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#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_pymol.py
# Purpose: viz running LIGGGHTS simulation via PyMol
# Syntax: viz_pymol.py in.liggghts Nfreq Nsteps
# in.liggghts = LIGGGHTS input script
# Nfreq = dump and viz shapshot every this many steps
# ... | CFDEMproject/LIGGGHTS-PUBLIC | python/examples/viz_pymol.py | Python | gpl-2.0 | 1,892 | [
"PyMOL"
] | 10f765bb8db41a804ed14dd2e5e9a287d42a2ae23d08810c2d76f601bf48f532 |
""" DIRAC JobDB class is a front-end to the main WMS database containing
job definitions and status information. It is used in most of the WMS
components
The following methods are provided for public usage:
getJobAttribute()
getJobAttributes()
getAllJobAttributes()
getDistinctJobAttributes... | calancha/DIRAC | WorkloadManagementSystem/DB/JobDB.py | Python | gpl-3.0 | 72,060 | [
"DIRAC"
] | d15f1687d6b18be01b06fd1c42a8ef479d31435d684af05a797d63eb1170374d |
"""Basic UI test that checks if the stack analysis is visible for the newly created project."""
from splinter import Browser
import time
import os
from urllib.parse import urljoin
SLEEP_BETWEEN_PAGES = 15
SLEEP_BEFORE_CLICK = 15
class Context:
"""Class that holds context for the UI tests."""
def __init__(s... | tisnik/fabric8-analytics-common | ui-tests/test.py | Python | apache-2.0 | 10,299 | [
"VisIt"
] | a502d799af214617ced9873ebca3415a5483de57206887f366f9e730c19b0486 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/gui/editors/discounteditor.py | Python | gpl-2.0 | 5,161 | [
"VisIt"
] | 0301e49af6007b19818588cb9587b07f9672548f48aba24085ae7850ad4d2106 |
import os
import sys
from utils import *
import operator
from time import localtime, strftime
import argparse
import re
from Bio import SeqIO
from abifpy import Trace
import pylab
from Bio.Blast import NCBIXML
from Bio.Blast import NCBIWWW
from Bio import Entrez
# usage: python /home/williamslab/scripts/python/blast_s... | richrr/scripts | python/blast_search_and_parse_indivi_queries.py | Python | gpl-3.0 | 11,742 | [
"BLAST",
"BioPerl",
"Biopython"
] | 94077ce5a6a66d0a6ebe89c9eaabb4eba035aff81220c85686a9f4ee5c1103eb |
#!/usr/bin/env python3
import optparse
import re
def parse_options():
"""
Parse the options guiven to the script
"""
parser = optparse.OptionParser(description='Get unmatched blast queries')
parser.add_option('-f', '--fasta', dest='fasta_file',
help='Query fasta file used du... | ARTbio/tools-artbio | tools/blast_unmatched/blast_unmatched.py | Python | mit | 2,034 | [
"BLAST"
] | 2e5bc8b14ceb907d1aa7d09912be3c01a6c92bb2c845d0d21f3bf2452af85324 |
import numpy as np
from .control import model_setup
from .cp_confocal import threed
from .cp_triplet import trip
from .cp_mix import double_pnum
# 3D + 3D + TT Gauß
# Model 6043
def CF_Gxyz_gauss_3D3DTT(parms, tau):
u""" Two-component three-dimensional free diffusion
with a Gaussian laser profile, includ... | paulmueller/PyCorrFit | pycorrfit/models/model_confocal_tt_3d_3d.py | Python | gpl-2.0 | 5,161 | [
"Gaussian"
] | 99f554b9e299c3c19230765ea26576bce2ad4e76b6e18e28ada2b045fdc9b449 |
#!/usr/bin/python
import numpy as np
import pylab as pl
from auryntools import *
# This code snipped assumes that you have run the example simulation
# sim_coba_binmon with mpirun and default paramters.
# This generates spk output files under /tmp/
num_mpi_ranks = 4
seconds = 0.1
filenames = [ "/tmp/coba.%i.e.spk"... | idiot-z/auryn | tools/python/merged_spike_raster.py | Python | gpl-3.0 | 533 | [
"NEURON"
] | fa33cf03c86f953ff63d3350445dd22a70a643e0362c9c41557cb22bae601410 |
#!/usr/bin/env python
"""
Adds Manually created builds and chrom info to Galaxy's info tables
Usage:
python add_manual_builds.py input_file builds.txt chrom_length_dir
"""
import sys,os
def add_manual_builds(input_file, build_file, chr_dir):
#determine existing builds, so as to not overwrite
existing_builds... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/cron/add_manual_builds.py | Python | gpl-3.0 | 1,728 | [
"Galaxy"
] | a53bf2c24e969754d711896a1ef12dca1cf221e13432ed2477a834005e10498d |
# -*- coding: utf-8 -*-
# Copyright 2013 by Petra Kubincova
import sys
try:
import Bio.bgzf as bgzf
except ImportError as e:
print "Missing Biopython module"
sys.exit(0)
import seq_structures as seq
def write_bgzf(writer, data):
if len(data) > seq.MAX_LEN:
raise BaseException()
else:
... | kpetra/maptool-python | bgzf_tool.py | Python | mit | 3,548 | [
"Biopython"
] | 42f79c1999648383b1be5588f58c32f63ce427b46db1ecabfe5a007611bebd0c |
from sympy import factorial, sqrt, exp, S, assoc_laguerre, Float
def R_nl(n, l, r, Z=1):
"""
Returns the Hydrogen radial wavefunction R_{nl}.
n, l
quantum numbers 'n' and 'l'
r
radial coordinate
Z
atomic number (1 for Hydrogen, 2 for Helium, ...)
