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# -*- coding: utf-8 -*-
from math import pi
import numpy as np
import ase.units as units
from gpaw.lfc import BaseLFC, LocalizedFunctionsCollection as LFC
from gpaw.wavefunctions.fdpw import FDPWWaveFunctions
from gpaw.hs_operators import MatrixOperator
import gpaw.fftw as fftw
from gpaw.lcao.overlap import... | ajylee/gpaw-rtxs | gpaw/wavefunctions/pw.py | Python | gpl-3.0 | 31,771 | [
"ASE",
"GPAW"
] | 518b3f7284b4278f0970ebce348257548b3cfee39616e368a5e994acc374bf3d |
# -*- coding: utf-8 -*-
import pytest
import sys
from aerospike import exception as e
from .as_status_codes import AerospikeStatus
try:
from collections import Counter
except ImportError:
from counter26 import Counter
from .test_base_class import TestBaseClass
aerospike = pytest.importorskip("aerospike")
try... | aerospike/aerospike-client-python | test/new_tests/test_select_many.py | Python | apache-2.0 | 13,592 | [
"ASE"
] | 90e6dd05dd559ded448169c7dd42a9560ee116e9699a6ac97449b0850fd267b3 |
# -*- coding: utf8 -*-
from __future__ import division # confidence high
from __future__ import with_statement
import itertools
import sys
import warnings
import numpy as np
import pyfits as fits
from pyfits.card import _pad
from pyfits.util import encode_ascii, _pad_length, BLOCK_SIZE, StringIO
from pyfits.tests ... | ClaudioNahmad/Servicio-Social | Parametros/CosmoMC/prerrequisitos/plc-2.0/lib/python2.7/site-packages/pyfits-3.2.2-py2.7-linux-x86_64.egg/pyfits/tests/test_header.py | Python | gpl-3.0 | 94,744 | [
"BLAST"
] | be044e72049c2ba1f65466a2ae1f66dd4fb339541564d56fe8fafd8f81299736 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImageNormalize()
| jeromevelut/Peavip | Testing/ImageNormalize.py | Python | gpl-3.0 | 127 | [
"ParaView"
] | 27dfe8a5d27d7ea677e25ec62f9998818ae9a153dcdb4ce5d5ec4911b914bc9b |
""" Utility Class for threaded agents (e.g. TransformationAgent)
Mostly for logging
"""
import time
from DIRAC import gLogger
AGENT_NAME = ""
class TransformationAgentsUtilities(object):
"""logging utilities for threaded TS agents"""
def __init__(self):
"""c'tor"""
self.debug = False
... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/Agent/TransformationAgentsUtilities.py | Python | gpl-3.0 | 2,817 | [
"DIRAC"
] | 99782f9ec2020bc76a10e2a25b46d79827885549a1e7f8a810168e40e396f9c8 |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | eemirtekin/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 57,479 | [
"VisIt"
] | 30f7023471bc0191d61c4be7367b901a82b91678d61911e5b0201198d58f988a |
# This file is part of Androguard.
#
# Copyright (C) 2012, Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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:/... | xtiankisutsa/MARA_Framework | tools/androguard/androguard/decompiler/dad/instruction.py | Python | lgpl-3.0 | 38,627 | [
"VisIt"
] | e6e692275c375a03024b2f25f957a6c6e1c0456053a5066ff8e056e3b124e705 |
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
import os
import numpy as np
import montage_wrapper as montage
import shutil
import sys
import glob
import time
from matplotlib.path import Path
from scipy.ndimage import zoom
from pdb import set_trace
_TOP_DIR = '/data/tycho/0/leroy.42/allsky/'
_INDEX_DIR ... | arlewis/galaxy_cutouts | versions/extract_stamp_v5.py | Python | mit | 23,457 | [
"Galaxy"
] | edcf82b6a348fa166f9c6b87acb99f27e1a944d84668987f7a67450eacef0ca9 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
# pylint: skip-file
im... | mohamed--abdel-maksoud/chromium.src | build/android/pylib/android_commands.py | Python | bsd-3-clause | 73,010 | [
"Galaxy"
] | b54ec76cca460518863ae90de5d71b866e5b88fea2f90fabfc242bf5b1b7bdb6 |
"""
Observational constrains and simulational results related to black hole masses.
:requires: NumPy
:version: 0.1
:author: Sami-Matias Niemi
:contact: sniemi@unc.edu
"""
import os
import numpy as np
#This should be global, as all observational data are in the same place
#Note however that because the data is in Dr... | sniemi/SamPy | astronomy/blackholes.py | Python | bsd-2-clause | 2,128 | [
"Galaxy"
] | 0986c038c09e65243f2a242ca8526a9ad163fb73bd87b4bb82dd9f30062bceb8 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VASP or other electronic
structure codes. For example, ... | Dioptas/pymatgen | pymatgen/entries/computed_entries.py | Python | mit | 7,271 | [
"VASP",
"pymatgen"
] | 1ff5cbb3f8d16f703c9146bc4da9fffb0bec1716dcd59433886d81db24f3bbfe |
# $Id$
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Trajectories
============
Write centered trajectories. Trajectories will be stored under the
base dir / trj.
- full fitxy
- fitxy at 100 ps inte... | jandom/GromacsWrapper | gromacs/analysis/plugins/trajectories.py | Python | gpl-3.0 | 5,775 | [
"Gromacs"
] | 2fd694f22e18cbdd4ae8057a16f306e885d10f83f78b01be23ee76fea11ae1b6 |
# encoding: utf-8
"""
Enable wxPython to be used interacive by setting PyOS_InputHook.
