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"""ASEr Setup Script."""
from setuptools import setup, find_packages
from codecs import open
from os import path
from os import listdir
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
long_description = f.... | TheFraserLab/ASEr | setup.py | Python | mit | 1,637 | [
"ASE",
"pysam"
] | 06541891230d98800f9094ce5468b09f3e56a06c1161204af3d6c038901456aa |
# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).
"""Definition of the Atoms class.
This module defines the central object in the ASE package: the Atoms
object.
"""
import warnings
from math import cos, sin
import numpy as np
from ase.atom import Atom
from ase.data import atomic_numbers, ... | askhl/ase | ase/atoms.py | Python | gpl-2.0 | 56,652 | [
"ASE"
] | b90a1950b1738545fc2ead7f34a6811c2dad72ee97185de16ba9c4f93c2aa292 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Mayo Clinic
# 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 copyright notice, this
# list... | hsolbrig/shexypy | shexypy/shexyparser/parser_impl/ShExDocVisitor_impl.py | Python | mit | 31,570 | [
"VisIt"
] | 72e7b7d9399f752d7e55131d9f51cab3bacc21d459b72f6580565395ce4a1093 |
# Author: Pietro Sormanni
## FUNCTIONS FOR SEQUENCE PROCESSING OF INPUTS ####
import sys
from .structure_processor import NUM_EXTRA_RESIDUES
def get_CDR_simple(sequence ,allow=set(["H", "K", "L"]),scheme='chothia',seqname='' \
,cdr1_scheme={'H':range(26-NUM_EXTRA_RESIDUES,33+NUM_EXTRA_RESIDUES),'L'... | eliberis/parapred | parapred/full_seq_processor.py | Python | mit | 7,698 | [
"Biopython"
] | bbd6070fe120c40d97c77a51963f76092d27202fd6f377afdb9eac1b8a23afb6 |
# Copyright 2006-2009 by Peter Cock. 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.
#
# This module is for reading and writing FASTA format files as SeqRecord
# objects. The co... | bryback/quickseq | genescript/Bio/SeqIO/FastaIO.py | Python | mit | 7,812 | [
"Biopython"
] | e5178a3f6bdf275e26a063dafb382d6ad9451847ee9aabdc06d53038f57270a8 |
from dark.blast.hsp import printHSP
def printBlastRecord(record):
"""
Print a BLAST record.
@param record: A BioPython C{Bio.Blast.Record.Blast} instance.
"""
for key in sorted(record.__dict__.keys()):
if key not in ['alignments', 'descriptions', 'reference']:
print('%s: %r' %... | bamueh/dark-matter | dark/blast/records.py | Python | mit | 1,064 | [
"BLAST",
"Biopython"
] | c1d62d0fb9060896713d6f4d19648ab8f5434db2cebf8b44a1f3e333dd59cd9f |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 James Buren and 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... | tuffy/python-audio-tools | audiotools/mpc.py | Python | gpl-2.0 | 12,755 | [
"Brian"
] | 51d8844339acf8c30a433aa203a0d4159b74ae214eaf2dc9b5444bbdd8c7d695 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | kaarolch/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 14,083 | [
"Brian",
"Galaxy"
] | d257b02023314a5772e7b2129486d199555262da122dcae3d2a890e4cf22b42c |
"""
Testing for Gaussian Process module (sklearn.gaussian_process)
"""
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# License: BSD 3 clause
from nose.tools import raises
from nose.tools import assert_true
import numpy as np
from sklearn.gaussian_process import GaussianProcess
from sklearn.gaussian_process ... | aabadie/scikit-learn | sklearn/gaussian_process/tests/test_gaussian_process.py | Python | bsd-3-clause | 6,813 | [
"Gaussian"
