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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Automatic electric field computation
------------------------------------
:download:`examples/auto_efield.py` demonstrates how
drift can be added self-consistently by calculating the
electric field generated from the concentration profile
of charged species.
::
$ p... | chemreac/chemreac | examples/auto_efield.py | Python | bsd-2-clause | 7,622 | [
"ChemPy"
] | 856fda06f2c649c8ecae599b0cabddfe977a70167a0a68b4c98a87818458f1d6 |
from setuptools import setup
import sys
setup(
name='localcider',
version='0.1.19',
author='Alex Holehouse',
author_email='alex.holehouse@wustl.edu',
packages=['localcider', 'localcider.tests', 'localcider.backend', 'localcider.backend.data'],
scripts=[],
url='http://pappulab.github.io/loca... | Pappulab/localCIDER | setup.py | Python | gpl-2.0 | 775 | [
"Biopython"
] | 194581fddad8b9343f8bd13ee151ed5095e0210364142fc273998a8e66e7f330 |
#!/usr/bin/python
"""
Exp5_Bumpers -- RedBot Experiment 5
Now let's experiment with the whisker bumpers. These super-simple switches
let you detect a collision before it really happens- the whisker will
bump something before your robot crashes into it.
This sketch was written by SparkFun Electronics, with l... | MrYsLab/pymata-aio | examples/sparkfun_redbot/sparkfun_experiments/Exp5_Bumpers.py | Python | agpl-3.0 | 2,938 | [
"VisIt"
] | e88c0a523b8060113f8b3e187d76413f2f877510d6f7cfbcd7b92929ccd4a867 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/test_species.py | Python | gpl-3.0 | 4,134 | [
"CRYSTAL",
"VASP"
] | 6cc25b603455c38f785c169e7450f9c8072b77e161f3556b6d6a57ab557ba03c |
import numpy as np
pi = np.pi
one = 1
radians_per_cycle = pi * 2
degrees_per_cycle = 360.
degrees_per_radian = degrees_per_cycle / radians_per_cycle
radians_per_degree = radians_per_cycle / degrees_per_cycle
deg_per_day = 180. / np.pi * 60 * 60 * 24
msun = 1.9892e33
rsun = 6.9598e10
lsun = 3.8418e33
mearth = 5.9764e... | chkvch/on_GP | v2/const.py | Python | gpl-2.0 | 2,702 | [
"Avogadro"
] | a7915d5cc66f6077a8a5ca812b790930d8020001f73d78b45e00380083c95c90 |
# Copyright (C) 2018 The HDF Group
#
# This examaple creates several HDF5 long string(>netCDF java limit 32767) datasets and attributes.
#
#
import h5py
import numpy as np
from random import choice
from string import lowercase
#
# Create a new file using defaut properties.
#
n = 32768
big_str="".join(choice(lowercase) ... | OPENDAP/hdf5_handler | data/src/t_big_str_dset.py | Python | lgpl-2.1 | 525 | [
"NetCDF"
] | f077e3771a6c04e0110ccf012daf4fc5fd011cc78c81de243d24ecf93e50c95d |
# -*- coding: utf-8 -*-
import os
from PIL import Image
import os.path
import time
import torch
import torchvision.datasets as dset
import torchvision.transforms as trn
import torch.utils.data as data
import numpy as np
from PIL import Image
import numbers
# /////////////// Data Loader ///////////////
def resize(i... | hendrycks/robustness | ImageNet-C/create_c/make_imagenet_c_inception.py | Python | apache-2.0 | 21,073 | [
"Gaussian"
] | 5ded86cc6be53a899f31ee1d059dfc3ea2fbc59668f73c06699c42a9abe6aceb |
import pygame
import screen
import networking
import gui
from game import stardate
ship_tracks_bitmaps = (
[0x001400, 0x001400, 0x043804, 0x087008, 0x489038, 0x489038, 0x087008, 0x043804],
[0x043804, 0x001400, 0x001400, 0x043804, 0x087008, 0x489038, 0x489038, 0x087008],
[0x087008, 0x043804, 0x001400, 0x0... | pjotrligthart/openmoo2-unofficial | game/gui/main_screen.py | Python | gpl-2.0 | 9,719 | [
"Galaxy"
] | 1be20ce39a1bb11fe2ea5619d100eb30743bfa5ceb2516d561e6c6455f78be7f |
from math import sqrt
import numpy as np
import ase.parallel as mpi
from ase.calculators.singlepoint import SinglePointCalculator
from ase.io import read
class NEB:
def __init__(self, images, k=0.1, climb=False, parallel=False,
world=None):
"""Nudged elastic band.