Authors: Robin Dunn, Brian Granger, Ondrej Certik
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/lib/inputhookwx.py | Python | apache-2.0 | 6,189 | [
"Brian"
] | 1512c7130cff628fd3aa6e60ced1329354e25591f5dab848abd564bc9058e0b2 |
# -*- coding: utf-8 -*-
"""
sphinx_pypi_upload
~~~~~~~~~~~~~~~~~~
setuptools command for uploading Sphinx documentation to PyPI
:author: Jannis Leidel
:contact: jannis@leidel.info
:copyright: Copyright 2009, Jannis Leidel.
:license: BSD, see LICENSE for details.
"""
import sys
import os
i... | blundeln/pylens | third_party/sphinx_pypi_upload.py | Python | bsd-3-clause | 5,744 | [
"VisIt"
] | c37bf7f3e173b7dc3cc8118830b241e6faf2f4ad5c6c87b10cb909cfe5075966 |
import sys
import os
debug = 0
def getGC_content(dnaString, as_fraction=True):
if len(dnaString) == 0:
return None
if dnaString.count('N') > len(dnaString) * 0.05:
raise Exception("too many NNNs in assembly sequence")
return None
gc = 0
gc += dnaString.count('G')
gc += dn... | Joshmoss11/x-seq | deeptools/utilities.py | Python | gpl-3.0 | 7,414 | [
"pysam"
] | 7b71170c908071089b9aa8336b50f2aee103b9f0d12746b403c211a9f510a958 |
# Autodetecting setup.py script for building the Python extensions
#
import sys, os, importlib.machinery, re, optparse
from glob import glob
import importlib._bootstrap
import importlib.util
import sysconfig
from distutils import log
from distutils.errors import *
from distutils.core import Extension, setup
from dist... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.5.9/Python-3.5.9/setup.py | Python | apache-2.0 | 100,155 | [
"VisIt"
] | d455987798639122e842af0fdb0278f85d56404d63e71708be037944afca9252 |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#*****************************************************************************
# Copyright (C) 2008-2009 The IPython Development Team
# Copyright (C) 2001-2008 Fernando Perez <fperez@colorado.edu>
# Copyright (c) 2001 Janko Hauser <... | mastizada/kuma | vendor/packages/ipython/IPython/Release.py | Python | mpl-2.0 | 4,136 | [
"Brian"
] | 51f9437dbdfa9c0de0ada8a353657ef2755cbb7ede403ef8cc78ed16cf6a1c7f |
from giotto.programs import Program, Manifest
from giotto.programs.shell import shell
from giotto.programs.tables import syncdb, flush
from giotto.views import BasicView
management_manifest = Manifest({
'syncdb': Program(
name="Make Tables",
controllers=['cmd'],
model=[syncdb],
view... | priestc/giotto | giotto/programs/management.py | Python | bsd-2-clause | 614 | [
"BLAST"
] | 472f9236d1ff1ef9f86853bd3e4db75c5d9b70b6c72d3258d426b79f23bc1799 |
# Licensed to the StackStorm, Inc ('StackStorm') under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use th... | tonybaloney/st2 | st2common/st2common/middleware/cors.py | Python | apache-2.0 | 3,927 | [
"GULP"
] | 078ad210cc9592d270b1a1b55810b51c3dcdb3d62a3a05fd06856d2e6c96eee8 |
"""MonitoredQueue classes and functions.
Authors
-------
* MinRK
* Brian Granger
"""
#
# Copyright (c) 2010 Min Ragan-Kelley, Brian Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as pub... | takluyver/pyzmq | zmq/devices/monitoredqueuedevice.py | Python | lgpl-3.0 | 4,448 | [
"Brian"
] | 1ee338777e9afa66e9c29222c6311eb4fa2ef8819ef543f584e4e41276706881 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2010 Jack Grigg
# Copyright (C) 2011 Krzysztof Tarnowski (krzysztof.tarnowski@ymail.com)
# Copyright (C) 2009, 2010, 2011 OpenHatch, Inc.
# Copyright (C) 2011 Jairo E. Lopez
#
# This program is free software: you can redistribute it a... | campbe13/openhatch | mysite/base/tests.py | Python | agpl-3.0 | 24,825 | [
"VisIt"
] | 8c930ac2311cd31d040dc29c9b401c9b69724359338ce0702cbecf12249d0409 |
#!/usr/bin/env python
from __future__ import print_function, division
import os
import scipy as sp
import scipy.linalg as LA
import scipy.spatial.distance as sp_dist
from ase.atoms import Atoms
from ase import units
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
import ase.io
import theano
import... | marcocaccin/LearningMetaDynamics | test_mlsample.py | Python | gpl-2.0 | 14,903 | [
"ASE",
"CP2K",
"Gaussian",
"LAMMPS"
] | 58adc04028e9902d9b8f4133006f977523541354a33d13a7e4ad4642398bf747 |
# Copyright 2017 The TensorFlow Authors All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | jiaphuan/models | research/fivo/models/vrnn.py | Python | apache-2.0 | 19,176 | [
"Gaussian"
] | 7cbbe23d2b20d9d07e175793154fb85c3cd60e466cee3981c1d2ef5213150482 |
#! /usr/bin/env python
import re
import math
import collections
import numpy as np
import time
import operator
from scipy.io import mmread, mmwrite
from random import randint
from sklearn import cross_validation
from sklearn import linear_model
from sklearn.grid_search import GridSearchCV
from sklearn import preproces... | Goodideax/CS249 | predict_gbm_combine_1000.py | Python | bsd-3-clause | 14,602 | [
"Gaussian"
] | bdebf5683b9288ccc5ddcfa8470254b8e7b160fa8e5151871c92c96788b6724a |
#!/usr/bin/env python
from __future__ import print_function
import json
import optparse
import os.path
import sys
from load_db import create_table
from query_db import describe_tables, get_connection, run_query
"""
JSON config:
{ tables : [
{ file_path : '/home/galaxy/dataset_101.dat',
table_name ... | blankclemens/tools-iuc | tools/query_tabular/query_tabular.py | Python | mit | 4,768 | [
"Galaxy"
] | cbba6288096b56141163e8c1a153fa1be9b4b36a425a42927040c68aacbf924d |
#!/usr/bin/env python
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
################################################... | INNUENDOWEB/INNUca | src/SPAdes-3.10.1-Linux/share/spades/spades_pipeline/spades_logic.py | Python | gpl-3.0 | 20,535 | [
"BWA"
] | 0f94be32c5bf23688938d4d9044135be5e1dfde6b11fdaaee2a2ac0afd993d98 |
#!/usr/bin/env python3
"""
Allows sampling and hyper-parameter search from outside of Python.
