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import os
import warnings
import numpy as np
from astropy.convolution import Gaussian1DKernel, Gaussian2DKernel
from astropy.io import fits
from astropy import wcs
import astropy
import multiprocessing
from .. import cubes, Cube, CubeStack
from ...spectrum.models import n2hp, ammonia_constants
from ...spectrum.models.... | allisony/pyspeckit | pyspeckit/cubes/tests/test_cubetools.py | Python | mit | 15,106 | [
"Gaussian"
] | cd82b6faff07b07ad02b32320d23777230d9946c0799122c37bf3afdfb477b99 |
###############################################################################
# Copyright 2015-2019 University of Florida. All rights reserved.
# This file is part of UF CTS-IT's NACCulator project.
# Use of this source code is governed by the license found in the LICENSE file.
#######################################... | ctsit/nacculator | nacc/lbd/ivp/builder.py | Python | bsd-2-clause | 21,964 | [
"VisIt"
] | 076e6029125164b4458ded638046b69079c547873f98d58d3b1c8ce8afabcc5a |
# box
# Copyright 2013-2014 Dipen Patel
# See LICENSE for details.
import urllib
import httplib
import json
from error import ERRORCODES, BoxError
import mimetypes
BOX_API_VERSION = "/2.0"
BOX_API_URL = "api.box.com"
BOX_DOWNLOAD_URL = "dl.boxcloud.com"
BOX_API_UPLOAD_URL = "upload.box.com"
class BoxClient(object)... | dipen30/boxapi | box/client.py | Python | mit | 13,730 | [
"VisIt"
] | eb07801e83c3f0d43f6b0e970e8f90f2da70f84327a8ab6087a2f512882c877e |
import vtk
def ReadPolyData(filename):
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
return reader.GetOutput()
def WritePolyData(input,filename):
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(filename)
writer.SetInputData(input)
writer.Write(... | kayarre/Tools | vtk/smooth_polydata.py | Python | bsd-2-clause | 919 | [
"VTK"
] | 7e5bb2d564ba0fb724b8a2d36a4b0682f1068abc391599572c3265c55933dd01 |
# 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 NcbiRmblastn(AutotoolsPackage):
"""RMBlast search engine for NCBI"""
homepage = "http... | iulian787/spack | var/spack/repos/builtin/packages/ncbi-rmblastn/package.py | Python | lgpl-2.1 | 904 | [
"BLAST"
] | e38ee9ba300f864277887f1976d42e78ad18c521fbdf2eaac9b1c2d395a191fb |
import os
from subprocess import Popen, PIPE, STDOUT
from ase import Atoms
from ase.calculators.turbomole import Turbomole
# Delete old coord, control, ... files, if exist
for f in ['coord',
'basis',
'energy',
'mos',
'statistics',
'control']:
if os.path.exists(f):... | askhl/ase | ase/test/turbomole/turbomole_H2.py | Python | gpl-2.0 | 752 | [
"ASE",
"TURBOMOLE"
] | 530d9391f8d868f59c4ae83f1788fb637a2dfcd31a8229ae8dd0df8dcbb3fd01 |
#!/usr/bin/env python
import pysam
import argparse
import sys
import time
import logging
import multiprocessing
DEFAULT_MIN_SOFT_CLIP=20
DEFAULT_MIN_SOFT_CLIP_MAPQ=10
DEFAULT_MIN_SOFT_CLIP_MATE_MAPQ=10
DEFAULT_BAD_MAP_MAX_SOFT_CLIP=50
DEFAULT_BAD_MAP_MIN_MAPQ=10
DEFAULT_BAD_MAP_MIN_MATE_MAPQ=10
DEFAULT_BAD_MAP_MIN_NM... | bioinform/breakseq2 | breakseq2/breakseq_pre.py | Python | bsd-2-clause | 6,295 | [
"pysam"
] | 24381efa19767dd74ef531ee0105a8420652df83bfc62c21a85cd437ee2dc381 |
from argparse import ArgumentParser, FileType, ArgumentDefaultsHelpFormatter
from csv import DictReader
from io import StringIO
from itertools import groupby
from operator import itemgetter
from tempfile import NamedTemporaryFile
from micall.core.denovo import write_contig_refs
def parse_args():
parser = Argumen... | cfe-lab/MiCall | micall/utils/contig_blaster.py | Python | agpl-3.0 | 3,252 | [
"BLAST"
] | f38f078f2db33eab592ca3c829c84df5b684cbf191219476e07c2374b112a86b |
# $Id: octopus_conf_handler.py 2016-12-17 $
# Author: Coen Meerbeek <coen@buzzardlabs.com>
# Copyright: BuzzardLabs 2016
import splunk.admin as admin
import splunk.entity as en
# import your required python modules
'''
Copyright (C) 2005 - 2010 Splunk Inc. All Rights Reserved.