Everything is in Hartr... | flacjacket/sympy | sympy/physics/hydrogen.py | Python | bsd-3-clause | 4,437 | [
"DIRAC"
] | 3c1468889557906490a2b73aa38ddb71a9ee18ded907fab92888bdf7687ad619 |
"""
BigchainDB: A Scalable Blockchain Database
For full docs visit https://docs.bigchaindb.com
"""
from setuptools import setup, find_packages
# get the version
version = {}
with open('bigchaindb/version.py') as fp:
exec(fp.read(), version)
# check if setuptools is up to date
def check_setuptools_features():
... | stanta/darfchain | darfchain_docker_vagrant/setup.py | Python | gpl-3.0 | 3,948 | [
"VisIt"
] | 8b7bd7c48e08bf8d270780353992fabec9ecb6231b7caa8210ecac79c2996922 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | SNoiraud/gramps | gramps/gen/filters/rules/person/_hasaddresstext.py | Python | gpl-2.0 | 1,909 | [
"Brian"
] | 138e86b3806efd0bf5f12ed4767e34ba31d0e97143c2e9849e34644ed5231c6d |
"""
This file provides kernels for par loops.
These are contained in this file as functions so that they can be tested separately.
"""
import numpy as np
from firedrake import dx
from firedrake.parloops import par_loop, READ, INC, WRITE
from pyop2 import ON_TOP, ON_BOTTOM
class GaussianElimination(object):
"""
... | firedrakeproject/gusto | gusto/kernels.py | Python | mit | 15,143 | [
"Gaussian"
] | cf835bba0335a462f2f9431ce8e5690fd8cd2b1c9cde04283e72eec68fa02e6f |
'''Color functions for PyMOLProbity plugin.'''
from pymol import cmd
def get_pymol_color(color):
"""Return the PyMOL color corresponding to a Kinemage color name."""
color_list = {
# Color names defined in the KiNG source that aren't included in a
# standard PyMOL installation are listed her... | jaredsampson/pymolprobity | pymolprobity/colors.py | Python | mit | 1,139 | [
"PyMOL"
] | 655a881665f7b1c9d5804261f8ded088805a3ab1494815af4861e17ab95024fe |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'MailItTemplate.content_html_template'
db.add_column(u'mai... | TEDICpy/write-it | mailit/migrations/0003_auto__add_field_mailittemplate_content_html_template.py | Python | gpl-3.0 | 11,683 | [
"VisIt"
] | 17c6476141cc740dd201372577dd5934e6f684cd031786d9db72d3d911e07c4c |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# 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 l... | userzimmermann/robotframework-python3 | src/robot/result/rerunmerger.py | Python | apache-2.0 | 2,580 | [
"VisIt"
] | ae8f52591717899a387c70efda8c54b9edb9a8a8d591cc1d4b2f054860a8e671 |
from moviepy.editor import VideoFileClip
import matplotlib.pyplot as plt
import matplotlib.image as mplimg
import numpy as np
import cv2
blur_ksize = 5 # Gaussian blur kernel size
canny_lthreshold = 70 # Canny edge detection low threshold
canny_hthreshold = 150 # Canny edge detection high threshold
# Hough transfo... | framefreeze/HangDriver | lane_detection/lanedetection2.py | Python | mit | 5,523 | [
"Gaussian"
] | e9617b3b64028d59b67ed85511b361265f17c61727f9a399c6323f4f5f69e6a6 |
from __future__ import print_function
"""Module for calculating phonons of periodic systems."""
import sys
import pickle
from math import sin, pi, sqrt
from os import remove
from os.path import isfile
import numpy as np
import numpy.linalg as la
import numpy.fft as fft
has_spglib = False
try:
from pyspglib impor... | suttond/MODOI | ase/phonons.py | Python | lgpl-3.0 | 27,222 | [
"ASE",
"GPAW"
] | cd510241fc7b314adf06477d013f9c2ef949ec89cf6651221a2a4678bd9b731e |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
import numpy as np
from unittest import TestCase
from os import sep, remove, rmdir
from tempfile import mkdtemp
import tarfile
from glob import glob
from exatomic.base import resourc... | exa-analytics/exatomic | exatomic/va/tests/test_va.py | Python | apache-2.0 | 24,371 | [
"Gaussian",
"NWChem"
] | 222729fa009b637e68713de88f725e1a0e5e505d4f3e2916252964aa570010ae |
# -*- coding: utf-8 -*-
## Ranking of records using different parameters and methods on the fly.
##
## This file is part of Invenio.
## Copyright (C) 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public... | pamoakoy/invenio | modules/bibrank/lib/bibrank_drank_sorter.py | Python | gpl-2.0 | 12,825 | [
"Octopus"
] | c5cc392e46d643904e7f8ffcd72d6ede69b48a4c1e14f1671f02d1114305deca |
"""
This is the boilerplate default configuration file.
Changes and additions to settings should be done in the config module
located in the application root rather than this config.