Note: ROPT_NPROC is currently unsupported, until I find a way to cleanly kill all
sub-processes.
Example:
ROPT_NSEARCH=16 ROPT_NPROC=4 ropt.py python example.py run --lr='Choice([0.1,0.2,0.3])' --wd='uniform(0,10... | seba-1511/randopt | bin/ropt.py | Python | apache-2.0 | 5,907 | [
"Gaussian"
] | cbf64f8603de2033d35059b139af491b4755560cb4426d7dba72fa38d707420e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2015 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/LICENS... | dougfelt/nototools | nototools/generate_website_2_data.py | Python | apache-2.0 | 56,431 | [
"VisIt"
] | 6c03a212690b3bec165ba9e662391fb59488165bc16701806f1e3f47c08aa040 |
# Copyright (c) 2015,Vienna University of Technology,
# Department of Geodesy and Geoinformation
# All rights reserved.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND F... | TUW-GEO/SMDC-performance | smdc_perftests/datasets/ascat.py | Python | bsd-3-clause | 9,343 | [
"NetCDF"
] | 8c508e406ef3dd366624588af3f02a701ab02188667087970cd73e7d08535551 |
import ternary
import matplotlib.pyplot as plt
def _generate_heatmap_data(scale=5):
from ternary.helpers import simplex_iterator
d = dict()
for (i, j, k) in simplex_iterator(scale):
d[(i, j, k)] = _color_point(i, j, k, scale)
return d
def _en_to_enth(energy,concs,A,B,C):
enth = abs(energy ... | wsmorgan/iid | scripts/triangle.py | Python | mit | 12,251 | [
"VASP"
] | 0f53b484acee377b7ac246ff3e92766761d99ce024fe18e17c33128bc0113d74 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent any type of spectrum, essentially any
x y value pairs.
"""
from typing import List, Union, Callable
import numpy as np
import scipy.stats as stats
from monty.json ... | richardtran415/pymatgen | pymatgen/core/spectrum.py | Python | mit | 7,665 | [
"Gaussian",
"pymatgen"
] | 64d38daac79a0b38865a65b27587270af1ec53917faf4b54fd59d3947457dd49 |
('\\AC', '∿'),
('\\aleph', 'ℵ'),
('\\Alpha', 'Α'),
('\\alpha', 'α'),
('\\amalg', '⨿'),
('\\angle', '∠'),
('\\approx', '≈'),
('\\approxeq', '≊'),
('\\asymp', '≍'),
('\\backepsilon', '϶'),
('\\backprime', '‵'),
('\\backsim', '∽'),
('\\backsimeq', '⋍'),
('\\barwedge', '⊼'),
('\\because', '∵'),
('\\Beta', '... | Template-Latex/Template-Informe | test/unicode_replacer.py | Python | mit | 13,865 | [
"Bowtie"
] | bf4edb495ea8f783f3515d76b205ed8455deb4f24b3c83b4fd51f9a2be8091f0 |
#import production
from asap3 import *
from asap3.md.verlet import VelocityVerlet
from cPickle import *
from numpy import *
#from Asap.Trajectories.NetCDFTrajectory import *
import sys, os, time
from asap3.testtools import *
from asap3.mpi import world
openkimmodel = "EMT_Asap_Standard_Jacobsen_Stoltze_Norskov_AlAgAu... | auag92/n2dm | Asap-3.8.4/Test/parallel/parallelOpenKIM_NeighPure_F.py | Python | mit | 5,058 | [
"ASE",
"OpenKIM"
] | a95f0b96b4f38cd61dc5881c2989fab70ba2f8c6e291dfeab0b6d441252409d1 |
#
# File : mkdir.py
# This file is part of RT-Thread RTOS
# COPYRIGHT (C) 2006 - 2018, RT-Thread Development Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of th... | armink/rt-thread | tools/mkdist.py | Python | apache-2.0 | 14,498 | [
"CDK"
] | 00950b5727cf910558790b0f5bd31b12c76743b647dd3224e374202fe0f37c3a |
########################################################################
# $HeadURL $
# File: RemoveReplica.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 07:45:06
########################################################################
""" :mod: RemoveReplica
===================
.. module: Re... | sposs/DIRAC | DataManagementSystem/Agent/RequestOperations/RemoveReplica.py | Python | gpl-3.0 | 6,797 | [
"DIRAC"
] | b7ad710a53a709499ae18682b537d280829c228efeb8dbcdd5fc7e1b437e020c |
# -*- coding: utf-8 -*-
{
'# selected': '# được lựa chọn',
"'Cancel' will indicate an asset log entry did not occur": "'Hủy' sẽ chỉ dẫn một lệnh nhập không thực hiện được",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a... | flavour/ifrc_qa | languages/vi.py | Python | mit | 374,132 | [
"VisIt"
] | c67d07f376d26d71629e30b84ac087cabdfc15356add7f0c0b92af4f4cbf5954 |
"""Vimdoc plugin management."""
from collections import OrderedDict
import io
import json
import os
import warnings
import vimdoc
from vimdoc import error
from vimdoc import parser
from vimdoc import regex
from vimdoc.block import Block
# Plugin subdirectories that should be crawled by vimdoc.
DOC_SUBDIRS = [
'pl... | google/vimdoc | vimdoc/module.py | Python | apache-2.0 | 19,130 | [
"VisIt"
] | fc84ae5597e485cb7b6b64eb09e9f33e0f8d4d42ea1fe9f1fc3069f40d58ec71 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform fitting of structures.