images: list ... | grhawk/ASE | tools/ase/neb.py | Python | gpl-2.0 | 10,627 | [
"ASE"
] | 80d3d143b11fe1e320355a211fd167c8dff9c57f2b342d85f87d71c33b140081 |
"""
Qualityscore class
"""
import data
import logging
from galaxy.datatypes.sniff import *
from galaxy import util
log = logging.getLogger(__name__)
class QualityScore ( data.Text ):
"""
until we know more about quality score formats
"""
file_ext = "qual"
class QualityScoreSOLiD ( QualityScore ):
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/qualityscore.py | Python | gpl-3.0 | 3,890 | [
"Galaxy"
] | 830360f93cf57040055d48c69aa81b6979d957fdaa2a4d748441502ed1999d6a |
"""
gts v0.01
genetic test sequencer
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
... | enikesha/ga-bitbot | gts.py | Python | gpl-3.0 | 19,971 | [
"Brian"
] | 3c5c6f2ace9fc3b8ffbb5961ee7ff05bf63fe9223c9753338d962039b35a3e7e |
#!/usr/bin/env python
"""
ctabulate.py
Author: Ben Langmead
Date: 4/23/2012
Contact: langmea@cs.jhu.edu
"""
import os
import argparse
import pysam
import sys
import string
import unittest
import copy
import site
import errno
import reference
import logging
from collections import defaultdict
base_path = os.path.dir... | BenLangmead/bsmooth-align | experimental/ctabulate.py | Python | gpl-3.0 | 32,794 | [
"pysam"
] | d36b82692c3707cd913226bacfdcbdfc0650abeaec0da2e1d754af88cb36e3cd |
from . import header
import pyfits,pywcs
from numpy import nanmin,nanmax,linspace
from scipy import ndimage
def contour(image,levels=None,ext=0,align='pix',wcs=None,sigma=None,**args):
"""image - string with FITS image or the data as a numpy array
levels - either an integer number of levels, or a list or num... | nlchap0/nlcpython | nlcplot/contour.py | Python | mit | 2,868 | [
"Gaussian"
] | ade8a9791ebc05b1c1a60d2db9a8bda68f3f4786e4d9eec9323127fa284a83bb |
# Copyright 2020 Makani Technologies 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... | google/makani | config/base_station/sim/gs_imus_sim.py | Python | apache-2.0 | 8,529 | [
"Gaussian"
] | 67cb8c2b6eb89e82782549e3c2f82f976b20516118d976b68b6d36de5cb1b073 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# 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 versi... | arunkgupta/gramps | gramps/gui/plug/report/_webreportdialog.py | Python | gpl-2.0 | 1,985 | [
"Brian"
] | f5aa841f973f78d2d00292cbec23f225ef43f16ff1c99c532611a7253623a179 |
"""
Install and manage python packages
usage: pip.py [-h] [--verbose] sub-command ...
optional arguments:
-h, --help show this help message and exit
--verbose be more chatty
List of sub-commands:
sub-command "pip sub-command -h" for more help on a sub-command
list list packages inst... | cclauss/stash | bin/pip.py | Python | mit | 48,279 | [
"VisIt"
] | d59c60ed9d1e0317ba2471491ab770927b4f4e77da0b8ec95da42539f93fb8b7 |
"""
Normalization functions for the st analysis package
"""
import numpy as np
import pandas as pd
from collections import Counter
import multiprocessing
import rpy2.robjects.packages as rpackages
from rpy2.robjects import pandas2ri, r, numpy2ri
import rpy2.robjects as ro
ro.conversion.py2ri = numpy2ri
base = rpackage... | SpatialTranscriptomicsResearch/st_analysis | stanalysis/normalization.py | Python | mit | 6,803 | [
"Bioconductor"
] | 31a2d0b0931b1e13945628c450e8a5b348a2143410eaf36885f0b3f78d256a68 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from contextlib import contextmanager
from copy import deepcopy
from cStringIO import StringIO
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse... | rismalrv/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 20,949 | [
"VisIt"
] | 6a03b578168e538ae15b675987d4edfce45bba6dfca7f6fd541486d35e1edd08 |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#-----------------------------------------------------------------------------
# Copyright (c) 2008, IPython Development Team.
# Copyright (c) 2001, Fernando Perez <fernando.perez@colorado.edu>
# Copyright (c) 2001, Janko Hauser <jhauser@zscout.de>... | vicky2135/lucious | oscar/lib/python2.7/site-packages/IPython/core/release.py | Python | bsd-3-clause | 4,386 | [
"Brian"
] | c67693474aa657c29a2d4cb6421e068b3972d9393becdfa2818421f0a7b9c8e3 |
# -*- coding: utf-8 -*-
import numpy as np
from shapely.geometry.polygon import Polygon
import netCDF4 as nc
import itertools
from shapely.ops import cascaded_union
from shapely import prepared
import time
from multiprocessing import Process, Queue, Lock
from math import sqrt
from util.ncconv.helpers import make_shapel... | OpenSource-/OpenClimateGIS | src/openclimategis/util/ncconv/in_memory_oo_multi_core.py | Python | bsd-3-clause | 42,480 | [
"NetCDF"
] | 1205ca0433f0fc65e0a70e0ab1f52b3f7a1f369dee2e734d68416bf19ab7920a |
"""
Test prediction of reflections using the scan-varying reflection
predictor.
"""
from __future__ import annotations
import math
from cctbx.sgtbx import space_group, space_group_symbols
from dxtbx.model import ScanFactory
from dxtbx.model.experiment_list import Experiment, ExperimentList
from libtbx.phil import p... | dials/dials | tests/algorithms/spot_prediction/test_scan_varying_predictor.py | Python | bsd-3-clause | 4,739 | [
"CRYSTAL"
] | 466beb40bfc248ad35f8d831252111ae8df33591600b1eafb813433f2fbad24a |
"""Summary of tensorflow basics.
some basic tf ops like numpy
tensor.eval()
tensor.get_shape()
reshape
Parag K. Mital, Jan 2016."""