] | a8842645515903ed6a5b18458477a8e32d54d359ae69c10f186e8be6e16c4603 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/grad/test/test_cisd.py | Python | apache-2.0 | 3,518 | [
"PySCF"
] | f51036633a9050755998dfdfd84e1bb157b0b84b78a0d8f3b8bc1c8ffc75fe99 |
#
# Copyright (C) 2001,2003 greg Landrum and Rational Discovery LLC
#
""" unit tests for the QuantTree implementation """
import io
import unittest
from rdkit import RDConfig
from rdkit.ML.DecTree import BuildQuantTree
from rdkit.ML.DecTree.QuantTree import QuantTreeNode
from rdkit.TestRunner import redirect_stdou... | bp-kelley/rdkit | rdkit/ML/DecTree/UnitTestQuantTree.py | Python | bsd-3-clause | 8,450 | [
"RDKit"
] | e41051038e702a99e5dee7da999802b334f1888ecaf53720ff78e846a77fa71f |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | sanketloke/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 68,901 | [
"Gaussian"
] | 2acbd3c3221ddc6968c071461808301025c6da76033f0b810a7b9b2e1cdf869f |
# 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/LICENSE-2.0
#
# Unless required by applicable law or ... | wijnandb/CodeCult-Scratch | modules/analytics/clustering.py | Python | apache-2.0 | 47,710 | [
"VisIt"
] | 7bf1b1035d2b0fbbc70aca80ed8278d64d32925a8bd500dafa73e31cc8d47cd5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes for parsing the FEFF output files.
Currently supports the xmu.dat, ldos.dat output files are for non-spin case.
"""
import re
from collections import OrderedDict, defaultdict... | gmatteo/pymatgen | pymatgen/io/feff/outputs.py | Python | mit | 15,146 | [
"FEFF",
"pymatgen"
] | 450408644d67e43748395f1a2c682eba0ce07e4de94dd8b0e6ebea327c169519 |
# the ttwotheta motor and detector
# test xpd sim of motor movement
import numpy as np
from ophyd.sim import SynSignal, motor1, motor2
from lmfit import Model, Parameter, Parameters
from lmfit.models import VoigtModel, LinearModel
from lmfit.lineshapes import voigt
class SynGaussPeaks(SynSignal):
"""
Evaluat... | NSLS-II-XPD/ipython_ophyd | profile_collection/simulators/10-motors-dets-sim.py | Python | bsd-2-clause | 3,925 | [
"Gaussian"
] | f1b6e3e9a14ccf04f6671f7d5490a34556996d482bcb4fba1d31ffd0b8aa602f |
#!/usr/bin/env python
__all__ = [ 'read_beta_hf_string' ]
import os,sys, re, argparse, ctypes, multiprocessing, functools
import numpy as np
import math as m
#from particles import *
from matplotlib import pyplot as plt
from .molecules import Atom
from .template import Template
try:
from applequist.gaussian i... | fishstamp82/moltools | moltools/read_dal.py | Python | mit | 45,486 | [
"Dalton",
"Gaussian"
] | 34cf75861eef659357b2ecf9fd8b18767da7c9edd8f24057d17722e43b520647 |
"""Convert BAM/SAM to FASTQ format*
@name
sequence
+name
quality score (phred33)
files may be SAM or BAM (autodetected)
If the file(s) contain paired-end sequences, we will write to two files
(in the current working directory)
If the files contain single end sequences, we will write to stdout by default
Output is alwa... | benjschiller/seriesoftubes | seriesoftubes/converters/bamtofastq.py | Python | artistic-2.0 | 6,093 | [
"pysam"
] | 9398f8b15753dd81f6eb8bbf7c26f31b3826b6e0167c04df90b4af3d026d7f41 |
# Copyright 2013 Yajie Miao Carnegie Mellon University
# 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
#
# THIS CODE IS PROVIDED *AS IS* B... | yajiemiao/pdnn | layers/rbm.py | Python | apache-2.0 | 9,456 | [
"Gaussian"
] | 487d40cd334bafb06293388650a8c28fe09ed8c450e1697ad48254431fb77b03 |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. 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.
