text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import asyncio
import discord
import googleapiclient.errors
import necrobot.exception
from necrobot.util import server
from necrobot.botbase.command import Command
from necrobot.botbase.commandtype import CommandType
from necrobot.botbase.necrobot import Necrobot
from necrobot.test import msgqueue
from necrobot.config... | incnone/necrobot | necrobot/test/cmd_test.py | Python | mit | 13,163 | [
"BLAST"
] | f0fc4af9c791ba24d2507f72fe2110456a7659133f2b3088e9f4dc7d45534c2f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | tiagocardosos/stoq | stoqlib/gui/dialogs/missingitemsdialog.py | Python | gpl-2.0 | 6,822 | [
"VisIt"
] | c4bc05914d45ae7f38393073517e2304504965e244f2358531113923c4bf021b |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import product
import numpy as np
from scipy.sparse import csr_... | thilbern/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 30,960 | [
"Brian"
] | efbec029336e6b793d124eecc923a13b638a77e67c211a7602a6d40ce6109557 |
import numpy as np
import pytest
from pysisyphus.Geometry import Geometry
from pysisyphus.helpers import geom_loader
from pysisyphus.linalg import get_rot_mat
from pysisyphus.intcoords import (
Bend,
Bend2,
BondedFragment,
CartesianX,
CartesianY,
CartesianZ,
DistanceFunction,
DummyTorsi... | eljost/pysisyphus | tests/test_wilson/test_wilson.py | Python | gpl-3.0 | 14,211 | [
"Jmol"
] | 31c4d14216a037fef6cc9ea4f04729295ae7e96f756f136a20564ab24ee1d111 |
from time import sleep
from subprocess import call
from datetime import datetime
import sys
import os
import time
import shutil
import argparse
from PIL import Image
path_to_watch = "new/"
#path_to_watch = "/Users/ns/Dropbox/Pirates/new/"
path_to_raw = "original/"
path_to_print = "forPrinting/"
#path_to_print = "/... | nstoker/nppPhotos | test.py | Python | lgpl-3.0 | 6,252 | [
"Gaussian"
] | 7bb1fbb6bb9473d5d4a5d58bad09732d17edc0ede2f669321782fcc950084de3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
These plugins modify the behavior of py.test and are meant to be imported
into conftest.py in the root directory.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import __future__
from ... | joergdietrich/astropy | astropy/tests/pytest_plugins.py | Python | bsd-3-clause | 31,389 | [
"VisIt"
] | 546f5521e9bb31f4e90b0adf2067ec975ea3fb20c5efbb58664ce01d72428a77 |
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2017, Anaconda, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENSE.txt, distributed with this software.
#---------------------------------------------------... | Karel-van-de-Plassche/bokeh | bokeh/__init__.py | Python | bsd-3-clause | 2,304 | [
"VisIt"
] | d92bec2c354641a9fec346484164e1886866f89029bf6a85703712a489f94c75 |
# -*- coding: utf-8 -*-
#
# mbuild documentation build configuration file, created by
# sphinx-quickstart on Wed Oct 1 08:59:12 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | iModels/mbuild | docs/conf.py | Python | mit | 10,588 | [
"MDTraj"
] | 4e0af9e58b11d9dfa059312b01e81b032dc9a67c6963879bed04eb4f3c774c4f |
# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
from contextlib import contextmanager
from distutils.version import LooseVersion
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil imp... | adykstra/mne-python | mne/utils/_testing.py | Python | bsd-3-clause | 16,450 | [
"Mayavi"
] | 7f7678645d0c5977dcd3960c826959657ed938ef7ea703b5975c5f084476526b |
import io
# From: http://www.redblobgames.com/pathfinding/a-star/implementation.html#python-dijkstra
import heapq
from itertools import permutations
class PriorityQueue:
def __init__(self):
self.elements = []
def empty(self):
return len(self.elements) == 0
def put(self, item, prio... | GuillaumeDD/AdventOfCode2016 | day24.py | Python | gpl-3.0 | 5,998 | [
"VisIt"
] | ca321eaaae8930be83b228f40786cc6081344c0dd631a3d81112117a04701777 |
"""Utilities for interpretability tools."""
import numpy as np
from scipy import ndimage
def gaussian_blur(image: np.ndarray, sigma: float) -> np.ndarray:
"""Applies a Gaussian blur to a 3D (WxHxC) image.
Args:
image: 3 dimensional ndarray / input image (W x H x C).
sigma: Standard deviation for Gaussian... | google/ai-weather-climate | interpretability/utils.py | Python | apache-2.0 | 498 | [
"Gaussian"
] | 1f9c69e109047b0f500a674c078082c1924e762d30f2b76ccdd7bd1fbd1ee0c8 |
# 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)
#
# Original Author: Mark Olesen <mark.olesen@esi-group.com>
#
# Legal Notice
# ------------
# OPENFOAM is a trademark own... | LLNL/spack | var/spack/repos/builtin/packages/openfoam-org/package.py | Python | lgpl-2.1 | 16,158 | [
"ParaView"
] | 25d568a75908b7178c8da9f2ab8dbb4194d793007dbee985cae3179b7a6c29af |
# 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.
"""Nodes for PPAPI IDL AST."""
