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#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2011'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Contains class for common routines for loading all CANON data
Mike McCann
MBARI 22 April 2012
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
... | stoqs/stoqs | stoqs/loaders/IOOS/__init__.py | Python | gpl-3.0 | 4,853 | [
"NetCDF"
] | 098b8eb69e101ad323dc892d8abc7bf75d14bb99e0dd9800ae49bb21cd9745a5 |
# This work is licensed under the Creative Commons Attribution 4.0 International License.
# To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
# author : Morad Edwar
# license : Creative Commons
# version : 1.0
# email : me@morad-edwar.com
# status : Beta
import requests
from lxml import... | Morxander/pythonsitemap | sitemap.py | Python | cc0-1.0 | 2,527 | [
"VisIt"
] | 351947c991a0ab4707a3f4dd18b1dd3315d1b287028ef452433401a2876f5a90 |
#
# 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... | commial/miasm | miasm/expression/expression.py | Python | gpl-2.0 | 61,740 | [
"VisIt"
] | 41fd1c53bf10bb58245460306c63fd43de85aa7402cd6d05d4cf3c98d4fec7fd |
"""DIRAC RPC Client utilities."""
import logging
from contextlib import contextmanager
import rpyc
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
@contextmanager
def dirac_api_client(host="localhost", port=18861):
"""RPC DIRAC API client context."""
conn = rpyc.connect(host, port, confi... | alexanderrichards/LZProduction | lzproduction/rpc/DiracRPCClient.py | Python | mit | 2,208 | [
"DIRAC"
] | d453f2c039d94fea91338fe409e4733a53537a2c4766a715941e2584d649698c |
# Copyright (c) 2018 PaddlePaddle 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 appli... | reyoung/Paddle | python/paddle/fluid/layers/nn.py | Python | apache-2.0 | 290,420 | [
"NEURON"
] | 615151ae99a5b6d6af12f46b357aa19cf58cdc0bf1850bbb62ecadfa73dd65b4 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/orca/learn/mpi/mpi_estimator.py | Python | apache-2.0 | 16,518 | [
"ORCA"
] | 16b10cc3e8f4efcb6b353c647e3e11df89e23eeff22a3d2110026153d06230d8 |
# Copyright 2020, The TensorFlow Federated Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/federated | tensorflow_federated/python/aggregators/differential_privacy.py | Python | apache-2.0 | 17,313 | [
"Gaussian"
] | d883e2d03daf6b65dd908cafa1590dd2e8fcd307618978438ac99e50bd023a7f |
#!/usr/bin/env python
"""
Copyright (c) 2006-2013 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
class PRIORITY:
LOWEST = -100
LOWER = -50
LOW = -10
NORMAL = 0
HIGH = 10
HIGHER = 50
HIGHEST = 100
class SORT_ORDER:
FIRST = 0
SECOND = 1
... | aron-bordin/Tyrant-Sql | SQL_Map/lib/core/enums.py | Python | gpl-3.0 | 8,910 | [
"Galaxy"
] | 6677e639ce7d08dec3bb317f342a153e1d8233fad9252eaf303a0df77c409df6 |
#!/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/range/minmax.py | Python | lgpl-2.1 | 826 | [
"MOOSE"
] | f3a46466491c6417c62180839dc2f86fb72da2428014433a6df8dbe4ae4abc68 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os
from xml.dom import minidom
from zeroinstall.injector import namespaces
from __main__ import die
mydir = os.path.dirname(__file__)
def get_choice(msg, options):
pri... | pombredanne/0template | create.py | Python | lgpl-2.1 | 2,315 | [
"VisIt"
] | 0afca9ba468982ab05b0c87310ef5748bb71fa623fc0247232ef5eeb49018ca5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Jerome Rapinat, B. Malengier
# 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 ... | pmghalvorsen/gramps_branch | gramps/plugins/quickview/lineage.py | Python | gpl-2.0 | 8,542 | [
"Brian"
] | 5efc13966550b4131297886c1718bf3cac0d0f7510e0539d824aa558e23eda8a |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2013 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 yo... | jmartinm/invenio | modules/docextract/lib/refextract_regression_tests.py | Python | gpl-2.0 | 127,271 | [
"DIRAC"
] | dbf8df8f4d66cccb5d44a15f479055befb33d0a172d2d424727ff5e27f03b1b2 |
# -*- coding: utf-8 -*-
#
# This file is part of Harvesting Kit.
# Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021 CERN.
#
# Harvesting Kit 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 ... | inspirehep/harvesting-kit | harvestingkit/elsevier_package.py | Python | gpl-2.0 | 50,664 | [
"VisIt"
] | b83f2343c4c4aecdcccc8f83e3618c55802fc592543f12fef56e9daa5329fe86 |
#!/usr/bin/env python
man_page_text = """
Usage (example):
postprocess_coeffs.py ttree_assignments.txt < file.template > file_new.template
Moltemplate users would like to be able to use commands with wildcards like:
bond_coeff @bond:*/A/* harmonic 533.7 120.0
pair_coeff @atom:A* @atom:B* lj/cut 0.35 2.7
as short... | quang-ha/lammps | tools/moltemplate/moltemplate/postprocess_coeffs.py | Python | gpl-2.0 | 12,657 | [
"LAMMPS"
] | eb7fd7f12a70504de67dd1c357e50057335dfacee5934d7b93819b25c1b6d6d9 |
# -*- coding: utf-8 -*-
import os
import json
import posixpath
from seaserv import seafile_api
from django.urls import reverse
from seahub.test_utils import BaseTestCase
from seahub.utils import check_filename_with_rename
from seahub.utils.file_revisions import get_all_file_revisions
from tests.common.utils import ... | miurahr/seahub | tests/api/endpoints/test_file_view.py | Python | apache-2.0 | 25,173 | [
"VisIt"
] | 2a214384d4620f4a97b3a305e720f3e5a623e123ce33b37ddc70ea28d11a041a |
import copy
import arybo.lib.mba_exprs as EX
class CachePass(object):
def __init__(self):
self.__cache = {}
def visit_wrapper(self, e, cb):
ret = self.__cache.get(id(e), None)
if ret is not None:
return ret
ret = cb(e)
self.__cache[id(e)] = ret
retur... | quarkslab/arybo | arybo/lib/exprs_passes.py | Python | bsd-3-clause | 1,607 | [
"VisIt"