Description: This skeleton python scrip... | cmeerbeek/splunk-addon-octopus-deploy | TA-OctopusNT-Fwd/bin/octopus_conf_handler.py | Python | mit | 2,769 | [
"Octopus"
] | 5f0b1349d75acb7023deea204bba77a2050a0a88662b42167fc83d9425c7fa66 |
#
# Copyright (C) 2013-2019 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) any later... | KaiSzuttor/espresso | testsuite/python/rigid_bond.py | Python | gpl-3.0 | 1,886 | [
"ESPResSo"
] | 6f78504aafb5157e56cf3beb79510eecff6ad5d34c9c5912eb85ceda39cf6fb5 |
import functools
from typing import List, Any
import numpy as np
import scipy.sparse as sp
import pytest
from sklearn.metrics import euclidean_distances
from sklearn.random_projection import johnson_lindenstrauss_min_dim
from sklearn.random_projection import _gaussian_random_matrix
from sklearn.random_projection im... | kevin-intel/scikit-learn | sklearn/tests/test_random_projection.py | Python | bsd-3-clause | 13,557 | [
"Gaussian"
] | 1b4b950dd931d7016a16e6c22bf953efdb669fc66c4fbd7a10a2485555b7412c |
# -*- 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... | kain88-de/mdanalysis | package/MDAnalysis/analysis/psa.py | Python | gpl-2.0 | 83,800 | [
"MDAnalysis"
] | f981f67f978815fd3f8b3154e1506bcd7a8bb3c381c7098f34852747b1b1a4ab |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/qiime2 | qiime2/core/testing/plugin.py | Python | bsd-3-clause | 21,565 | [
"Octopus"
] | fa9468976d648a7cb8db49c09e497c3c5e09d7139a51072e53cab21516486a68 |
#!/usr/bin/env python
# Functions:
# parse_indexes
#
# indexes_matrix
# select_cols_str
# select_cols_substr
# add_column
# copy_column
# add_desc_for_gmx
#
# add_header_line
# fill_empty_headers
# remove_header_line
# reorder_headers_alphabetical
# upper_headers
# lower_headers
# hash_headers
# remove_duplicate_heade... | jefftc/changlab | scripts/slice_annot.py | Python | mit | 110,648 | [
"ADF"
] | 63a379fadc816b2c74e12914809de696131d68ada7c10e1717dcf7d30852279f |
import argparse
import torch
import pickle
import numpy as np
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
# Training settings
parser = argparse.ArgumentParser(description='PyTorch semi-supervised MNIST')
parser.add_argument('--batch-size', type... | fducau/AAE_pytorch | script/aae_supervised.py | Python | gpl-3.0 | 8,911 | [
"Gaussian"
] | ca1dc18f30633253478f48f3bc12bb68c97148cc694afd56d3d95df4b48cd465 |
"""Deal with Motifs or Signatures allowing ambiguity in the sequences.
This class contains Schema which deal with Motifs and Signatures at
a higher level, by introducing `don't care` (ambiguity) symbols into
the sequences. For instance, you could combine the following Motifs:
'GATC', 'GATG', 'GATG', 'GATT'
as all fa... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/NeuralNetwork/Gene/Schema.py | Python | apache-2.0 | 26,134 | [
"Biopython"
] | 12fdf797ef5c7010f1d0ae43530385fa3832ffc3d5ba09dd3677f7ada53829d5 |
"""This module adds support to easily import and export NumPy
(http://numpy.scipy.org) arrays into/out of VTK arrays. The code is
loosely based on TVTK (https://svn.enthought.com/enthought/wiki/TVTK).
This code depends on an addition to the VTK data arrays made by Berk
Geveci to make it support Python's buffer p... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/util/numpy_support.py | Python | bsd-3-clause | 8,928 | [
"VTK"
] | b04829d049ac33fcede1d36612d043cdaaabde8be04789e96ff7d47c3b7cdba8 |
#!/usr/bin/env python
################################################################################
#
# qe_extractor.py
#
# Pulls all sorts of information from a QE output file and writes to standard
# output, e.g. the command "qe_extractor.py INPUTFILE homo" uses the number of
# electrons and the output KS eigenva... | kaneod/physics | python/qe_extractor.py | Python | gpl-3.0 | 8,488 | [
"ESPResSo",
"Quantum ESPRESSO"
] | 6bcae61c994939915867671d118ee729cde78b72206d9295a23535f671f0d8b9 |
import numpy as np
from astropy.io import fits
from astropy.io import ascii
from glob import glob
import pdb
import os
def collate(path, jobnum, name, destination, optthin=0, clob=0, high=0, noextinct = 0, noangle = 0, nowall = 0, nophot = 0, noscatt = 1):
"""
collate.py ... | danfeldman90/EDGE | collate.py | Python | mit | 28,085 | [
"VisIt"
] | 3b675186035fe616a62d831e6dde446c9594379dcdacb34619fab208ffdec0ee |
# 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 Blat(Package):
"""BLAT (BLAST-like alignment tool) is a pairwise sequence
alignment... | iulian787/spack | var/spack/repos/builtin/packages/blat/package.py | Python | lgpl-2.1 | 842 | [
"BLAST"
] | 8009f3d99d50afff6dc3f9bd3ce7221dabf809af4e9f3caf1da461bf6d68f81f |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Jun 9, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Jun 9, 2012"
import unittest
import... | yanikou19/pymatgen | pymatgen/matproj/tests/test_rest.py | Python | mit | 9,825 | [
"pymatgen"
] | 5fe1a641d342c1455feec49d1771ffade26f706aaf3ac4ef26159581f3c6609f |
#-----------------------------------------------------------------------------
# Copyright (c) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part of this software.
#-----... | ellisonbg/pyzmq | zmq/tests/__init__.py | Python | lgpl-3.0 | 7,203 | [
"Brian"
] | 515a38277390a0c3e61f83ad2bde503ceed2a24f03f10832b4d57fd459899ed3 |
#!/usr/bin/python
########################################################################
# File : DIRACbenchmark.py
# Author : Andrew McNab
########################################################################
""" DIRAC Benchmark 2012 by Ricardo Graciani, and wrapper functions to
run multiple copies in ... | hgiemza/DIRAC | WorkloadManagementSystem/Client/DIRACbenchmark.py | Python | gpl-3.0 | 8,236 | [
"DIRAC"
] | c125e2a3b376d1f4572b0faf03fd502e5c25da13bd92100928478bfd30ac9bb8 |
"""
============= DON'T MODIFY THIS FILE ============
This is the boilerplate default configuration file.
Changes and additions to settings should be done in
/bp_content/themes/<YOUR_THEME>/config/ rather than this config.