from idl_namespace import IDLNamespace
from idl_node import IDLNode
from idl_option import GetOption
from idl_visitor imp... | androidarmv6/android_external_chromium_org | ppapi/generators/idl_ast.py | Python | bsd-3-clause | 5,841 | [
"VisIt"
] | 990260f707c7ca9b9f71c7a2df690e457712136ca44e95bd0f3fcec8a8e12319 |
# shallowstore.py - shallow store for interacting with shallow repos
#
# Copyright 2013 Facebook, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from mercurial import util
from mercurial import store as storemod
import stat
... | pycontribs/remotefilelog | remotefilelog/shallowstore.py | Python | gpl-2.0 | 1,703 | [
"VisIt"
] | 48fc5383d394fa18ae75ebf6ed58995e58f07eb5ecc44738be36d216bb9fb859 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | pkreissl/espresso | testsuite/python/lb_slice.py | Python | gpl-3.0 | 6,007 | [
"ESPResSo"
] | dedbef23a86862a9f962087305f035831562a0dfd3531df6a456ff407de862f7 |
"""
Predicting potential dopants
"""
import warnings
import numpy as np
from pymatgen.analysis.structure_prediction.substitution_probability import (
SubstitutionPredictor,
)
from pymatgen.core.periodic_table import Element, Species
def get_dopants_from_substitution_probabilities(structure, num_dopants=5, thre... | vorwerkc/pymatgen | pymatgen/analysis/structure_prediction/dopant_predictor.py | Python | mit | 7,420 | [
"pymatgen"
] | 93335422d0dbf6d559cca7fc23463bc698a0932134d8076ba9caeadcfdb51173 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Jan 22, 2013
@author: Bharat Medasani
"""
import unittest
from pymatgen.command_line.gulp_caller import *
from pymatgen.core.structure import Structure
from monty.os.path import which
from pym... | montoyjh/pymatgen | pymatgen/command_line/tests/test_gulp_caller.py | Python | mit | 11,557 | [
"GULP",
"VASP",
"pymatgen"
] | e493333974692e6d00740600ab7861e08f932733e9f907932f501a220b4ebab6 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, 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 (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import re
import pyte... | bcoca/ansible | test/units/galaxy/test_api.py | Python | gpl-3.0 | 50,779 | [
"Galaxy"
] | 7e8c717764d1df96faac8a365ad83bd2d233d52803b0aeebc55ec94a87a93109 |
from lettuce import step, world
from questionnaire.features.pages.home import HomePage
from questionnaire.features.pages.step_utils import assign, create_user_with_no_permissions
from questionnaire.features.pages.users import LoginPage
from questionnaire.models import Theme
@step(u'Given that I am logged in as a regio... | eJRF/ejrf | questionnaire/features/themes_regional_steps.py | Python | bsd-3-clause | 1,221 | [
"VisIt"
] | 3acde015181c1583cdc720d622b08c0ea95880372afad2d927e97729cd789479 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2014 Michael Cook <mcook@mackal.net>
#
# GPLv3
"""
Processes an eqlog file and generates SQL to update factions
Should work with a full log, but cleaning up the log will be quicker
The file needs at least the zone enter messages, faction m... | mackal/faction.py | faction.py | Python | gpl-3.0 | 36,016 | [
"CRYSTAL"
] | 86cd449615906c0b7469c1b8474a9daa8bd1ae0fef95188eaf0d2053547f5665 |
## This file is part of Invenio.
## Copyright (C) 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 License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your ... | kaplun/Invenio-OpenAIRE | modules/websession/lib/websession_templates.py | Python | gpl-2.0 | 103,262 | [
"VisIt"
] | 565cb0fb021855d098a31a526a596a1d734f59972b1e41afb18fde537b366058 |
#!/usr/bin/env python
#---------------- EDIT JOB NAME -------------------
#$ -N SiteAnalysis
#--------------------------------------------------
#$ -S /usr/bin/python
#$ -v PYTHONPATH=/home/oliver/Library/python-lib
#$ -v LD_LIBRARY_PATH=/opt/intel/cmkl/8.0/lib/32:/opt/intel/itc60/slib:/opt/intel/ipp41/ia32_itanium/sha... | iwelland/hop | doc/examples/siteanalysis_gsbp.py | Python | lgpl-3.0 | 4,814 | [
"MDAnalysis"
] | 07843d8c08541c569b0b46dbd369e9ee3265e5115b21e258c00df6acbccde61d |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | uncertainty_baselines/models/resnet50_het_rank1.py | Python | apache-2.0 | 18,089 | [
"Gaussian"
] | a6579240e04bc5c993202f9170794518d1e4546fe7724483a722f358826e117a |
# -*- coding: utf-8 -*-
# The MIT License (MIT)
#
# Copyright (c) 2018, TU Wien
#
# 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 without limitation the rights
... | TUW-GEO/ecmwf_models | tests/tests_era5/test_era5_download.py | Python | mit | 5,198 | [
"NetCDF"
] | 15d170e79c67e1e83b9cf41242c0f13b14a36e2287d110eb8c182041dab72589 |
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from matplotlib.widgets import Slider
from scipy.stats import norm
import matplotlib.mlab as mlab
import numpy as np
__author__ = 'Robbert Harms'
__date__ = "2016-09-02"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
class Sampl... | cbclab/MDT | mdt/visualization/samples.py | Python | lgpl-3.0 | 7,835 | [
"Gaussian"
] | 6e62b1bc176c30c26c630d5753c11ed86a7e40e3a6807e909782f448942d07f1 |
"""This demo program uses of the interface to TAO solver for
variational inequalities to solve a contact mechanics problem in
FEnics. The example considers a heavy elastic circle in a box of the
same size.