"""
import abc
import itertools
import numpy as np
from monty.json import MSONable
from pymatgen.analysis.defects.core import Defect, Inters... | davidwaroquiers/pymatgen | pymatgen/analysis/structure_matcher.py | Python | mit | 48,204 | [
"pymatgen"
] | d22a30fa655d88cffa3a4263ae565662f42b418d3bdc208561fded0d0c68ff36 |
# coding=utf-8
# Copyright 2022 The Edward2 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... | google/edward2 | experimental/sngp/gaussian_process_test.py | Python | apache-2.0 | 7,326 | [
"Gaussian"
] | 86644802814f000c454939199b0598aacbada3023884c68c654f1f1fa3885f66 |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2020 Brian Langenberger
# 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 Licens... | tuffy/python-audio-tools | audiotools/__init__.py | Python | gpl-2.0 | 204,620 | [
"Brian"
] | f177fe78310ddfc63aa96fabac503f748be2626dc624c65d78c40a4be1a58937 |
# -*- 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/c16128/Generate16128Centreline.py | Python | gpl-2.0 | 1,027 | [
"VTK"
] | 00caa57ae231aeb85f7d95858918faae542d792de811f32bbc38344619f68c59 |
# -*- coding: utf-8 -*-
from sys import path as sys_path
sys_path.append('../')
from subprocess import call
from util.fs_util import get_dir, get_dist_path, copy_file
from image_info import get_info, get_orientation
import logging
logging.basicConfig(format = u'%(filename)s[LINE:%(lineno)d]# %(levelname)-8s [%(asct... | poserg/photo-groupinator | importer/graphic/convert.py | Python | gpl-2.0 | 3,027 | [
"Gaussian"
] | 69933c0f071155b81b6be6e92fe378221860e725be36ace1a058de0aebcf1db9 |
""" The Notification service provides a toolkit to contact people via email
(eventually SMS etc.) to trigger some actions.
The original motivation for this is due to some sites restricting the
sending of email but it is useful for e.g. crash reports to get to their
destination.
Another use-case is... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Service/NotificationHandler.py | Python | gpl-3.0 | 11,354 | [
"DIRAC"
] | f7b7016a7ad1cfea9d8f9738d4393a28721f2eb9f4527129f819f0f450b7c012 |
# -*- coding: utf-8 -*-
# (c) 2016, Adrian Likins <alikins@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at you... | s-hertel/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 59,253 | [
"Galaxy"
] | 3bafb0c813a9279ed569347bb0de18cdb05f632a586ac3c44773ff367f5f27fa |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_tilleditor.py | Python | gpl-2.0 | 7,093 | [
"VisIt"
] | 8bc9f4ccb1eb5b41b3016b3c42fb859fedfb53a3a2d11f9ceb009b3039a4939f |
""" Class that contains client access to the production DB handler. """
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.ProductionSystem.Utilities.StateMachine import ProductionsStateMachine
@createClient("Production/ProductionManager")
class ProductionClien... | DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/Client/ProductionClient.py | Python | gpl-3.0 | 5,666 | [
"DIRAC"
] | 170bd06084cbff478223767e1f74c610a63a5285fdfc08d8817e6e08f0ef4c05 |
#!/usr/bin/env python
"""Download strips of the global bathymetry"""
import sys
import os
import matplotlib.pyplot as plt
import clawpack.clawutil.data as data
import clawpack.geoclaw.topotools as topotools
def form_etopo_URL(lower, upper, file_name="etopo1.nc", file_format="netcdf"):
URL = "https://maps.ngd... | mandli/surge-examples | global/topo/get_topo.py | Python | mit | 2,235 | [
"NetCDF"
] | 70debbb10592c2f8a37746d89be337fda49fdb5c55176387d97d22c4686d494f |
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0
"""
An RPC client class using ZeroMQ as a transport and
the standard Python threading API for concurrency.
Authors
-------
* Alexander Glyzov
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2012-2014. Brian Granger,... | Alidron/demo-nao | alidron-env/lib/python2.7/site-packages/netcall/threading/client.py | Python | mpl-2.0 | 9,962 | [
"Brian"
] | f0ee3eedc505c9a84029a84024dbfd2caaa6825a6b2d0b3ddc26358305106b7b |
"""
Cave decoding/conversion logic.
Included here are the (encoded) caves from Boulderdash I on the Commodore-64.
More info including the decoding algorithm:
https://www.elmerproductions.com/sp/peterb/rawCaveData.html#rawCaveDataFormat
https://www.elmerproductions.com/sp/peterb/insideBoulderdash.html
http://www.bd-fan... | irmen/bouldercaves | bouldercaves/caves.py | Python | gpl-3.0 | 30,816 | [
"BLAST",
"Firefly"
] | 8318a8c1787caa02a984c835de80328a7c26956b6868d6870043e9daca0cf963 |
# Copyright (C) 2017-2018 Michael Freitag, Shahin Amiriparian, Sergey Pugachevskiy, Nicholas Cummins, Björn Schuller
#
# This file is part of auDeep.
#
# auDeep 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, ... | auDeep/auDeep | audeep/cli/generate.py | Python | gpl-3.0 | 5,742 | [
"NetCDF"
] | a58aaeb4148aaedadd4f156a83d3195a2379b9e243a477542deb511552f31bd1 |
import os
import sys
import numpy as np
import nibabel as nb
import nighresjava
from ..io import load_volume, save_volume, load_mesh_geometry, save_mesh_geometry
from ..utils import _output_dir_4saving, _fname_4saving,_check_available_memory
def levelset_to_mesh(levelset_image, connectivity="18/6", level=0.0,
... | nighres/nighres | nighres/surface/levelset_to_mesh.py | Python | apache-2.0 | 4,662 | [
"VTK"
] | 9e7d6e79841805ae07938176d8b30bfdc029d25cf95cf46bbdec166b6835ac39 |
#!/usr/bin/python
"""
Copyright 2017-2018 University of Cincinnati
All rights reserved. See LICENSE file at:
https://github.com/AS4SR/website
Additional copyright may be held by others, as reflected in the commit history.