"""Unit test for ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SCOP_Scop.py | Python | gpl-2.0 | 5,661 | [
"Biopython"
] | d9b9e648d40a872ca0c3f869e89a6454acb267eb50981ceb24a2f90859511c83 |
# 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.
"""Test hoomd.hpmc.update.QuickCompress."""
import hoomd
from hoomd.conftest import operation_pickling_check
import pytest
import math
# note: The parameterize... | joaander/hoomd-blue | hoomd/hpmc/pytest/test_quick_compress.py | Python | bsd-3-clause | 6,587 | [
"HOOMD-blue"
] | 9f851d4cf6cfec816cf0aa5cf13e847a441da034dbb4bcb92520315e487a0e74 |
# -*- coding: utf-8 -*-
from .base import FunctionalTestCase
from .pages import game
DATE_REGEX = r'\[\d{1,2}-\d{1,2} \d{2}:\d{2}\] '
class LogTests(FunctionalTestCase):
"""Tests for logging events"""
def test_shows_new_game_message_on_game_creation(self):
self.story('Alice is a user who starts a new ... | XeryusTC/18xx-accountant | accountant/functional_tests/test_log.py | Python | mit | 21,085 | [
"Amber"
] | 29997ef29b9515d1e09c9a20bebc9887a1d201471a7f06667d9e99bff901a244 |
#
# @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/p4util/solvers.py | Python | lgpl-3.0 | 37,813 | [
"Psi4"
] | a25fcc64d52c18ae007f58d26ead6aa8a3171af86e4de8dc00c02746570d2890 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/ao2mo/r_outcore.py | Python | apache-2.0 | 13,798 | [
"PySCF"
] | e29d7b8fe9f2a8671260154e3ccf4520c3d3575b791ed106404c7126c23179e0 |
"""
This is the client of the Monitoring service based on Elasticsearch.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Utilities.Plotting.FileCoding import codeRequestInFileId
__R... | yujikato/DIRAC | src/DIRAC/MonitoringSystem/Client/MonitoringClient.py | Python | gpl-3.0 | 3,209 | [
"DIRAC"
] | d183f3d8b68125edb6882e9e9331a0727f5b23105a0e281e16ce695c30bc0552 |
# -*- 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 Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/search/paymentreceivingsearch.py | Python | gpl-2.0 | 5,433 | [
"VisIt"
] | 073fdd4446d33176ad85637cff270db9f6c1d21e5b8625cc5cb17a5d4dd2b0f0 |
# -- TRAINING for [250, 300] window
from keras.layers import containers
from keras.models import Sequential, model_from_yaml
from keras.layers.core import Dense, Dropout, AutoEncoder, MaxoutDense, Activation, Merge
from keras.layers.advanced_activations import PReLU
from keras.layers.embeddings import Embedding
from ke... | ml-slac/deep-jets | training/plotscript.py | Python | mit | 24,160 | [
"Gaussian"
] | 8b10d457a85c89ca5ed97557936041c869dcf6f73cf908c673c5814ab5613583 |
"""The Iteration/Expression Tree (IET) hierarchy."""
import abc
import inspect
import numbers
from cached_property import cached_property
from collections import OrderedDict, namedtuple
from collections.abc import Iterable
import cgen as c
from devito.data import FULL
from devito.ir.equations import DummyEq
from dev... | opesci/devito | devito/ir/iet/nodes.py | Python | mit | 36,966 | [
"VisIt"
] | c68aa96a30b46ce4e686f5ac673c319b9e6c6b83fdd8c2569a677647e26fda89 |
from DIRAC import S_ERROR, S_OK, gLogger
from DIRAC.ResourceStatusSystem.Client.ResourceStatus import ResourceStatus
class FTSRoute(object):
"""
This class represents the route of a transfer: source, dest and which server
"""
def __init__( self, sourceSE, targetSE, ftsServer ):
"""
:param sourc... | vmendez/DIRAC | DataManagementSystem/private/FTSAbstractPlacement.py | Python | gpl-3.0 | 2,654 | [
"DIRAC"
] | 0f5f33c9d0473a9f23ca5b0fb50c75935e25bf707335f769240e2ece242c31ab |
""" CStoJSONSynchronizer
Module that keeps the pilot parameters file synchronized with the information
in the Operations/Pilot section of the CS. If there are additions in the CS,
these are incorporated to the file.
