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import math
import logging
#from fibonacci_heap_mod import Fibonacci_heap
from spat.priority_queue import PriorityQueue
def no_handicap(key):
return 0.0
def identity_projection(key):
return key
class MarkovGraph:
""" Represents a markov chain as a graph of virtual nodes.
A markov chain is a stoch... | eti-p-doray/gis-upir | spat/markov.py | Python | mit | 4,911 | [
"VisIt"
] | b2ca561a0864fb97feb690090f67ef1847156f5015e3cac1e9d0f33c40c8364a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division
import warnings
import numpy as np
import matplotlib.pylab as plt
from pymatgen import Composition
from pymatgen.analysis.phase_diagram import GrandPotentialPhaseDiagram
from p... | nisse3000/pymatgen | pymatgen/analysis/interface_reactions.py | Python | mit | 18,427 | [
"pymatgen"
] | e5ed8a2b9821fe10ad040b022b57106afd82cfb2c262d2a0c2978e9b6cd34457 |
"""
Various bayesian regression
"""
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from ._base import LinearModel, _rescale_data
from ..base import RegressorMixin
from ._base import _deprecate_normalize
from ..utils.extmath imp... | kevin-intel/scikit-learn | sklearn/linear_model/_bayes.py | Python | bsd-3-clause | 26,806 | [
"Gaussian"
] | 62c7c2978b396eb5345ecd829a3a7c26b268c44fef0752ce4a37f79458728050 |
#!/usr/bin/env python3
"""This module contains classes for representing the static, global resources
and paths to them.
Resources are static file such as genomes, indices, but also databases that
are shared read-only by various programs. The following resource types exist
and need to be versioned in the manner descri... | holtgrewe/shellfish | resources.py | Python | bsd-3-clause | 8,670 | [
"BWA"
] | 5f015565ed99744c02c5eaa9fab698d13fdc6851b3b7573d7b5a8e25a2ab3321 |
# -*- coding: utf-8 -*-
"""
Created on Sun May 10 12:39:33 2015
Author: Josef Perktold
License: BSD-3
"""
import warnings
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_equal
from statsmodels.discrete.discrete_model import Poisson, Logit, Probit
from statsmodels.genmod.generalized... | bashtage/statsmodels | statsmodels/base/tests/test_penalized.py | Python | bsd-3-clause | 25,636 | [
"Gaussian"
] | a12d67b050bf694d96ec2be7e81870f3d2a1ccd990bc707e2755965260f51514 |
# coding=utf-8
from collections import namedtuple
from functools import total_ordering
from heapq import heappush, heappop
from itertools import count, zip_longest
INITIAL_START = object()
class SumTuple(tuple):
"""
A handy class for storing priority-costs. Acts just like a regular tuple, but addition
a... | Mumbleskates/mumblecode | src/mumblecode/graphs.py | Python | mit | 10,489 | [
"VisIt"
] | 4aaa2267da023e3f92ae70d7e92be1bd472774a6fdae68f9e42a9da61f5e49fb |
# Copyright 2015 Vince Veselosky and contributors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | veselosky/chephren | chephren/domain.py | Python | apache-2.0 | 16,367 | [
"VisIt"
] | 99b088bc18b4fc093921434fc6fb48b230fae6380480e3fc27a7f456c4f1e06f |
# -*- coding: utf-8 -*-
"""Implements the transformation and optimzation features.
"""
from collections import defaultdict
from ast import *
import copy, sys
from gmpy import mpz
from tasty import state
from tasty.tastyc.bases import (has_parent_node, get_fqnn, add_keyword,
CALL_TYPE_CTOR, CALL_TYPE_METHOD, C... | tastyproject/tasty | tasty/tastyc/transformation.py | Python | gpl-3.0 | 22,923 | [
"VisIt"
] | a7db3fa7f85ce635a49092ef66326e0897e87599cda223fb0c5355af5c559f79 |
import numpy as np
import dolfin
from dolfin import *
from mpi4py import MPI as pyMPI
comm = pyMPI.COMM_WORLD
mpi_comm = MPI.comm_world
#load mesh,boundaries and coefficients from file
mark = {"Internal":0, "wall": 1,"inlet": 2,"outlet": 3 }
#read mesh and boundaries from file
mesh = Mesh()
hdf = HDF5File(mesh.mpi_... | BradHub/SL-SPH | hdg_test/2d/cg_test.py | Python | mit | 2,253 | [
"ParaView"
] | ea71f0cacaca8295eb10193d9822028f36761a556875bcc8058e3a04b20999e0 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | vhosouza/invesalius3 | invesalius/gui/task_navigator.py | Python | gpl-2.0 | 98,487 | [
"VTK"
] | 6a34990255b6b310fe2aa7b5fa0d8c35f83930e03254513a0cb79b1859b6e11e |
#!/usr/bin/python
"""Test of Orca's support for mouseovers."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
sequence.append(KeyComboAction("<Control>Home"))
sequence.append(KeyComboAction("Down"))
sequence.append(utils... | GNOME/orca | test/keystrokes/firefox/mouseover_javascript_alert.py | Python | lgpl-2.1 | 1,409 | [
"ORCA"
] | 3be35de2db8c13f4822f2de3772e52a46b6842ba372ada8430fa4132af38c4d0 |
import ocl
import camvtk
import time
import vtk
if __name__ == "__main__":
print(ocl.version())
myscreen = camvtk.VTKScreen()
stl = camvtk.STLSurf("../stl/demo.stl")
#stl = camvtk.STLSurf("../stl/pycam-textbox.stl")
print("STL surface read")
myscreen.addActor(stl)
stl.SetWirefr... | aewallin/opencamlib | examples/python/pathdropcutter_test_2.py | Python | lgpl-2.1 | 3,664 | [
"VTK"
] | 8162f2dbdd59a98cf5c0942e7582b9a262de1dd124a0588988bad1d9fba87251 |
#!/usr/bin/python -tt
#
# Copyright 2009-2010 Facebook, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | bcwalrus/git-tutorial | src/gitreview/git/repo.py | Python | apache-2.0 | 26,568 | [
"Octopus"
] | fe18e50cdf5a86f9738184362e53c86f7e0a69685dfcd0ca80f4accfae2e4b6b |
#!/usr/bin/env python
# encoding: utf-8
# Default parameters work for formation_of_diffractons/
import numpy as np
import clawpack.petclaw as pyclaw
# Medium structure
medium_type='piecewise-constant'
def qinit(state,A,x0,y0,varx,vary):
r""" Set initial conditions:
Gaussian stress, zero velocities."""