"""
# Copyright (C) 2012 Corrado Maurini
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you ca... | akshmakov/Dolfin-Fijee-Fork | demo/undocumented/contact-vi-tao/python/demo_contact-vi-tao.py | Python | lgpl-3.0 | 3,297 | [
"VTK"
] | a461b1372f40eb962ebdd0f260d440147e6d0b5b229cdc1280e91918f8a858f3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##########################################################
#
# autore: Damiano Lollini
# nome prog: Video To Ogv
# date: 26/03/2012
# ver: 1.1
# descrizione: converte vari formati video in ogv
# vers python: 2.7
#
######################################################... | damnemo/videotoogv | images.py | Python | gpl-3.0 | 171,434 | [
"ASE"
] | 6001374f09ba18b5a8bda9d31204d595e51bc14333f5cb7ca03e134e0d3ca809 |
#
# Copyright (c) 2010, 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 copyrigh... | bp-kelley/rdkit | rdkit/Chem/FunctionalGroups.py | Python | bsd-3-clause | 5,470 | [
"RDKit"
] | 4e98e022ed3cf7f4a2d6ddd51414ea4b4c625998cdbf4cb8cec10ab5f1b33773 |
# -*- coding: utf-8 -*-
import abc
import numpy as np
from scipy._lib._util import check_random_state
from ..utils import (_chol, _chol_downdate, _chol_update, _chol_logdet,
_chol_solve, _normal_rvs, _normal_logpdf, _wishart_rvs,
_wishart_logpdf, _t_logpdf)
class GenericMixture(object):
"""
... | tscholak/imm | imm/models/mixtures.py | Python | apache-2.0 | 46,272 | [
"Gaussian"
] | 36ee9c120ca532c48168008979b1c8ca2b0ad92072e3ea91756c5ce8eac20177 |
from django.test import TestCase, tag
from ..visit import Crf, FormsCollection, FormsCollectionError
class TestFormsCollection(TestCase):
def test_forms_collection_empty(self):
crfs = []
try:
FormsCollection(*crfs)
except FormsCollectionError as e:
self.fail(f'For... | botswana-harvard/edc-visit-schedule | edc_visit_schedule/tests/test_forms_collection.py | Python | gpl-2.0 | 1,008 | [
"VisIt"
] | 348fbd11b8d74ab8ed94a6a55ecdb88c0cc11995dad5c5624bd02ac9d01e9f47 |
# 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/FixPositions.py | Python | gpl-3.0 | 1,793 | [
"ESPResSo"
] | ff56e4d25d99899e6f2bc99dfc1f36073355cca1ac2fc090bc7095383d5776b2 |
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 5 17:58:07 2015
@author: andrea.insabato@upf.edu
Decision-making attractor neural network with integrate & fire neurons with AMPA, GABA and NMDA synapses
from Wang (2002).
TODO: check consistency with Wang data
"""
#!/usr/bin/env python
# -*- coding: utf-8 -*-
unitsC... | andins/ANN_Wang_python | ANN_wang2002.py | Python | gpl-2.0 | 7,763 | [
"Brian",
"Gaussian",
"NEURON"
] | 5c061f326a3a620e50e050a49c45177a90457aa88a9d40ba24d4fe3d67037020 |
import copy
import pyscf.pbc.tools.make_test_cell as make_test_cell
import numpy
import numpy as np
from pyscf.pbc.tools.pbc import super_cell
from pyscf.pbc import gto
from pyscf.pbc import cc as pbcc
from pyscf.pbc import scf as pbcscf
from pyscf.pbc.cc.eom_kccsd_rhf import EOMIP, EOMEA
from pyscf.pbc.cc.eom_kccsd_rh... | sunqm/pyscf | pyscf/pbc/cc/test/test_eom_krccsd.py | Python | apache-2.0 | 25,374 | [
"PySCF"
] | 82d1cf903c1d454696294e6d7358b50c0f7adad9375a2a0e9aea76828f9bd2da |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@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 ... | haad/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 32,087 | [
"Galaxy"
] | ad4794ee9c87f55cb7dc771c50cb21f094a95236581a2eefe82a244e146603b4 |
import MySQLdb
import time
import random
#import threading
import db_conf
import sys
class pham_comparator:
def compare(self, pB, pC, compare_type):
for b_pham in pB.phams:
for c_pham in pC.phams:
match = 0. ... | byuphamerator/phamerator-dev | phamerator/pham_comparator2.py | Python | gpl-2.0 | 2,209 | [
"BLAST"
] | 70b4bb6e829b99321f04d96b8b51a41b485fb1d24e5832e32b00c7ab74078e77 |
import numpy as np
import matplotlib.pyplot as plt
# generate measures from gaussian distribution
x = np.arange(0, 10, 1)
# values computed from "measured"
y = np.log(x)
# add some error samples from standard normal distribution
xe = 0.1 * np.abs(np.random.randn(len(y)))
# draw and show errorbar
plt.bar(x, y, yer... | pletisan/python-data-viz-cookbook | 3367OS_Code/3367OS_03_Code/3367OS_03_CODE_1stDraft/ch03-code/ch03-rec12-errorbar.py | Python | mit | 607 | [
"Gaussian"
] | c8c7d7828308328c5b2d3b905e945850bd0771b58915832d9e5ae0f59a37f048 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | b-carter/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 228,099 | [
"Brian"
] | 4433230107e5f93d1504f29b5f88ab7d73ad51649d20b20b0e8fa96d023411d5 |
# A module to determine the accumulated dose as a function of exposure epoch
# for a given set of images, assuming:
#
# (i) the set is complete
# (ii) the set come from a single (logical) crystal
#
# This is to work with fortran program "doser"
from __future__ import annotations
import collections
from scitbx.arra... | xia2/xia2 | src/xia2/Modules/DoseAccumulate.py | Python | bsd-3-clause | 928 | [
"CRYSTAL"
] | 0891c9f740e5200a2da021eba47dbc5a5d3e66a9d03179ba3628e3d5879bdac1 |
#!/usr/bin/python
########################################################################
# 15 May 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subproce... | pdl30/chipseq_misc | chip_track_norm.py | Python | gpl-2.0 | 2,935 | [
"HTSeq",
"pysam"
] | 40fdee58efee2cc8799fd5a4a1273d13053c9c3c4893b9643cdcdfa29bced1a3 |
#!/usr/bin/env python
# LICENSE
#
# Copyright (c) 2010-2017, GEM Foundation, G. Weatherill, M. Pagani, D. Monelli
#
# The Hazard Modeller's Toolkit (openquake.hmtk) is free software: you can
# redistribute it and/or modify it under the terms of the GNU Affero General
# Public License as published by the Free Software ... | gem/oq-hazardlib | openquake/hmtk/seismicity/max_magnitude/kijko_nonparametric_gaussian.py | Python | agpl-3.0 | 10,283 | [
"Gaussian"
] | 59551d2daa9c2ac40dd35f3d62cc7e6b67d6c870ceb30886d609651ecc4dd6b4 |
#!/usr/bin/env python
"""
Script that helps setting the token of the elements in RSS.