The module uploads to a web server the latest version of the pilot scripts.
"""
import os
import... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Utilities/PilotCStoJSONSynchronizer.py | Python | gpl-3.0 | 14,299 | [
"DIRAC"
] | a2d2b2077a89ce5df44f32787a6ef41611ccd3ee5d66ba481cfce2cc6c8f8dcc |
#!/bin/env python
# -*- coding: utf-8 -*-
import os,re, sys, shutil
from Sire.IO import *
from Sire.Mol import *
from Sire.CAS import *
from Sire.System import *
from Sire.Move import *
from Sire.MM import *
from Sire.FF import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Maths import *
from Sire.Base ... | chryswoods/Sire | wrapper/Tools/FDTISingleFree.py | Python | gpl-2.0 | 59,222 | [
"Amber"
] | 6cf35c94e3e15a08e270321e7e4d2212b8eaa2fdb63abf8f9dc35bfcdbdbc46b |
#!/usr/bin/env python
from xml.dom.minidom import parse, parseString
import getopt
import sys
class DomHandler():
def __init__(self, file_name):
self.dom = parse(file_name)
def setValue(self, attr_name, attr_value):
result = False
for node in self.dom.getElementsByTagName('parameter'):
if node.getAttribut... | zillians/supercell | scripts/set_xml.py | Python | agpl-3.0 | 1,678 | [
"VisIt"
] | db0ba7713e12002b747ba65340dfc90c6d88fe6ac1214ae03914de76ee387857 |
#!/usr/bin/python
"""
Copyright 2015 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/getResourceByImage.py | Python | gpl-3.0 | 9,438 | [
"Galaxy"
] | dab5a5de5a9bfc72d3dfbbeb4fa18137ceb6f24fd9787fee3cc9873ab678c01b |
#!/usr/bin/env python
# encoding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/cantherm/qchemTest.py | Python | mit | 6,019 | [
"ChemPy"
] | a6b19c1ba0e4d6dc54c8699e1d42cb3132504ac51ff4e627819d5958741e6420 |
from __future__ import print_function
if __name__ == '__main__':
import matplotlib
matplotlib.use('Agg')
import pylab as plt
import os
import tempfile
import time
import numpy as np
import fitsio
from astrometry.util.fits import fits_table, merge_tables
from astrometry.util.file import trymakedirs
from astr... | gregreen/legacypipe | py/legacypipe/common.py | Python | gpl-2.0 | 86,929 | [
"Galaxy",
"Gaussian"
] | ffa9960f6cd8f81f6b147570847d5ef6cecd16d7d853b36d1cd864d617aca775 |
import numpy as np
from diffraction import Site
# Crystal Structure
lattice_parameters = (5.5876, 5.5876, 13.867, 90, 90, 120)
chemical_formula = 'BiFeO3'
formula_units = 6
g_factor = 2
space_group = 'R3c'
# Atomic sites
sites = {
'Bi1': Site('Bi3+', (0, 0, 0)),
'Fe1': Site('Fe3+', (0, 0, 0.2212)),
... | noahwaterfieldprice/bfo | bfo/constants.py | Python | gpl-2.0 | 613 | [
"CRYSTAL"
] | a4807ba7f67a7a8f2976d1a0f793181ff81324d29bbb3cd1935e95b8bbebfc7c |
"""Next-gen alignments with TopHat a spliced read mapper for RNA-seq experiments.