# %% Import tensorflow and pyplot
import tensorflow as tf
import matplotlib.pyplot as plt
# %% tf.Graph represents a collection of tf.Operations
# You can create operations by writi... | trhongbinwang/data_science_journey | deep_learning/tensorflow/tutorials/tutorial2/01_basics.py | Python | apache-2.0 | 4,605 | [
"Gaussian"
] | 9f1b5c9b3eeb1e8c1dc0603199aaaef33516db5e32958a746c2f9a8cd1ad377e |
__all__ = ['AbundanceFunction', 'add_scatter', 'rematch', 'LF_SCATTER_MULT']
import numpy as np
from scipy.optimize import curve_fit
try:
from fiducial_deconv_wrapper import fiducial_deconvolute
except (OSError, ImportError):
_has_fiducial_deconvolute = False
else:
_has_fiducial_deconvolute = True
LF_SCAT... | manodeep/yymao-abundancematching | AbundanceMatching/AbundanceFunction.py | Python | mit | 13,873 | [
"Gaussian"
] | 20103734c898f1485f007733b7b5fac2bb6c05729de43bc826942f688b64a9cb |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
bonds_by_type.py reads a LAMMPS data file (or an excerpt of... | SGenheden/lammps | tools/moltemplate/src/bonds_by_type.py | Python | gpl-2.0 | 16,079 | [
"LAMMPS"
] | 7c1dc8d8017aeeb34c21697d0d010d663342e14c581e31f906030e177e812276 |
import numpy as np
from ..numerics.utilities import my_trapz
from .stochastic_process import StochasticProcess
from ..src.gaussian_moments import GaussianMoments
class OrnsteinUhlenbeck(StochasticProcess):
"""
Information about the Ornstein - Uhlenbeck process:
https://en.wikipedia.org/wiki/Ornstein%E2%... | vrettasm/VGPA | code/dynamics/sp_ornstein_uhlenbeck.py | Python | gpl-3.0 | 6,818 | [
"Gaussian"
] | 9ca16f458f652afa65d0c71f8ef571e21a8c62630e0f6d7e3c9d77339a6d506b |
from __future__ import absolute_import
import io
import os
import six
import zlib
import base64
import msgpack
import inspect
from parsimonious.grammar import Grammar, NodeVisitor
from parsimonious.exceptions import ParseError
from sentry import projectoptions
from sentry.stacktraces.functions import set_in_app
from... | beeftornado/sentry | src/sentry/grouping/enhancer.py | Python | bsd-3-clause | 20,863 | [
"VisIt"
] | 1024530d74b297ff35001e677e6e4c0cf309456ab4312eafc9c2e45fb17065a5 |
"""
Acceptance tests for Studio related to the split_test module.
"""
import math
from bok_choy.promise import Promise
from nose.plugins.attrib import attr
from selenium.webdriver.support.ui import Select
from base_studio_test import StudioCourseTest
from common.test.acceptance.fixtures.course import XBlockFixtureDe... | Lektorium-LLC/edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 47,182 | [
"VisIt"
] | e211b7e5843bc4a3a9c30864dda3f61983769f6f4fa4273b615c8035ac778c4f |
import os
import shutil
import tempfile
import numpy as np
from numpy.testing import assert_almost_equal as eq
from ..core import cmi, ce, ncmi
from ..metrics import (AlphaAngleTransferEntropy, ContactTransferEntropy,
DihedralTransferEntropy)
import mdtraj as md
from msmbuilder.example_dataset... | cxhernandez/mdentropy | mdentropy/tests/test_tent.py | Python | gpl-3.0 | 2,246 | [
"MDTraj"
] | 77a8ef823599827702135fcd1a073e0f8d3b22d9b67e81d5837720e288f95512 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
#
# Maintainer: Jonathan Lange
import sys
import traceback
from zope.interface import implements
from twisted.python import reflect
from twisted.python.failure import Failure
from twisted.trial import util
from twisted.trial.unittest import Tes... | openhatch/oh-mainline | vendor/packages/twisted/twisted/trial/test/test_pyunitcompat.py | Python | agpl-3.0 | 6,659 | [
"VisIt"
] | ed7352d736482c45ec1c87424559bddf4e2bfa7aa577f52987fb34ed9996077a |
__author__ = 'Simon Birrer'
"""
this file contains standard routines
"""
from collections import namedtuple
import numpy as np
import scipy.ndimage.interpolation as interp
import scipy
from numpy import linspace, meshgrid
import copy
import mpmath
def dictionary_to_namedtuple(dictionary):
dictionary.pop("__nam... | sibirrer/astrofunc | astrofunc/util.py | Python | mit | 33,823 | [
"Gaussian"
] | 366be866b3436f5a7c254ca6ebce76668f036f09cd6e825b505a8d4a243abd49 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/cameras/__init__.py | Python | mit | 1,392 | [
"VisIt"
] | e60875120325d322f309c97de69afc1e55c31c1320e80c676ccd0f7236f6c43b |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Integration tests for loading and saving netcdf files."""
# Import iris.tests first so that some things can be initialised ... | pp-mo/iris | lib/iris/tests/integration/test_netcdf.py | Python | lgpl-3.0 | 24,683 | [
"NetCDF"
] | 710d1aa09b93a05a16ffd2c51c670f5d06af5d4e68168b0e5fb629b5b8b82bb5 |
'''Flatten nested progns, open progns with single expressions, and
replace empty progns with nops
'''
from __future__ import absolute_import
from __future__ import with_statement
from ..compiler import ir as I
from ..compiler import bind
from ..compiler.walk import IRWalker
from ..compiler.purity import purep
de... | matthagy/Jamenson | jamenson/transform/progn_flatten.py | Python | apache-2.0 | 1,562 | [
"VisIt"
] | e8171fd9a1702ce7563c5bfdfeeb99caeb5da7854701bc8771129dad8c506df9 |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <htt... | sharkerz/deluge-yarss-plugin | yarss2/lib/feedparser/feedparser.py | Python | gpl-3.0 | 156,379 | [
"NetCDF",
"VisIt"
] | 92da42dc9e86e546782ed55b6b6c5fef8cf7064b9fbcd78c31fc0ec84611cc61 |
raise "Use https://github.com/keflavich/h2co_modeling/blob/master/h2co_modeling/constrain_parameters.py instead"
"""
Functions for fitting temperature (and density and column) from the line ratio
plus whatever other constraints are available
"""
import inspect
import time
import os
import numpy as np
from scipy.ndimag... | keflavich/APEX_CMZ_H2CO | analysis/constrain_parameters_4to3.py | Python | bsd-3-clause | 26,715 | [
"Gaussian"
] | 240f6545d0dd435e17f9fd95522453fbeb9309813fd7d1ee5686e04aad36f595 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# REF [site] >> https://github.com/aleju/imgaug
import os, sys
if 'posix' == os.name:
swl_python_home_dir_path = '/home/sangwook/work/SWL_github/python'
else:
swl_python_home_dir_path = 'D:/work/SWL_github/python'
sys.path.append(swl_python_home_dir_path + '/src')
#---... | sangwook236/SWDT | sw_dev/python/rnd/test/machine_learning/imgaug_test.py | Python | gpl-3.0 | 25,926 | [
"Gaussian"
] | 6deb97e2fb4cf3b2e52b126c61f08062eabb0525c0e722f92263e2086fd2d4e6 |
# coding: utf-8
# # Sequence Annotation Hunter
#
# Compares two sequences and identifies similar features.
#
# Useful in the case of identifying elements of a shuffled sequence.
#
# Requires an original annotated og_reference_sequence.ape file and a new_reference_sequence.ape file located in the notebook folder.