"""
config = {
# webapp2 sessions
'webapp2_extras.sessions' : {'secret_key': '_PUT_KEY_HERE_YOUR_SECRET_KEY_'},
# webapp2 authenticatio... | jackie6chang/aits | boilerplate/config.py | Python | lgpl-3.0 | 4,185 | [
"VisIt"
] | 13b2b5b5ac64b1f080740c9ad9acb92da7488779d4af8c48142c4c28b8502ca3 |
"""
:codeauthor: Jayesh Kariya <jayeshk@saltstack.com>
"""
import pytest
import salt.modules.moosefs as moosefs
from tests.support.mock import MagicMock, patch
@pytest.fixture
def configure_loader_modules():
return {moosefs: {}}
def test_dirinfo():
"""
Test if it return information on a directory l... | saltstack/salt | tests/pytests/unit/modules/test_moosefs.py | Python | apache-2.0 | 1,323 | [
"MOOSE"
] | b3bf121e523926dc88cf1a6bbd20b0159c937d2090e9817f1d0ed369db57141c |
from ase.atoms import string2symbols
abinitio_energies = {
'CO_gas': -626.611970497,
'H2_gas': -32.9625308725,
'CH4_gas': -231.60983421,
'H2O_gas': -496.411394229,
'CO_111': -115390.445596,
'C_111': -114926.212205,
'O_111': -115225.106527,
'H_111': -1... | mhoffman/catmap | tutorials/1-generating_input_file/generate_input.py | Python | gpl-3.0 | 5,160 | [
"ASE"
] | 94cdf175ed4cc9856ff5fe1c5f160a2a8f10a30b5ff5d3b2daa7ae68a13501d8 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is vasp high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides vasp python interface to physical inpu... | pylada/pylada-light | tests/vasp/test_uparams_attribute.py | Python | gpl-3.0 | 7,548 | [
"CRYSTAL",
"VASP"
] | a53fb5c8af00b70daa84c40236b4bca22316a81b3ad6fce10405cb6eda1448e5 |
"""
Common functions for tests
"""
__author__ = 'Dan Gunter <dkgunter@lbl.gov>'
__date__ = '10/29/13'
# Stdlib
import json
import logging
import os
import subprocess
import sys
import tempfile
import traceback
import unittest
# Third-party
from mongomock import MongoClient
import pymongo
# Package
from matgendb.query_... | migueldiascosta/pymatgen-db | matgendb/tests/common.py | Python | mit | 4,261 | [
"VASP"
] | c1a2deaadda81d7e1ae3700734fe58f23b37277d846fea2b67f89fab3f6b32fa |
#!@Python_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | lothian/psi4 | psi4/run_psi4.py | Python | lgpl-3.0 | 14,586 | [
"Psi4"
] | eeae13b268cc02944ac3aa6e5252c3e6bcbf15829f1c5b73d9cab4f3276deae6 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/tutorials/ChemicalBistables/mapkFB.py | Python | gpl-2.0 | 3,118 | [
"MOOSE"
] | eef69f615bbd5449682a8edbc20e2618c0c4be640eaed032c3f68ebdb1fa0eee |
#!/usr/bin/env python
# -*- coding: utf-8 -*- #
import json
import sys
import re
import random
from twitterbot import TwitterBot
# from os.path import expanduser
class InsultBird(TwitterBot):
def bot_init(self):
"""
Initialize and configure your bot!
Use this function to set options and ... | brianshumate/insult-bird | insult-bird.py | Python | mit | 4,896 | [
"Brian"
] | 10efabf1b64738dc1ce019bfc8601b068a4a8a4155e7dc3adcc508d122158523 |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2008 VMware, Inc.
# All Rights Reserved.
#
# 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 ... | execunix/vinos | xsrc/external/mit/MesaLib/dist/src/gallium/tools/trace/model.py | Python | apache-2.0 | 6,211 | [
"VisIt"
] | 827fb335a0fc87c203baab587c903a9cc61f7e5815dbe81023ac94254c567d75 |
def codegen_helper():
import clr
clr.AddReference("IronPython")
from IronPython.Compiler import Ast
def get_Subclass_of(rt):
for y in [getattr(Ast, x) for x in dir(Ast)]:
yt = clr.GetClrType(y)
if rt == yt: continue
if yt.IsAbstract: continue
if ... | IronLanguages/ironpython3 | Tests/transform.py | Python | apache-2.0 | 7,398 | [
"VisIt"
] | 3caf511894eb50046c4fcdfd6ce8c3371e43234970c193ea7cb57bd2e76eec55 |
"""
Several utilities to reduce clutter in my policy gradient codes.
(c) April-June 2017 (mostly) by Daniel Seita
"""
import numpy as np
import tensorflow as tf
import scipy.signal
import sys
def gauss_log_prob_1(mu, logstd, x):
"""
Calls `gauss_log_prob` with a broadcasted version of logstd. Assumes that
... | DanielTakeshi/rl_algorithms | utils/utils_pg.py | Python | mit | 5,503 | [
"Gaussian"
] | 9d527ce5363d0f34b4845b4531b9437d784e87ed9a5f8cd4197a5226b9dc7c09 |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import time
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..jsinterp import JSInterpreter
from ..swfinterp import SWFInterpreter
from ..compat import (
compa... | nyuszika7h/youtube-dl | youtube_dl/extractor/youtube.py | Python | unlicense | 150,830 | [
"ADF"
] | e3dc14438db66b361899b823fba7937576fb283841ecf156196e1769c9fe5b68 |
## DensityProfiles.py
## Dr. Harold Barnard and Jonathan Terry
## 8/21/2014
import numpy as np
import matplotlib.pyplot as plt
## Aggregation of various density profiles, maintaining the total density profile of
## the target material.
## Used for statistics management in simulation
class TargetRegion(object):
d... | hbar/python-ChargedParticleTools | lib/ChargedParticleTools/DensityProfiles.py | Python | mit | 5,843 | [
"Gaussian"
] | 0d6eec3a0805c7846ea7c0a9a40a09b3fee9b572e6f13246f36801a440169206 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | mairin/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 23,922 | [
"VisIt"
] | e2305bc988a2be30f0f851d792552d62e4056b90c7782453cba2ea0d7b90f75c |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/exp1/v1-first-half/lm_v4.py | Python | mit | 25,619 | [
"NEURON"
] | 06d79fcad3650b5638f492f42b3c016d4ac063a460ea90605ccf140b7d30b2dd |
import sys
import os
import pysam
import difflib
IS_PYTHON3 = sys.version_info[0] >= 3
if IS_PYTHON3:
from itertools import zip_longest
from urllib.request import urlopen
else:
from itertools import izip as zip_longest
from urllib2 import urlopen
def checkBinaryEqual(filename1, filename2):
'''r... | daler/pysam | tests/TestUtils.py | Python | mit | 3,266 | [
"pysam"