http://tophat.cbcb.umd.edu
"""
import os
import shutil
from contextlib import closing
import glob
import numpy
import pysam
try:
import sh
except ImportError:
sh = None
from bcbio.pipeline import config_utils
from bcbio.ngsali... | SciLifeLab/bcbio-nextgen | bcbio/ngsalign/tophat.py | Python | mit | 15,665 | [
"Bowtie",
"pysam"
] | 5cf61edbf3bcaf03ee61c47f83a5ce2d03c2e64683e0f48309715321770298d5 |
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import numpy as np
from . import MinCovDet
from ..utils.validation import check_is_fitted
from ..metrics import accuracy_score
from ..base import OutlierMixin
class EllipticEnvelope(OutlierMixin, MinCovDet):
"""An object for detecting... | kevin-intel/scikit-learn | sklearn/covariance/_elliptic_envelope.py | Python | bsd-3-clause | 8,336 | [
"Gaussian"
] | fe68be627c5dc1e15c341abf1fc35578e7e9f24b8db415e3e634f001c6b93cec |
# Copyright 2004 by Harry Zuzan. 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.
#Edited for speed for BioGui. Core function was preserved.
"""
Classes for accessing the inform... | fxb22/BioGUI | Utils/CelFileReader.py | Python | gpl-2.0 | 2,077 | [
"Biopython"
] | 9b6eb8ea421d224122475df2ca21bf35f53497e6e5bc505e90ea81d28dfad050 |
"""
Morlet Wavelet Analysis
=======================
Perform time-frequency decomposition using wavelets.
In this tutorial we will use Morlet wavelets to compute a time-frequency
representation of the data.
This tutorial primarily covers the ``neurodsp.timefrequency.wavelets`` module.
"""
###########################... | voytekresearch/neurodsp | tutorials/timefreq/plot_MorletWavelet.py | Python | apache-2.0 | 11,349 | [
"Gaussian"
] | 31202551aa6efb8c45ae9fdc21e160f331ad093a6ee612d62f90c07053de9a7c |
"""
# Copyright Nick Cheng, Brian Harrington, Danny Heap, 2013, 2014, 2015
# Distributed under the terms of the GNU General Public License.
#
# This file is part of Assignment 2, CSCA48, Winter 2015
#
# This is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | venkatkorapaty/Regex | regextree.py | Python | gpl-2.0 | 6,972 | [
"Brian"
] | 0a81df54bb5ae6f8dcfa99c3767155aac7e48ffbebd42cb4daf0047b37eb572e |
#!/usr/bin/env python
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# MSMTools 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... | gph82/PyEMMA | setup.py | Python | lgpl-3.0 | 9,557 | [
"MDTraj"
] | 82c262023203058cd09e81df5c2b9d664b406d60e3318742a7ab9b1ef4268a54 |
import os
import numpy as np
from shutil import copy
from subprocess import call
import quantumpropagator.GeneralFunctionsSystem as gfs
def launchSPfromGeom(geom):
'''
geom -> xyz name (with path)
given a xyz into a folder it launches the corresponding molcas calculation
'''
folder_path = ('.'... | acuzzio/GridQuantumPropagator | src/quantumpropagator/molcas.py | Python | gpl-3.0 | 2,768 | [
"MOLCAS"
] | 00cbf8527be862db7764c31dc18ab4a2d612cf75becf3d1929fbe3564b8db867 |
# This is the tutorial script.
# Most icons used in this script are from the Tango icon library (http://tango.freedesktop.org/)
# Created by Toni Sagrista
from __future__ import division
from gaia.cu9.ari.gaiaorbit.script import EventScriptingInterface
headerSize = 25
textSize = 13
twdelay = 0.01
arrowH = 7
gs = Ev... | vga101/gaiasky | assets/scripts/tutorial/tutorial.py | Python | mpl-2.0 | 19,757 | [
"Galaxy"