] | 98273972d6bb68c4344f6631577bb96aabf737bd39f5be1a34483ae2cd32d704 |
# Copyright (c) 2001, Stanford University
# All rights reserved.
#
# See the file LICENSE.txt for information on redistributing this software.
#
# Authors:
# Brian Paul
"""The SPUDialog class builds a dialog with a set of options specified by
the caller. Options can be boolean, integer, float or string.
"""
impor... | excid3/chromium | mothership/tools/spudialog.py | Python | bsd-3-clause | 9,499 | [
"Brian"
] | 2306dc4831bb761226dcef495e3247f8b21c961b639a473d7780229959331fe1 |
#!/usr/bin/env python3
"""
Wurstmineberg: All The Items
"""
import sys
#sys.path.append('/opt/py')
import bottle
import contextlib
import json
import pathlib
import re
import sys
bottle.debug()
#try:
#import uwsgi
#is_dev = uwsgi.opt['is_dev'] == 'true' or uwsgi.opt['is_dev'] == b'true'
#except:
#is_... | wurstmineberg/alltheitems.wurstmineberg.de | alltheitems/__main__.py | Python | mit | 12,447 | [
"VisIt"
] | 58d8767a374f78c2528b46a914573f2435af57d3b5524d522f1f8d93b43800d3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Emacs: treat this as -*- python -*-
from __future__ import print_function
from optparse import OptionParser
parser = OptionParser(usage='%prog [options] output_prefix.\nExample of call:\n'+
'python %prog --dir=. --pattern="b256H2O_120_04x04m64.grid... | marcindulak/gpaw-on-aws | benchmark/scaling.py | Python | bsd-2-clause | 8,611 | [
"GPAW"
] | b815cea2d216ecb74a00ff3057f36cca061280f08252d31a2fbe16d754172c99 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/l10n/l10n.py | Python | gpl-2.0 | 1,931 | [
"VisIt"
] | 54cdbe676505dcec117dd43abed22b115775cfd57e2fa1fcda9290090d33710e |
# Curves force analysis software
# JWA (c)2009
# Analyse force curves
import numpy as np
import scipy.signal.signaltools as signaltools
import mlpy
import stats
import time
def find_peaks_wavelet(x,y,gap_thresh=5,window=10,ridge_thresh=10,snr_thresh=0.0,peak_thresh=0.0,scaleCutoff=(4.0,32.0),order=4,verbose=False):
... | jarmond/Curves | curves/analyse.py | Python | gpl-3.0 | 21,522 | [
"Gaussian"
] | ff831879522d282934da8af88b466a9fd08244709afe9b025e84411d6df58c3b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | sam-m888/gramps | gramps/gui/plug/_dialogs.py | Python | gpl-2.0 | 12,066 | [
"Brian"
] | bf81c527b1181bcdf730edccb08de0efc79754f3101eab48ecb8d2c96bcfefe0 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2020 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
#... | appleseedhq/blenderseed | translators/cycles_shaders.py | Python | mit | 5,153 | [
"VisIt"
] | 5f2f1cbfbbb635654581fe6f91982a7343bc9fa69899dc6eb839648ab1c46bf5 |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework 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
... | alexandrul-ci/robotframework | src/robot/result/visitor.py | Python | apache-2.0 | 3,960 | [
"VisIt"
] | 078f679c372ebac83a7928a867491931da5a560fd30eddc7cf9758906b8d174a |
import logging, time
from astropy import coordinates as coord, units as u
import mechanize, httplib, StringIO
import astroquery, requests
from astroquery.irsa import Irsa
import numpy as np
import pandas as pd
import itertools
from astropy.cosmology import Planck13 as cosmo
#custom modules for the RGZ catalog
import c... | willettk/rgz-analysis | python/processing.py | Python | mit | 13,922 | [
"Galaxy"
] | faba7c792a6f93cd57212aac5047bc41c74c2ddd91f63050d59c099b1d1f5208 |
"""Objects used to represent Nengo networks as instantiated on SpiNNaker.
"""
from copy import copy
from collections import namedtuple, defaultdict, deque
from itertools import chain
from nengo import LinearFilter
import numpy as np
from .ports import EnsembleInputPort, InputPort, OutputPort
from six import iteritems, ... | project-rig/nengo_spinnaker | nengo_spinnaker/builder/model.py | Python | mit | 39,752 | [
"VisIt"
] | 6d9ffb2fe677ca4ac0bfdfd50c30082c5a4ba77c605147e7aa670da1592fe599 |
# -----------
# User Instructions
#
# Familiarize yourself with the code below. Most of it
# reproduces results that you have obtained at some
# point in this class. Once you understand the code,
# write a function, cte, in the run class that
# computes the crosstrack
# error for the case of a segmented path. You will
... | rhyswat/udacity | robotics_ai/slam1.py | Python | gpl-2.0 | 18,034 | [
"Gaussian"
] | 8aefc3bee4a67e0d9c213eb39f377fbaa03294717c7c1d0a28a1ffa5d4f9adf4 |
"""This module contains BayesianOptimization- and BOLFI-classes."""