... | ketch/effective_dispersion_RR | numerical_experiments/2D-propagation/quadrants_figure/cz-disp/psystem_lin.py | Python | bsd-2-clause | 10,117 | [
"Gaussian"
] | 15189b6ec1a3dfeecc4b8c6cdc17d53af721285f2132f06c09646e494c1d7484 |
# -*- coding: utf-8 -*-
"""
Created on 25 Jun 2014
@author: Éric Piel
Copyright © 2014-2015 Éric Piel, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License version 2 as published by the Free Software Foundation.
Odem... | delmic/odemis | src/odemis/acq/stream/_static.py | Python | gpl-2.0 | 38,810 | [
"Gaussian"
] | 2a645d1fabba136c42e522cec1bd0202cdebc1ccd7f2a209f2e97b492a91c032 |
# Taken by JXP from github sixtenbe
import numpy as np
#from math import pi, log
import pylab
from scipy import fft, ifft
from scipy.optimize import curve_fit
'''
i = 10000
x = np.linspace(0, 3.5 * pi, i)
y = (0.3*np.sin(x) + np.sin(1.3 * x) + 0.9 * np.sin(4.2 * x) + 0.06 *
np.random.randn(i))
'''
def _datacheck... | profxj/xastropy | xastropy/xutils/peaks.py | Python | bsd-3-clause | 28,307 | [
"TINKER"
] | 6d7b02b8cf0b3ab371e170bcfd2058a98889f58f8c70e55cd9ada1ee68179526 |
from pyscf.gto import Mole
from pyscf.scf import RKS, RHF
from pyscf.tdscf import TDDFT, TDHF
from pyscf.tdscf.proxy import PhysERI, TDProxy, mk_make_canonic, molecular_response, orb2ov
from pyscf.tdscf.common_slow import format_frozen_mol
import numpy
from numpy import testing
import unittest
from test_common import... | gkc1000/pyscf | pyscf/tdscf/test/test_proxy.py | Python | apache-2.0 | 8,490 | [
"PySCF"
] | a832474c300f8114c3a90391d340489272a046e8039dd12cf3557efd03222c74 |
"""
Tests of neo.io.exampleio
"""
import warnings
import unittest
import quantities as pq
import numpy as np
from neo.io.nestio import ColumnIO
from neo.io.nestio import NestIO
from neo.test.iotest.common_io_test import BaseTestIO
class TestNestIO_Analogsignals(BaseTestIO, unittest.TestCase):
ioclass = NestIO... | samuelgarcia/python-neo | neo/test/iotest/test_nestio.py | Python | bsd-3-clause | 29,084 | [
"NEURON"
] | 35200e48348b00381d66958f0bb658955929771c5717fc13ae11739fa04fbec6 |
# Copyright (c) 2004 Robert L. Campbell
from pymol import cmd
import glob
def load_models(files,obj,discrete=0):
"""
load_models <files>, <object>, <discrete=0>
loads multiple files (using filename globbing)
into a single object (e.g. from modelling or NMR).
use discrete=1 if you want to color individual s... | wjurkowski/ppibench | vegas/scripts/load_models.py | Python | apache-2.0 | 615 | [
"PyMOL"
] | 1bc6450710ef15c3d0ae95d64d53b79c7a82e06068b7d3e18deb6bbe2e3d0989 |
# Project - OneClickCut - "To segment 3D ROI, like tumor, leison from given 3D volume"
# Author: Guoqing Bao
# Supervisor: Sidong Liu; Weidong Cai;
# The University of Sydney
# 2017-05-08
#---------------------------------------------------------------------------
# Implement simple paint effect.
# This class used fo... | bobking8/OneClickCut | Segmentor/Marker.py | Python | gpl-3.0 | 15,894 | [
"VTK"
] | 311aa5c7032840e6e318d6f098e8c7a59fc70d7e3f9ff1615dea64b5895014ea |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | ReptarX/erosdb | config/urls.py | Python | bsd-3-clause | 1,276 | [
"VisIt"
] | 2a50883a8778cbe18afe2b99c52468345403099f3d7de9aee65fc95563d91bf3 |
#
# @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 redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/procrouting/dft/hyb_functionals.py | Python | lgpl-3.0 | 16,716 | [
"Psi4"
] | 7d7e094aef0004da98ffc54968d2ee5f72cfd01c229149cbab2d36e1677e8bb9 |
"""Some test functions for bivariate interpolation.