#... | MLKaufman/seq-annotator | seq_annotation.py | Python | mit | 5,646 | [
"Biopython"
] | e346dd068d0e0e98077a51cbd6cd6589a6e083f29b010ad12313e324ea38f448 |
# Copyright 2016 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | tkzeng/molecular-design-toolkit | moldesign/orbitals/gaussians.py | Python | apache-2.0 | 15,367 | [
"Gaussian"
] | a7004bfacea709c3fe68cbed4d876c235eb74374f8a341cd51f8afd9e6773a2a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Mar 5, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Sh... | aykol/pymatgen | pymatgen/alchemy/tests/test_transmuters.py | Python | mit | 4,541 | [
"pymatgen"
] | 48f9f9559902289e2d7360ac2d9006fff435edf79f69e4df59260f0e60330c97 |
"""
Python implementation of the fast ICA algorithms.
Reference: Tables 8.3 and 8.4 page 196 in the book:
Independent Component Analysis, by Hyvarinen et al.
"""
# Authors: Pierre Lafaye de Micheaux, Stefan van der Walt, Gael Varoquaux,
# Bertrand Thirion, Alexandre Gramfort, Denis A. Engemann
# License: BS... | nhejazi/scikit-learn | sklearn/decomposition/fastica_.py | Python | bsd-3-clause | 19,076 | [
"Gaussian"
] | abf9b1a806a21e78437fcd029ef3b162475a97c9238c6a4bb9923f053acb2a35 |
#!/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.
'''Unit tests for misc.GritNode'''
import os
import sys
if __name__ == '__main__':
sys.path.append(os.path.join(os.path.dirname... | guorendong/iridium-browser-ubuntu | tools/grit/grit/node/misc_unittest.py | Python | bsd-3-clause | 15,813 | [
"xTB"
] | 06980303d4cf951b061867de8b872404889f14f136412022ad72294b7319c640 |
#!/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.
"""Compile Android resources into an intermediate APK.
This can also generate an R.txt, and an .srcjar file containing the prope... | Passw/gn_GFW | build/android/gyp/compile_resources.py | Python | gpl-3.0 | 21,899 | [
"Galaxy"
] | 4a710a9814aff5711590b644411ac592d565c58ff31786282256dfee8d9d7d56 |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
t_shelf = 3.2*3600 # time approaching continental slope
t_harbor = 3.5*3600 # time approach... | clawpack/adjoint | examples/adjoint_CrescentCity_26hrs/setrun.py | Python | bsd-2-clause | 14,673 | [
"NetCDF"
] | d34269a149362a3a56275d7a622a2198eb3bd481c1bead41e20c6b92926b5b9f |
# .. coding: utf8
# $Id: __init__.py 7544 2012-12-12 22:04:49Z milde $
# Author: Engelbert Gruber, Günter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributio... | ktan2020/legacy-automation | win/Lib/site-packages/docutils/writers/latex2e/__init__.py | Python | mit | 122,198 | [
"VisIt"
] | 8fc697e99fd633bff57d665abb7a27a6a6494d7bb49b355fe7fd3baf09818d23 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import Chem
from rdkit import six
from rdkit.VLib.Supply import SupplyNode
class SDSupplyNode(SupplyNode):
""" SD supplier
Sample Usage:
>>> import os
>>> from rdkit import RDConfig
>>> fileN = os.path.join(... | rvianello/rdkit | rdkit/VLib/NodeLib/SDSupply.py | Python | bsd-3-clause | 1,391 | [
"RDKit"
] | b5d1d6f2bd5aae0f33e0c424d4dd8df33cfc63c0e14e365fc556822640df98f0 |
#
# Samples a 2d Gaussian using Umbrella sampling in the temperature (parallel version)
#
# Usage:
# > mpirun -np N python -u gaussian.py
# where "N" is the number of cores to run on, e.g. 4
#
import usample.usample
import numpy as np
import emcee
#
# Sample a 2D Gaussian
#
# Define the log probability function:
#
... | c-matthews/usample | gaussian_mpi.py | Python | gpl-3.0 | 1,432 | [
"Gaussian"
] | 1cfabd9eee930803ea6345402fb9215f0d2eb45cd9a5f55a29ba5a432dddaf57 |
from mayavi import mlab
from data_diameter_slice import compute_funnel_coordinates, compute_outline_coordinates
from numpy import linspace, sqrt, pi
# -------
# OPTIONS
# -------
FILENAME = 'funnel_diameter_slice.png'
IMAGE_SIZE = (1600, 900)
BACKGROUND_COLOR = (0, 0, 0)
FUNNEL_COLORMAP = 'Blues'
HIGHLIGHT_EDGE = Tru... | grollins/funnel-graphics | plot_funnel_diameter_slice.py | Python | mit | 1,187 | [
"Mayavi"
] | 3167b47ea093302b98214f1984f76e09e33a3e9ebb0fa727cdd73d4136bb4b19 |
# coding=utf-8
#Monte Carlo integration in 6 dimensions
#Translated by Kyrre Ness Sjøbæk
import numpy,math
import sys
def integrand(x):
"""Calculates the integrand
exp(-a*(x1^2+x2^2+...+x6^2)-b*[(x1-x4)^2+...+(x3-x6)^2])
from the values in the 6-dimensional array x."""