] | 70cefbe072cbdbf9a2833f1943320292c4009477fada87c2e9d91b04aa4db026 |
# -*- coding: utf-8 -*-
#
# * Copyright (c) 2009-2017. Authors: see NOTICE file.
# *
# * 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... | cytomine/Cytomine-python-datamining | cytomine-applications/ldm_model_builder/build_dmbl_model.py | Python | apache-2.0 | 18,236 | [
"Gaussian"
] | a8528602f131d940e503e10301eb8dd8a4c74fdcbf20414cce0704cd327d34e5 |
from django.db import models
from edc_base.model.fields.custom_fields import OtherCharField
from edc_base.model.models import BaseUuidModel
from edc_base.audit_trail import AuditTrail
from edc_constants.choices import DRUG_ROUTE
from edc_constants.choices import YES_NO
from edc_visit_tracking.models import CrfInlineMo... | botswana-harvard/microbiome | microbiome/apps/mb_infant/models/infant_fu_new_med.py | Python | gpl-2.0 | 2,336 | [
"VisIt"
] | d98c07568157667aea2881eae7a06a1456eeb57c353040fb724bc91914788bc6 |
import time
from vtk.web import testing
dependencies_met = True
try:
# import modules for automating web testing using a real browser
import selenium, Image
from selenium import webdriver
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Web/Applications/FileViewer/test/test_pv_web_fileviewer_can_test.py | Python | gpl-3.0 | 3,472 | [
"ParaView",
"VTK"
] | da2ece4f58ee8503756e996dd6f012eb4c5dd5ad9b2e19cf788e1b36bf7c6fc1 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_applicant.py | Python | apache-2.0 | 9,979 | [
"VisIt"
] | 0382b8504b2f907478076159f4730fb1d06c45294c33dea3014e3920f15f082a |
import sys
sys.path.insert(1, "../../../")
import h2o
def link_correct_default(ip,port):
# Connect to h2o
h2o.init(ip,port)
print("Reading in original prostate data.")
h2o_data = h2o.upload_file(path=h2o.locate("smalldata/prostate/prostate.csv.zip"))
print("Compare models with link unspecified and canonical lin... | bikash/h2o-dev | h2o-py/tests/testdir_algos/glm/pyunit_link_correct_default_largeGLM.py | Python | apache-2.0 | 2,018 | [
"Gaussian"
] | a5053796f46b419a2ea0531832756899bbcba63e456a509b87708b4d6292a25a |
# Copyright (c) 2012-2014 The GPy authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from scipy import stats, special
from . import link_functions
from .likelihood import Likelihood
from .gaussian import Gaussian
from ..core.parameterization import Param
from ..cor... | jameshensman/GPy | GPy/likelihoods/mixed_noise.py | Python | bsd-3-clause | 3,283 | [
"Gaussian"
] | a3650c47fe70af8ccd500171677a00c9efb52bb420225ef3ad4a082b6e93b45c |
import time
class FileObjectError(Exception):
def __init__(self, value):
self.value = value
def __str__(self):
return repr(self.value)
# Biopython read_fasta implementation
def SimpleFastaParser(file):
"""Generator function to iterate over Fasta records (as string tuples).
For each re... | nauer/BI-Army-Knife | src/Examples.py | Python | apache-2.0 | 3,073 | [
"Biopython"
] | c7efbffd05ac60299c3b8c9d62d1f8316875a0f52a4953cb29298408b589a499 |
from ase import *
class Bader:
'''class for running bader analysis and extracting data from it.
ACF.dat contains the coordinates of each atom, the charge
associated with it according to Bader partitioning, percentage of
the whole according to Bader partitioning and the minimum distance
to the surf... | freephys/python_ase | ase/calculators/jacapo/utils/bader.py | Python | gpl-3.0 | 5,653 | [
"ASE"
] | f675dd0ec7af7fa26380b8ad8c76c2de83f69894be19b14186916dbeb7a634b8 |
# ocean
from django.db import models
from django.contrib.gis.db import models
from django.contrib.gis.geos import Point
from django.utils import timezone
from django.contrib.gis.geos import GEOSGeometry
# from django.contrib.gis.geos import LineString
from django.contrib.gis.geos import Polygon, MultiPolygon
from djang... | cttgroup/oceanhub | proto/data-refining/back/workdir/ocean/models.py | Python | apache-2.0 | 8,027 | [
"NetCDF"
] | 3a346abdece1f3787dc515188d5b5d741d6963dc8233df8c531dda9300441cdb |
##!/home/alpha/anaconda/bin/python
## -*- coding: utf-8 -*-
"""
This Python module calculates the Credit Value Adjustment for a single netting set of plain vanilla
interest rate swaps.
The code is based on the IPython Notebook of Matthias Groncki (see reference below).
References:
"CVA Calculation with QuantLib and... | carljohanrehn/xvapy | py/cva_calculation.py | Python | bsd-2-clause | 24,700 | [
"Gaussian"
] | 2a4551897b35edba00fefe67fb9dc9ed13d377bd48bbcd87649c78d46034b9ab |
#
# Copyright 2019-2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Softw... | libAtoms/matscipy | matscipy/electrochemistry/poisson_nernst_planck_solver.py | Python | lgpl-2.1 | 45,577 | [
"Avogadro",
"Matscipy"
] | 6522ac2719013a112ded2d668658dd29f8a0e25ce9300e6b0e924cad58ad5053 |
"""
# 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 includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_0004.py | Python | gpl-3.0 | 3,909 | [
"Brian"
] | a9f9043114e2d3abaa772bea6940cc1967d0225e7686aceb2f066ecbd1a9dede |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/pyside/widgets/checkbox.py | Python | gpl-3.0 | 1,324 | [
"Brian"
] | 8ba662fbbbcac5f70d4206e6aa3d6eba753c6d210b4bb4d0aaefa7b7fb4fe429 |
# INPUT FILE for adco_transect_preprocessor
# Set options in this file in order to use process adcp transects using the
# For further information on setting these options, the ADCP Python Documentation
#
# IMPORTANT: This options file is uses Python 2.X code convenctions, meaning:
# 1) there may not be any tab chara... | esatel/ADCPy | adcpy/trn_pre_input_RIO.py | Python | mit | 4,988 | [
"NetCDF"
] | f0b4dc3113885cbae0a6558db38bdeada9b2c45507eb97cdad7e25bdfad7ce2c |
#!flask/bin/python
# Author: Johan Beekhuizen, Deltares
# Author: Joan Sala Calero, Deltares
# This work is based on the Flask Upload Tool by Ngo Duy Khanh (https://github.com/ngoduykhanh/flask-file-uploader)
# which in turn is based on the jQuery-File-Upload (https://github.com/blueimp/jQuery-File-Upload/)
import os
... | switchonproject/sip-html5-data-upload | app.py | Python | lgpl-3.0 | 30,051 | [
"NetCDF"