"""
import os
config = {
# webapp2 sessions
'webapp2_extras.sessions': {'secret_key': ... | joshainglis/sa-tools | bp_includes/config.py | Python | lgpl-3.0 | 4,390 | [
"VisIt"
] | 33046706804d80ee531fe91c04182144e054f492f1aae3c6b754a961f612e64b |
""" Write ccData object to file """
from __future__ import print_function
from os.path import join
from qcl import templates
from qcl import periodictable as pt
def xyzfile(ccdata, fname, append=False):
"""xyzfile"""
if append:
permission = 'a'
else:
permission = 'w'
with open(fname... | ben-albrecht/qcl | qcl/write.py | Python | mit | 7,255 | [
"MOPAC"
] | ccfe6fba9e7985a07f3e6de1eab20ab93f671a3c6ddcd27e343e82cefa9313c7 |
"""
basic support for running library as script
"""
import os
import os.path as op
import shutil
import signal
import sys
import logging
from httplib import HTTPSConnection
from urllib import urlencode
from socket import gethostname
from subprocess import PIPE, call
from optparse import OptionParser as OptionP, Optio... | sgordon007/jcvi_062915 | apps/base.py | Python | bsd-2-clause | 53,020 | [
"BWA",
"Bowtie"
] | c4a68f410e696153233b0bd9801443ef3f27b83f4ea8f1121b0fdc10d77e7ef2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract fragments for molecules in given SDF files and save then into JSON.
Path and circular fragments use different indexing method, so they may collide.
Usage:
python extract_fragments.py
-i {input file or directory with input files}
-o {path to ... | davidhoksza/bayescreen | biochem_tools/extract_fragments.py | Python | mit | 13,552 | [
"RDKit"
] | 7102294c5025b93d1a096627167a8273b07311cee7bb6dd41763025656c9143b |
# Modified by FrancoisMalan 2011-12-06 so that it can handle an input with larger
# extent than its source. Changes constitute the padder module and pad_source method
import gen_utils
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
class prob... | nagyistoce/devide | modules/filters/probeFilter.py | Python | bsd-3-clause | 4,578 | [
"VTK"
] | 92b35d2357c0875073216146deb3799cd342907b1f66ee35c016b8acb32ddbd3 |
from __future__ import print_function
from __future__ import absolute_import
import sys
from metatlas import metatlas_objects as metob
from metatlas.io import h5_query as h5q
import qgrid
from metatlas.helpers import metatlas_get_data_helper_fun as mgd
from matplotlib import pyplot as plt
from matplotlib import colo... | biorack/metatlas | metatlas/interfaces/pactolus_tools.py | Python | bsd-3-clause | 45,482 | [
"RDKit"
] | 9b12acf39fdcb01cf8830d877fbdeb5a5822a7d7b3229eaa27ba9f8f18c04ec8 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | christianbrodbeck/nipype | nipype/interfaces/fsl/model.py | Python | bsd-3-clause | 69,529 | [
"Gaussian"
] | 2e33f326178064e910303e7cb5ebcf585988dff72f0ecb21498b4c2c02e77397 |
import fauxfactory
import pytest
from cfme import test_requirements
from cfme.ansible_tower.explorer import TowerCreateServiceDialogFromTemplateView
from cfme.infrastructure.config_management import AnsibleTower
from cfme.utils.testgen import config_managers
from cfme.utils.testgen import generate
from cfme.utils.upda... | izapolsk/integration_tests | cfme/tests/infrastructure/test_config_management.py | Python | gpl-2.0 | 8,785 | [
"VisIt"
] | 40a293222457f202505adca01b1ebad95714c792747959c227769468603e003d |
# -*- coding: utf-8 -*-
"""
Lexer for the NesC language.
http://nescc.sourceforge.net/
:copyright: 2008 by Peter Vizi
:license: GPLv3, see LICENSE for more details.
"""
import re
try:
set
except NameError:
from sets import Set as set
from pygments.scanner import Scanner
from pygments.lexer im... | petervizi/pygments-nesc | lexer/__init__.py | Python | gpl-3.0 | 5,072 | [
"NetCDF"
] | dda6c73e67c586c82e08cb0eace34550e9427c32b23437cd9f9505cd83c1105b |
import os
import pysam
from os import path
from ...fileop import PosixFileSystem
from ....util import Utility
def run_sam_to_bam(*args, **kwargs):
paramindex = 0
if 'data' in kwargs.keys():
data = kwargs['data']
else:
if len(args) == paramindex:
raise ValueError("Argument not gi... | mainulhossain/phenoproc | app/biowl/libraries/pysam/adapter.py | Python | mit | 1,304 | [
"pysam"
] | a151cb5b7a73e9e625612db5177c7e59906d4d2fe26f4fe2f14423e135dee0c1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date_... | dongsenfo/pymatgen | pymatgen/apps/borg/tests/test_queen.py | Python | mit | 1,323 | [
"pymatgen"
] | fa8dc8d955f408d1a2f2e844e6a3229d0f9b3dacaf0947d925f665d1c0f76717 |
from setuptools import setup
setup(
name = 'plumbing',
version = '2.0.3',
description = 'Helps with plumbing-type programing in python',
long_description = open('README.md').read(),
license = 'MIT',
url = 'http://github.com... | DC23/plumbing | setup.py | Python | mit | 851 | [
"Biopython"
] | f393a7bbf02b852a47cceced94dcae754baf871d4114cdc0c14b8b15a1cbd4f5 |
#!/usr/bin/env python
"""
This module calculates thermal properties using different equations of state.