"""
import os
import sys
import shutil
#
# create "verticalmenubar.part" as verticalmenubar_str ... | AS4SR/website | create_html.py | Python | bsd-3-clause | 22,316 | [
"ASE"
] | 7905352bb4bd8f9aba10d73f721247ae205199c57844362a78c45a20ee57aab3 |
"""
This module implements a weighted Kernel Density Estimation (KDE).
The code is a modified version of Scipy gaussian_kde that adds support for
weights.
Only direct set of bandwidth is supported.
This code borrows from a mods done by Zachary Pincus (zachary.pincus@yale.edu):
http://mail.scipy.org/pipermail/scipy-u... | tritemio/FRETBursts | fretbursts/fit/weighted_kde.py | Python | gpl-2.0 | 4,364 | [
"Gaussian"
] | ecf7e2da7b1fea252cea9c07c68647f0e9ae13db45385097b125b38883eb49a1 |
# Copyright 2004 by Jason A. Hackney. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from string import join
from Bio.Alphabet import IUPAC
from Bio import File
from Bi... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/MEME/Parser.py | Python | apache-2.0 | 24,693 | [
"Biopython"
] | cf890f98f81da5260f8ea8a70752c5e52965b7fa083872f230c5c47d8d65d847 |
"""Known matrices related to physics"""
from sympy import Matrix, I
def msigma(i):
"""Returns a Pauli matrix sigma_i. i=1,2,3
See also:
http://en.wikipedia.org/wiki/Pauli_matrices
"""
if i==1:
mat=( (
(0, 1),
(1, 0)
) )
elif i==2:
mat=( (
... | hazelnusse/sympy-old | sympy/physics/matrices.py | Python | bsd-3-clause | 2,087 | [
"DIRAC"
] | 634fd8421eafa2e9a3e1cb9a9e71390de0d4f8c4dbad4085d9e1db622e4d3cdf |
# An instrumentation script template that tricks the software into decrypting
# data that it previously encrypted
# Dependencies: Immunity Debugger
# Author: Brian Yip
import immlib
def main(args):
imm = immlib.Debugger()
encrypted_file = open('''Path to encrypted file''', "rb")
in_file = encrypted_f... | itsbriany/Security-Tools | reverse-engineering/self_decrypt_template.py | Python | mit | 1,384 | [
"Brian"
] | c40e30be3699554d98d5457b5a67ac09ab5a63ac3fbad56550f199fcc7707440 |
"""This manages the lookup table used to map values to colors.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
import os.path
import sys
import subprocess
# Enthought library imports.
from traits.api import Instance, Range, Bool, Array, \
... | dmsurti/mayavi | mayavi/core/lut_manager.py | Python | bsd-3-clause | 16,440 | [
"Mayavi",
"VTK"
] | c773365fc03e9cef95b83facff4a7011ab75fe0a629b56d975ba27ed9425367c |
#
# Generate crystal given a size and element.
#
# Check list for supported elements.
#
# Author: Gonzalo Aguirre <graguirre@gmail.com>
#
import sys, getopt
import numpy as np
def usage():
print >> sys.stderr, "Options:"
print >> sys.stderr, " -h Show help"
print >> sys.stderr, " -e <element> Ele... | graguirre/CrystalGen | crystal-gen.py | Python | gpl-2.0 | 2,047 | [
"CRYSTAL"
] | 22f6460cade1fad7ab7e7003df869f9f67c54501fea3ba62225b967151738f29 |
#!/usr/bin/env python
"""RNAalignment
Example::
# STOCKHOLM 1.0
AACY023581040 --CGUUGGACU------AAA--------AGUCGGAAGUAAGC-----AAU-C------GCUGAAGCAACGC---
AJ630128 AUCGUUCAUUCGCUAUUCGCA-AAUAGCGAACGCAA--AAG------CCG-A-------CUGAAGGAACGGGAC
target --CGUUGA... | m4rx9/rna-pdb-tools | rna_tools/tools/rna_calc_evo_rmsd/RNAalignment.py | Python | mit | 2,737 | [
"Biopython"
] | cddd6894457876e8d9d5c854dd3f5bf081fd4d0c1e66933daf1cdc51df8afac8 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/alignment/_indexing.py | Python | bsd-3-clause | 8,571 | [
"scikit-bio"
] | 794d67f9be941b1842cb60d79d06bcd0d4e73f8f1468cfe704ac11517d9b9f14 |
##############################################################################
# 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/qmcpack/package.py | Python | lgpl-2.1 | 12,703 | [
"ESPResSo",
"QMCPACK",
"Quantum ESPRESSO"
] | f1886b36e359afadfb78695a5b8bc9129a2efaa9300c2ec311e0f06a91ac4ea2 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/core/lib/db.py | Python | gpl-2.0 | 19,321 | [
"Brian"
] | 63913c6d6bcd71d1d78788dbd5a3ada49b39c55bbc4eb2d14a7faf7397612f74 |
from __future__ import print_function
import logging
import yaml
import numpy as np
import orca
import pandas as pd
from . import misc
from ..models import util
logger = logging.getLogger(__name__)
def from_yaml(net, cfgname):
print("Computing accessibility variables")
cfg = yaml.load(open(misc.config(cfg... | apdjustino/urbansim | urbansim/utils/networks.py | Python | bsd-3-clause | 1,780 | [
"ORCA"
] | 0760f5a0a1a84f1d0158ac50648bb9ff50c94f30d995475335acfd8ca4566764 |
from __future__ import print_function
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, Help, oops
from ase.io.pov import write_pov
from ase.gui.status import formula
from os.path import basename