] | e6169db42bbd6c044c46fded7d44f5e288a873a1dbd3f0701c57efea84107744 |
# $Id$
##
## This file is part of pyFormex 0.8.9 (Fri Nov 9 10:49:51 CET 2012)
## pyFormex is a tool for generating, manipulating and transforming 3D
## geometrical models by sequences of mathematical operations.
## Home page: http://pyformex.org
## Project page: http://savannah.nongnu.org/projects/pyformex/
##... | dladd/pyFormex | pyformex/plugins/vtk_itf.py | Python | gpl-3.0 | 8,856 | [
"VTK"
] | 40d740651898145b1cbb7a63b65504b6a290e051f9f1056101917575625da8b0 |
#! /usr/bin/env python
'''
jsSHA HMAC Test Result Generator
Version 1.0 Copyright Brian Turek 2009
Distributed under the BSD License
See http://jssha.sourceforge.net/ for more information
'''
import hashlib
import hmac
def main():
'''
main()
Calculates the HMAC of the test vectors given in FIPS-198a for full
... | a2n/jsSHA | test/HMACGen.py | Python | bsd-3-clause | 3,154 | [
"Brian"
] | a0ce03c2656cdd76d46ac8172f0927f70f8cbb13d0a7d3140b900043366da692 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/mongodb/__init__.py | Python | lgpl-2.1 | 1,650 | [
"MDTraj"
] | 4b00e741669a3ee0157efebf9501fb0e3e8c16b613d63965e66ccae8adeca093 |
# Copyright 2017 Battelle Energy Alliance, 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 t... | idaholab/raven | scripts/TestHarness/testers/NetCDFDiffer.py | Python | apache-2.0 | 3,769 | [
"NetCDF"
] | f513c8a864d7b74fae660b79e13d91e19ba47cb495c2c14809471a5d90fa250d |
"""Astronomical and physics constants.
This module complements constants defined in `astropy.constants`,
with gravitational paremeters and radii.
Note that `GM_jupiter` and `GM_neptune` are both referred to the whole planetary system gravitational parameter.
Unless otherwise specified, gravitational and mass paramet... | poliastro/poliastro | src/poliastro/constants/general.py | Python | mit | 15,064 | [
"Brian"
] | 34e000b009c2ac2853440f55ce1a3f5d025af42ab3f5576abdb3d240ce80659a |
# -*- coding: utf-8 -*-
r"""
Linear elasticity with given displacements.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,
where
.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_{il} \delta_{jk}) +
\lambda \ \d... | vlukes/sfepy | examples/linear_elasticity/linear_elastic.py | Python | bsd-3-clause | 2,483 | [
"VTK"
] | fd9f4525221349fca65435cc8c0821ae73f02559be64910237e70fc9497b6266 |
"""
flatten_obj.py - Flatten multi-state pymol objects into a single state.
<https://pymolwiki.org/index.php/Flatten_obj>
This is particularly useful for dealing with biological assemblies, which are
loaded as multi-state objects when fetched using `fetch PDBID, type=pdb1`. It
can also be used as a quick way to combi... | mmagnus/rna-pdb-tools | rna_tools/tools/PyMOL4RNA/external_flatten_object.py | Python | gpl-3.0 | 11,652 | [
"PyMOL"
] | a9647219f4261f22ee4cf62597ea1714ea37a4583489e45c4e7d7d7163f5f85b |
#! /usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010 (ita)
"""
This file is provided to enable compatibility with waf 1.5, it will be removed in waf 1.7
"""
import sys
from waflib import ConfigSet, Logs, Options, Scripting, Task, Build, Configure, Node, Runner, TaskGen, Utils, Errors, Context
# the following... | Theragon/kupfer | waflib/extras/compat15.py | Python | gpl-3.0 | 9,248 | [
"VisIt"
] | dfce0e467fa6834fecee7dc70ab46cbed99a98e9bb699389c391011ae6c97691 |
import multiprocessing
import tempfile
import time
import numpy
import vtk
import i18n
import converters
# import imagedata_utils as iu
from scipy import ndimage
# TODO: Code duplicated from file {imagedata_utils.py}.
def ResampleImage3D(imagedata, value):
"""
Resample vtkImageData matrix.