] | 8c49d1253b3a70c90af3b7da34d6da0fd1b06a12467449f3f8e3c4bafa49b3ce |
#######################################################################
#
# Copyright (C) 2001-2014, Michele Cappellari
# E-mail: cappellari_at_astro.ox.ac.uk
#
# This software is provided as is without any warranty whatsoever.
# Permission to use, for non-commercial purposes is granted.
# Permission to modify for pers... | zpace/MaNGA-fitting | ppxf_util.py | Python | mit | 12,458 | [
"Galaxy",
"Gaussian"
] | 37d499dff64fd5825c0a9bebf152b3da4a52d1a8da94a89eb6241a2492d12f8c |
# -*- coding: utf-8 -*-
'''
param_file.py
'''
import numpy as np
import logging
from .log import LOG_NAME
from .write import write_param_file
from .share import NcGlobals, SECSPERDAY, MAX_NC_CHARS
from .pycompat import iteritems, pyrange, pyzip
from . import plots
import os
from datetime import date
# ---------------... | UW-Hydro/RVIC | rvic/core/param_file.py | Python | gpl-3.0 | 20,513 | [
"NetCDF"
] | ed3139b057e831633dc5e16b19ab75fc93cd59f5d8de277189039e1bac66de30 |
#!/usr/bin/python
"""
This module includes a few basic functions useful for the pygme
Multi Gaussian Expansion models (Monnet et al. 1992, Emsellem et al. 1994)
python module.
For questions, please contact Eric Emsellem at eric.emsellem@eso.org
"""
"""
Importing the most import modules
This module requires NUMPY and S... | emsellem/pygme | pygme/mge_miscfunctions.py | Python | bsd-3-clause | 19,673 | [
"Galaxy",
"Gaussian"
] | 4945963b080de4a714077392ad6911697f22be7b83696ca3365135510c2d01bd |
# -*- coding: UTF-8 -*-
#
# Copyright (c) 2014, Yung-Yu Chen <yyc@solvcon.net>
#
# 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... | yungyuc/solvcon | solvcon/cloud.py | Python | bsd-3-clause | 13,444 | [
"VTK"
] | 3d645f0fda97233ba5799119b8725947b062ca96f9e4c6baf86d9c84354f07f2 |
#/###################/#
# Import modules
#
#ImportModules
import ShareYourSystem as SYS
#/###################/#
# Build the model
#
#Definition an instance
MyBrianer=SYS.BrianerClass(
).mapSet(
{
'BrianingNeurongroupDict':{
'N':100,
'model':
'''
dv/dt = (-(v+60*mV)+11*mV + 5.*mV*sqrt(20.*ms)*... | Ledoux/ShareYourSystem | Pythonlogy/build/lib/ShareYourSystem/Standards/Recorders/Brianer/01_ExampleCell.py | Python | mit | 1,259 | [
"Brian"