from os import system
import numpy as np
class Render(gtk.Window):
finish_list = ['ase2','... | suttond/MODOI | ase/gui/render.py | Python | lgpl-3.0 | 15,733 | [
"ASE",
"Jmol",
"VMD"
] | faa15208c416c808ed1ceae7ea9044bcd591d7d07e3b1e99625c0dc04e7fb80d |
import gc
import os
import os.path as op
from os.path import join as pjoin
import sys
import pytest
from mayavi import mlab
import nibabel as nib
import numpy as np
from numpy.testing import assert_array_equal, assert_array_less
from unittest import SkipTest
from surfer import Brain, io, utils
from surfer.utils impo... | nipy/PySurfer | surfer/tests/test_viz.py | Python | bsd-3-clause | 17,650 | [
"Mayavi"
] | 4a8f23a688df668bfc6876d32f7f8bcedab7c009021044f04b179326c960a8e0 |
import numpy as np
import pandas as pd
import mdtraj as md
#os.system("hmsm means-ghmm --filename hmms.jsonlines --lag-time 1 --n-states 3 -o out.csv --dir Trajectories --top system.subset.pdb --ext h5 -a AtomIndices.dat")
name = "atompairs"
df = pd.read_csv("./samples-%s.csv" % name)
for k, row in df.iterrows():
... | hainm/MSMs | attic/src/code/hmsm/save_pdbs.py | Python | gpl-2.0 | 432 | [
"MDTraj"
] | c57e62348de3edd41e99c5a0518204451943a657bf5888c29fe6cec97e62c9bd |
#
# Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | rvianello/rdkit | rdkit/Chem/FunctionalGroups.py | Python | bsd-3-clause | 5,065 | [
"RDKit"
] | 4cc32eb5b37231493259e42b68605fe0449d2b9ebfd4838dc3eedd505eb1c17d |
#!/usr/local/sci/bin/python
# PYTHON3
#
# Author: Kate Willett
# Created: 16 October 2015
# Last update: 10 April 2019
# Location: /data/local/hadkw/HADCRUH2/UPDATE2014/PROGS/PYTHON/
# GitHub: https://github.com/Kate-Willett/Climate_Explorer/tree/master/PYTHON/
# -----------------------
# CODE PURPOSE AND OUTPUT
# --... | Kate-Willett/Climate_Explorer | PYTHON/ReadNetCDF.py | Python | cc0-1.0 | 16,111 | [
"NetCDF"
] | 2b7761a2c8bf140782ade355ad7506888f8ad03b0de4268b983b06a03b85d6ba |
########################################################################
# $HeadURL$
# File : CREAMComputingElement.py
# Author : A.T.
########################################################################
""" CREAM Computing Element
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement ... | avedaee/DIRAC | Resources/Computing/CREAMComputingElement.py | Python | gpl-3.0 | 14,251 | [
"DIRAC"
] | 111e3bd5bb058b191b36743973a0eb1cff368c1a72880b7d5cd382f87bb60b44 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# gulp browserify example documentation build configuration file, created by
# sphinx-quickstart on Sat Mar 1 22:50:10 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are pres... | juhamust/gulp-browserify-example | conf.py | Python | mit | 8,325 | [
"GULP"
] | 973999c60c13c4b45df449e320c14e362601e365021f84bc29d87c22fede6e2f |
#!/usr/bin/env python
"""A web application that retrieves other websites for you.
To start serving the application on port 8088, type
python webproxy.py
To start the server on some other interface/port, use
python -m gevent.wsgi -p 8000 -i 0.0.0.0 webproxy.py
"""
from gevent import monkey; monkey.patch_all()
i... | mgadi/naemonbox | sources/psdash/gevent-1.0.1/examples/webproxy.py | Python | gpl-2.0 | 4,295 | [
"VisIt"
] | 1c7d5d9f8f6017b796bffdf7f3dfc6dfd27d6d98f2437a91bfae338663f5ae6c |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTreeMapToPolyData(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkTreeMapToPolyData.py | Python | bsd-3-clause | 491 | [
"VTK"
] | cf3f707f3baeac9e9f2d4cd68ab0ada94a5a594aa0986f1c8a52aa75842569ab |
#!/usr/bin/python
import os
sTypes = ['smooth','Gaussian','fBm']
| dronir/EM | python/makeBatch.py | Python | gpl-3.0 | 67 | [
"Gaussian"
] | 051b6d8e8c594daed473e53ba44bcbfe4d8b5eaa5cc61f360f563a831bccbf8e |
# manifest.py - manifest revision class for mercurial
#
# Copyright 2005-2007 Olivia Mackall <olivia@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import heapq
import itertool... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/mercurial/manifest.py | Python | apache-2.0 | 77,284 | [
"VisIt"
] | 719788a11df649e611a13e798976099b191647126872457dc07b986ebcc053e1 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | naturali/tensorflow | tensorflow/python/ops/template.py | Python | apache-2.0 | 11,931 | [
"VisIt"
] | a2f7e882b699c1f52da225e9c1c3db0491053497146f2dff7818b1a7a42342ab |
#!/usr/bin/env python
"""
replicate file in the FileCatalog
Can work in two modes.
In the first mode, yuser provides the destination SE with option "-D".
In the second mode, when no destination is given, drepl will look for COMDIRAC configuration options "replication_scheme" and "replication_ses".