__all__ = ['BayesianOptimization', 'BOLFI']
import logging
import matplotlib.pyplot as plt
import numpy as np
import elfi.methods.mcmc as mcmc
import elfi.visualization.interactive as visin
import elfi.visualization.visualization as vis
from elfi.l... | elfi-dev/elfi | elfi/methods/inference/bolfi.py | Python | bsd-3-clause | 22,416 | [
"Gaussian"
] | cdb7f8924fa87be22ee712db1774ffffe85ee1a68546348e59bc3588271f9333 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/__init__.py | Python | gpl-2.0 | 1,312 | [
"VisIt"
] | a3eb29d724e223fe262a1e806bec74fce4601654d6d8ee81934faa6ba50dcde9 |
import numpy as np
from Neuron import Neuron
class NeuronLayer:
def __init__(self, nNeurons, nInputEachNeuron):
self.nNeurons = nNeurons
self.neurons = np.array([Neuron(nInputEachNeuron) for _ in range(nNeurons)]) | holandajunior/ExtremeLearningMachine | src/NeuronLayer.py | Python | mit | 220 | [
"NEURON"
] | 42669fd24bbd91e5a77e278867942d32aef850961a79d915cb5e3f77867a6cd9 |
# -*- coding: utf-8 -*-
#
# Tint documentation build configuration file, created by
# sphinx-quickstart on Sun Dec 28 02:00:17 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | 8468/tint | docs/conf.py | Python | mit | 8,186 | [
"Brian"
] | 6b69ff268a66cd5fc01e0c5caa54af4183ea50f206c7494cb6cd6b1793b1eda2 |
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.PathFinder import getAgentSection
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.Core.Utilities.JDL import loadJDLAsCFG, d... | vmendez/DIRAC | WorkloadManagementSystem/Client/JobState/JobManifest.py | Python | gpl-3.0 | 8,782 | [
"DIRAC"
] | edb8854ddfb68583187d697bd671428c271f9672e39cf6f045a1c415f5ed03aa |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | localprojects/Change-By-Us | lib/web/template.py | Python | agpl-3.0 | 47,321 | [
"VisIt"
] | 57c9a6595211f00c242dca75f3ac58bf7aa8f4ef164e5507d0906810168e2033 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for non-standard space-group settings
"""
from fractions import Fraction
import numpy as np
import re
from pymatgen.core import Lattice
from pymatgen.util.string import transf... | mbkumar/pymatgen | pymatgen/symmetry/settings.py | Python | mit | 7,200 | [
"pymatgen"
] | 65469854557e0ebdf84c0ac93e50eecd220d89b09227c4db245ef3cf16db1af5 |
#!/usr/bin/env python
# Greg Von Kuster
"""
Subtract an entire query from another query
usage: %prog in_file_1 in_file_2 begin_col end_col output
"""
import sys, re
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
# Older py compatibility
try:
... | volpino/Yeps-EURAC | tools/new_operations/subtract_query.py | Python | mit | 3,107 | [
"Galaxy"
] | 2c309235b8959927683717960633dd21d76f63c23de25531b3e8291f7de36659 |
import os
import argparse
import json
import pydot
from PyV8 import *
__author__ = 'flier'
class CallGraph(object):
def __init__(self, name):
self.graph = pydot.Dot(name, graph_type='digraph')
self.funcs = {}
self.callstack = []
@staticmethod
def parseCmdLine():
parser ... | pombredanne/python-v8 | demos/callgraph.py | Python | apache-2.0 | 2,359 | [
"VisIt"
] | ef261b63725d1d4842bf2990bfde98374c12e5b4fc65557297bbde865c6281ef |
# -*- coding: utf-8 -*-
''' Display of diagrams (forces, moments, ...) on linear elements'''
__author__= "Luis C. Pérez Tato (LCPT) , Ana Ortega (AO_O) "
__copyright__= "Copyright 2016, LCPT, AO_O"
__license__= "GPL"
__version__= "3.0"
__email__= "l.pereztato@ciccp.es, ana.ortega@ciccp.es "
import geom
import vtk
f... | lcpt/xc | python_modules/postprocess/xcVtk/control_var_diagram.py | Python | gpl-3.0 | 5,317 | [
"VTK"
] | c4ea827845e0d81d159a02e32121585845c16098ac17a0c112e3dcbb933b9357 |
#!/usr/bin/env python
"""
This module is a Python implementation of the GIBBS algorithm.