a = 1.0
b = 0.5
x2 = nu... | CompPhysics/ComputationalPhysics2 | doc/Programs/LecturePrograms/programs/MCIntro/python/program4.py | Python | cc0-1.0 | 1,242 | [
"Gaussian"
] | 20d0b534e8445d8c5aa2ade1f202207e33a39a0276030cb0335fc6d406df51dc |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, e... | dursobr/Pythics | pythics/examples/hello_world.py | Python | gpl-3.0 | 834 | [
"Brian"
] | a5dd3662985721dff2b71afe17722d2bb996df914cf43a5bac61e7967dc9c8ab |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistribution and use in ... | hainm/scikit-xray | skxray/core/recip.py | Python | bsd-3-clause | 8,818 | [
"CRYSTAL"
] | 710545f47b6f0f0a6db03b5cd72cdecc75a4159d7fcc8b50e061bac2ccc7d6dc |
# disable missing docstring
# pylint: disable=C0111
import json
from lettuce import world, step
from nose.tools import assert_equal, assert_true # pylint: disable=E0611
from common import type_in_codemirror, open_new_course
from advanced_settings import change_value
from course_import import import_file, go_to_import... | torchingloom/edx-platform | cms/djangoapps/contentstore/features/problem-editor.py | Python | agpl-3.0 | 9,464 | [
"VisIt"
] | 9b9582832a2e9d0384182caf8427aa89a813e13448b2c9776083a8c81e6b6863 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# @File: libddd.py
#
# @Author: Jondy Zhao(jondy.zhao@gmail.com)
#
# @Create Date: 2014/12/18
#
# @Description:
#
# GDB Extension script.
#
from __future__ import with_statement
import ast
import fnmatch
import locale
import os
import sys
import string
import gdb... | jondy/pyddd | libddd.py | Python | gpl-2.0 | 58,416 | [
"VisIt"
] | 69851e155f69032165301e5bca4ff25dd1085562a97a03521eddb1a6bfced7c3 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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... | simplegeo/ipaddr | test/ipaddr_test.py | Python | apache-2.0 | 47,742 | [
"FEFF"
] | 69fae38ecfba2e124fd4ac0dbad7554532d04b04eaea6bcf6ed7169d217768e3 |
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of cha... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/molecule/generatorTest.py | Python | mit | 19,738 | [
"RDKit"
] | 04a4fb20b6b0516b0e75a2930772b25ac04d13454f93144773a545aebb93dd02 |
"""feedfinder: Find the Web feed for a Web page
http://www.aaronsw.com/2002/feedfinder/
Usage:
feed(uri) - returns feed found for a URI
feeds(uri) - returns all feeds found for a URI
>>> import feedfinder
>>> feedfinder.feed('scripting.com')
'http://scripting.com/rss.xml'
>>>
>>> feedfinder.fe... | dfm/ugly | ugly/feedfinder.py | Python | mit | 12,937 | [
"Brian"
] | 0523a666def2ba9978cbab458c490e65bcac664f4718ed70c46ce716216934a1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Functions for use with the GEOS-Chem chemical transport model (CTM).
Use help(<name of function>) to get details on a particular function.
NOTE(S):
- This module is underdevelopment vestigial/inefficient code is being removed/updated.
- Where external code is used credi... | tsherwen/AC_tools | AC_tools/GEOSChem_bpch.py | Python | mit | 193,004 | [
"NetCDF"
] | 09287508221e31f5a707d37c134a1b4b74e003ef8cf5c8bc025699331bbd6220 |
#-------------------------------------------------------------------------------
# rbtlib: setup.py
#
# Rbt setup script.
#
# Credit to Eli Bendersky's pss/setup.py.
#-------------------------------------------------------------------------------
# The MIT License (MIT)
# Copyright (c) 2016 Brian Minard
#
# Permission... | bminard/rbtlib | setup.py | Python | mit | 3,417 | [
"Brian"
] | ae1b082d61afda3c87bfc29a1cd8923ac36588cf8a9f6d0ffc4b4992a9f4fe8f |
from django.conf import settings
from django.urls import include, path
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
path("", TemplateView.as_view(template_name="pages/home... | mistalaba/cookiecutter-django | {{cookiecutter.project_slug}}/config/urls.py | Python | bsd-3-clause | 1,748 | [
"VisIt"
] | 382271d3cd58a1a2bd97db92e649c78d7792719ab21bb41364195535021a3b69 |
#! /usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Scraper
==========
Given, the ANDROID-APP-URL, this module is meant to be able
to extract an agreed upon set of features about the app
- [x] Name
- [x] Company
- [x] AppCategory
- [x] AppId
- [x] AppVer
- [x] Price
- [x] Rating
- [
(OneStarRating, OneStarR... | seekshreyas/obidroid | scraper.py | Python | mit | 11,253 | [
"VisIt"
] | adb11ae5d054e2764f0b0b22d86a92f9761c8d817e1454a8fbbf665c5fd41d9f |
#!/usr/bin/env python
"""[License: GNU General Public License v3 (GPLv3)]
This file is part of FuMa.
FuMa 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 opti... | ErasmusMC-Bioinformatics/fuma | fuma/ParseBED.py | Python | gpl-3.0 | 4,654 | [
"HTSeq"
] | cee1c38f6945ddc71f1095f0d50fb73f813c7b17847a9b2ef695702efe0c2b7b |
"""Functions for to connect SEA outputs to the E3FP pipeline.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import os
from rdkit import Chem
from fpcore.fconvert import string2ascii, ascii2string
from e3fp.config.params import read_params
from e3fp.conformer.util import mol_from_sdf
from e3fp.fingerprint.fprint ... | keiserlab/e3fp-paper | e3fp_paper/pipeline.py | Python | lgpl-3.0 | 3,238 | [
"RDKit"
] | 60967a527b749075301c3b9dbb183eead683f5a62213529409f0860b0a31e707 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Module description
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
simplecrawler is a module to do http request smartly.