"""
from __future__ import division
import warnings
import sys
import subprocess
import unittest
import pymatgen
from pymatgen.agl_thermal.agl_polynomial import polfit
from pymatgen.agl_thermal.agl_polynomial impor... | ctoher/pymatgen | pymatgen/agl_thermal/agl_eqn_state.py | Python | mit | 37,058 | [
"pymatgen"
] | 34a4b161c3a1c381982ff96fddd673d4b1522afd90c174234a912578a40d208e |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren1)
iren = vtk... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/TestFlyingEdges2D.py | Python | bsd-3-clause | 1,383 | [
"VTK"
] | 3dbb395c2b585f2a3586a4eac72fe683621f15f8ec2b7cc846591ff7bf408f42 |
# Copyright 2015 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 agreed to in writing, s... | googleapis/python-api-core | tests/unit/test_page_iterator.py | Python | apache-2.0 | 21,887 | [
"BLAST"
] | 09f40ab9e57f32e892c719a334ddc22532c05b1437d664a57b4c3e0a4f975df5 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/PyscesMiniModel.py | Python | bsd-3-clause | 18,529 | [
"PySCeS"
] | 045edf580199b1792c5417c1246d5a120b7748321dbc57009337e11cbedb7822 |
#!/usr/bin/env python
##############################################################
# B a r a K u d a
#
# Generate netcdf files of cross-sections
#
# L. Brodeau, 2016
##############################################################
import sys
import numpy as nmp
from netCDF4 import Dataset
import b... | brodeau/barakuda | python/exec/cross_sections.py | Python | gpl-2.0 | 3,545 | [
"NetCDF",
"ORCA"
] | 5492994ffe5f0da9e6e225d8e2a8f0a5dc31ae84ae99a371821241e7e422ce95 |
# Copyright 2013 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs 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, ... | JoseBlanca/seq_crumbs | crumbs/seq/seq.py | Python | gpl-3.0 | 9,686 | [
"Biopython"
] | c67736aee94f997388f084ce61a9b61ac9d6328822d3c0e75c1d73dbcdb53d98 |
# This script exercsises some of the idiosyncracies
# of the descriptor class and PBLAS on a realistic
# case. See the BLACS descriptor documentation
# in trunk/gpaw/blacs.py for some discussions of
# these idiosyncracies.
import numpy as np
from gpaw.blacs import BlacsGrid, parallelprint
from gpaw.mpi import world... | qsnake/gpaw | gpaw/test/big/miscellaneous/pblacs_oblong.py | Python | gpl-3.0 | 972 | [
"GPAW"
] | 28a5d47158147e63e8cb3786726f976b84f845b577a5c6a755fc59ea2ea8ad19 |
"""
=============================================
Integration and ODEs (:mod:`scipy.integrate`)
=============================================
.. currentmodule:: scipy.integrate
Integrating functions, given function object
============================================
.. autosummary::
:toctree: generated/
quad ... | aeklant/scipy | scipy/integrate/__init__.py | Python | bsd-3-clause | 3,826 | [
"Gaussian"
] | 6d7b544523f9fee7eabb865648cf9562e0aa9f90e2c274a08452c6214571f590 |
from __future__ import print_function
from six import iteritems
import vtk
from vtk import vtkQuad
from numpy import array, arange, cross
from pyNastran.converters.LaWGS.wgs_reader import LaWGS
from pyNastran.gui.gui_objects.gui_result import GuiResult
class LaWGS_IO(object):
def __init__(self):
... | saullocastro/pyNastran | pyNastran/converters/LaWGS/wgs_io.py | Python | lgpl-3.0 | 6,233 | [
"VTK"
] | 85d454ef4e6432031cabeae107f5868391f2c95ff0cace87743ab006ce13f039 |
#!/opt/miniconda/bin/python3
import sys
import subprocess
from textwrap import fill
import pandas as pd
from Bio import SeqIO
readfile = sys.argv[1]
allrefs = dict([(s.id.split('_')[0], str(s.seq))
for s in SeqIO.parse('/analyses/Diagnostics/Repositories/SmaltAlign/References/flugenomes_nonmixed.fast... | medvir/SmaltAlign | select_ref.py | Python | mit | 1,691 | [
"BWA"
] | c67e65456a25c9e9555486897c05125489336f6494073bad5ef52d3c07d101d2 |
#!/usr/bin/env python
import io
import netCDF4
import numpy
import m6plot
import m6toolbox
import matplotlib.pyplot as plt
import os
try: import argparse
except: raise Exception('This version of python is not new enough. python 2.7 or newer is required.')
def run():
parser = argparse.ArgumentParser(description='''... | nicjhan/MOM6-examples | tools/analysis/TS_drift.py | Python | gpl-3.0 | 3,201 | [
"NetCDF"
] | e627840032caf7ec0f2458786999d5fd10ef8b166d3c3a531863a1b699f88521 |
######################################################################
# Simple script to test VTK export of periodic cell
######################################################################
# enable periodic cell
O.periodic=True
# insert some bodies
sp = randomPeriPack(radius=1,initSize=(10,20,30),memoizeDb='/tmp/v... | bcharlas/mytrunk | examples/test/vtkPeriodicCell.py | Python | gpl-2.0 | 865 | [
"VTK"
] | 3b93c5c29d599b48dc7894fd57c023f516eb614a67bbf9c7b8f46f4ad20abe66 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rmvgridowner - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms... | heromod/migrid | mig/cgi-bin/rmvgridowner.py | Python | gpl-2.0 | 1,112 | [
"Brian"
] | 62d3c6bcef12c5953a8a7ba3d909bbd7d04141a5cda21763b76eee8850f747b8 |
"""Handle surfaces."""
from __future__ import absolute_import, division, print_function
from nibabel.freesurfer.io import read_geometry
import numpy as np
from scipy.io.matlab.mio import loadmat
def vertex_values_to_colors(vertex_values):
"""Convert vertex values to RGB representation.