Most of these have been yoinked from ACM TOMS 792.
http://netlib.org/toms/792
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import xrange
import numpy as np
from .triangu... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/delaunay/testfuncs.py | Python | bsd-2-clause | 21,168 | [
"Gaussian"
] | 1efb4ee045f45404b41253a2b6d29547d2d3ea264e1a17c51f39c723c07ee604 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/py-deeptools/package.py | Python | lgpl-2.1 | 2,156 | [
"pysam"
] | 0b0f29650b8e03b5d374828920cad8abab36c7b670049c3fb2659d72d050430b |
import numpy as np
import os
from iri12py import iri_sub as iri12
from iri16py import iri_sub as iri16
from iri16py import read_ig_rz, readapf107
from .constants import DIR_FILE, nan
IONS = ['O+', 'H+', 'HE+', 'O2+', 'NO+']
# Global variable indicating if IRI 2016 has been initialized with the contents
# of the iono... | timduly4/pyglow | src/pyglow/iri.py | Python | mit | 7,646 | [
"Brian"
] | 8fd063450f74a98388825089ba639aac6ebe7f80e625cdb3d7e8fc3d520403fb |
import os, functools, time
import multiprocessing as mp
from multiprocessing.managers import BaseManager
import threading
import numpy as np
#from sklearn import preprocessing
import cv2 as cv
#import imgaug as ia
from imgaug import augmenters as iaa
from swl.machine_learning.data_generator import Data2Generator
from s... | sangwook236/sangwook-library | python/test/language_processing/synth90k_data.py | Python | gpl-2.0 | 44,117 | [
"Gaussian"
] | 3c3b94d9be63b8653bc69691022e979c43dbc5ed265a49b80e80e2273337afb3 |
#!/usr/bin/python
#=============================================================================================
# A module implementing Bayesian analysis of isothermal titration calorimentry (ITC) experiments
#
# Written by John D. Chodera <jchodera@gmail.com>, Pande lab, Stanford, 2008.
#
# Copyright (c) 2008 Stanfo... | choderalab/bayesian-itc | examples/sampl4_notebook/ITC.py | Python | gpl-3.0 | 67,766 | [
"Avogadro"
] | 5592b4a2c5ba99a32644c94df0d3fdadf96dfd517f85041ae124b8d527fa3fd9 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Parsers for XTB output files and directories
"""
import logging
import os
import re
from monty.json import MSONable
from pymatgen.core import Molecule
from pymatgen.io.xyz import XYZ
__author__ = "Alex Epstein"
__copyrigh... | vorwerkc/pymatgen | pymatgen/io/xtb/outputs.py | Python | mit | 7,016 | [
"pymatgen",
"xTB"
] | e7f8cc7abf781ef335f9ea6b45d384ed976d15bf104c26c6235c3efff3349961 |
import discord
from discord.ext import commands
from discord import utils
from cogs.utils.dataIO import fileIO
from cogs.utils.chat_formatting import *
from __main__ import settings, send_cmd_help
import os
import re
import string
import datetime
class BotInfo:
def __init__(self, bot):
self.bot = bot
... | FishyFing/FishBot | cogs/botinfo.py | Python | gpl-3.0 | 6,074 | [
"VisIt"
] | d8afe139da662b2f0d62ef320756c58fa23f6407ac0f22ff0a372ec0428552c6 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Code is originally adapted from MILK: Machine Learning Toolkit
# Copyright (C) 2008-2011, Luis Pedro Coelho <luis@luispedro.org>
# License: MIT. See COPYING.MIT file... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sklearn/tree/tree.py | Python | agpl-3.0 | 27,669 | [
"Brian"
] | ecd10024d4347d15fe50fe69628ad15f0a88f868c77c7572751d2642743c7204 |
#######################################
# Copyright 2019 PMP SA. #
# SPDX-License-Identifier: Apache-2.0 #
#######################################
import pytest
import os
import glob
import tarfile
import tempfile
import shutil
from rpackutils.packinfo import PackInfo
from rpackutils.packinfo import Pack... | sgubianpm/RPackUtils | tests/test_bioconductor.py | Python | gpl-2.0 | 8,932 | [
"Bioconductor"
] | c04c760dbbd62743407d9520631028954d897d9726fc4bf04df435cc27fa9fe3 |
#!/usr/bin/python
#
# Copyright (c) 2012, Psiphon 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 Foundation, either version 3 of the License, or
# (at your option) any later v... | thispc/psiphon | psi_client.py | Python | gpl-3.0 | 17,333 | [
"VisIt"
] | 47bd05d87e9716068d2313f9713408a3cfeb1d4528b0e8e8d077c124a3e02bd3 |
#
# Copyright (C) 2011 EADS France, Fabrice Desclaux <fabrice.desclaux@eads.net>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any late... | mrphrazer/miasm | miasm/expression/expression_helper.py | Python | gpl-2.0 | 20,658 | [
"VisIt"
] | 4f48539e733ff88af8023bf592788a067c39fd1293f0c5a903da8b0aeac3ff39 |
# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
from typing import Tuple
import numpy as np
from ...core.interfaces import IDifferentiable, IModel
from ..kernels.quadrature_kernels import QuadratureKernel
class IBaseGaussianProcess(IModel, IDifferent... | EmuKit/emukit | emukit/quadrature/interfaces/base_gp.py | Python | apache-2.0 | 3,475 | [
"Gaussian"
