
import openeye as oe
genConformers = oe.oeomega.OEOmega()
genConformers.SetMaxConfs(20)
genConformers.SetStrictStereo(False)
# For testing
sys.argv.append('/home/pgupta13/prep_ligand/protomers_2J79_GTL.smi')
sys.argv.append('protom... | CCBatIIT/AlGDock | Pipeline/backup/parameterize_OpenEye.py | Python | mit | 3,947 | [
"Amber"
] | ba8232812042e5cd1aca3513d2e3d3d142639d96296c6f6d70f0fbf806551f27 |
import argparse
import cStringIO
import deploy_config
import getpass
import hashlib
import os
import pprint
import re
import service_config
import socket
import string
import subprocess
import sys
import telnetlib
import time
import urllib2
import uuid
from log import Log
from service_config import ServiceConfig
from ... | linyiqun/minos | client/deploy_utils.py | Python | apache-2.0 | 40,759 | [
"Galaxy"
] | b910dbacff4730fc503eef3ba9aacfc1f360bac775b608032161ab8dc3569bce |
import numpy as np
import pytest
from cached_property import cached_property
from conftest import skipif
from devito import (Grid, Constant, Function, TimeFunction, SparseFunction,
SparseTimeFunction, Dimension, ConditionalDimension, SubDimension,
SubDomain, Eq, Ne, Inc, NODE, O... | opesci/devito | tests/test_mpi.py | Python | mit | 85,117 | [
"VisIt"
] | 05a43af642bfb0b8b290a06c372495ef6eb6943cbed7e7a594b253b950370b5b |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http:/... | stuart-knock/tvb-framework | tvb/interfaces/web/entities/context_model_parameters.py | Python | gpl-2.0 | 16,171 | [
"Gaussian"
] | 07e46fc14ef40c5b180a004f9ef4fc25ffe4051abd861940e7ea50b646e3bdab |
'''
Steps for problem.feature lettuce tests
'''
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from common import i_am_registered_for_the_course
from problems_setup import PROBLEM_DICT, answer_problem, problem_has_answer, add_problem_to_course
@... | syjeon/new_edx | lms/djangoapps/courseware/features/problems.py | Python | agpl-3.0 | 7,043 | [
"VisIt"
] | e822d12724273e3d6bc30e905fb9f8535268e3b559b39577f6517c5d570c7269 |
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields, rdtrajectory
from rdkit.Chem.rdtrajectory import Snapshot, \
Trajectory, ReadAmberTrajectory, ReadGromosTrajectory
import os,sys
import unittest
from rdkit import RDConfig
def feq(v1, v2, tol=1.0e-4):
return... | adalke/rdkit | Code/GraphMol/Wrap/testTrajectory.py | Python | bsd-3-clause | 20,262 | [
"Amber",
"RDKit"
] | a9f3bcc6f5523e0602aca88253c332311510c51286c00b92b8876a3c7ad1641b |
'''
#=============================================================================
# FileName: prepare_ligands.py
# Desc:
# Author:
# Email:
# HomePage:
# Version: 0.0.1
# LastChange: 2014-06-26 06:53:27
# History:
#===========================================================... | Jianlong-Peng/pytools | PDB/prepare_ligands.py | Python | gpl-2.0 | 1,034 | [
"Pybel"
] | e62eac2d24ed45ab2124c09aa2d33a7d3f01f7cbf17e7351c5d527ba4b8a3738 |
__author__ = 'chris hamm'
#NetworkServer_r9D
#Created: 1/10/2015
#Added lists for the server to use to keep track of things that have happened and still need to be done
#(In progress) (May not be implemented) A list of all messages that have been received from clients and who sent them
#A list that records all... | COCS4950G7/COSC4950 | Source/Rainbow/NetworkServer.py | Python | gpl-3.0 | 77,026 | [
"ADF"
] | 4fb4bddb1cac5a9d16c2ba52563d01f8e250f7ed24e5220fda0c2bde8f21d54d |
#!/usr/bin/env python
# encoding: utf-8
"""
inorder-successor-in-bst.py
Created by Shuailong on 2016-05-17.
https://leetcode.com/problems/inorder-successor-in-bst/.
"""
# Definition for a binary tree node.
class TreeNode(object):
def __init__(self, x):
self.val = x
self.left = None
sel... | Shuailong/Leetcode | solutions/inorder-successor-in-bst.py | Python | mit | 1,260 | [
"VisIt"
] | 5f10a5a51289b2550c0546c686510e32f2bb14d71086af5218b611a24d258692 |
"""
===========================
Formaldehyde mm-line fitter
===========================
This is a formaldehyde 3_03-2_02 / 3_22-221 and 3_03-2_02/3_21-2_20 fitter.
It is based entirely on RADEX models.
Module API
^^^^^^^^^^
"""
from __future__ import print_function
import numpy as np
from . import hyperfine
from . im... | low-sky/pyspeckit | pyspeckit/spectrum/models/formaldehyde_mm.py | Python | mit | 18,978 | [
"Gaussian"
] | 1b417af1848fd6221c0673abe7c78f66a77a189fe7d052c199dea4ff112d8e28 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.