Parameters
-... | fnielsen/brede | brede/surface/core.py | Python | gpl-3.0 | 9,816 | [
"Mayavi"
] | 3f78104daf57f322461e37dcc0f68d1ce253df54b5582a51fdd099a1227c25bc |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | caseyrygt/osf.io | tests/factories.py | Python | apache-2.0 | 17,903 | [
"Brian"
] | e8f3fadf0bd35f9cec5e9b1ff70da04a261c9e09b9bd296cad10a7cc54844c4f |
#!/usr/bin/env python
# http://arxiv.org/pdf/1512.09300.pdf
import pickle,subprocess, argparse, urllib
from astropy.io import fits
import scipy.ndimage.interpolation as intp
import numpy as np
import os,re
import math
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import chainer
from chain... | nushio3/UFCORIN | script/suntomorrow-VAEGAN/main-vectorizer.py | Python | mit | 18,295 | [
"Gaussian"
] | 1dda3b2d0200dcfed86c55d7c4fd3e1438630b869b82376f7d6882b6941f1d7f |
from keys import *
from simulation_params import *
import nest
import numpy.random as random
# Neuron parameters
iaf_neuronparams = {'E_L': -70., # Resting membrane potential in mV
'V_th': -50., # Spike threshold in mV
'V_reset': -67., # Reset membrane... | research-team/NEUCOGAR | NEST/cube/dopamine/3d/scripts/synapses.py | Python | gpl-2.0 | 2,943 | [
"NEURON"
] | e6ba039c1b1cb860ccaa7ed8af2f042a7004ef81b899f0ca135a1668d4487767 |
""" Coarse Ricci matrix. """
import numpy as np
import numexpr as ne
import scipy.linalg as sl
from pyfftw import zeros_aligned
def add_AB_to_C(A, B, C):
"""
Compute C += AB in-place.
This uses gemm from whatever BLAS is available.
MKL requires Fortran ordered arrays to avoid copies.
Hence we wo... | siudej/Ricci | Ricci.py | Python | bsd-3-clause | 4,298 | [
"Gaussian"
] | 64e70d5766f6b7eeb7e137a36a58221dd750ace47ac2e9531db5c24661e8ff59 |
import matplotlib
matplotlib.use('Agg')
print "importing stuff..."
import numpy as np
import pdb
import matplotlib.pylab as plt
from scipy import special
from .context import aep
from .context import config
# import sys
# import os
# sys.path.insert(0, os.path.abspath(
# os.path.join(os.path.dirname(__file__), '.... | thangbui/geepee | examples/gplvm_aep_examples.py | Python | mit | 13,286 | [
"Gaussian"
] | c3fbd69a1503cadd9bd462760d8936fb6b2d7b4790bb25e24205e98b0e43c50b |
# TODO: Add properties to solver
#TODO: snapshot_format not available in this version. update later.
__author__ = 'hugh'
bl_info = {
"name": "Create Caffe solution",
"category": "Object",
}
import bpy
import random
import time
import os
tab = ' '
tab2 = tab + tab
tab3 = tab2 + tab
def getFillerString(fi... | codeaudit/caffe-gui-tool | CaffeGenerate.py | Python | unlicense | 21,253 | [
"Gaussian"
] | b20ae35165f77ba8b58786b30a1e602ed4ca067316ada922c7f3916055978420 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_8000/brian2_benchmark_COBAHH_nosyn_8000.py | Python | gpl-3.0 | 3,350 | [
"Brian"
] | c1c3f066f51c9393e1c7f6d20cf69656ebbbf3bc699d8083f3e6a18d50fa9048 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements an interface to the Henkelmann et al.'s excellent
Fortran code for calculating a Bader charge analysis.
This module depends on a compiled bader executable available in the path.
Please download the library at http://theory.c... | rousseab/pymatgen | pymatgen/command_line/bader_caller.py | Python | mit | 5,733 | [
"VASP",
"pymatgen"
] | caee80a66cc9feadd2746698e22cda8a9ebd0626a18aa04320f6538cf303b532 |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | vistrails/core/system/linux.py | Python | bsd-3-clause | 7,566 | [
"VTK"
] | 138dbfadfda3fcf51a3c0acf7f9370beeb26a5eb68b0e6b74712be3070ff9ad2 |
import unittest
from timeseries import *
# import .timeseries
import io
import sys
from contextlib import redirect_stdout
import numpy as np
class MyTest(unittest.TestCase):
def test_astlexpar(self):
data = open("./samples/example1.ppl").read()
ast = pype.parser.parser.parse(data, lexer=pype.lexer... | Planet-Nine/cs207project | tests/test_pype.py | Python | mit | 6,223 | [
"VisIt"
] | ff2950df34e5f70f8563f8d4d1032abf236adbeb5ade8d57809fc6ce4b1a8175 |
import os
import optparse
import subprocess
from multiprocessing import Pool
directory = ""
results = "results.data"
extension = ""
aligned_extension = ".tab"
datatype = ""
perlpath = "/home/galaxy-dist/tools/osiris/tree-manipulation/"
def unescape(string):
mapped_chars = {
'>': '__gt__',
'<': '_... | xibalbanus/PIA2 | osiris_phylogenetics/phylostatistics/phytab_LB_pruner.py | Python | mit | 3,591 | [
"Galaxy"
] | 4089009e78ce53f08ff11d27cfe3a9f917c3ee619b64db4962e8514832b7458e |
import os
import logging
import synapse.glob as s_glob
import synapse.common as s_common
import synapse.lib.cell as s_cell
import synapse.lib.msgpack as s_msgpack
logger = logging.getLogger(__name__)
defport = 65521 # the default neuron port
class Neuron(s_cell.Cell):
'''
A neuron node is the "master cell"... | vivisect/synapse | synapse/neuron.py | Python | apache-2.0 | 3,346 | [
"NEURON"
] | fc130c5b69eaed6864580c07aae17f08b1b10b13e1d3b4b99d3e4233f16ecf88 |