"""
spaci... | givanaldo/invesalius3 | invesalius/data/surface_process.py | Python | gpl-2.0 | 7,484 | [
"VTK"
] | 3875793f6e62003f2ffb5cb2ebd96b46e1f7ead3401082fdbe6b7963e9f3fd4e |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | shiwalimohan/RLInfiniteMario | system/codecs/Python/src/rlglue/environment/EnvironmentLoaderScript.py | Python | gpl-2.0 | 1,627 | [
"Brian"
] | ae82043da81be1c0fdcdf9668c67c1742eabf0dfdc5403cce7c27d58a12c1c62 |
from director.shallowCopy import shallowCopy
import director.vtkAll as vtk
from vtk.util import numpy_support
import numpy as np
def numpyToPolyData(pts, pointData=None, createVertexCells=True):
pd = vtk.vtkPolyData()
pd.SetPoints(getVtkPointsFromNumpy(pts.copy()))
if pointData is not None:
for ... | patmarion/director | src/python/director/vtkNumpy.py | Python | bsd-3-clause | 2,528 | [
"VTK"
] | 64e531246623a6f321ba006a0898199633fe895c7d417fe1c2a52f905fbcb1f6 |
import sys
import unittest
sys.path.append('./code')
from models import GSM, Distribution
from tools import logmeanexp, mapp
from numpy import zeros, all, abs, array, square, log, pi, sum, mean, inf, exp
from numpy import histogram, max, sqrt
from numpy.random import randn, rand
from scipy import integrate
from scip... | lucastheis/isa | code/models/tests/gsm_test.py | Python | mit | 3,467 | [
"Gaussian"
] | e35dc55af92afc19504d7087f90fc8f7fb1d2d5e81ab2a02c2755eaf7544af54 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/selected_ci.py | Python | apache-2.0 | 41,715 | [
"PySCF",
"exciting"
] | dbe8d213cf43ab2e29a62d9decb89a8eb925d09fe27d2a2da44db80be5119513 |
from os.path import join, abspath, dirname, getsize, curdir
from netCDF4 import Dataset
from flyingpigeon import config
import logging
logger = logging.getLogger(__name__)
DIR_SHP = config.shapefiles_dir()
def has_Lambert_Conformal(resource):
"""
Check if grid is organised as Lambert_Conformal
:param res... | KatiRG/flyingpigeon | flyingpigeon/ocgis_module.py | Python | apache-2.0 | 12,205 | [
"NetCDF"
] | 020efe488f0baa9ab851e31f615d034b594278dbe5d3be3bff6a37d752d515a8 |
# -*- coding: utf-8 -*-
'''
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General Public License is a fre... | juergenhamel/cuon | cuon_client/Cuon.py | Python | gpl-3.0 | 83,624 | [
"VTK"
] | 672545f7c9a06f453ec21942b8db021e8bfd76b26754c30c8e44f7cedb3ced77 |
########################################################################
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/WorkloadManagementSystem/private/DIRACPilotDirector.py $
# File : PilotBundle.py
# Author : Ricardo Graciani
########################################################################
... | sposs/DIRAC | Resources/Computing/PilotBundle.py | Python | gpl-3.0 | 6,349 | [
"DIRAC"
] | 8e3a4209999016a04d5c4c49de137155b8c9967f444de846ba66c54bbfde82e8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Appcelerator Titanium Mobile
# Copyright (c) 2011 by Appcelerator, Inc. All Rights Reserved.
# Licensed under the terms of the Apache Public License
# Please see the LICENSE included with this distribution for details.
#
# Android Application Script
#
import os, sys, s... | arnaudsj/titanium_mobile | support/android/android.py | Python | apache-2.0 | 11,939 | [
"VisIt"
] | 4ff0c17ce3f44d508fa81cb93b7b17d7305e4aaaec7d31c483c131db0510da7b |
from hamcrest import *
from test.features import BrowserTest
from test.features.support import table_from
class GenerateHighVolumeServicesPages(BrowserTest):
def test_all_services_table(self):
self.browser.visit("http://0.0.0.0:8000/high-volume-services/by-transactions-per-year/descending.html")
... | imclab/transactions-explorer | test/features/test_generate_high_volume_services.py | Python | mit | 952 | [
"VisIt"
] | 9abd79d739ee515c87ba3299f64b2eec72a46474ece9bcf96ee3fe962f573b3c |
import matplotlib.pyplot as plt
from pycbc import distributions
# Create a mass distribution object that is uniform between 0.5 and 1.5
# solar masses.
mass1_distribution = distributions.Uniform(mass1=(0.5, 1.5))
# Take 100000 random variable samples from this uniform mass distribution.
mass1_samples = mass1_distribut... | ahnitz/pycbc | examples/distributions/mass_examples.py | Python | gpl-3.0 | 1,651 | [
"Gaussian"
] | d355e4629af4d944e3de1f17ee7af603a96f84175ef1230ec3834264b099a427 |
import tensorflow as tf
import numpy as np
class SOM(object):
"""
2-D Self-Organizing Map with Gaussian Neighbourhood function
and linearly decreasing learning rate.