Features:
1. Automatically handle html encoding problem. You can also name the encoding.
2. You can login website ... | MacHu-GWU/angora-project | angora/crawler/simplecrawler.py | Python | mit | 9,767 | [
"VisIt"
] | c1662e0aee67bffc36062e9a3f6fb23441997ba49de0052ca802890e0edcbe40 |
"""
tools for dealing with frozen atoms. Especially in relation to neighbor lists
.. currentmodule:: pele.utils.frozen_atoms
.. autosummary::
:toctree: generated/
FreezePot
makeBLJNeighborListPotFreeze
"""
import numpy as np
import pele.potentials.ljpshiftfast as ljpshift
from pele.potentials.... | kjs73/pele | pele/utils/frozen_atoms.py | Python | gpl-3.0 | 17,542 | [
"PyMOL"
] | 67350560200682ed62e15fb3728d134f301ae33a4d2b9e9d2c8a323fd88e66e7 |
# 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 *
import datetime as dt
class Lammps(CMakePackage, CudaPackage):
"""LAMMPS stands for Large-scale ... | rspavel/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 9,495 | [
"LAMMPS",
"NetCDF"
] | e2e1593a2aaeb6b7b5e221c33f969a439b8479d801cdcacc6358a5a82a9e33e5 |
# -*- coding: utf-8 -*-
COLORS = (
('black', 'Black'),
('white', 'White'),
('red', 'Red'),
('Yellow', 'Yellow'),
)
FUEL_TYPES = (
('benzin', 'Benzin'),
('petrol', 'Petrol'),
)
BRANDS = (
('bmw', 'BMW'),
('jaguar', 'Jaguar'),
('volkswagen', 'Volkswagen'),
('mercedes', 'Mercedes... | COEXCZ/django-adminfilter | example/car/choices.py | Python | isc | 359 | [
"Jaguar"
] | 63d63eb1f5a6871a9f525beb503f250999acd7348915747225a58435f41bfa95 |
# Copyright (c) 2014-2018 Matteo Degiacomi and Valentina Erastova
#
# Assemble 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 version.
# Assemb... | degiacom/assemble | System.py | Python | gpl-3.0 | 12,775 | [
"Gromacs"
] | 39fca6925a3df1fe4e411c265835a7865651b2079cb6b646f8e38ba8671ea758 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | arunkgupta/gramps | gramps/gui/dbman.py | Python | gpl-2.0 | 32,851 | [
"Brian"
] | e81e6f1d55d28a3a8d82168e041cf953beef2647a3d0d9d39ac9555fa300914c |
# -*- coding: utf-8 -*-
from collections import defaultdict
from datetime import datetime
from pymisp import MISPAttribute, MISPEvent, MISPObject
import json
arch_type_mapping = {'ANDROID': 'parse_apk', 'LINUX': 'parse_elf', 'WINDOWS': 'parse_pe'}
domain_object_mapping = {'@ip': ('ip-dst', 'ip'), '@name': ('domain', ... | VirusTotal/misp-modules | misp_modules/lib/joe_parser.py | Python | agpl-3.0 | 24,869 | [
"Galaxy"
] | ce12731e3d25d4f9abc557eafd590142911885a37f86d4351cbb60d0aa49e987 |
# Copyright 2014-2017 The ODL contributors
#
# This file is part of ODL.
#
# This Source Code Form is subject to the terms of the Mozilla Public License,
# v. 2.0. If a copy of the MPL was not distributed with this file, You can
# obtain one at https://mozilla.org/MPL/2.0/.
"""Figures of merit (FOMs) for comparison ag... | aringh/odl | odl/contrib/fom/supervised.py | Python | mpl-2.0 | 21,932 | [
"Gaussian"
] | c29f970a8bf1dd37888ab0070fd9c317b58cf8efd31b7518362ea9150acd452f |
"""
Utility methods common to Studio and the LMS.
"""
from bok_choy.promise import BrokenPromise
from selenium.webdriver.common.action_chains import ActionChains
from common.test.acceptance.pages.lms.create_mode import ModeCreationPage
from common.test.acceptance.pages.lms.pay_and_verify import FakePaymentPage, Paymen... | ahmedaljazzar/edx-platform | common/test/acceptance/pages/common/utils.py | Python | agpl-3.0 | 5,794 | [
"VisIt"
] | 3e2f37afae776644d0f10b073a6a40d5681bde1c34ffd7ca214b6bf9248cb14f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0015_staff_is_site_coordinator'),
]
operations = [
migrations.AddField(
model_name='visit',
... | koebbe/homeworks | visit/migrations/0016_auto_20150504_1406.py | Python | mit | 660 | [
"VisIt"
] | 2aa6d4f60ed6a37dd07e69fe3572f48c0ee44a401a917e027d0993f8dbbd8d7d |
"""
PHYLIP multiple sequence alignment format (:mod:`skbio.io.phylip`)
==================================================================
.. currentmodule:: skbio.io.phylip
The PHYLIP file format stores a multiple sequence alignment. The format was
originally defined and used in Joe Felsenstein's PHYLIP package [1]_,... | johnchase/scikit-bio | skbio/io/phylip.py | Python | bsd-3-clause | 10,543 | [
"BioPerl",
"scikit-bio"
] | ca5da491686166b14b83d4456077fd6e79c38ec4c0ef94742069404c6f17e1e2 |
#!/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.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/combStreamers.py | Python | gpl-3.0 | 2,503 | [
"VTK"
] | 1957e8df0e619f3e10e62828b066ea90c134d1a92188f6f16b349b5cf3244977 |
#!/usr/bin/python3
# Uses Python Imaging Library fork (Pillow) to render galaxy maps
# Requirements, installation:
# pip3 install Pillow
# on Debian Linux, requirements should be installed:
# - compiler (build-essential)
# - zlib devel files (zlib1g-dev)
# - libjpeg, libjpeg-devel
import io
import logging
import sqli... | minlexx/xnova_galaxy_parser | site_uni5/classes/img_gen_pil.py | Python | gpl-3.0 | 5,534 | [
"Galaxy"
] | cd3d290cf477bddc675b1ef352e2b2148cd9171c3b4aab6a4c2b96c2680471d7 |
#!~/source/ParaView-3.12.0-Linux-x86_64/bin/pvpython
from paraview.simple import *
restratification_after_oodc_ = XMLPartitionedUnstructuredGridReader( FileName=['/tamay/mensa/fluidity/mli_250m_4/mli_0.pvtu'])
AnimationScene2 = GetAnimationScene()
restratification_after_oodc_.PointArrayStatus = ['Pressure', 'Density... | jungla/ICOM-fluidity-toolbox | plot_pv_3.py | Python | gpl-2.0 | 1,645 | [
"ParaView"
] | 3c3fa9cc52301997de8d7bed3c5ac6d6cc71d78be1cb9ebcb3df79bbfe763484 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008-2010, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | NetNow/wmi-samba | pysamba/twisted/callback.py | Python | gpl-2.0 | 1,818 | [
"VisIt"
] | abafeb014fb7604afd31990bc5eb0435b506c89136a814121b31d457d1ec4e12 |
"""
Author: Remi Lafage <remi.lafage@onera.fr>
This package is distributed under New BSD license.