] | 816b988a31fe2d988f0a84d17d45fec06b98cfaa9f528e70b0ea14add4239d0b |
import numpy as np
import math_utils
import neural_net
# Create some toy data to check your implementations
input_size = 4
hidden_size = 10
num_classes = 3
num_inputs = 5
# The toy model is a 2-layer network: it has one hidden layer and one output
# layer.
def init_toy_model():
model = {}
# Layer 1 has 10 ... | eliben/deep-learning-samples | cs231n/run_nn.py | Python | unlicense | 1,830 | [
"NEURON"
] | edb17eea803d7d5a0e1a80a46a893b81dc90651490d2a4c0d38d4565dc79d95c |
###BAMtoExonBED
#Author Nathan Salomonis - nsalomonis@gmail.com
#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
#to use, co... | nsalomonis/AltAnalyze | import_scripts/BAMtoExonBED.py | Python | apache-2.0 | 24,152 | [
"pysam"
] | 48665df56577b421b76f614cf71be39acfe9d05b5591cef1909b4f9a42967280 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | backmari/moose | python/chigger/graphs/Line.py | Python | lgpl-2.1 | 7,589 | [
"MOOSE",
"VTK"
] | 596c01c4d979186955e01c97f8bc2a32b631b520f76e1a20b7b03ccbac7f3458 |
#!/usr/bin/env python
"""A kernel that creates a new ASCII file with a given size and name.
"""
__author__ = "The ExTASY project <vivek.balasubramanian@rutgers.edu>"
__copyright__ = "Copyright 2015, http://www.extasy-project.org/"
__license__ = "MIT"
from copy import deepcopy
from radical.ensemblemd.exceptions... | radical-cybertools/ExTASY | examples/coam-on-stampede/kernel_defs/tleap.py | Python | mit | 4,161 | [
"Amber",
"NetCDF"
] | 5164009848d0829caf2c20bd1a83d39a186ea32edbeb14982d1ae7f2aa0e5a6a |
"""
End-to-end tests for the main LMS Dashboard (aka, Student Dashboard).
"""
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.dashboard import DashboardPage
from common.test.a... | edx/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard.py | Python | agpl-3.0 | 5,600 | [
"VisIt"
] | 2414dfe07ece384c128ddc2d334052ea44af808427d6ce8ecf6f2fa5e9a17d42 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkCylinderSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkCylinderSource.py | Python | bsd-3-clause | 475 | [
"VTK"
] | a066600d3b482c64da5df0ad0b69e9214658253699346dc1b4a0214538659d39 |
#* 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/licenses/lgpl-2.1.html
import os
i... | nuclear-wizard/moose | python/MooseDocs/extensions/listing.py | Python | lgpl-2.1 | 9,231 | [
"MOOSE"
] | ad9e8cb84b4c577f7aa6b7c7fb07dac0e70f20828cc8c128bb5f04bb7bd7ce12 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/runners/lmtp/server.py | Python | lgpl-3.0 | 900 | [
"VisIt"
] | ebc60391813c469d48e2d34048182025ffa84f4f09f1fa7ac5657acc709707b8 |
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao import mf, conv_yzx2xyz_c
from pyscf import gto, scf as scf_gto
mol = gto.M( verbose = 1,
atom = '''
H 0 0 0
H 0 0.757 0.587''', basis = 'cc-pvdz',)
conv = conv_yzx2xyz_c(m... | gkc1000/pyscf | pyscf/nao/test/test_0047_dens_elec_gto2nao.py | Python | apache-2.0 | 902 | [
"PySCF"
] | c5b74a5c8d103aa754823a051e697a69e6dbb32eeb06ed6efed0567f6ec25f8b |
import mapy
from mapy import FEM
from vtk import *
from random import random
def randomrgb():
r = random() * 255
g = random() * 255
b = random() * 255
return [r, g, b]
class FEMView(FEM):
def __init__(self, model):
FEM.__init__(self)
self.points = vtkPoints()
x1min = 1000000.... | saullocastro/mapy | mapy/renderer/__init__.py | Python | bsd-2-clause | 3,848 | [
"VTK"
] | 2c3d0f5bd58305eb8ed7a433bfeabd347b1a0554f120e066ebceab53af210eac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#################################################
# insiliChem OpenMM launcher #
# --------------------------------------------- #
# By Jaime RGP <jaime@insilichem.com> @ 2016 #
#################################################
import sys as _sys
imp... | insilichem/ommprotocol | ommprotocol/__init__.py | Python | lgpl-3.0 | 2,487 | [
"OpenMM"
] | 06b61e91fc32152b1fca386019554e1cd521fa2e795cd9b484582abdd0eba4e3 |
# Copyright (C) 2012,2013,2016
# 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... | fedepad/espressopp | src/interaction/Interaction.py | Python | gpl-3.0 | 3,181 | [
"ESPResSo"
] | 42bc37eb5b1b956522441323ffd0bb461be2a3a1f63d5b70dd354f281be1e13c |
"""
Tests for creating bundles/archives of formatted data
"""
import os
import zipfile
import tarfile
import pytest
import basis_set_exchange as bse
from .common_testvars import fake_data_dir
_bundle_types = bse.bundle.get_archive_types()
_bundle_exts = [v['extension'] for v in _bundle_types.values()]
def _extract... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/tests/test_bundle.py | Python | bsd-3-clause | 3,081 | [
"NWChem",
"Psi4"
] | ea71e65e9125a0bf2d5f2171d4a7e376ebec0ec5b683bb0b53d43b109749c459 |
import os.path
from urllib import urlretrieve
url = 'http://wiki.fysik.dtu.dk/ase-files/'
def setup(app):
pass
for file in ['ase/ag.png',
'ase/dft/water_divide_surf.png',
'ase/ase-talk.pdf']:
if os.path.isfile(file):
continue
urlretrieve(url + os.path.basename(file)... | askhl/ase | doc/images.py | Python | gpl-2.0 | 328 | [
"ASE"
] | 7a17e98f7662a441acca1c8918adb705dc5f349adf349677ce9f7bc4b0ab7f7f |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/area_codes/time_window/hmm_crossvalidation_area_400ms.py | Python | mit | 16,114 | [
"Gaussian",
"Mayavi"
] | 9a5bb30fb09032d5e9a28ec3b640723da8e3addd6a68f0b7fa93d9d84d2ac150 |
#
# @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 redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/diatomic.py | Python | lgpl-3.0 | 11,372 | [
"Psi4"
] | 4622320e3df238cd2717b88123f8a5efe820f0e167aecc2a9edfa63af59df686 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Miyamoto! Level Editor - New Super Mario Bros. U Level Editor