If found, those va... | calancha/COMDIRAC | Interfaces/scripts/drepl.py | Python | gpl-3.0 | 3,393 | [
"DIRAC"
] | 21e3b462f659ce9ed8c161fbaf2e779d6a463d77a4143ffdbc89ff48cf625bcc |
#
# Copyright (C) 2001-2017 greg Landrum
#
# @@ 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.
#
from __future__ import print_function
import unittest
... | rvianello/rdkit | rdkit/Chem/UnitTestSATIS.py | Python | bsd-3-clause | 1,358 | [
"RDKit"
] | 87fbda5d4485b2095d90dc9ad8cc8105bb43482f175ebbb76eff64af677f4f5d |
#
# @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/qcdb/util/regex.py | Python | lgpl-3.0 | 2,596 | [
"Psi4"
] | 7ce8145cce4acf9cf0ef680b7181002414da790abc23008e60221a55cf8c9e77 |
#! /usr/bin/python
import os
import json
import arff
FLAG_NAMES = [
u'nvcc:--no-align-double',
u'nvcc:--use_fast_math',
u'nvlink:--preserve-relocs',
u'nvcc:--relocatable-device-code=',
u'nvcc:--ftz=',
u'nvcc:--prec-div=',
u'nvcc:--prec-sqrt=',
u'ptxas:--... | phrb/gpu-autotuning | weka/generate_arff.py | Python | lgpl-3.0 | 5,720 | [
"Gaussian"
] | f089b837eebff736ff37e9ffff7be416281b9d695d4c4df761908fccc253883f |
"""
Load and save a set of chosen implementations.
@since: 0.27
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from zeroinstall import _, zerostore
from zeroinstall.injector import model
from zeroinstall.injector.policy import get_deprecated_singlet... | rammstein/0install | zeroinstall/injector/selections.py | Python | lgpl-2.1 | 17,140 | [
"VisIt"
] | 81315067ce1305148baca95db50528f9640e6397f2a659fddae7c19cea8f94f6 |
############
# GATK Best Practices
############
# rule GATK:
# input: bam="{base}/{sample}/{sample}.bwa.dd.bam",
# bai="{base}/{sample}/{sample}.bwa.dd.bam.bai",
# ref=config["reference"],
# phase1=config["1000G_phase1"],
# mills=config["Mills_and_1000G"]
# output:
# bam="{base}/{sample}/{sample}.bwa.fi... | seandavi/snakewrappers | bio/bw_gatk_best_practices/wrapper.py | Python | mit | 2,073 | [
"BWA"
] | 75df402d98b72f92a1a0d3adbc38b106acb09f2f907ce8c93d884d179f44a519 |
# -*- coding: utf-8 -*-
#
# Twenty47 documentation build configuration file, created by
# sphinx-quickstart on Fri May 9 16:48:24 2014.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | gary-dalton/Twenty47 | docs/conf.py | Python | mit | 7,728 | [
"Dalton"
] | 5323a4330c47afc3cd658cc398f3f65e7c43b6a02be102c8d07d6adc2c48ed8e |
from ase.cluster import Icosahedron
from ase.ga.particle_crossovers import CutSpliceCrossover
from random import shuffle
ico1 = Icosahedron('Cu', 5)
ico1.info['confid'] = 1
ico2 = Icosahedron('Ni', 5)
ico2.info['confid'] = 2
op = CutSpliceCrossover({(28, 29): 2.0, (28, 28): 2.0, (29, 29): 2.0},
... | PHOTOX/fuase | ase/ase/test/ga/particle_operators.py | Python | gpl-2.0 | 1,433 | [
"ASE"
] | e711b49853934a03a3cc6da6bcf9d7d1b064c2e6bb4d2c169c338d3263073d14 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-talent | scripts/fixup_talent_v4beta1_keywords.py | Python | apache-2.0 | 8,359 | [
"VisIt"
] | 391df6625b4b48fe40de60a6e009ac1e3afe553eb3784a8186f4f6a8cd89e8ef |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | windskyer/nova | nova/tests/unit/network/test_manager.py | Python | gpl-2.0 | 167,357 | [
"FEFF"
] | 27c9484dd01f4f91ac24741c0531159e96b10b834a742d97dcb887a78a62bcda |
'''
S transform (time-frequency transformation)
Submodule of the Modular EEg Toolkit - MEET for Python.
the 'standard' S transform:
----------------------------
Stockwell, Robert Glenn, Lalu Mansinha, and R. P. Lowe. "Localization of
the complex spectrum: the S transform." Signal Processing,
IEEE Transactions on 44.... | neurophysics/meet | meet/tf.py | Python | mit | 8,365 | [
"Gaussian"
] | 50f1a7de5ab30be964d72647465a782369dec3e40d36e819bf2852fc55f7a0e5 |
# Custom library
import data_reader
# Standard libraries
import datetime
import os
import sys
import time
# Third-party libraries
import numpy as np
import tensorflow as tf
# Short form of Boolean value
T, F = True, False
class optimise_hyperparameters :
def __init__(self, use_single_U = True, U = 5, U1 = 5, U... | kchng/Quantum_machine_learning | TF_HSF_CNN0i_core.py | Python | apache-2.0 | 29,560 | [
"NEURON"
] | 2ab844826abd5c4bd784a1483ccd9ac6c237592f732af48e014e12d942f471fd |
# confdistmatrix.py --- Conformational distance matrix calculator
# Copyright (C) 2014 Wouter Boomsma, Matteo Tiberti
#
# 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 Li... | encore-similarity/encore | encore/confdistmatrix.py | Python | gpl-3.0 | 16,732 | [
"MDAnalysis"
] | d5e0bf2d21aae0f9a16aafbfcfd02ffd3d83c0e224b398f8d8dd3e7fd562863f |
from mdt import CompositeModelTemplate
__author__ = 'Francisco.Lagos'
class S0T1_MI_EPI(CompositeModelTemplate):
"""Inversion recovery model.