"""
import matplotlib
matplotlib.use("Agg")
import unittest
import numpy as np
from sys import argv
from smt.applications import MOE, MOESurrogateModel
from smt.utils.sm_test_case import SMTestCase
from smt.problems i... | SMTorg/smt | smt/applications/tests/test_moe.py | Python | bsd-3-clause | 16,036 | [
"MOE"
] | 28d0583233e18d5932d33a5d0b188f75b949e160d8f0cee565959e5836755e75 |
# slicer imports
import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
#
# Vesselness Filtering using VMTK based Tools
#
class VesselnessFiltering(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/... | vmtk/SlicerExtension-VMTK | VesselnessFiltering/VesselnessFiltering.py | Python | apache-2.0 | 32,651 | [
"Gaussian",
"VTK"
] | fdc1c5550477134549738af0c8c7104293882f6bf1728a3b04f5ac6ce0afcb0f |
"""
msg.py: Basic classes for message passing
"""
from __future__ import division
from __future__ import print_function
import numpy as np
# Import other sub-packages
import vampyre.common as common
class MsgHdl(object):
def __init__(self):
"""
Base class for Gaussian message passing handler
... | GAMPTeam/vampyre | vampyre/estim/msg.py | Python | mit | 17,002 | [
"Gaussian"
] | 75d86d9cbd6a98b1d3742758a60a84de0566eba7f6c42a92eb2205d8eb764e48 |
import app.config as config
from rdflib import Graph, URIRef, Dataset
import requests
import json
import traceback
# This is old style, but leaving for backwards compatibility with earlier versions of Stardog
QUERY_HEADERS = {'Accept': 'application/sparql-results+json',
'SD-Connection-String': 'reaso... | CLARIAH/wp4-csdh-api | src/app/util/sparql_client.py | Python | mit | 5,765 | [
"VisIt"
] | e4a2620964a951ff4187829634cd117e097bf9f5f95544e0282e73b5defad7b4 |
"""Convert to and from Roman numerals
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004/05/05 21:57:20 ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage8/roman81.py | Python | mit | 2,041 | [
"VisIt"
] | 614e966189f4ae62576b7fffd7d8f4a16eedc5e6818345eae5c22707cb42f9e1 |
#!/usr/bin/python
__author__ = 'george'
import multiprocessing
import os
import sys
import pysam
### External imports ###
from numpy import array, hstack, arange, zeros
### My imports ###
from fluff.util import ( normalize_data, get_absolute_scale, split_ranges,
mirror_clusters, cluster_profile )
from fluff.... | simonvh/fluff | fluff/commands/heatmap.py | Python | mit | 8,525 | [
"pysam"
] | 94d61178eeb0f97a60638f98c67c9ee87ec61d1b392d67b85a17f5fa0ce7d734 |
from inspect import getsource
from utils import argmax, argmin
from games import TicTacToe, alphabeta_player, random_player, Fig52Extended, infinity
from logic import parse_definite_clause, standardize_variables, unify, subst
from learning import DataSet
from IPython.display import HTML, display
from collections impor... | jo-tez/aima-python | notebook.py | Python | mit | 43,431 | [
"Gaussian"
] | fd2da534a0eeac83045fb397750c17b6321538db61c0f4e10480cec4827d6b92 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/fst/tests/test_get_features.py | Python | bsd-3-clause | 35,896 | [
"NEURON"
] | 5a7bfe2474c51e259e68d19751450b303365e1332e1b1a350f4b9e581354fd5d |
# Copyright 2013 by Kamil Koziara. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Module giving acces to I/O modules through generic methods.