# Copyright (C) 2009-2021 Treeki, Tempus, angelsl, JasonP27, Kinnay,
# MalStar1000, RoadrunnerWMC, MrRean, Grop, AboodXD, Gota7, John10v10,
# mrbengtsson
# This file is part of Miyamoto!.
# Miyamoto! is fre... | aboood40091/Miyamoto | sprites.py | Python | gpl-3.0 | 385,594 | [
"CRYSTAL"
] | c406127cb72b3d3d6c4608386ad1fa4e3ddf8800edb188e6b5e7c95c8fad49de |
class BrowserHistory(object):
def __init__(self, homepage):
"""
:type homepage: str
"""
self.hindex = 0
self.history = [homepage]
def visit(self, url):
"""
:type url: str
:rtype: None
"""
self.history[:] = self.history[:self.hind... | fy0/my-leetcode | 1472.design-browser-history/main.py | Python | apache-2.0 | 783 | [
"VisIt"
] | e35b8af3717be4d04c4a331198f19eb2c5b5bed807dfec0f74b5531f8f384116 |
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Version 2.0 (the "License")... | PeterLauris/aifh | vol2/vol2-python-examples/lib/aifh/normalize.py | Python | apache-2.0 | 8,702 | [
"VisIt"
] | 599f40ed6d5fa9d1c598e21f41a39c8949443a1d92902e469405f112eee5d0ee |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2010 Brian G. Matherly
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published b... | sam-m888/gprime | gprime/display/name.py | Python | gpl-2.0 | 44,810 | [
"Brian"
] | 3e64a04b6a1001570e212aa74f8e6bb57301ab6a93145523ed1f4e0813b34d12 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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... | CDSherrill/psi4 | psi4/share/psi4/basis/primitives/dunning_prepend_and_checknew.py | Python | lgpl-3.0 | 2,192 | [
"Molpro",
"Psi4"
] | ab21ab4ada44cba039da6ea5f7b8044a7f1c71e1a85962d72786db88853dbace |
""" ProxyRepository class is a front-end to the proxy repository Database
"""
__RCSID__ = "$Id$"
import time
import random
import types
import hashlib
import urllib
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Security.X5... | arrabito/DIRAC | FrameworkSystem/DB/ProxyDB.py | Python | gpl-3.0 | 46,936 | [
"DIRAC"
] | 98a07342f0e0f33548a33c0a79d186e49017b5d591af1f7d0e9d96da57caff18 |
# coding: utf-8
# # Convert OOI Parsed JSON to NetCDF file
# using CF-1.6, Discrete Sampling Geometry (DSG) conventions, **`featureType=timeSeries`**
# In[2]:
get_ipython().magic('matplotlib inline')
import json
import pandas as pd
import numpy as np
from pyaxiom.netcdf.sensors import TimeSeries
# In[6]:
infile... | rsignell-usgs/notebook | OOI/from_ooi_json.py | Python | mit | 2,291 | [
"NetCDF"
] | 6e18aff6fcae56770a0cd8f5a8973b689d8f261a367a2658824467c102de7c6d |
# coding=utf-8
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | aisk/grumpy | compiler/block_test.py | Python | apache-2.0 | 10,677 | [
"VisIt"
] | b585f841ae2fdf4f21b97e9f0dd17295de7336f5016c803a4d55237621b232a9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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 redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 161,069 | [
"Psi4"
] | 99802b1ce8e559c469071550d7e7ea80651a0bf6330988b313cd1b9d10d0a472 |
from pygments.lexer import RegexLexer, words, include, default
from pygments.token import *
LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
"balance", "bond_coeff", "bond_style", "bond_write", "boundary", "box",
"clear", "comm_modify", "comm_style",
"compute_modify", "create_atoms", "crea... | jeremiahyan/lammps | doc/utils/sphinx-config/LAMMPSLexer.py | Python | gpl-2.0 | 5,042 | [
"LAMMPS"
] | 856e15bd0f83a7d4751fb7ca7c454081b256eb2fb3bb45cd3e6d1534b8682acc |
#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import mimetypes
import time
from flask import Blueprint
from flask import url_for
from flask import request
from flask import session
from flask i... | migeruhito/sagenb | sagewui/blueprints/base.py | Python | gpl-3.0 | 8,392 | [
"Jmol"
] | 6e5937962472d8b45ef480077712f5b71ee30c6174fa2e2d80dde71b7660c5ce |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | brain-research/deep-molecular-massspec | parse_sdf_utils_test.py | Python | apache-2.0 | 28,886 | [
"RDKit"
] | 64986260e5cf609ccafc355be1989148bd818dde25ddfc9a2dd3c0cdf652a93c |
import numpy as np
from astropy.io import fits,ascii
import matplotlib.pyplot as plt
from astropy.table import Table
from astroquery.simbad import Simbad
from astropy.coordinates import SkyCoord
import astropy.constants as c
import astropy.units as u
import os
# TODO: Work masks into resample method.
# TODO: Change ... | jchowk/pyND | pyND/gbt/GBTspec.py | Python | gpl-3.0 | 15,210 | [
"Gaussian"
] | be12d5a94baa539eca67a4fb8c72b2c39f7f5eb3a5a2002234425f1efde6e565 |
#!/home/ehermes/local/bin/python
import sys
import os
import commands
import math
'''
This program takes, as input, a generic template file, and creates
input files using geometries from all .xyz files that are
located in the pwd and match a user-identified prefix.