"""
from __future__ import division
import warnings
import sys
import subprocess
import unittest
import pymatgen
from pymatgen.agl_thermal.agl_ev_check import evsort
from pymatgen.agl_thermal.agl_ev_check import evtsort
from pyma... | ctoher/pymatgen | pymatgen/agl_thermal/agl_gibbs.py | Python | mit | 66,625 | [
"pymatgen"
] | bb70ebd8105b6a7d49733ed885a9c8581b6f35212ad0444e32f577db6ba7ec67 |
from setuptools import setup
setup(
name="valueadded",
version="1.1.1",
description="A client library for valueadded.io",
long_description="Visit https://github.com/valueadded/valueadded-python for more information.",
packages=["valueadded"],
install_requires=[
"requests>=2.10,<3"
]... | valueadded/valueadded-python | setup.py | Python | bsd-3-clause | 709 | [
"VisIt"
] | f17aa22e3737cf505b2006dbfcb9bd10cb42dd057686cad031f4a840f0f3e313 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
import re
from math import sin, cos, pi, sqrt
import string
from pymatgen.electronic_structure.core import Magmom
from monty.json import M... | tallakahath/pymatgen | pymatgen/core/operations.py | Python | mit | 21,597 | [
"CRYSTAL",
"pymatgen"
] | 793d5b4a1fa84077747a28d9f5e084f3158f9ba57a2661376ca5bdd150e100cb |
# -*- coding: utf-8 -*-
"""The config functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import atexit
from functools import partial
import json
import os
import os.path as op
import platform
import shutil
import sys
import tempfile
import numpy as np
from .check import _valid... | Teekuningas/mne-python | mne/utils/config.py | Python | bsd-3-clause | 19,152 | [
"Mayavi",
"VTK"
] | cd0bdd4f42254b3d899c60e441443d987416a9b04423ecc1a870157389a1ba71 |
import sys
import time
import socket
TIMEOUT = 30
class Firefly:
def __init__(self, port):
self._port = port
def _get_the_dataz(self, s):
ret = ""
s.settimeout(TIMEOUT)
while True:
data = s.recv(4096)
if not data:
break
ret =... | ACAHNN/adscape | code/firefly.py | Python | mit | 1,553 | [
"Firefly"
] | 709a51782b64bb8ee130f73e4b5279175ba14f6054a49f18914ebbcb3554e1b6 |
from __future__ import absolute_import, division, print_function
import textwrap
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED, EXIT_OK, EXIT_USAGEERROR
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request, tmpdir_... | ddboline/pytest | testing/test_conftest.py | Python | mit | 18,111 | [
"VisIt"
] | a8927c24e07a333143c8ff7be99237a52147111405bb3f880cec092d994ed8b0 |
from __future__ import division
from builtins import range
from past.utils import old_div
import numpy as np
import matplotlib.pyplot as plt
import math
import scipy.signal
def diff(voltage):
d_voltage = voltage[0:-1] - voltage[1:]
return d_voltage
def signal_diff(voltages):
#Work with normalized voltages:
vmin ... | nanophotonics/nplab | nplab/experiment/dynamic_light_scattering/dls_signal_postprocessing.py | Python | gpl-3.0 | 3,949 | [
"Gaussian"
] | d5a9f442b4bcc77bfba2da118ac6e32b77ef6268e665dca342bb4495972adfef |
"""
The Python Wrapper of all ISC anomaly detector training methods.
"""
# --------------------------------------------------------------------------
# Copyright (C) 2014, 2015, 2016, 2017 SICS Swedish ICT AB
#
# Main author: Tomas Olsson <tol@sics.se>
#
# This code is free software: you can redistribute it and/or modi... | STREAM3/pyisc | _pyisc_modules/BaseISC.py | Python | lgpl-3.0 | 20,400 | [
"Gaussian"
] | 56f7bc27ab612dbc0ba1302b3e3b7fb13eec23c9fdd36e8d84a37532c4b09a21 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# 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 RDKit source tree.
#
"""Cluster tree visual... | ptosco/rdkit | rdkit/ML/Cluster/ClusterVis.py | Python | bsd-3-clause | 15,377 | [
"RDKit"
] | 8f6f5e55afc096121da6fe4dd871c6d7651df44b64d13c64704c3b1dee3207f9 |
import cv2
import numpy as np
from matplotlib import pyplot as plt
import math as m
import process
import os
import random as r
"""
Sorting methods for determining most likely corners
"""
def uLeftSort(pt):
return pt[0] + pt[1]
def lLeftSort(pt):
return -1*(pt[0] - pt[1])
def uRightSort(pt):
return -1*(p... | agundy/BusinessCardReader | cardscan/findCard.py | Python | mit | 10,748 | [
"Gaussian"
] | d3e40252ed1f807b89d8e7808fd264574be8ab79531824292f81dfdb6b0fc8dd |
#!/usr/bin/env python
#script to read .tst format and make surfaces in pymol
#ryan coleman
import math
import string
import sys
import os
import tstdata
def tstConvexHull(execKHull, tstFileName, execQHull=False, runKHull=False):
tstD = tstdata.tstData(tstFileName) # read the file into the data structure
tempFile... | ryancoleman/traveldistance | src/tstConvexHull.py | Python | gpl-2.0 | 5,513 | [
"PyMOL"
] | 519e897712297aacc2e0b9e3ff5a7941e4f671056b303053613e8081a2515a95 |
import numpy as np
class Invdisttree:
""" inverse-distance-weighted interpolation using KDTree:
invdisttree = Invdisttree( X, z ) -- data points, values
interpol = invdisttree( q, nnear=3, eps=0, p=1, weights=None, stat=0 )
interpolates z from the 3 points nearest each query point q;
For example, interpol... | ArchaeoPY/ArchaeoPY | Positional/invdisttree.py | Python | gpl-2.0 | 3,697 | [
"Gaussian"
] | 83e93ba3126196bf9a512183f3307dddb5b9957c7073ab8faff8b6b5222e5903 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements more advanced transformations.