It can acquire or release the token.
If the releaseToken switch is used, no matter what was the previous token, it will be set to rs_svc (RSS owns it).
If not set, the token will be set to whatever username is defined on the proxy lo... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_set_token.py | Python | gpl-3.0 | 6,569 | [
"DIRAC"
] | 262c52a6870d01897e51178f3c6d82a741291ceecf8058f2508ee64ad2057228 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 8,
'resolution': 0... | research-team/NEUCOGAR | NEST/cube/integration/integration-10/neuromodulation.py | Python | gpl-2.0 | 30,026 | [
"NEURON"
] | fc7b4a21e11e6f2914a3f731f0a47dda009a7b575b791377f627d1b630a9d8f6 |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os.path
from ._paml import Paml
from . import _parse_yn00
# TODO - Restore use of... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/PAML/yn00.py | Python | mit | 5,398 | [
"Biopython"
] | 655e5cb3a5484d6a252d299ccf8ceaaf93bfdf30595447114100304c6a97dec9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import random
from collections import OrderedDict
import gzip
import json
import numpy as np
import pandas as pd
from ruamel.yaml import YAML
from pymatgen import Molecule, Element, La... | tschaume/pymatgen | pymatgen/io/lammps/tests/test_data.py | Python | mit | 45,867 | [
"CHARMM",
"LAMMPS",
"pymatgen"
] | 29e88367c539081cb1994ae6f788196223866cfce5feb17564186f4406c5c34c |
from setuptools import setup, find_packages
from mutgen.version import __version__
setup(name='mutgen',
version=__version__,
url='http://github.com/fhcrc/mutgen',
description='Generate mutations under a motif based mutation model',
author="Christopher Small",
entry_points={
... | fhcrc/mutgen | setup.py | Python | gpl-3.0 | 501 | [
"Biopython"
] | 3dba28fd2713b4192d3f711522a74821ddd4e2fbe4dea63b4985f9d826febebc |
# residue atoms mean stdev
bonds = [
( 'ALA', ('CB', 'CA'), 1.5259, 0.0163 ),
( 'ALA', ('N', 'CA'), 1.4601, 0.0108 ),
( 'ALA', ('O', 'C'), 1.2329, 0.0104 ),
( 'ALA', ('C', 'CA'), 1.5255, 0.0112 ),
( 'ALA', ('C', '+N'), 1.3299, 0.0094 ),
( 'CYS', ('CB', 'CA'), 1.5310, 0.0126 ),
... | bjornwallner/proq2-server | apps/modeller9v8/modlib/modeller/library_restraints/bonds.py | Python | gpl-3.0 | 8,158 | [
"Gaussian"
] | 9d5ee401269eff8859574186a43fa1571b04e6217b66c57088510e9cbda29b74 |
#
# @BEGIN LICENSE
#
# QCDB: quantum chemistry common driver and databases
#
# Copyright (c) 2011-2017 The QCDB Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of QCDB.
#
# QCDB is free software; you can redistribute it and/or modify
# it ... | loriab/qcdb | qcdb/vecutil.py | Python | lgpl-3.0 | 11,226 | [
"Psi4"
] | e129c4aeb727ad6673df33aaccd8b91bbdb7cbb0ff2cecb7ee12690373953bad |
import os
from pymatgen.io.vasp.outputs import Vasprun, Outcar
class UData(object):
def __init__(self, U=None):
self.U = U
self.a = None
self.b = None
self.c = None
self.alpha = None
self.beta = None
self.gamma = None
self.charges = None
... | gVallverdu/myScripts | VASP/readU.py | Python | gpl-2.0 | 5,603 | [
"VASP",
"pymatgen"