] | fbd88d4f30082f13230b9845e674b56021e7de22dbc873742a9e9435b4fe5e82 |
#!/usr/bin/env python2
# * **************************************************************** **
# File: audio.py
# Requires: Python 2.7+ (but not Python 3.0+)
# Note: For history, changes and dates for this file, consult git.
# Author: Brian Danilko, Likeable Software (brian@likeablesoftware.com)
# Copyright 2015-2017 M... | Bdanilko/EdPy | src/lib/audio.py | Python | gpl-2.0 | 8,576 | [
"Brian"
] | 05197e76145e7eceab4c9da58eebabe7da2fbe437d627e9066fec19944b01174 |
import re
import os
import random
import pickle
import warnings
import shlex
import shutil
from copy import deepcopy
from collections import defaultdict, Counter
from subprocess import call, Popen, PIPE
import glob
import numpy as np
import pandas as pd
import matplotlib
# try:
# os.environ['DISPLAY']
# except Ke... | ManuSetty/wishbone | src/wishbone/wb.py | Python | gpl-2.0 | 59,061 | [
"Gaussian"
] | 6a334d9d01b7f2c8357196a468aeaf4c9fd89b718ad90204fa70f8827e77df90 |
from starcluster.clustersetup import ClusterSetup
from starcluster.logger import log
class BowtieInstaller(ClusterSetup):
def run(self, nodes, master, user, user_shell, volumes):
for node in nodes:
log.info("Installing Bowtie 1.0.1 on %s" % (node.alias))
node.ssh.execute('wget -c -P /opt/software/bowtie http:... | meissnert/StarCluster-Plugins | bowtie_1_0_1.py | Python | mit | 952 | [
"Bowtie"
] | ddd320e2e547fbafc224d0fb088f122d855653cfc8ff513431260946ce0af8ea |
#!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 28.05.2021
# Author: Moritz Smolka
# Contact: moritz.g.smolka@gmail.com
#
from dataclasses import dataclass
import re
import itertools
import pysam
#for: --dev-cache
import os
import sys
import pickle
#... | fritzsedlazeck/Sniffles | src/sniffles/leadprov.py | Python | mit | 23,639 | [
"pysam"
] | 9c83eac4a2ec76a59e69ba9c7feb491d0056236c680de70e3b2cd32640affe75 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your opt... | GRArmstrong/invenio-inspire-ops | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 148,279 | [
"VisIt"
] | 6938be33b511189a8bf0b688e9f53ac0d89ded45cf3359754e09fd8a7632bd47 |
# coding: utf-8
import numpy as np
from .. import img_as_float
from ..restoration._denoise_cy import _denoise_bilateral, _denoise_tv_bregman
def denoise_bilateral(image, win_size=5, sigma_range=None, sigma_spatial=1,
bins=10000, mode='constant', cval=0):
"""Denoise image using bilateral filt... | michaelaye/scikit-image | skimage/restoration/_denoise.py | Python | bsd-3-clause | 11,219 | [
"Gaussian"
] | ce1a0ffb0b8ce3b6c4b30374b7ab1b454a8b4e7b2f908bf6b883118c4d43965b |
from collections import OrderedDict
from edc_constants.constants import REQUIRED, NOT_REQUIRED, ADDITIONAL, NOT_ADDITIONAL
from edc_visit_schedule.classes import (
VisitScheduleConfiguration, site_visit_schedules,
CrfTuple, MembershipFormTuple, ScheduleTuple, RequisitionPanelTuple)
from microbiome.apps.mb.con... | botswana-harvard/microbiome | microbiome/apps/mb_infant/visit_schedule/infant_birth_visit_schedule.py | Python | gpl-2.0 | 16,747 | [
"VisIt"
] | 60defb77eb9365f5f74423e0f78b9b3f2a9ac77ea5173b75c8b38ecbb5468480 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.moltemplate.org
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The origi... | quang-ha/lammps | tools/moltemplate/moltemplate/lttree_check.py | Python | gpl-2.0 | 144,120 | [
"LAMMPS"
] | 5d388bf9bac006c8b02eb1943d5b8ab7dce4c2e86630ad48049647fa8f395c36 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | modules/geochemistry/test/tests/kinetics/quartz_dissolution.py | Python | lgpl-2.1 | 1,106 | [
"MOOSE"
] | a8115ac9e014eec731f3d2388943a95612ee4080cb84797c07928a38baea9e96 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpa... | pgergov/belmis | config/urls.py | Python | mit | 1,805 | [
"VisIt"
] | 9b62843fd013a4e7f10a7324307a2b96dcfaa841e1ab583d6f74fbeb78a5ea34 |
#!/usr/bin/env jython
# copyright 2002 the Brothers Wilcox
# <mailto:zooko@zooko.com>
#
# This file is part of OvP.
#
# OvP is open source 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 Lic... | zooko/ogresvpixies | OvP.py | Python | gpl-2.0 | 7,593 | [
"VisIt"
] | 304c951b3a48219f22d001991739c2ccb1863c8be46599df76a57bbca29f8af5 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may n... | kwhitehall/climate | mccsearch/code/mccSearchUI.py | Python | apache-2.0 | 12,928 | [
"NetCDF"
] | 45c8411ea587fe839cea9f9447ad000b10fe517a39db5f320077b4115515227a |
"""
======================================
Decision Tree Regression with AdaBoost
======================================
A decision tree is boosted using the AdaBoost.R2 [1] algorithm on a 1D
sinusoidal dataset with a small amount of Gaussian noise.