File prefix is user specified. Template file should... | mvanvleet/workflow-for-force-fields | scripts/create_molpro_files_from_xyz.py | Python | gpl-3.0 | 3,561 | [
"Molpro"
] | f34abd87cb891af65e69f89d02f9d0cd9e9b99c1f35499f5dd2c3caec371afe4 |
import nipype.interfaces.io as nio # Data i/o
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.camino as camino
import nipype.interfaces.fsl as fsl
import nipype.interfaces.camino2trackvis as cam2trk
import nipype.in... | JohnGriffiths/nipype | nipype/workflows/dmri/camino/connectivity_mapping.py | Python | bsd-3-clause | 25,076 | [
"DIRAC",
"ParaView",
"VTK"
] | d8072642b88ef32161366c12a8f98b67d89ac84ee734ddbbed83e8e614c845d3 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from contextlib import contextmanager
from bok_choy.web_app_test import WebAppTest
from datetime import datetime
from nose.plugins.attrib import attr
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptan... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 35,347 | [
"VisIt"
] | 0095c27eb08dc9cbd89da4eb4a3e1a340bd227127ddb08a82d6d73d562364892 |
# coding: utf8
"""Streamlink extracts streams from various services.
The main compontent of Streamlink is a command-line utility that
launches the streams in a video player.
An API is also provided that allows direct access to stream data.
Full documentation is available at https://streamlink.github.io.
"""
__tit... | ethanhlc/streamlink | src/streamlink/__init__.py | Python | bsd-2-clause | 2,124 | [
"Brian"
] | e588a41319d0dc36b41895d1708288857930f1650c8d2c021ad9e7eb19d5254b |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
#####... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/basak.py | Python | bsd-3-clause | 14,559 | [
"RDKit"
] | 76d79a767bf25d3dfc47ed0d7176d5d9d6bfb754422bffcd791af3242c371fc5 |
"""Galaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import tempfile
import uuid
from . import (
CloudProvider,
CloudEnvironment,
CloudEnvironmentConfig,
)
from ..util import (
find_executable,
... | j-carl/ansible | test/lib/ansible_test/_internal/cloud/galaxy.py | Python | gpl-3.0 | 7,757 | [
"Galaxy"
] | 9e8e2dd8d444c2b1cb79adb655b6e00633c8b4b428a0dd1e9ec61f054cb274f5 |
#!/usr/bin/env python
"""Lots of training- and classification-related utilities, written (mostly) by Neeraj Kumar.
Licensed under the 3-clause BSD License:
Copyright (c) 2011, Neeraj Kumar (neerajkumar.org)
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are perm... | neeraj-kumar/nkpylib | trainutils.py | Python | bsd-3-clause | 77,102 | [
"Gaussian"
] | bf9c554855905958487d1c81c20f38f29adb3a2aa8baaec2758374e7e223513d |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import math
import sys
import warnings
from scipy.lib.six import callable, string_types, get_method_function
from scipy.lib.six import exec_
from sc... | kmspriyatham/symath | scipy/scipy/stats/distributions.py | Python | apache-2.0 | 232,477 | [
"Gaussian"
] | 596ddfd2d6645fc54cdac67fb8f3721886eac9caab3daa3c4ee070b1c2ce8cb9 |
"""
Function to convert xyz coordinates to pdb
"""
from simtk.openmm.app import pdbfile as openmm_pdb
from simtk.openmm import unit as openmm_unit
from simtk.unit import angstrom as openmm_angstrom
__all__ = ["coords2pdb"]
def coords2pdb(coords, top, pdbfname):
"""
coords = 3*N x 1 numpy array
top ... | js850/PyGMIN | pygmin/amber/coords2pdb.py | Python | gpl-3.0 | 1,407 | [
"OpenMM",
"PyMOL"
] | d92c7f5a896745822a21113a47ffcda7119c0c8575f29ab775e4c62a59749b8f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrappers for ABINIT main executables"""
from __future__ import unicode_literals, division, print_function
import os
import numpy as np
from monty.string import list_strings
from six.moves import map, cStrin... | czhengsci/pymatgen | pymatgen/io/abinit/wrappers.py | Python | mit | 13,729 | [
"ABINIT",
"pymatgen"
] | a75fa0c5bf02e574a7dcde9b5d3b7fd7ef69a9532e8917c70650630f3e46ed4b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2018 David Arroyo Menéndez
# Author: David Arroyo Menéndez <davidam@gnu.org>
# Maintainer: David Arroyo Menéndez <davidam@gnu.org>
# This file is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | davidam/python-examples | scikit/scikit-naivebayes.py | Python | gpl-3.0 | 2,467 | [
"Gaussian"
] | 8fe27ff3e70074b1c1fefa53dcaee01379a05e9403e2b22fa0e8a2ca7dcb1027 |
#!/usr/bin/env python
import urllib2,urllib,simplejson,sys,httplib,json,pickle,psycopg2,os,traceback,re,subprocess,time
from mwapy.ephem_utils import GPSseconds_now
from datetime import datetime
import numpy as np
n_d = 2
update_d_all=False
fusionname='/nfs/blank/h4215/aaronew/MWA_Tools/eorlive/FConn.p'
client_id='105... | ryandougherty/mwa-capstone | MWA_Tools/eorlive/add_obs_data.py | Python | gpl-2.0 | 24,125 | [
"Bowtie",
"VisIt"