"""
#To check if the SOM has been trained
_trained = False
def __init__(self, m, n, dim, n_iterations=100, alpha=None, sig... | uqyge/combustionML | som/som.py | Python | mit | 9,210 | [
"Gaussian",
"NEURON"
] | 280e244b65b8f3a93347b6f26bdcec7622da66751b59b607f011e947912c7892 |
import os
from django.test import TransactionTestCase
from django.contrib.auth.models import Group
from django.conf import settings
from hs_core import hydroshare
from hs_core.hydroshare.utils import resource_post_create_actions
from hs_core.testing import TestCaseCommonUtilities
from utils import assert_ref_time_ser... | ResearchSoftwareInstitute/MyHPOM | hs_file_types/tests/test_reftimeseries_metadata_user_zone.py | Python | bsd-3-clause | 5,406 | [
"NetCDF"
] | 6eb30682515ed60baced6e2d5cc1d44b488cbf2a3e061b5e14ec845cc9ddd3a3 |
# $Id$
#
# Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
# 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... | rdkit/rdkit-orig | Projects/DbCLI/CreateDb.py | Python | bsd-3-clause | 20,427 | [
"RDKit"
] | 205a089b933831ad049f4edde4c323cbafc1308a5ca1914564ef4d3f36ac1d49 |
# -*- coding: utf-8 -*-
"""
========================================================================
Transforming positions and velocities to and from a Galactocentric frame
========================================================================
This document shows a few examples of how to use and customize the
`~ast... | stargaser/astropy | examples/coordinates/plot_galactocentric-frame.py | Python | bsd-3-clause | 7,979 | [
"Galaxy"
] | 1bb6b9f163b33a096befcf7b88b8323f9312d7b4eb453c4f9ba7c792ee2c8f83 |
from string import atoi,atof
import sys,os,commands
def get_interface(pdb,interfaceid):
cmd="curl --compressed http://eppic-web.org/ewui/ewui/fileDownload?type=interface\&id=%s\&interface=%s > %s-%s.%s.pdb"%(pdb,interfaceid,pdb,pdb,interfaceid)
os.system(cmd)
chains=commands.getoutput("cat %s-%s.%s.pdb | grep SEQR... | kumar-physics/general-scripts | python/sp.py | Python | gpl-3.0 | 1,860 | [
"PyMOL"
] | 17134a42ceaaa1d91320c4614c4ded2afabd00c0762d18bdaec69bf3148783ab |
from collections import defaultdict
import logging
import pickle
import json
from typing import Dict, Optional, Tuple
from ray.tune import ExperimentAnalysis
from ray.tune.sample import Domain, Float, Quantized
from ray.tune.suggest.variant_generator import parse_spec_vars
from ray.tune.utils.util import unflatten_dic... | robertnishihara/ray | python/ray/tune/suggest/bayesopt.py | Python | apache-2.0 | 15,477 | [
"Gaussian"
] | fd28f068eaa6d310c41303f76d39f54a02415e411e5bcaab61860bc96c815497 |
import sympy.mpmath
from sympy.mpmath import *
from sympy.mpmath.libmp import *
import random
def test_type_compare():
assert mpf(2) == mpc(2,0)
assert mpf(0) == mpc(0)
assert mpf(2) != mpc(2, 0.00001)
assert mpf(2) == 2.0
assert mpf(2) != 3.0
assert mpf(2) == 2
assert mpf(2) != '2.0'
a... | mattpap/sympy-polys | sympy/mpmath/tests/test_basic_ops.py | Python | bsd-3-clause | 14,066 | [
"Gaussian"
] | 31382082556c1560ee2ff2370ffd04d35ed2f17530dbf4107962bed740db9059 |
"""Test options handling."""
import os
import sys
from collections import OrderedDict
import pytest
sys.path.append(os.path.abspath('.'))
import fyrd
def test_help():
"""Check that the output of option_help() matches saved output."""
if os.path.isfile(os.path.join('tests', 'options_help.txt')):
ofile ... | MikeDacre/fyrd | tests/test_options.py | Python | mit | 5,648 | [
"pysam"
] | 80f1cd1101614cd8b5fdc4b1427a938f81bda20380109ab3e1a3985f0bf64ef0 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe.utils import add_days, getdate, cint, cstr
from frappe import throw, _
from erpnext.utilities.transaction_base import Transa... | treejames/erpnext | erpnext/support/doctype/maintenance_schedule/maintenance_schedule.py | Python | agpl-3.0 | 9,573 | [
"VisIt"
] | e6e4297f2e95e76a0a9da9338bae6c7440d2937e5e212ba1ee233323da566338 |
''' This is a test of the chain
ResourceManagementClient -> ResourceManagementHandler -> ResourceManagementDB
It supposes that the DB is present, and that the service is running
The DB is supposed to be empty when the test starts
'''
from __future__ import absolute_import
from __future__ import division
fr... | yujikato/DIRAC | tests/Integration/ResourceStatusSystem/Test_ResourceManagement.py | Python | gpl-3.0 | 12,762 | [
"DIRAC"
] | 4d0f8ec5b80fd9c713e3db697b0b502b074c8581f283d9925008f89891c56e86 |
"""DIRAC Administrator API Class
All administrative functionality is exposed through the DIRAC Admin API. Examples include
site banning and unbanning, WMS proxy uploading etc.
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import os
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.... | fstagni/DIRAC | Interfaces/API/DiracAdmin.py | Python | gpl-3.0 | 31,575 | [
"DIRAC"
] | 9b0e2c59b869f537a5e9fc24d51cd012a8fac38d2da993e06a68971495aec6fa |
import sys
import numpy as np
from mpi4py import MPI
from uvw.parallel import PRectilinearGrid, PImageData
from uvw import DataArray
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
if comm.Get_size() != 4:
if rank == 0:
print('Please execute with 4 MPI tasks', file=sys.stderr)
sys.exit(1)
N = 20
# Domain bo... | prs513rosewood/uvw | examples/parallel_mpi.py | Python | mit | 1,555 | [
"Gaussian"
] | d02fd0b4d109f26612218777f48664e195f28e93d023dbe0639c593fbb7e0064 |
from __future__ import absolute_import, division, print_function
import pprint
import sys
import textwrap
import pytest
from _pytest.main import Session, EXIT_NOTESTSCOLLECTED, _in_venv
class TestCollector(object):
def test_collect_versus_item(self):
from pytest import Collector, Item
assert not... | ddboline/pytest | testing/test_collection.py | Python | mit | 32,740 | [
"VisIt"
] | cad8298c234618b42a1d380ec58e8c7e5b30e6115f04b9df5b25bf2bca096d4b |
# Copyright: (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Copyright: (c) 2016, Toshio Kuratomi <tkuratomi@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import ... | kustodian/ansible | lib/ansible/cli/__init__.py | Python | gpl-3.0 | 20,535 | [
"Galaxy"
] | 11b4273604b3d61540324e8e940176823749ad0ef7f8b3f3467293b0b729f597 |
import csv
import os
import pytest
import shutil
import subprocess
from morphct import run_MorphCT
from morphct.definitions import TEST_ROOT
from testing_tools import TestCommand
from morphct.code import helper_functions as hf
from morphct.code import transfer_integrals as ti
class dummy_chromophore:
def __init__... | matty-jones/MorphCT | tests/test_orca_retrials.py | Python | gpl-3.0 | 4,210 | [
"ORCA"
] | 1cbbe73625c83ebc35450457e25af02f1cb23ff4217b3c27a44407030856159c |
#!/usr/bin/python
"""
Automaticaly generate Medobs 'visit template' by selecting office, start/end times and interval.