] | 6f4e883949f78459c92a9ec9f89e54f73cc34d40b663e1e85e3a8ddd26dbf196 |
#! /usr/bin/env python
#
# Copyright (c) 2016 Jakub Krajniak <jkrajniak@gmail.com>
#
# Distributed under terms of the GNU GPLv3 license.
#
import argparse
import datetime
import numpy as np
import gromacs_topology_new
parser = argparse.ArgumentParser('Mix table')
parser.add_argument('--top', default='topol.top')
par... | MrTheodor/bakery | examples/network_backmapping/ab2/chemical_reaction/mix_table.py | Python | gpl-3.0 | 3,753 | [
"Gromacs"
] | 908ac493f27aae022c5c4d50c865215b5e672b6c3748f24a89bb8cda76085f30 |
# creates: Al110slab.png
from math import sqrt
from ase import Atoms, Atom
from ase.io import write
from ase.data.colors import jmol_colors
a = 4.0614
b = a / sqrt(2)
h = b / 2
atoms = Atoms('Al2',
positions=[(0, 0, 0),
(a / 2, b / 2, -h)],
cell=(a, b, 2 * h),
... | qsnake/gpaw | doc/exercises/neb/plot.py | Python | gpl-3.0 | 868 | [
"ASE"
] | bc95637c5087a23026a98925c02da5af0d91c6b08ee51d6896d35673223bf9ef |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/settings/custom.py | Python | apache-2.0 | 827 | [
"Galaxy"
] | 21f62b768d4741108c80e795652ab13dcc33f9961fa840dfc7bcdd31a06fb53b |
from ase import *
from gpaw import GPAW
from gpaw.xc.bee import BEEF_Ensemble
import numpy as np
xc = 'BEEF-vdW'
d = 0.75
# H2 molecule
h2 = Atoms('H2',[[0.,0.,0.],[0.,0.,d]])
h2.center(vacuum=2.)
cell = h2.get_cell()
calc = GPAW(xc=xc)
h2.set_calculator(calc)
e_h2 = h2.get_potential_energy()
f = h2.get_forces()
ens ... | ajylee/gpaw-rtxs | gpaw/test/beefvdw.py | Python | gpl-3.0 | 891 | [
"ASE",
"GPAW"
] | 5113a0493455d5a2d00efecd59e7fe1729088fd9e6b4a43d9c87b06ffbcab29e |
from PyQt4 import QtGui, QtCore
#@@TODO: Cuando abro un caso (tutorial) que no tiene el .config de arranqe
#no me deja agregar figuras
#cambiar a:
#from petroSym.petroSym_ui import petroSymUI
#from petroSym.popUpNew import *
#from petroSym.popUpNewFigure import *
#from petroSym.figureResiduals import *
#from petroSym... | jmarcelogimenez/petroSym | petroSym/petroSym.py | Python | gpl-2.0 | 55,774 | [
"ParaView"
] | f9b64dc8bc947b4f8cb92db93fb39ad4d637f1b6ac993f101c964e1113cb8add |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/exodus/ExodusColorBar.py | Python | lgpl-2.1 | 3,690 | [
"MOOSE"
] | 755c05d5416579c3136219278c435a0efe5548e21233456a26d7deed4494119b |
import pytest
pytest_plugins = [
'encoded.tests.features.browsersteps',
'encoded.tests.features.customsteps',
]
@pytest.fixture(scope='session')
def app_settings(server_host_port, elasticsearch_server, postgresql_server):
from .. import test_indexing
return test_indexing.app_settings(server_host_port... | kidaa/encoded | src/encoded/tests/features/conftest.py | Python | mit | 3,520 | [
"VisIt"
] | e5bc584ab1cc041f0bc487744cd8daff9812e5ea992f49aa7a0cd8b6dc67cc9e |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# 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... | trendelkampschroer/PyEMMA | pyemma/util/tests/statistics_test.py | Python | bsd-2-clause | 2,581 | [
"Gaussian"
] | e71d34fc24ac666038794002f49dec62e486332a2d61a07f3a96849a2ecd63ec |
"""
Tests for discussion pages
"""
from uuid import uuid4
from .helpers import UniqueCourseTest
from ..pages.lms.auto_auth import AutoAuthPage
from ..pages.lms.courseware import CoursewarePage
from ..pages.lms.discussion import (
DiscussionTabSingleThreadPage,
InlineDiscussionPage,
InlineDiscussionThreadP... | Unow/edx-platform | common/test/acceptance/tests/test_discussion.py | Python | agpl-3.0 | 21,753 | [
"VisIt"
] | 17c38064dca66bc7d1d0a81ee812711bdd2128cee68a342de38ba8f54f959bb3 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 4000
k = 3000
testMehrotra = Tru... | birm/Elemental | examples/interface/QPAffine.py | Python | bsd-3-clause | 4,826 | [
"Gaussian"
] | bcb1853538c6434bdb1c0478c90e8370632c94f5d46a54000dfbc786b67ccd00 |
import numpy as np
from scipy import linalg
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.validation import check_array
from ut.ml.sk.decomposition.wpca_utils import check_array_with_weights, weighted_mean, has_integer_value
class WPCA(BaseEstimator, TransformerMixin):
"""Weighted P... | thorwhalen/ut | ml/sk/decomposition/wpca.py | Python | mit | 9,044 | [
"Gaussian"
] | 4a76f5473ef35cc947bc1d703a4e38b8bbd7c55537a371cade0b44b02a1d4c87 |
# basic dependencies
import os
import sys
import subprocess
from glob import glob
import math
# main dependencies: numpy, nibabel
import numpy
import nibabel
# nighresjava and nighres functions
import nighresjava
from ..io import load_volume, save_volume
from ..utils import _output_dir_4saving, _fname_4saving, \
... | nighres/nighres | nighres/registration/surface_antsreg.py | Python | apache-2.0 | 28,283 | [
"Brian"
] | 39f077068a0f0ca83d435090988b5fe1a231cf3aa6ce7c3eebf9ed88dc93e2d7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
import os
from pymatgen.phasediagram.entries import PDEntryIO, PDEntry, \
GrandPotPDEntry, TransformedPDEntry
from pymatgen.core.period... | aykol/pymatgen | pymatgen/phasediagram/tests/test_entries.py | Python | mit | 4,546 | [
"pymatgen"
] | 92c8814b95799ef8023019e9fcbce380c3491ea5e19302d0b690576bee1a77ca |
'''This module contains the ComplexityVisitor class which is where all the
analysis concerning Cyclomatic Complexity is done. There is also the class
HalsteadVisitor, that counts Halstead metrics.'''