# Copyright 2013-2018 The Meson development team
# 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 agree... | pexip/meson | mesonbuild/dependencies/base.py | Python | apache-2.0 | 102,150 | [
"NetCDF"
] | 8e2be49e6b557cec8fc0bf03e69fc25ef98de1b2583531a105a4eb70e9c0cf7d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements modules for input and output to and from Qchem
""" | dongsenfo/pymatgen | pymatgen/io/qchem/__init__.py | Python | mit | 189 | [
"pymatgen"
] | eb1151064bfeee78a40de32525e686513f552bda7b7ca4b51184b08de345f066 |
from __future__ import unicode_literals
import json
import nexmo
import pytz
import six
from context_processors import GroupPermWrapper
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from decimal import Decimal
from django.conf import settings
from django.contrib.auth.models import U... | tsotetsi/textily-web | temba/orgs/tests.py | Python | agpl-3.0 | 142,450 | [
"VisIt"
] | 144c3a48f19d5406d464e37e06fa63c554a84cee81b9bd673437598abc789df5 |
#!/usr/bin/env python3
"""K. Miernik 2012
k.a.miernik@gmail.com
Distributed under GNU General Public Licence v3
Gaussian peak fitting class
"""
import math
import numpy as np
import os
import sys
import time
from lmfit import minimize, Parameters, report_errors
from Pyspectr.exceptions import GeneralError as G... | ntbrewer/Pyspectr | Pyspectr/peak_fitter.py | Python | gpl-3.0 | 6,244 | [
"Gaussian"
] | 98ab0559519eb2f276bffa8f883db7ba3a704d5d758446aae65af345bc612e48 |
#!/usr/bin/python
import sys
import argparse
import multiprocessing
import logging
import vcf
import random
import math
import pysam
def annotate_vcfs(bam, chromosomes, vcfs):
func_logger = logging.getLogger("%s-%s" % (annotate_vcfs.__name__, multiprocessing.current_process()))
random.seed(0)
# Load inde... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/EGG-INFO/scripts/annotate_vcf_bam.py | Python | apache-2.0 | 7,657 | [
"pysam"
] | 29744e7f3edd24d8af2c446e30d7261ae44bd65801afc6c3901ecb08ecf3d7de |
"""TIP3P potential, constraints and dynamics."""
from math import pi, sin, cos
import numpy as np
import ase.units as units
from ase.parallel import world
from ase.md.md import MolecularDynamics
qH = 0.417
sigma0 = 3.15061
epsilon0 = 0.1521 * units.kcal / units.mol
rOH = 0.9572
thetaHOH = 104.52 / 180 * pi
class T... | slabanja/ase | ase/calculators/tip3p.py | Python | gpl-2.0 | 5,975 | [
"ASE"
] | 87c562cffbfd8e3e83f9b19187386e819d46892664dc4768bac23321563d651b |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/many2oneeditor.py | Python | gpl-2.0 | 14,748 | [
"VisIt"
] | 3b08c6484b8f7646e887e4a40bbc0c6662f9dc274da3968d501c22c3285094d9 |
import numpy as np
from gpaw import debug
from gpaw.io.tar import Reader, Writer
from gpaw.utilities import is_contiguous
from gpaw.analyse.observers import Observer
from gpaw.transformers import Transformer
from gpaw.tddft import attosec_to_autime, eV_to_aufrequency
# -----------------------------------------------... | qsnake/gpaw | gpaw/tddft/fourier.py | Python | gpl-3.0 | 11,388 | [
"GPAW",
"Gaussian",
"NetCDF"
] | c1d814a163b38b45413d6657e9054cb4533da8f1f212687d0763aa9a4a637214 |
# Copyright 2014-2018 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/data/nist.py | Python | apache-2.0 | 2,567 | [
"Avogadro",
"PySCF"
] | 33010f2ff0fd9df989ae19ab3bb0e9aa1af1a5ed726586c069fba2a420fd51ac |
from collections import OrderedDict
import pytest
from diffraction import Crystal, Site
CALCITE_ATOMIC_SITES = OrderedDict([
("Ca1", ["Ca2+", [0, 0, 0]]),
("C1", ["C4+", [0, 0, 0.25]]),
("O1", ["O2-", [0.25706, 0, 0.25]])
])
class TestCreatingFromSequence:
def test_can_create_from_sequence(self):
... | noahwaterfieldprice/diffraction | tests/functional/create_crystal_test.py | Python | gpl-2.0 | 5,308 | [
"CRYSTAL"
] | 90330f6756760ab2998e4b4927d950db2083ab77f8686b97b8ef1b85e2b47c31 |
import ovh
import ConfigParser
import string
import warnings
from random import choice
from prettytable import PrettyTable
class EmailManager :
''' This class uses the ovh Python API and provide some
functionalities to interact with email accounts
Arguments:
niceoutput Optional.... | rubendibattista/ovh-python-email-manager | ovhem/em.py | Python | bsd-2-clause | 5,365 | [
"VisIt"
] | eeb2344758f0d9129a81054701d232c2bab06bf5285aeba0cbb2c6e3f46f5832 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
"""
A web crawler for networks’ international calling costs.
"""
from __future__ import print_function
import json
import os
import re
import sys
import time
import textwrap
import argparse
import logging
import coloredlogs
try:
from selenium import webdriver
... | luigi-riefolo/network_crawler | network_crawler/network_crawler.py | Python | mit | 9,914 | [
"VisIt"
] | d62ee6454ab65d37a4529561694306e7629383d6fae80be545f4a66fd080b2f5 |
#neuro.py - a basic set of neural network functions
#these are almost entirely based on the functions
#provided in the textbook (Data Science from Scratch)
#This is not an efficient nor robust implementation.