"""
import logging
import math
import warnings
from fractions import Fraction
from itertools import groupby, product
from math import gcd
from string import ascii_lower... | materialsproject/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 88,058 | [
"ASE",
"CRYSTAL",
"pymatgen"
] | c791b75ba92b3c9a1900dd80657f93fe8c6b988de010a25622427bb0f97830fc |
from __future__ import print_function
import sys
import random
import os
from builtins import range
import time
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.deeplearning import H2ODeepLearningEstimator
from h2o.grid.grid_search import H2OGridSearch
class Test_deeple... | michalkurka/h2o-3 | h2o-py/dynamic_tests/testdir_algos/deeplearning/pyunit_deeplearning_gridsearch_over_all_params_large.py | Python | apache-2.0 | 21,366 | [
"Gaussian"
] | 40ea9a38e9b8ac2fb9f7594398391290e8aae7b020b6136687f30c3812e16369 |
# Configuration file for jointcal
from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask
# Select external catalogs for Astrometry
config.astrometryRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.astrometryRefObjLoader.ref_dataset_name='pan-starrs'
config.astrometryRefObjLoader.filterMap = {
... | LSSTDESC/ReprocessingTaskForce | config/w_2018_07/cfht/jointcalConfig.py | Python | gpl-2.0 | 1,555 | [
"VisIt"
] | 0df9c883dd935397977b5aef58a723324a0f566cf4ebe2310cd6a7edf6647b30 |
import ocl as cam
import camvtk
import time
import vtk
import datetime
if __name__ == "__main__":
myscreen = camvtk.VTKScreen()
myscreen.setAmbient(1,1,1)
#stl = camvtk.STLSurf(filename="demo.stl")
stl = camvtk.STLSurf(filename="demo2.stl")
print("STL surface read")
myscreen.addActor(stl... | aewallin/opencamlib | examples/python/old/kdtree_tst.py | Python | lgpl-2.1 | 5,359 | [
"VTK"
] | ce36ce285740498bf5ceeff2b0708889c052cff61a0d89d3afd076a6532cd84b |
# Support for the Numato Opsis - The first HDMI2USB production board
from collections import OrderedDict
from litex.build.generic_platform import *
from litex.build.xilinx import XilinxPlatform, iMPACT
from platforms.tofe_lowspeedio import *
_tofe_io = OrderedDict([
# A pairs - 2 x Diff CLK, 6 x Diff IO
# -... | cr1901/HDMI2USB-litex-firmware | platforms/opsis.py | Python | bsd-2-clause | 32,434 | [
"CRYSTAL"
] | 335977b41011d4dc932a1caddddb22cc04ad739a200171259c1e91a521c6c541 |
# -*- coding: utf-8 -*-
import os
from sys import executable
import types
from os.path import join
from stat import ST_MTIME
from docutils import nodes, utils
from docutils.parsers.rst.roles import set_classes
def mol_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
n = []
t = ''
while t... | qsnake/gpaw | doc/ext.py | Python | gpl-3.0 | 4,885 | [
"GPAW"
] | 868f25969e784489ac627ef79d21b30ffea46286c440f96510bbec79015b3f50 |
import unittest
import numpy as np
import cpnest.model
class GaussianModel(cpnest.model.Model):
"""
A simple gaussian model with parameters mean and sigma
"""
names=['mean','sigma']
bounds=[[-5,5],[0.05,1]]
data = np.array([x for x in np.random.normal(0.5,0.5,size=10)])
analyticZ = np.log(0... | johnveitch/cpnest | tests/test_verbosity.py | Python | mit | 1,294 | [
"Gaussian"
] | 631e54abb457db75a76406a7b09fa6312fd873bc36b7ba82ec7e0629ab904e3c |
"""Test the DataRecoveryAgent"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
from collections import defaultdict
from mock import MagicMock as Mock, patch, ANY
from parameterized import parameterized, param
import DIRAC
from DIRAC impor... | yujikato/DIRAC | src/DIRAC/TransformationSystem/test/Test_DRA.py | Python | gpl-3.0 | 24,656 | [
"DIRAC"
] | 85ded02c7ae00c6a9789cb71260b51fb6d5e1ab4dd9b3fd2112f25917bc08d5d |
"""Support the ElkM1 Gold and ElkM1 EZ8 alarm/integration panels."""
import logging
import re
import voluptuous as vol
from homeassistant.const import (
CONF_EXCLUDE, CONF_HOST, CONF_INCLUDE, CONF_PASSWORD,
CONF_TEMPERATURE_UNIT, CONF_USERNAME)
from homeassistant.core import HomeAssistant, callback # noqa
fro... | jnewland/home-assistant | homeassistant/components/elkm1/__init__.py | Python | apache-2.0 | 7,969 | [
"Elk"
] | 8350d0c4b4174b115989050ddc8340a93b58553435e2b275beb2d326db8e636a |
__author__ = "William Batista Aguiar Motta"
__email__ = "william.b.motta@aluno.unb.br"
__license__ = "GPL"
import ast
import sys
import codecs
class CallCollector(ast.NodeVisitor):
def __init__(self):
self.calls = []
self.current = None
def visit_Call(self, node): ... | cisalhante/matricula-o-matic | extract_outline.py | Python | gpl-3.0 | 1,600 | [
"VisIt"
] | f70bb5564f0d0fdbac1ede4c8111432085aa61382de6d3d2b8a382b013fa6e26 |
from django.core.management.base import BaseCommand, CommandError
from bugle.models import Blast
from django.contrib.auth.models import User
import re, sys
class Command(BaseCommand):
help = """
Ensures that all @username mentions are added to the mentions DB table
""".strip()
requires_model_valid... | devfort/bugle | bugle_project/bugle/management/commands/populate_short_from_subversion.py | Python | bsd-2-clause | 863 | [
"BLAST"
] | 591c11a1f4b0b6fae558767ae24c6755285c38bf42e73621b2e93a2e97349730 |
##############################################################################
# Copyright (c) 2013-2017, 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... | wscullin/spack | var/spack/repos/builtin/packages/paraview/package.py | Python | lgpl-2.1 | 6,121 | [
"NetCDF",
"ParaView"
] | a3e408b505be2b94c3d861a705e8c30e2e6bf6712dbc916f29a94503af9d9e36 |
"""
.. _tut_forward:
Head model and forward computation
==================================
The aim of this tutorial is to be a getting started for forward
computation.
For more extensive details and presentation of the general
concepts for forward modeling. See :ref:`ch_forward`.