This is made to model the MI-EPI sequence, a multi inversion recovery EPI (Renvall et Al. 2016).
The Model is based on Stikov et al.'s three parameter model.... | cbclab/MDT | mdt/data/components/standard/composite_models/relaxometry.py | Python | lgpl-3.0 | 1,296 | [
"Gaussian"
] | 6f1aa955742fb7883a7842b16db8a307fe9ac46015bd6c11043c88bed1cca31a |
"""
Basic molecular features.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "MIT"
from deepchem.feat import Featurizer
class MolecularWeight(Featurizer):
"""
Molecular weight.
"""
... | ktaneishi/deepchem | deepchem/feat/basic.py | Python | mit | 3,311 | [
"RDKit"
] | 14e61114e54eeed87b057825230ca9471cd6f1a9ee2ce7b9c46e2e3912f016f4 |
#!/usr/bin/env python
#
# thapbi_santi_otus.py
#
# Script to identify OTUs from metabarcoding reads.
#
# This is an almost direct translation of a pipeline written by Santiago
# Garcia, to generate OTU clusters from metabarcoding ITS reads in
# Phytophthora.
#
# (c) The James Hutton Institute 2016
# Author: Leighton Pr... | widdowquinn/THAPBI | santi_script/thapbi_santi_otus.py | Python | mit | 13,428 | [
"BLAST"
] | df764f8a675f2bf3ea2122bbf749502fcac579e3b0cd0582ed163f0c134eee37 |
import OpenGL.GL as gl
import OpenGL.arrays.vbo as glvbo
import gl_program
class SpikeProgram(gl_program.GLProgram):
"""Render a series of ints as white dots."""
def __init__(self, width, height):
self.width = width # size of the grid
self.height = height # size of the grid
s... | tcstewar/opengl_texture_rendering | pygame/spiker.py | Python | gpl-2.0 | 2,169 | [
"NEURON"
] | e566e6749cf32340ead67b2fcaf3f9e21be4217d2f2f143bcbf0c907a37cfc44 |
#!/usr/bin/env python
"""[License: GNU General Public License v3 (GPLv3)]
This file is part of FuMa.
FuMa is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your opti... | ErasmusMC-Bioinformatics/fuma | setup.py | Python | gpl-3.0 | 1,715 | [
"HTSeq"
] | a9a622c717fae6769fc604492b7ba48242bd4f4966e737546e0e82a4fa64f1f6 |
#Copyright 2009 Brian Meeker
#
#This file is part of pyFish.
#
#pyFish is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#pyFish is distri... | palebluedot2/pyfish | src/pyFish/Core.py | Python | gpl-3.0 | 9,922 | [
"Brian"
] | f180768bbb0caf0481d5dbe8df6f4d1ad80c2d57fd62e7750beb4a53b9e9c419 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RKegggraph(RPackage):
"""KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor... | rspavel/spack | var/spack/repos/builtin/packages/r-kegggraph/package.py | Python | lgpl-2.1 | 1,444 | [
"Bioconductor"
] | da75159b222971795f36852061ff087f93908b2a30b0190703a59972c407e48b |
config.parse.translation = {'filter': 'FILTER',
'ccdnum': 'DETECTOR',
'calibDate': 'CALIBDATE',
}
config.register.columns = {'filter': 'text',
'ccdnum': 'int',
'calibDate': 'text',
... | lsst/obs_decam | config/ingestCuratedCalibs.py | Python | gpl-3.0 | 652 | [
"VisIt"
] | 640f61ef1433709cbaf40d89fafe05d557384f32c0b51337251bc00af432a3f1 |
"""
Calculating Exposure Times and Limiting Magnitude
=================================================
This file provides a simple functions to calculate exposure times or limiting magnitudes.
:requires: NumPy
:requires: SciPy
:requires: matplotlib
:version: 0.4
:author: Sami-Matias Niemi
:contact: s.niemi@ucl.ac.... | sniemi/EuclidVisibleInstrument | ETC/ETC.py | Python | bsd-2-clause | 14,220 | [
"Galaxy"
] | fa0c88e4743ff52ef39acf7f15ef7902b2c7dcf9bd3bbf2b743378596ca6aac7 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/periodictable.py | Python | gpl-2.0 | 78,237 | [
"CFOUR",
"Psi4"
] | 6b730ece28ec60637ed7cd89c29b53b6bbd643d42510ddd05332a7f1dfa15fb8 |
#trida, ktera bude reprezentovat strukturu pro initdata
class InitData:
def __init__(self, filepath = None, ablator_exe = "Ablator.exe"):
self.filepath = filepath
self.ablator_exe = ablator_exe
if(filepath == None):
self.set_default()
else:
if ablator_exe ==... | vaanwizard/ablator | python/models/init_data.py | Python | gpl-2.0 | 10,966 | [
"Gaussian"
] | 9956b60f6ccdde4ce6e8ec2ebaa291f68455dbc7d4528148524eac623408c32b |
from ase import Atom, Atoms
from gpaw import GPAW, PoissonSolver
from gpaw.test import equal
from gpaw.xc.hybrid import HybridXC
a = 6. # Size of unit cell (Angstrom)
c = a / 2
# Hydrogen atom:
atom = Atoms([Atom('H', (c, c, c), magmom=1)],
cell=(a, a, a), pbc=False)
# gpaw calculator:
calc = GPAW... | qsnake/gpaw | gpaw/test/atomize.py | Python | gpl-3.0 | 2,589 | [
"ASE",
"GPAW"
] | 643d9128fe1eefa9e03f6196c1893ba2da9fb5572409a7406fd4cd1cdac191b4 |
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