] | fb87d58628c1f721e5c31fe14025fdd48514024849b1ea4cdc73697e57ad65b0 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_job_service.py | Python | apache-2.0 | 358,754 | [
"Octopus"
] | 059740a0b7f36883dcb0f0df0525cc414c24aca4ab21d08a55e655686f934c84 |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c216/Generate216Centreline.py | Python | gpl-2.0 | 993 | [
"VTK"
] | ca4a67290ff0d325fd6009cd627d0abd25701336f1141141dc82448e9185e131 |
#!/usr/bin/env python
import vtk
def main():
# Create the first graph
g0 = vtk.vtkMutableUndirectedGraph()
v1 = g0.AddVertex()
v2 = g0.AddVertex()
v3 = g0.AddVertex()
g0.AddEdge(v1, v2)
g0.AddEdge(v2, v3)
g0.AddEdge(v1, v3)
# Create points
points = vtk.vtkPoints()
... | lorensen/VTKExamples | src/Python/Graphs/SideBySideGraphs.py | Python | apache-2.0 | 2,048 | [
"VTK"
] | f1ffb99cadcc0e56762638fbc25b98ff371f6608c2d0ceb80f19c6fa11f863cb |
from numpy import *
from numpy.random import *
from plotting.plot_images import *
from plotting.myplot import *
from plotting.covariance_ellipse import *
from spikes.spikes import *
import matplotlib.image as img
import matplotlib.cm as cm
import matplotlib.gridspec as gridspec
def new_g_pairs(make):
# make: make i... | zsomko/visualcortex | python/spikes/poster.py | Python | gpl-2.0 | 45,824 | [
"Gaussian",
"NEURON"
] | 9665cb084285ce00272052cb0cf7eed442209e9b2282f35081f78bae0828a0e2 |
# 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 the G... | kkreis/espressopp | src/analysis/VelocityAutocorrelation.py | Python | gpl-3.0 | 1,836 | [
"ESPResSo"
] | d2f412418251452f797a8d388bc6be46db42f46314ad6c596ff19e70eaaa4128 |
import numpy as np
def hello(name = 'no name'):
"""
name is welcome by saying hello
input: name - the welcome name
"""
print('Hello {name}!'.format(**locals()))
print('2015-3-2, 2:45pm')
def check_mol_similarity():
from rdkit import Chem
from rdkit import DataStructs
from rdk... | jskDr/jamespy | jlib.py | Python | mit | 5,262 | [
"RDKit"
] | 247e6da63639f7ba25be979faa690d0ed3850cd5a18805ee5035c0b26b58d806 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_g2gtools
----------------------------------
Tests for `g2gtools` module.
"""
import unittest
# import os
# import shutil
# import pysam
# from . import bamsam, chain
class TestG2gtools(unittest.TestCase):
def setUp(self):
# self.path = os.path.rea... | churchill-lab/g2gtools | tests/test_g2gtools.py | Python | mit | 1,771 | [
"pysam"
] | dedcfb5128856ffda66ef70f0eff15eb178377865324c237eb7dac4a34b75a8f |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/stats/distance/_bioenv.py | Python | bsd-3-clause | 9,911 | [
"scikit-bio"
] | baa6bb1ea55a7153b91cb0296f08ab652d087bf92c8ae4f79776bb4853bfb37f |
import inspect
import warnings
from functools import partial
from itertools import chain, repeat
from collections import defaultdict
from collections.abc import Sequence, Mapping
from . import query as hiku_query
from .graph import Link, Maybe, One, Many, Nothing, Field
from .result import Proxy, Index, ROOT, Referen... | vmagamedov/hiku | hiku/engine.py | Python | bsd-3-clause | 14,304 | [
"VisIt"
] | a8e9d985929b89033aa5f8aec466853b6ba227685fc3c3de3cbd8a4e4e9d9aa6 |
# data file for refs that can be migrated into a plain json, first of merges
# of development from the developmental notebook
# from periodic table.com the first google hit for all comparitive data
expt_ref= {'Ag':{'a0':4.0853 ,
'B':100 ,
'dB':5.87,
'elec': 11 },
... | joshgabriel/dft-crossfilter | benchmark-view/refs.py | Python | mit | 4,631 | [
"VASP",
"WIEN2k"
] | 2f0af55d4adc619ca7bc6887f4809244ce9215d9c734330d40fe4b7be86ab2ca |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q
import pytz
import logging
import smtplib
impor... | kamalx/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 89,356 | [
"VisIt"
] | 24249e19dd7c711281a9cf9eb49fe7330dc709413d0395d25049dd1a25cc9646 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
"""
import time
from datetime import datetime, timedelta
from textwrap import dedent
import ddt
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import ... | cpennington/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 48,187 | [
"VisIt"
] | a81ff468dd94d2454a6f64d5c220cabfc6e73ae85282af62b440b7ac37ff5c5a |
from pele.amber import amberSystem
import playground.group_rotation.group_rotation as group_rotation
import pele.amber.read_amber as read_amber
import time
# create new amber system
# It turns out that these are the only names that we can use, since we rely on
# countatoms.f90 from AMBGMIN to determine the number o... | kjs73/pele | playground/amber/driverr.py | Python | gpl-3.0 | 1,949 | [
"Amber",
"OpenMM"
] | 842fa6b86a1b72819a81f19943b44f4df40bfbd0db887b999fbbecca228d33e7 |
from __future__ import print_function
"""
Test systems for perses automated design.