"""
fro... | arkatebi/SwissProt-stats | Ontology/IO/__init__.py | Python | gpl-3.0 | 5,651 | [
"Biopython"
] | 345708ca7066eed105710a3d88711f8905789aff18cfa89b9667c92ddb9f4c3e |
# 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/integrator/LBInit.py | Python | gpl-3.0 | 4,700 | [
"ESPResSo"
] | c35112404af2825bbf24cca5275baeca1dbf34531a4899095a1046da931d1843 |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
"""
@package TargetPredict
@brief Main file of the program
@copyright [GNU General Public License v2](http://www.gnu.org/licenses/gpl-2.0.html)
@author Adrien Leger - 2015
* <adrien.leger@gmail.com>
* <adrien.leger@inserm.fr>
* <adrien.leger@univ-nantes.fr>... | a-slide/TargetPredict | src/TargetPredict.py | Python | gpl-2.0 | 9,668 | [
"BLAST"
] | d9e4019d71cf50bed7a00a91dbcd298c1cb1c52716b7cfca74497380aa190735 |
import IMP
import IMP.test
import IMP.atom
def get_all_atoms(pdb):
atoms = {}
residues = IMP.atom.get_by_type(pdb, IMP.atom.RESIDUE_TYPE)
for ni, res in enumerate(residues):
resatoms = IMP.atom.get_by_type(res, IMP.atom.ATOM_TYPE)
for a in resatoms:
aid = '%d:' % (ni + 1) \
... | shanot/imp | modules/atom/test/test_charmm_stereochemistry.py | Python | gpl-3.0 | 3,890 | [
"CHARMM"
] | d9f1607787e2eb0e2c46117fcae680ebd831b80cf1cc4b0570d13cfddeebfa13 |
#!/usr/bin/env python
"""
command line tool to remove local and remote proxies
"""
import sys
import os
import DIRAC
from DIRAC import gLogger, S_OK
from DIRAC.Core.Security import Locations
from DIRAC.Core.Base import Script
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.FrameworkSystem.Client.ProxyMa... | andresailer/DIRAC | FrameworkSystem/scripts/dirac-proxy-destroy.py | Python | gpl-3.0 | 4,939 | [
"DIRAC"
] | 2a049e33ce1b63b06e3c83860e97f7f194f6ed8ab82d29d0f69f6b3710bd3c92 |
#!python
"""\
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ http://peak.telecommunity.com/DevCenter/EasyInstall
"""
import sys, os.path, ... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/setuptools-0.6c11/setuptools/command/easy_install.py | Python | bsd-3-clause | 63,580 | [
"VisIt"
] | 09fae78299fabb116c5aa2d14f788d732555bac65cf410e037cac39dbd21ab24 |
# Copyright 2013-2021 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 Berkeleygw(MakefilePackage):
"""BerkeleyGW is a many-body perturbation theory code for exc... | LLNL/spack | var/spack/repos/builtin/packages/berkeleygw/package.py | Python | lgpl-2.1 | 9,216 | [
"BerkeleyGW"
] | db1e84953f9a29690fc405398629583a114f8f929046a00cd2a0f0a86b0565df |
from hashkernel import (
reraise_with_msg, ensure_string, utf8_reader)
from hashstore.utils import failback
from hashstore.utils.fio import (ensure_directory, read_in_chunks)
from hashstore.utils.ignore_file import (
ignore_files, parse_ignore_specs, check_if_path_should_be_ignored)
from hashkernel.bakery impor... | walnutgeek/hashstore | hashstore/bakery/cake_scan.py | Python | apache-2.0 | 11,359 | [
"NEURON"
] | 9f94e9106de542c94a2dea0fdf5646d43ed666b53f9957bd6651d4c33c4c4181 |
# coding: utf-8
import pandas as pd
import pysam
import argparse
import sys
import os
def main(args):
assert not os.path.isfile(args.outfile)
mag_bam_file = args.mag_bam_file
mag = args.mag_name
mag_contig_list = args.mag_contig_list
sag_bam_file = args.sag_bam_file
sag = args.sag_name
sa... | EnvGen/toolbox | scripts/sag_vs_mag/new_bam_file_with_read_groups.py | Python | mit | 2,677 | [
"pysam"
] | 1d7b355776f49e15586756be80554165e20f28d91e1088bf77086bfe56a67493 |
#!/usr/bin/env python
import numpy as np
from scipy import stats
def asymgauss(x, mu, sigma_lower, sigma_upper):
"""
Program calculates an asymmetric Gaussian distribution (ie. a Gaussian
with different standard deviations above and below the mean) for a given
mean and standard deviations. There... | lauralwatkins/toolbox | toolbox/asymgauss.py | Python | bsd-2-clause | 984 | [
"Gaussian"
] | f7787c0df7d2eb8671fa176b158afdcfb5c8df77681ea51d4e47770e001d3dbb |
import os
import re
from PIL import Image
import math
import copy
import pickle
from collections import OrderedDict
from picklefield.fields import PickledObjectField
from django.db import models
from django.conf import settings
from django.db.models import Count,Sum,Q
from django.core.exceptions import ObjectDoesNotE... | mmcauliffe/django-buckeye-corpus | buckeyebrowser/models.py | Python | gpl-3.0 | 85,930 | [
"COLUMBUS"
] | 5a9192e0dc84e8f02c1b84603f7f2dd666506a795024eb6548a55e74cf2fe866 |
#!/usr/bin/env python
"""
DESCRIPTION
This script is provides helpful definitions for interactively visualizing
manufactured quantities within a Mayavi
(http://code.enthought.com/projects/mayavi/) or IPython session. It is
/not/ a standalone program and should be %run from within an 'python
-wthre... | manufactured-solutions/analytical | navier_stokes/navier_stokes_comp_transient_powerlaw/vizcoeffs.py | Python | lgpl-2.1 | 5,862 | [
"Mayavi"
] | f4947daa51d2db64d13f37d6819ccad2529ec05575c3f7bbb05e8bf155aa7f97 |
#!/usr/bin/env python
#
# $File: MaPenetrance.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribu... | BoPeng/simuPOP | docs/MaPenetrance.py | Python | gpl-2.0 | 1,527 | [
"VisIt"
] | 0da319e80b573cace58c553434b8ea659d9cbbb7e2c78f488ab479d8e0ecdfd0 |
"""
Copyright (C) 2009-2015 Jussi Leinonen, Finnish Meteorological Institute,
California Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including wit... | josephhardinee/pytmatrix | pytmatrix/orientation.py | Python | mit | 4,819 | [
"Gaussian"
] | ab10e37bd52e85fafc01000ff79fbf7d865d313f61aa40ce8f65085302c6a328 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_poolgroupdeploymentpolicy.py | Python | gpl-3.0 | 5,862 | [
"VisIt"
] | 1c46b67f7b49dabe1ca0ef693a0d6ce7ede282dfed4652dc4f9d1fd669eed40b |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/controlling.py | Python | gpl-2.0 | 30,741 | [
"PyMOL"
] | 5b855d7acf72630456baa9c09abe9e11033d12a295319d71979a7a003d67616c |
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