#For educational purposes only.
from __future__ import division
import numpy as np
import math as math
import ... | armandosrz/DataScience-343 | Neuro/neuro.py | Python | apache-2.0 | 3,296 | [
"NEURON"
] | 34262d3f7c3a1f679aa3cfe580be35e3ac683d8f51f59451b13dcac628cfaff0 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-delete-user
# Author : Adrian Casajus
########################################################################
"""
Remove User from Configuration
"""
from __future__ import print_functio... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-delete-user.py | Python | gpl-3.0 | 1,587 | [
"DIRAC"
] | f0b00fd5acf4f77fac4dfe7e3c5acfe2104637aa6fdcd462d9c4946be60c811a |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
__RCSID__ = "$Id$"
from types import IntType, LongType, ListType, DictType, StringTypes, StringType, NoneType, BooleanType
from DIRAC.Core.DISET.... | vmendez/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 19,011 | [
"DIRAC"
] | 2d3779752c3f5dcd216391290255c10add6ea67491e3236e2da7ea8f3c2feb75 |
#!/usr/bin/env python
"""
==================
ModEM
==================
# Generate data file for ModEM
# by Paul Soeffky 2013
# revised by LK 2014
# revised by JP 2014
# edited by AK 2016
"""
import os
import matplotlib.cm as cm
import matplotlib.colorbar as mcb
import matplotlib.colors as colors
import matplotlib.g... | MTgeophysics/mtpy | legacy/modem_new.py | Python | gpl-3.0 | 313,405 | [
"ParaView",
"VTK"
] | a032e62073307ed7210b8ab25a56a399ab4b3c4fc3cc5d9ce8f9e93a8b8b9ee3 |
#
# Copyright (C) 2013,2014 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) any l... | olenz/espresso | testsuite/python/nonBondedInteractions.py | Python | gpl-3.0 | 3,803 | [
"ESPResSo"
] | 4240f8e814a93a9757d2226433dfefbba8bc53125e1ddcef05d98b0c4a1b7a32 |
#!/usr/bin/env python3
"""
This is the new SONAR setup/install script. It will check for
prerequisites and configure some helper files.
Usage: setup.py
"""
import os,subprocess,sys,glob
SONAR_HOME=os.getcwd()
if len(glob.glob("%s/commonVars.py"%SONAR_HOME))==0:
SONAR_HOME = sys.argv[0]
if not os.path.is... | scharch/SOAnAR | setup.py | Python | gpl-3.0 | 7,164 | [
"BLAST",
"BioPerl",
"Biopython"
] | 67b682b8efcf18620c470cae2c81f1ecfd9f59df18afc80420a110164360a4ae |
import functools
import math
import numpy
from .Exponential import *
class GaussianExponential:
"""
Implements the convolution of a Gaussian with a multiexponential.
The Gaussian is assumed to be centered at the origin, and the exponential
is assumed to be modulated by a Heaviside function (also star... | tsbischof/photon_correlation | python/photon_correlation/GaussianExponential.py | Python | bsd-3-clause | 1,391 | [
"Gaussian"
] | 39e53d448e7867b8fca63f40d3d1352d66fade5ce99283bf11de205a01529609 |
# -*- coding: utf-8 -*-
#
# rate_neuron_dm.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | tobikausk/nest-simulator | pynest/examples/rate_neuron_dm.py | Python | gpl-2.0 | 5,588 | [
"Gaussian",
"NEURON"
] | b15ca8f0fb3a0d5e42b1b4a4720c6474d78e48beabcad7a3de61c09e3dc47e84 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/orca/data/spark_pandas.py | Python | apache-2.0 | 1,686 | [
"ORCA"
] | 75c03ce80f81d31a2f0f74304792de8ed8b429ac579f4e9d88bbfb0d54800087 |
from __future__ import division
import algebra
import math
def step_function(x):
return 1 if x >= 0 else 0
def perceptron_output(weights, bias, x):
"""returns 1 if the perceptron 'fires'; 0 if not"""
return step_function(algebra.dot(weights, x) + bias)
def sigmoid(t):
return 1 / (1 + math.exp(-t))... | mjamesruggiero/tripp | tripp/neural_networks.py | Python | bsd-3-clause | 1,824 | [
"NEURON"
] | 43137e9ca6093bf1afe9760e5312b2a2a6344c0b170b3dec6685557b19a4f4e1 |
# coding: utf8
{
' Assessment Series Details': ' Assessment Series Details',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'# of Inter... | flavour/porto | languages/en-gb.py | Python | mit | 259,796 | [
"VisIt"
] | 523521af21a80d0a7a492f5e228b5f32e032afa8e92c9db86db0e5d9dcc5345e |
""" The Cloud Director is a simple agent performing VM instantiations
"""
import random
import socket
import hashlib
from collections import defaultdict
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.Helpers import CSGlobals, Registry... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/CloudDirector.py | Python | gpl-3.0 | 22,033 | [
"DIRAC"
] | 3a90042a96019739242b8d5bfef2cd16989a03a4236ffa9be14a28c0e8a86b0f |
# -*- coding: utf-8 -*-
"""
Copyright 2015, Institute for Systems Biology.
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 ... | IlyaLab/CombiningDependentPvaluesUsingEBM | Python/WorkFlow.py | Python | apache-2.0 | 4,079 | [
"Gaussian"
] | 63b8f8dff63cf12cac5929ff974da695a5c8398b6238faeed4a892082be4872c |
#!/usr/bin/env python
"""
Author: Ryan Golhar <ryan.golhar@bms.com>
Date: 12/23/14
This script creates a folder within a library in Galaxy.