"""
import mne
from mne.datasets i... | wronk/mne-python | tutorials/plot_forward.py | Python | bsd-3-clause | 6,837 | [
"Mayavi"
] | 2a9ef80682d4965e21c689867260341152d430b05c95538a84375d3416dc2a6e |
#! /usr/bin/python
import __main__
__main__.pymol_argv = ['pymol','-qc']
#__main__.pymol_argv = ['pymol','']
import sys,time,os
import pymol
pymol.finish_launching()
my_file = sys.argv[1]
end = my_file.find(".pdb")
file_name = my_file[0:end]
pymol.cmd.load(my_file,file_name)
#pymol.cmd.split_states(file_name)
#pymo... | demharters/git_scripts | align_intrafit_HO.py | Python | apache-2.0 | 583 | [
"PyMOL"
] | 5566beeb72539f90b0279eba50968663f1c2bceb97ec19a3b3255df5c0c1ab2c |
"""
Implementation of exact latent-function inference in a Gaussian process model
for regression.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
import numpy as np
import scipy.linalg as sla
from mwhutils.linalg import chol_update
from ._base import G... | mwhoffman/pygp | pygp/inference/exact.py | Python | bsd-2-clause | 4,559 | [
"Gaussian"
] | 5b231d1464d74f4c9a3db8b566a4c53737ff706f5c55b6e2b9a6762f37e9d94d |
#!/usr/bin/env python
from peacock.ExodusViewer.plugins.MeshPlugin import MeshPlugin
from peacock.ExodusViewer.plugins.BackgroundPlugin import BackgroundPlugin
from BlockHighlighterPlugin import BlockHighlighterPlugin
from peacock.base.PluginManager import PluginManager
from peacock.base.TabPlugin import TabPlugin
from... | yipenggao/moose | python/peacock/Input/InputFileEditorWithMesh.py | Python | lgpl-2.1 | 9,957 | [
"VTK"
] | 7095974ce803b6ecafeecce013535f01d00a6b296180e6a37b487dffc520b855 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import pytest
approx = pytest.approx
from sisl.unit.siesta import unit_group, unit_convert, unit_default, unit_table_si... | zerothi/sisl | sisl/unit/tests/test_unit_siesta.py | Python | mpl-2.0 | 1,720 | [
"SIESTA"
] | f32af2498078dca48277220b2759d8c2b25a8987b05c1211cfaf8f0cab1fc70a |
##############################################################################
# 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-crispresso/package.py | Python | lgpl-2.1 | 2,158 | [
"Biopython"
] | ce556efcc4ad3f230cbf1605c59a6f3a4765649f7bf1a7ab08db75250807c4b8 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/formats/netcdf.py | Python | lgpl-2.1 | 21,654 | [
"Amber",
"MDTraj",
"NetCDF"
] | a32a3cd4d820ad79ec8a94893f2cb80f0fefa2f8fce10285df7dcfc7278085a4 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/fileformats/grib/_load_convert.py | Python | lgpl-3.0 | 77,912 | [
"Gaussian"
] | 3dad1d7df9222679468111ef3dce11f4cf870a1fc5f0f3d6a7d7b33a8ffcbca7 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tornado/websocket.py | Python | bsd-2-clause | 47,684 | [
"VisIt"
] | 5322ce0787b6f14d8a4c49177eaa64696ca62e65756e9f5e440223be1d1ded24 |
import logging
import re
import os
import select
import signal
try:
import autotest.common as common
except ImportError:
import common
from autotest.client import utils, os_dep
from autotest.client.shared import error
from autotest.client.shared.utils import VersionableClass
class ServiceManagerInterface(Vers... | joyxu/autotest | client/shared/openvswitch.py | Python | gpl-2.0 | 18,583 | [
"ASE"
] | 13d1dc51ad22ba49d1630f160010f1341a279850303f96e839c7abe6adbdce4e |
#post processing, add sequence and additional annoation info if available
from urllib import urlencode
from galaxy.datatypes.images import create_applet_tag_peek
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
primary_data = out_data.items()[0][1]
#default params ... | dbcls/dbcls-galaxy | tools/visualization/LAJ_code.py | Python | mit | 2,169 | [
"Galaxy"
] | 3ac45d593a24bb0c9996eb2b5d198a425f53f3726e0c8cb67a52e760f8a893a2 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | corburn/scikit-bio | skbio/alignment/_tabular_msa.py | Python | bsd-3-clause | 24,570 | [
"scikit-bio"
] | bdb008df1c38292ca0b3dbd6fb6ed62923a58b072385e4b4e28a999193dd2b23 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement Action."""
from abc import ABCMeta, abstractmethod
from enum import IntEnum
from hoomd.logging import Loggable
from hoomd.operation import _HOOMDGe... | joaander/hoomd-blue | hoomd/custom/custom_action.py | Python | bsd-3-clause | 4,770 | [
"HOOMD-blue"
] | c6871e0f9098b00e011517f30ab6d9fe259b3bab7e35a816ff30fa3fefca99ad |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# MIT License
#
# Copyright (c) 2018 Miha Purg <miha.purg@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, in... | mpurg/qtools | qscripts-cli/q_amber2q.py | Python | mit | 9,720 | [
"Amber"
] | ea170c562d2fd759723c061c4511c3004a3458e4d1493ffb1784ad9d8a0d0759 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | testsuite/python/constant_pH_stats.py | Python | gpl-3.0 | 4,327 | [
"ESPResSo"
] | 7b45a1449f03e031bfdfeecd3a2dfcab3f219e8bcb95092040fd3ddaaecc7e7b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
A module to perform experimental thermochemical data analysis.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
... | matk86/pymatgen | pymatgen/analysis/thermochemistry.py | Python | mit | 3,335 | [
"pymatgen"
] | dcab3cf362d54eb262076df3a752398162b733eaba500768169af4477b6fe9d3 |
from unittest import mock
import sys
import numpy as np
import numpy.random
import dask.array as da