Running without any arguments prints list of available offices.
"""
import sys
import datetime
from django.core.management.base import BaseCommand, CommandError
from djcode.reservations.models import... | mmincikova/medobs | djcode/reservations/management/commands/medobstemplates.py | Python | gpl-3.0 | 2,066 | [
"VisIt"
] | e26c1b502853ff979480f36ff0ee32056c3ae74ef88f65ce18956e9a18f8a5d0 |
#
# File : mkdir.py
# This file is part of RT-Thread RTOS
# COPYRIGHT (C) 2006 - 2018, RT-Thread Development Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of th... | zhaojuntao/rt-thread | tools/mkdist.py | Python | apache-2.0 | 14,163 | [
"CDK"
] | 9eb14fe82a2951039e4e7e0a17b03e7007f6f322a03a441005b9aeb6f56a868e |
#!/usr/bin/env python
# Authors: 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.
"""
ttree Ttree is a simple program for recursively composing and ... | qipa/lammps | tools/moltemplate/src/ttree.py | Python | gpl-2.0 | 221,891 | [
"LAMMPS",
"NAMD",
"VisIt"
] | 6d93a16237cefc8f682dc5962843c62d80c1871683f524f65e7b419fff671fcb |
#! /usr/bin/env python
"""
Test NIFTI support in VTK by reading a file, writing it, and
then re-reading it to ensure that the contents are identical.
"""
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
from vtk.util.misc import vtkGetTempDir
VTK_DATA_ROOT = vtkGetDataRoot()
VTK_TEMP_... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/Image/Testing/Python/TestNIFTIReaderWriter.py | Python | gpl-3.0 | 4,659 | [
"VTK"
] | 311c9e468657cba65f84ff60cdcfe8801525f17bad3bb2dffdbefaa44724fdb6 |
#!/usr/bin/env python
class codata2016:
def __init__(self):
self.mp = 1.672621898e-27 # kg
self.me = 9.10938356e-31 # kg
# end def
# end class
# HELPER FUNCTIONS
# ======================================
from lxml import etree
def xml_print(node):
print etree.tostring(node,pretty_print=Tru... | Paul-St-Young/QMC | setup_unpolarized.py | Python | mit | 12,997 | [
"GAMESS",
"QMCPACK",
"pymatgen"
] | fb1750cd0fb9c669f59da40e2fb88cb535590532e4879bd8447fda34fa3f17e4 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/analysis/hbonds/hbond_analysis.py | Python | gpl-2.0 | 57,367 | [
"CHARMM",
"Gromacs",
"MDAnalysis",
"VMD"
] | 9ffce0c1143f95c611730e4161e46c6147a7dc9d0a76d1df7d6066bda9f05ffb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/custom/lib/__init__.py | Python | gpl-2.0 | 2,240 | [
"Brian"
] | 008e5b86134658413f6593b2e049454a225bcc3bc53bc29d034e55e174b93137 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para filmenoi
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os, sys
from core im... | Zanzibar82/pelisalacarta | python/main-classic/channels/filmenoi.py | Python | gpl-3.0 | 5,883 | [
"ADF"
] | e0bdb60bf88b178ef7cdf07fbd7af77a7294193b5057e1bdc35db8a3d03b1eea |
# -*- coding: iso-8859-1 -*-
'''Module for processing the data read from the output files of quantum chemical
software. '''
'''
orbkit
Gunter Hermann, Vincent Pohl, Lukas Eugen Marsoner Steinkasserer, Axel Schild, and Jean Christophe Tremblay
Institut fuer Chemie und Biochemie, Freie Universitaet Berlin, 14195 Berlin,... | orbkit/orbkit | orbkit/qcinfo.py | Python | lgpl-3.0 | 11,118 | [
"ASE"
] | a4e2add350338731cb9f4aab58c35abc880b9497faf526a74a7da6a236e865c7 |
#
# packages.py: package management - mainly package installation
#
# Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006 Red Hat, Inc.
# All rights reserved.
#
# 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... | mattias-ohlsson/anaconda | pyanaconda/packages.py | Python | gpl-2.0 | 12,756 | [
"VisIt"
] | 7a3408312e13b254e92fa4a3ba2142f8a0deaab88aad02258053f9dc2af688d2 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe
# License: BSD 3 clause
from itertools import product
import numbers
import numpy as np
from scipy import linalg
from ..utils import array2d, check_random_state
from ..utils i... | maxlikely/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 43,666 | [
"Gaussian"
] | 8187f99c381454a0bcd56743d6f9cca25b92870fd83e352b31ab9af47061defc |
#! /usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistr... | susilehtola/psi4 | psi4/versioner.py | Python | lgpl-3.0 | 14,574 | [
"Psi4"
] | 9f9127345ad664d4cc4ea906ab2f30ca9a61e249e63d5eee5a8e3c9d7c3e5104 |
#!/usr/bin/env python3
from bisect import bisect_left
import matplotlib
from utils import TANGO, filename
from matplotlib import pyplot, mlab
from numpy import linspace
matplotlib.rcParams['lines.linewidth'] = 2
matplotlib.rcParams['savefig.dpi'] = 300
def gaussian(x, mu, sigma):
return mlab.normpdf(x, mu, sigma)... | cpitclaudel/dBoost | graphics/gaussians-preview.pdf.py | Python | gpl-3.0 | 1,197 | [
"Gaussian"
] | 9a01a92bbf0064c88b8b410a52a09ca3885592ddecd6408d35d05045a8be4ad6 |
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | majidaldo/ansible | v2/ansible/plugins/lookup/url.py | Python | gpl-3.0 | 1,545 | [
"Brian"
] | 09d400ad8971e1e350fcebbda37a13be3716817165aec0c0a39375ebd2ada82b |
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