import ast
import operator
import collections
# Helper functions to use in combination with map()
GET_COMPLEXITY = op... | seansu4you87/kupo | projects/molt/venv/lib/python2.7/site-packages/radon/visitors.py | Python | mit | 13,792 | [
"VisIt"
] | bf8c0b745089bd8893f771803cbfacdf6a51a6d226efe494f18a4e4b7e0aafe2 |
# -*- coding: utf-8 -*-
# Define your item pipelines here
# We have no item pipelines, refer to settings.py to see how we deal with exporting data
# Import statements
import scrapy
from scrapy.contrib.spiders import CrawlSpider, Rule
from scrapy.http import Request
import string
from lyrics.items import LyricsItem
im... | CS205IL-sp15/workbook | demo_scrapeData/py/lyrics/lyrics/spiders/lyrics_scraper.py | Python | mit | 3,865 | [
"VisIt"
] | 3803925fd8589629a9d820629eba4c4c40288804f2526cced2094cb46340f05e |
from .utils import PyKEArgumentHelpFormatter
from . import kepmsg, kepio, kepkey
import math
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.cbook import is_numlike
from scipy.optimize import leastsq
from scipy.optimize import fmin
from scipy.interpolate import interp1d
from astropy.io impor... | gully/PyKE | pyke/kepcotrend.py | Python | mit | 40,071 | [
"Gaussian"
] | f1e138540cb26bf000eb6b22ebfbc3705a787793ffef80d91a91c5460cca9fc5 |
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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.... | Multiscale-Genomics/mg-process-fastq | tool/macs2.py | Python | apache-2.0 | 24,251 | [
"BWA"
] | 07ab2706d2ff906f13c6e04565affd8403018b44b24ca8b0ef0a9165128c92ed |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fr... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_pl.py | Python | gpl-2.0 | 33,712 | [
"Brian"
] | e714e75d4b04ffa4b1dd302e0b23a1076ed120bf56a43862a36418892ef479b8 |
"""
complete Pade analysis workflow
from E-V fitted data to
the precision data, plots and
histograms
GOAL: to be the one script that is used by
the database web app to be activated in part
on sensibly crossfiltered data
and also on the a complete new set of data
in an object oriented way.
"""
# must be executed within
... | joshgabriel/dft-crossfilter | CompleteApp/benchmark-precision/precision/precisions.py | Python | mit | 53,042 | [
"ASE",
"VASP"
] | 418b7a752cf2c25afcdca0e1e8efff26586e576add8c2aeb62c72f6927a0d7c2 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/vector/vector_x.py | Python | lgpl-2.1 | 622 | [
"MOOSE"
] | 4d2b145ff262d57db57ebd90daedbe0154817edb7d2e51936ec1b825426fbad5 |
"""
Statistics Library
Should eventually contain
- gaussian process regression
- compressed sensing for image reconstruction
- other relevant statistics tools, e.g. bayesian inference tools
- tree sturcture objects for e.g. functional fit propagation
- local crystallography
Submodules
----------
.. autosummary::
... | pycroscopy/pycroscopy | pycroscopy/stats/__init__.py | Python | mit | 419 | [
"Gaussian"
] | 58a67f38a70eeef0dc1cb0d4763d84e1a88451b61ca82b0f2e43a1ae5068be80 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Gary Burton - derived from _HasGalleryBase.py
#
# This program is free software; you can redistribute it and/or modify
# it under t... | Forage/Gramps | gramps/gen/filters/rules/source/_hasrepository.py | Python | gpl-2.0 | 2,676 | [
"Brian"
] | 20f8ad69822fe3de2813496e2c54f14cf477858cee7bc662a2c18583ebb54dfb |
import numpy as np
from dipy.viz import actor, window, widget, fvtk
from dipy.data import fetch_viz_icons, read_viz_icons
import numpy.testing as npt
from dipy.testing.decorators import xvfb_it
@xvfb_it
@npt.dec.skipif(not actor.have_vtk)
@npt.dec.skipif(not actor.have_vtk_colors)
def test_button_and_slider_widgets()... | JohnGriffiths/dipy | dipy/viz/tests/test_fvtk_widgets.py | Python | bsd-3-clause | 5,776 | [
"VTK"
] | 91390223b8bee41a7721604b08ae7d593e28d9550d1da7029573b89f6e3379d0 |
# 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/model/testsuite.py | Python | apache-2.0 | 5,521 | [
"VisIt"
] | 74c12a6e6c4aeb84e3e0078c2d9384cf281713af9055d2a9c6d82bc2d5cfc614 |
"""
Spatial working memory spiking neural circuit model
References:
J.D. Murray et al. Cerebral Cortex 2012
doi: 10.1093/cercor/bhs370
A. Compte, N. Brunel, P. Goldman-Rakic, X.-J. Wang Cerebral Cortex 2000
doi: 10.1093/cercor/10.9.910
Notice that with the Compte parameters, the spontaneous state takes ~10s
to reach... | xjwanglab/book | compte2000/compte2000.py | Python | mit | 13,229 | [
"Brian",
"NEURON"
] | 674064816a603a486d1f8ef75caf71ea0e5f6db605b11e6c71892e90f200f166 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/tensorflow/contrib/factorization/python/ops/gmm.py | Python | mit | 12,252 | [
"Gaussian"
] | 84ea68814ed55e5e3963e49f8ff65049a0a7ba14ed2fa92926ccd2e18c876eee |
#!/usr/bin/env python
# Copyright (c) 2001, Stanford University
# All rights reserved.
#
# See the file LICENSE.txt for information on redistributing this software.
#
# Authors:
# Brian Paul
""" graph.py
This module defines the GraphFrame class which is the top-level window
for creating/editing Chromium graphs.