Examples
--------
Alanine dipeptide in various environments (vacuum, implicit, explicit):
>>> from perses.tests.testsystems import AlaninDipeptideSAMS
>>> testsystem = AlanineDipeptideTestSystem()
>>> system_generator = testsystem.sy... | choderalab/perses | perses/tests/testsystems.py | Python | mit | 117,794 | [
"OpenMM"
] | 5726262e311e29b491ba1a2beb99f3eea74475e280b761d5a0340575b91e19e1 |
# Copyright: (c) 2013, James Cammarata <jcammarata@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)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | Dhivyap/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 59,135 | [
"Galaxy"
] | 505cf2148713a60c5f91ff911330494f588ff48f992625c10c725f0150c988f3 |
import random
import colorsys
import numpy as np
from itertools import izip_longest
def get_radial_img_data(width, height):
return get_data(width, height, gradient(RADIAL(0.5, 0.5), NO_NOISE,
[(1.0, (0xDD, 0xDD, 0xDD), (0x10, 0x12, 0x13)),]))
def get_gradient_img_data(width, height):
return get_data(... | caglar/Arcade-Universe | arcade_universe/gradient_textures.py | Python | bsd-3-clause | 2,875 | [
"Gaussian"
] | 37a4e949312785d29a4fae47abb1d35fa5f52ae3de9ff35f53e4f864573018a2 |
"""
pylearn2 Wrapper script
Author: Seyed Hamidreza Mohammadi
Date: 05/13/2014
Contains:
RegularAutoencoder
DenoisingAutoencoder
ContractiveAutoencoer
HigherOrderContractiveAutoencoer
DeepGeneralAutoencoder
MLP (Multilayer Perceptron)
"""
from abc import ABCMeta, abstractmethod
import copy
import pickle... | shamidreza/pylearn2_wrapper | pylearn2_wrapper.py | Python | gpl-2.0 | 24,473 | [
"Gaussian"
] | 1a7fdc4e5353bdab7a668f09a8c5f489f494389cdb4506d62f21c46d2c7a2fdb |
import datetime
import os
from django.conf import settings
import pymongo
import pysam
import sys
import gzip
import itertools
from collections import defaultdict
from xbrowse import Variant
from xbrowse import genomeloc
from vep_annotations import HackedVEPAnnotator
from population_frequency_store import PopulationFr... | macarthur-lab/xbrowse | xbrowse/annotation/annotator.py | Python | agpl-3.0 | 15,967 | [
"pysam"
] | f5cd282377022f1e67500fd0f962c6b57d7ae77c45bcfad40cfa01fa53ebddbd |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/rotational_gtensor/test/test_rhf.py | Python | apache-2.0 | 1,370 | [
"PySCF"
] | 5559b36c08e9c2de2f460dba8d363bae4ceac30ab5b2cc89ea8ebf25c489b67b |
from pylab import *
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cbook as cbook
import random
import time
from scipy.misc import imread
from scipy.misc import imresize
import matplotlib.image as mpimg
import os
os.chdir('C:/Users/Ramaneek/SkyDrive/Documents/University/Third Year/CSC320/project ... | RamaneekGill/CSC320-Winter-2014 | project 1/p1.py | Python | gpl-2.0 | 6,850 | [
"Gaussian"
] | bf622b889c84a76693122d8d2333849e27a242d37b658593c115e822156e25e6 |
from Bio import SeqIO
import glob
##########################################################################################
## Concatenates alignments from multiple fasta files into a single new file.
##
## Expects a directory of alignments in fasta format, with each individual sequence
## being named exact... | lcoghill/Utilities | concatenateFasta.py | Python | bsd-3-clause | 1,675 | [
"Biopython"
] | 183de631b01e6cb5d2386818a97f70f9bfba3ced5bcf52de162671cf082fd7e7 |
'''
Created on 13 Mar 2014
@author: maxz
'''
import unittest, itertools
#import cPickle as pickle
import pickle
import numpy as np
from GPy.core.parameterization.index_operations import ParameterIndexOperations,\
ParameterIndexOperationsView
import tempfile
from GPy.core.parameterization.param import Param
from GP... | ptonner/GPy | GPy/testing/pickle_tests.py | Python | bsd-3-clause | 9,340 | [
"Gaussian"
] | 038f42348c0f41b06a4b7276b6015d14dcdcb4828b6f8a7f4f83474c908bec9d |
#!/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... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_set_token.py | Python | gpl-3.0 | 6,797 | [
"DIRAC"
] | 99cbf5a454fc8407a9b6e4d46da678f999ab9fe0d27648b9794283551dce2659 |
import os
import pytest
import UWG
import math
class TestUWG(object):
"""Test for UWG.py
Naming: Test prefixed test classes (without an __init__ method)
for test autodetection by pytest
"""
DIR_UP_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
DIR_EPW_PATH = os.path.join... | saeranv/UWG_Python | tests/test_UWG.py | Python | gpl-3.0 | 10,402 | [
"EPW"
] | 03a8b6043d7d881ba9ff7e17573559cdd440ff2eb6a53b6cbe6486f861de3b96 |
import numpy as np
import matplotlib.pyplot as plt
from time import time
def converged_mixture_model(y, model_class, n_components, K_seq=3,
metric_function=None, break_when_breaking=True, **kwargs):
"""
Run a series of Gaussian mixture models with an increasing number of K
components.
"""
... | andycasey/snob | articles/chemical-tagging-gmm/experiments/slf-clustering-fake-ocs/utils.py | Python | mit | 2,926 | [
"Gaussian"
] | 28f11ad0d54b9ce64c78307d96ff0cf75869d46b8392ffa6a13f59d39aca824d |
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