Usage: create_library.py <API_KEY> <API_URL> <library_name> folder_name
Algorithm:
"""
import argparse
from string import split
from common import display, submit
import sys
ap... | golharam/rgtools | scripts/galaxy/api/create_folder.py | Python | lgpl-3.0 | 1,330 | [
"Galaxy"
] | f0dffd1bd478d42e33e06194979ab5db2ba21c076d37ceaf11e1ae55e3ad4d81 |
#
# Bugwarrior documentation build configuration file, created by
# sphinx-quickstart on Wed Apr 16 15:09:22 2014.
#
# 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 configuration valu... | ralphbean/bugwarrior | bugwarrior/docs/conf.py | Python | gpl-3.0 | 8,914 | [
"Brian"
] | ca1b8cfb56d51b8aadb9602b02c424d55046a5ccef677156c50d9bd98e49fab6 |
"""Manage IPython.parallel clusters in the notebook.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, d... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/html/services/clusters/clustermanager.py | Python | apache-2.0 | 5,921 | [
"Brian"
] | fb08645a4fb6b7fa5bd7819ffc34fe654786e17bfe63547a593f9b961918702f |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import pdbfixer
padding = 1.0 * u.nanometers
cutoff = 0.95 * u.nanometers
ff = app.ForceField('amber99sbnmr.xml', 'tip3p-fb.xml')
temperature = 293.
pressure = 1.0 * u.atmospheres
fixer = pdbfixer.PDBFixer("./1am7.pdb")
fixer.find... | choderalab/open-forcefield-group | nmr/code/build_T4.py | Python | gpl-2.0 | 631 | [
"OpenMM"
] | 7fa140ff8edbb8d7cd3a4ab8e85f0095e923ff1d47e2907bc1d60a898e1535c0 |
##############################################################################
# Copyright (c) 2013-2018, 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... | mfherbst/spack | var/spack/repos/builtin/packages/moab/package.py | Python | lgpl-2.1 | 8,028 | [
"NetCDF",
"VTK"
] | 09d8268aa57fd99e6f8d0d89bda5ff1ac854d59cd80fe853a11fa80dd6816ff9 |
"""
BSD 3-Clause License
Copyright (c) 2017, Mairie de Paris
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of cond... | LouisTrezzini/projet-mairie | api/franceocr/cni/mrz.py | Python | bsd-3-clause | 11,613 | [
"Gaussian"
] | 8104960311c099c1e83f787e73c15e93b7a575e9832c4e67595540a032d148cc |
"""
Classes for point set registration
Author: Jeff Mahler
"""
from abc import ABCMeta, abstractmethod
import copy
import IPython
import logging
import numpy as np
import scipy.spatial.distance as ssd
import scipy.optimize as opt
try:
import mayavi.mlab as mlab
except:
logging.warning('Failed to import mayavi... | mdlaskey/DeepLfD | src/deep_lfd/rgbd/registration.py | Python | gpl-3.0 | 18,495 | [
"Mayavi"
] | b66d6cfd12161e3026a7257f6208b2b421943f5532de04e313b008d926d50dc5 |
########################################################################
# $HeadURL$
# File : JobPathAgent.py
# Author : Stuart Paterson
########################################################################
"""
The Job Path Agent determines the chain of Optimizing Agents that must
work on the job prior to t... | Sbalbp/DIRAC | WorkloadManagementSystem/Agent/JobPathAgent.py | Python | gpl-3.0 | 5,598 | [
"DIRAC"
] | b971374bd92b3bfb84ef6db98206f0ad8e12b7e03b2b7278aa7b76582b334775 |
from tapiriik.settings import WEB_ROOT, HTTP_SOURCE_ADDR, GARMIN_CONNECT_USER_WATCH_ACCOUNTS
from tapiriik.services.service_base import ServiceAuthenticationType, ServiceBase
from tapiriik.services.service_record import ServiceRecord
from tapiriik.services.interchange import UploadedActivity, ActivityType, ActivityS... | dlenski/tapiriik | tapiriik/services/GarminConnect/garminconnect.py | Python | apache-2.0 | 40,482 | [
"VisIt"
] | 412728bcc2e1ceaeb67d6aa5f94608b7371b203a98cfdeaf455f51ac9bc36855 |
#
# @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/wrapper_database.py | Python | gpl-2.0 | 35,234 | [
"Psi4"
] | 18e6a05533257df6a21ebeabb6699a4d0b5086b67343a4a4d7050eabe7fd2a85 |
# plotting
from matplotlib import pyplot as plt;
from matplotlib import colors
import matplotlib as mpl;
from mpl_toolkits.mplot3d import Axes3D
if "bmh" in plt.style.available: plt.style.use("bmh");
# matplotlib objects
from matplotlib import mlab;
from matplotlib import gridspec;
# scientific
import numpy as np;
im... | eecs445-f16/umich-eecs445-f16 | lecture07_naive-bayes/Lec07.py | Python | mit | 5,343 | [
"Gaussian"
] | cdf74970a6800ec942280b22df253582bcc2a2e5d4719587e724a4a3f3bf8a67 |
import random
import math
from .interval import Interval
class Note(object):
"""A single note, defined by a pitch, octave, and (optional) accidentals."""
VALID_PITCHES = ('C', 'D', 'E', 'F', 'G', 'A', 'B')
"""List of valid pitch characters."""
VALID_ACCIDENTALS = ('#', '##', 'b', 'bb', None)
"""... | charlottepierce/music_essentials | music_essentials/note.py | Python | mit | 23,672 | [
"Gaussian"
] | 0567a0da912e52ad7a0d7537e0941f2b85e175a3ec5c9e00275befdd20256429 |
# Author:
# Tests for the yambopy library
#
#
import unittest
import sys
import os
import argparse
import subprocess
import filecmp
from yamboparser import YamboFile, YamboFolder
folder = os.path.dirname(os.path.realpath(__file__))+'/testdata/'
class TestFolder(unittest.TestCase):
def test_folder_list(sel... | henriquemiranda/yambopy | tests/parser/test_parser.py | Python | bsd-3-clause | 2,368 | [
"Yambo"
] | 52a37cc7cba2bfeae61a653420c3b1725f2561aa9c437e1946778d7613b44d7c |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/__init__.py | Python | lgpl-2.1 | 3,224 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF"
] | d85e5ffccc096c2af54af8dd223312e32df95b1b0c6781495d7c54f292de28ae |
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