"""... | alown/chromium | mothership/tools/graph.py | Python | bsd-3-clause | 51,080 | [
"Brian"
] | c85684018da4b864559b5ed5615a53e41889814a14c9a079a7fc721ae05d67ed |
""" Python test discovery, setup and run of test functions. """
import py
import inspect
import sys
import pytest
from _pytest.main import getfslineno
from _pytest.mark import MarkDecorator, MarkInfo
from _pytest.monkeypatch import monkeypatch
from py._code.code import TerminalRepr
import _pytest
cutdir = py.path.loca... | geraldoandradee/pytest | _pytest/python.py | Python | mit | 72,287 | [
"VisIt"
] | 6d42fb21e92950a5ac6ddd06b7b2c316feac95a869f0fafbdff2865806add788 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@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... | tedelhourani/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 42,306 | [
"VisIt"
] | 314654158e80b1151daabb00ffa7b9792cb02c7905c01338659e279a449cb9a0 |
#!/usr/bin/env/ python3
"""
Library of miscellaneous helper functions for Cyclops init/admin tasks.
Functions
---------
- `read_ICs` : Read initial conditions from the Polvani experiments
- `geopotential_transform` : Transform the height field from (u,v,h) to skew-Hermitian (u,v,phi)
- `inv_geopotential_transform` : ... | AGPeddle/Cyclops | source/cyclops_base.py | Python | mit | 7,973 | [
"Gaussian"
] | 2874c687e7bd7bd30170ebb5af0d192c04b9059803f354b86edc69562d9baf33 |
"""
Tests for discussion pages
"""
import datetime
from pytz import UTC
from uuid import uuid4
from nose.plugins.attrib import attr
from .helpers import BaseDiscussionTestCase
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from... | dkarakats/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 44,559 | [
"VisIt"
] | 8525ff37511af5b35615d3fb1d8b86a0e42dc596ef08caf4125f283369a0fdbe |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/metadata | setup.py | Python | apache-2.0 | 5,286 | [
"VisIt"
] | 9b963040e3eca05b622499903712f81d007a134d1455d9a9fd3f8e4c413a6a17 |
# sybase/base.py
# Copyright (C) 2010-2017 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | wildchildyn/autism-website | yanni_env/lib/python3.6/site-packages/sqlalchemy/dialects/sybase/base.py | Python | gpl-3.0 | 28,696 | [
"ASE"
] | 9f9d00aa8cfdeb67fd1cfc0090e8a3bce195fd3e962df0bfcf6deaaa2a603570 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | pwcberry/climate | examples/knmi_to_cru31_full_bias.py | Python | apache-2.0 | 8,082 | [
"NetCDF"
] | 9e5af542641838618c127d161b91933e27f358d4894ef36fcfe57b1a2d3bef78 |
# Copyright (c) 2010-2012 OpenStack Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | tipabu/swift | test/unit/obj/test_diskfile.py | Python | apache-2.0 | 380,728 | [
"VisIt"
] | 0add63bb2c736e43f5a92d9d94fc7841b1dea943e355ea79678a22bc7a17c7e8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | rmfitzpatrick/ansible | lib/ansible/modules/network/lenovo/cnos_factory.py | Python | gpl-3.0 | 5,013 | [
"VisIt"
] | e191f6883fa58fc2685ae246fc1df1c8880b1a8834c6aee7939dcc97fc920efb |
from vectors import Point
from heppy_fcc.particles.tlv.particle import Particle as BaseParticle
from heppy.utils.deltar import deltaR
import math
class PFObject(object):
'''Base class for all particle flow objects (tracks, clusters, etc).
Particle flow objects of different types can be linked together
form... | semkiv/heppy_fcc | fastsim/pfobjects.py | Python | gpl-3.0 | 5,755 | [
"VisIt"
] | 3795901129d511259f8e8a67ba2b87d7c14de54295b1ee9725b89cd9f31ed208 |
"""A simple filter that thresholds on input data.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2010, Enthought, Inc.
# License: BSD Style.
import numpy as np
# Enthought library imports.
from t... | dmsurti/mayavi | mayavi/filters/threshold.py | Python | bsd-3-clause | 10,670 | [
"Mayavi"
] | 7d563d8e74673c2e662fb9843ab99c58b3cfd95330c9ce1eef2e757b97303af7 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/gaussian.py | Python | gpl-3.0 | 12,214 | [
"Gaussian",
"ORCA"
] | ef1bd4e57fa55561db5285ab09d78a0ce3722baac54364a4ff6e84dc3cf3e284 |
# -*- coding: utf-8 -*-
#
# Sphinx-Gallery documentation build configuration file, created by
# sphinx-quickstart on Mon Nov 17 16:01:26 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file... | sphinx-gallery/sphinx-gallery | doc/conf.py | Python | bsd-3-clause | 13,709 | [
"Mayavi"
] | 55762886e114fcaac3f3de762d16d7ca33874cd54fa037656ed9c25f5c19ea5c |
"""Undocumented Module"""
__all__ = ['indent',
'StackTrace', 'traceFunctionCall', 'traceParentCall', 'printThisCall',
'doc', 'adjust', 'difference', 'intersection', 'union',
'sameElements', 'makeList', 'makeTuple', 'list2dict', 'invertDict',
'invertDictLossless', 'uniqueElements', 'disjoint', 'contains',
'replace', '... | matthiascy/panda3d | direct/src/showbase/PythonUtil.py | Python | bsd-3-clause | 94,270 | [
"Gaussian"
] | 314c9fc4f67f23a4166322854a1ccbd1d8bab253d6650d4949351bf3ade36c2e |
#!/usr/bin/env python
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar2QTAgg
import sys
import ephem
from PyQt4 import QtGui, QtCore
sys.path.append('./')
from telescope import *
from measurement imp... | varenius/salsa | Control_program/mapper.py | Python | mit | 40,971 | [
"Gaussian"
] | cd807245dbc4c7dfaa744437a629fd29d5f34b92e1d5b23724dc7cdbe81df7c8 |
from system.core.controller import *
import random
import time
class Ninjas(Controller):
def __init__(self, action):
super(Ninjas, self).__init__(action)
self.load_model('WelcomeModel')
self.db = self._app.db
def index(self):
#session initializers
if not 'gold' in s... | authman/Python201609 | Nguyen_Ken/Assignments/Pylot assignments/ninja_gold/app/controllers/Ninjas.py | Python | mit | 2,449 | [
"CASINO"
] | 25dff96412b59bc7da9aca716ceb989e74d604f2e50ad24da1817c757ea5127d |
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from tqdm import tqdm
class MovementPlanner:
def __init__(self, movement_variance, xlim=(-10, 10), ylim=(-10, 10), n_points=1000):
self.movement_var = movement_varianc... | jessegeerts/GazeVR-analysis | model.py | Python | mit | 3,300 | [
"Gaussian"
] | 8ccc34888ff0754ec67caa6cf2afbbebf40a29d700133fe51387ebd1bd19ec3f |
#-*- coding: utf-8 -*-
#! /usr/bin/env python
'''
#------------------------------------------------------------
filename: lab12_runTCcheckBatchNorm_spiraldata.py
To check Gradient Vanishing problem in
A Multi-Hidden Layers Fully Connected Neural Network.