from numpy.testing import assert_array_equal, assert_allclose
import pytest
from hyperspy import signals
from hyperspy.decorators import lazifyTestClass
from hyperspy.signal_tools import SpikesRemoval
from hyperspy.com... | CodeMonkeyJan/hyperspy | hyperspy/tests/signal/test_tools.py | Python | gpl-3.0 | 35,000 | [
"Gaussian"
] | 261b7720ac291ad92e3ab2cf9343a8cc7bdb4cee96293cbf8d3903365118b333 |
"""
Utilities to create replication transformations
"""
from DIRAC.TransformationSystem.Client.Transformation import Transformation
from DIRAC import gLogger, S_OK, S_ERROR
def createDataTransformation(flavour, targetSE, sourceSE,
metaKey, metaValue,
extraDat... | fstagni/DIRAC | TransformationSystem/Utilities/ReplicationTransformation.py | Python | gpl-3.0 | 3,512 | [
"DIRAC"
] | d0e6b5c3e2d908a8d71c9a296f7ceff33e6d02a32a6fbd0fcd29e3ffc2fe9604 |
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 2 2015
Main for MG_Synth. This main calls the necessary functions to create a
synthetic dataset for analysis of the metagenome regulatory network Bayesian
inference module
@author: ivanerill
"""
#imports getopt to handle the cmd line reading
import getopt
#imports the N... | ErillLab/CogsNormalizedPosteriorProbabilityThetas | MGtest/MG_synth.py | Python | gpl-3.0 | 13,849 | [
"BLAST"
] | 33c36e99015764742a3d3a55c7a741c5cf937cd8fb90403923a7e4d38cfefe16 |
#!/usr/bin/python
import apt_pkg
import apt
import logging
import json
import unittest
import xapian
from mock import patch
from piston_mini_client import PistonResponseObject
from testutils import setup_test_env
setup_test_env()
from softwarecenter.enums import (XapianValues,
AVAIL... | gusDuarte/software-center-5.2 | test/test_reinstall_purchased.py | Python | lgpl-3.0 | 15,432 | [
"BLAST"
] | 3045b154da864d4fcd77fdf7554b001f030293b1e93e5fc1ca01100b88b2cad4 |
# $HeadURL$
__RCSID__ = "$Id$"
import GSI
requiredGSIVersion = "0.3.9"
if GSI.version.__version__ < requiredGSIVersion:
raise Exception( "pyGSI is not the latest version (installed %s required %s)" % ( GSI.version.__version__, requiredGSIVersion ) )
GSI.SSL.set_thread_safe()
nid = GSI.crypto.create_oid( "1.2.42.4... | atsareg/VMDIRAC | VMDIRAC/Security/__init__.py | Python | gpl-3.0 | 643 | [
"DIRAC"
] | d0335e9fad54ebdfe12245c6d31cbe07bee7a720a89502b45e16a32492f38b68 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
#
# This program is free software; you can redistribute it and/or modify
# it u... | arunkgupta/gramps | gramps/plugins/docgen/psdrawdoc.py | Python | gpl-2.0 | 13,959 | [
"Brian"
] | 5402323cfbdb8309805a1aa396849692c0bbe5bda81e81c2d0efde033146e60b |
import numpy as np
import regreg.api as rr
import pandas as pd
from scipy.stats import norm as ndist
from scipy.optimize import bisect
from statsmodels.sandbox.stats.multicomp import multipletests
from ...tests.instance import gaussian_instance
from ...algorithms.lasso import lasso
from ...tests.flags import SET_SEED... | selective-inference/selective-inference | selectinf/randomized/tests/sandbox/test_cv_lee_et_al.py | Python | bsd-3-clause | 6,849 | [
"Gaussian"
] | 891b05131ced5625d4ef6c48a250e99a1c6ac1bf3ed2108645ca077017271ef7 |
########################################################################
# File : Utilities.py
# Author : Federico Stagni
########################################################################
"""
Utilities for Transformation system
"""
import ast
import random
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.C... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/Client/Utilities.py | Python | gpl-3.0 | 19,959 | [
"DIRAC"
] | 5160d8b922f2fbf99f4c5b15b8078f3824bb2d78aaba42fcf5ea39e68a74d31c |
"""
Tests for discussion pages
"""
from uuid import uuid4
import pytest
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.fixtures.discussion import (
Comment,
Response,
SingleThreadViewFixture,
Thread,
)
from common.test.acceptance.pages... | msegado/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 17,053 | [
"VisIt"
] | d0f2da8c5e5605cb24597ef1e023fd464a2165822a8fac4691de90ff4cd0a822 |
# -*- coding: utf-8 -*-
# please visit http://www.iptvxtra.net
import os,sys,xbmcplugin,xbmcgui,xbmc,xbmcaddon,urllib
addonID = 'plugin.audio.swr3'
addon = xbmcaddon.Addon(id = addonID)
addonPath = addon.getAddonInfo('path')
profilePath = addon.getAddonInfo('profile')
icon = xbmc.translatePath( os.path.join( addonPat... | noba3/KoTos | addons/plugin.audio.swr3/default.py | Python | gpl-2.0 | 750 | [
"VisIt"
] | afd33fe11caa996d7692f64866e692bc18ce8671fa80366fdc51021727e8fa55 |
import sys
import os
from collections import defaultdict
import pysam
import numpy as np
#Go one directory up and append to path to access the deepdna package
#The following statement is equiv to sys.path.append("../")
sys.path.append(
os.path.abspath(os.path.join(os.path.dirname(__file__),os.path.pardir)))
impo... | LarsDu/DeepNucDecomp | scripts/exon_stitch.py | Python | gpl-3.0 | 4,367 | [
"pysam"
] | c34b308a97589560808cd7f9362017813cf8d11dfd84a1f216674f40b6ebcc0a |
#!/usr/bin/python
"""
FoldX_runner Copyright (C) 2012 Jose Sergio Hleap
This script will run FoldX software for repair and mutations to alanine.
It will output a pickled dictionary of energies and the mutated files.
Check FoldX manual for more info.