This script aim to see how the "batch normalizat... | jwkanggist/EveryBodyTensorFlow | lab12_runTFcheckBatchNorm_spiraldata.py | Python | unlicense | 13,993 | [
"NEURON"
] | bb6f8e4e1987ae174de971e30e1d4dfcac3ad9d18a67dd5a13d3753dd4ae1d69 |
import os
import re
import external.cclib as cclib
import logging
from subprocess import Popen, PIPE
import distutils.spawn
from rmgpy.molecule import Molecule
from qmdata import CCLibData
from molecule import QMMolecule
class Mopac:
"""
A base class for all QM calculations that use MOPAC.
Classes s... | nyee/RMG-Py | rmgpy/qm/mopac.py | Python | mit | 13,879 | [
"MOPAC",
"cclib"
] | ed3fb1c9b78e9a840146658229ba3539c51467d6c9cf88da6f54f308b3746c33 |
# Data sources
database(
thermoLibraries = ['primaryThermoLibrary', 'GRI-Mech3.0'],
reactionLibraries = [],
seedMechanisms = [],
kineticsDepositories = ['training'],
kineticsFamilies = 'default',
kineticsEstimator = 'rate rules',
)
# Constraints on generated species
generatedSpeciesConstraints... | comocheng/RMG-Py | examples/rmg/1,3-hexadiene/input.py | Python | mit | 1,891 | [
"MOPAC"
] | fcec653b478e0e3ca6e76919f0031c127d3ce4587dac745b67cf9a83f4c1cf2b |
"""Main Lomb-Scargle Implementation"""
import numpy as np
from .implementations import lombscargle, available_methods
from .implementations.mle import periodic_fit, design_matrix
from . import _statistics
from astropy import units
from astropy.time import Time, TimeDelta
from astropy import units as u
from astropy.ti... | pllim/astropy | astropy/timeseries/periodograms/lombscargle/core.py | Python | bsd-3-clause | 29,161 | [
"Gaussian"
] | 594e77cc167826d021fb04c7263124173ef018052100eec9e87c78f8c8c38f86 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.community.AIX/ZenPacks/community/AIX/modeler/plugins/community/snmp/AIXSWInstalledMap.py | Python | gpl-2.0 | 1,720 | [
"VisIt"
] | 19d358100cc337e5b39d93040b603d2f001aaa676049d97b0995c39042cb0df6 |
#pylint: disable=no-init,invalid-name
from __future__ import (absolute_import, division, print_function)
from mantid.simpleapi import *
from mantid.api import *
from mantid.kernel import *
import math
import numpy
class USANSSimulation(PythonAlgorithm):
def category(self):
return "SANS"
def seeAlso... | ScreamingUdder/mantid | Framework/PythonInterface/plugins/algorithms/USANSSimulation.py | Python | gpl-3.0 | 6,477 | [
"Gaussian"
] | 10a697a88d6e7eb42d2047d5449ca058ec25f18185be396ebb6bfa3a7aa7ae84 |
import os
import textwrap
import unittest
from conans.model.ref import ConanFileReference, PackageReference
from conans.paths import CONANFILE, CONANFILE_TXT
from conans.test.assets.genconanfile import GenConanfile
from conans.test.utils.tools import NO_SETTINGS_PACKAGE_ID, TestClient
class TestPackageInfo(unittest.... | conan-io/conan | conans/test/integration/generators/package_info/package_info_test.py | Python | mit | 26,656 | [
"Galaxy"
] | df85570392650651da553ca8c1990876f4558f045dd8f81c861bb36146383e72 |
'''
Created on Jul 16, 2015
@author: sergio
'''
import numpy as np
import ctypes
import numpy.ctypeslib as npct
import matplotlib.pyplot as plt
import psycopg2
import time
import neurodb.neodb.core
from math import e, pow
from scipy.optimize import leastsq
import neurodb
import random
from sklearn.cluster import KMea... | sergiohr/NeuroDB | test/multip.py | Python | gpl-3.0 | 6,602 | [
"Gaussian"
] | 86291ee64902929e76b89612da1fd945c90626f99b71fd1ed479a198052cdf5b |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.