This program is free software: you can redistribute it and/or modify... | jshleap/StructBio | FoldX_runner.py | Python | gpl-3.0 | 6,180 | [
"CRYSTAL",
"FoldX"
] | 3df3a781c6914dd97a06d84f3692db63b818c85c70761f3ef61cc7832dce7589 |
"""
=======================================
Signal processing (:mod:`scipy.signal`)
=======================================
Convolution
===========
.. autosummary::
:toctree: generated/
convolve -- N-dimensional convolution.
correlate -- N-dimensional correlation.
fftconvolve --... | surhudm/scipy | scipy/signal/__init__.py | Python | bsd-3-clause | 12,436 | [
"Gaussian"
] | 247901111f52657beb179c2ee1d318755b0baec83dd41bc2db8cea56e9e92838 |
from numpy import array,median,std,mean,log,concatenate,sum,reshape,sqrt,dot,exp,histogram,float,empty,unique
from ctypes import c_double
import pynopticon
import pynopticon.slots
import _mpi_kmeans
class PairwiseDistances(object):
mertics = ['euclidean', 'cityblock', 'sqeuclidean', 'cosine', 'correlation', 'hammi... | jhmadhav/pynopticon | src/pynopticon/score.py | Python | gpl-3.0 | 5,722 | [
"Gaussian"
] | 778763a15c3b0ef10cae3092962b98d66491da787506f5a658aa2e3ba1258611 |
# -*- coding: utf-8 -*-
from pyqtgraph.Qt import QtCore, QtGui
from ..Node import Node
from scipy.signal import detrend
from scipy.ndimage import median_filter, gaussian_filter
#from pyqtgraph.SignalProxy import SignalProxy
import functions
from common import *
import numpy as np
try:
import metaarray
HAVE_MET... | robertsj/poropy | pyqtgraph/flowchart/library/Filters.py | Python | mit | 6,350 | [
"Gaussian"
] | 4cec796853d5814c0737a52e3bc234555c922b8051e95083ba0bc373576dc80f |
""" Class for the LCG File Catalog Client
"""
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Resources.Utilities import checkArgumentFormat
from DIRAC.Resources.Catalog.FileCatalogueBase import F... | marcelovilaca/DIRAC | Resources/Catalog/LcgFileCatalogClient.py | Python | gpl-3.0 | 66,168 | [
"DIRAC"
] | feb0f54fa5e5c01f8dc407b738c4881c59774ce2ea44df4203074266bb45cc75 |
#########################################################################################
#
# ERA_INTERIM.py
#
# Download ERA Interim data and create a movie from it.
#
#
# bethan.perkins@assimila.eu
# May 2014
#
#########################################################################################
# Import librari... | joelfiddes/toposubv2 | getERA/ERA_INTERIM.py | Python | gpl-3.0 | 18,438 | [
"NetCDF"
] | 55da8221e62fc0096acec3292fc5c5ce3a0a7bec612697e5a1be44ec8a9f5f38 |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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 later version.
#
# This program is distrib... | Microvellum/Fluid-Designer | win64-vc/2.78/Python/bin/2.78/scripts/addons_contrib/io_scene_fpx/fpx_spec.py | Python | gpl-3.0 | 176,319 | [
"CRYSTAL"
] | deb15db189740e819e912baf8615014a97dcdbb917736d1eae35e7a753ac72e8 |
import numpy as np
from menpo.image import Image
from menpofit.base import name_of_callable
from menpofit.aam.fitter import AAMFitter
from menpofit.clm.fitter import CLMFitter
from menpofit.fitter import MultilevelFitter
class SDFitter(MultilevelFitter):
r"""
Abstract Supervised Descent Fitter.
"""
d... | mrgloom/menpofit | menpofit/sdm/fitter.py | Python | bsd-3-clause | 10,184 | [
"Gaussian"
] | 267dec68ee3588f786d824596568ce06b5c102bebe046fa91d9618095778c18d |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 5.0
d = 1.0
x = d / 3**0.5
atoms = Atoms([Atom('C', (0.0, 0.0, 0.0)),
Atom('H', (x, x, x)),
Atom('H', (-x, -x, x)),
Atom('H', (x, -x, -x)),
Atom('H', (-x... | qsnake/gpaw | gpaw/test/degeneracy.py | Python | gpl-3.0 | 876 | [
"ASE",
"GPAW"
] | d7039273103985f6286af64a8042a606a54a840f33c5faa24e43dce945e42b87 |
# -*- coding: utf-8 -*-
from random import randint, choice
from PIL import Image, ImageFont
from PIL.ImageDraw import Draw
from django.http import HttpResponse, Http404
snippets = (
("%s << %s", lambda x, y: x << y, lambda: randint(0, 100), lambda: randint(0, 5)),
("%s >> %s", lambda x, y: x >> y, lambda: rand... | BusyJay/Django-Expression-Capture | utils/views.py | Python | mit | 2,967 | [
"VisIt"
] | ebf72359e5540c2dde5ed4d6e3add6a57a00bce6b19db3b1a37a0fe411918f7d |
#!/usr/bin/python
import os
import sys
import subprocess
import time
import glob
# Run Example:
# FeatureFinderMetabo -in {infile} -out {outfile} -ini {paramfile}
print "Inside " + __file__
# first parse input if environment vars is inputed as
# one single comma separated environment var
if "envparams" in os.enviro... | phnmnl/MTBLS233-POP | container-openms/bin/OpenMS.py | Python | apache-2.0 | 4,191 | [
"OpenMS"
] | 5d0fd55885636ce22cf2e33c18c5a5eff657c1c64f141260a0f484d5057c60bb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Craig J. Anderson
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Matt Keenan (matt.keenan@... | arunkgupta/gramps | gramps/plugins/textreport/descendreport.py | Python | gpl-2.0 | 17,655 | [
"Brian"
] | 6cd9d9e200de1ae2d4748954446bfe93204c85aba212cfb35c44b0bf22c73bcf |
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