299 boosts (300 decision trees) is compared with a single decision tr... | depet/scikit-learn | examples/ensemble/plot_adaboost_regression.py | Python | bsd-3-clause | 1,404 | [
"Gaussian"
] | f31e5cdaa1c3381fab5a942cd13dd01ecff44d5c20ccd2b1498f453e327abf6a |
from numpy.testing import assert_equal, assert_array_equal, assert_allclose
from nose.tools import assert_true, assert_raises, assert_not_equal
from copy import deepcopy
import os.path as op
import numpy as np
from scipy import sparse
import os
import warnings
from mne.utils import (set_log_level, set_log_file, _TempD... | yousrabk/mne-python | mne/tests/test_utils.py | Python | bsd-3-clause | 17,609 | [
"Mayavi"
] | 7e1e91de00ea1f615c522956d52428c42be43e2a4c2b3c70e7576d4f8c7b7e21 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | tbereau/espresso | samples/python/visualization.py | Python | gpl-3.0 | 6,903 | [
"ESPResSo",
"Mayavi"
] | d0dd0dc0b1b4b78c59db437aa2bd5dec3d84b2f049b641ac7cb043ad4e623d2c |
""" Class to manage connections for the Message Queue resources.
Also, set of 'private' helper functions to access and modify the message queue connection storage.
They are ment to be used only internally by the MQConnectionManager, which should
assure thread-safe access to it and standard S_OK/S_ERROR erro... | yujikato/DIRAC | src/DIRAC/Resources/MessageQueue/MQConnectionManager.py | Python | gpl-3.0 | 15,401 | [
"DIRAC"
] | aee591e14082795201d33c5ec9a473cb3deae4e88e214a825d84760c9da54db7 |
"""
A Tkinter based backend for piddle.
Perry A. Stoll
Created: February 15, 1999
Requires PIL for rotated string support.
Known Problems:
- Doesn't handle the interactive commands yet.
- PIL based canvas inherits lack of underlining strings from piddlePIL
You can find the latest version ... | jandom/rdkit | rdkit/sping/TK/pidTK.py | Python | bsd-3-clause | 16,569 | [
"RDKit"
] | 0c2dcbce16318886a434b2ba48970badab67523dd4bf6f60f5d35e0630319367 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/cc/test/test_uccsd_lambda.py | Python | apache-2.0 | 10,539 | [
"PySCF"
] | 6730675b24ce89cb9e0b3b436652c241db5fc5398d6b02b83551e8f0091241f9 |
"""Example using the operator of fixed-template linearized deformation.
The linearized deformation operator with fixed template (image) ``I`` maps
a given displacement field ``v`` to the function ``x --> I(x + v(x))``.
This example consider a 2D case, where the displacement field ``v``
is a Gaussian in each component... | kohr-h/odl | examples/deform/linearized_fixed_template.py | Python | mpl-2.0 | 2,749 | [
"Gaussian"
] | 843942aac519d9fb6c843727a1de87c577f8e17b6ab41359e4809f054989e4d7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import shutil
import subprocess
import matplotlib.pyplot as plt
import xml.etree.ElementTree as ET
import z2pack
# Edit the paths to your Quantum Espresso and Wannier90 here
qedir = '/home/greschd/software/spack/opt/spack/linux-ubuntu20.04-skylake/gcc-9.3.0/qu... | Z2PackDev/Z2Pack | examples/fp/espresso/6.2/Bi/run.py | Python | gpl-3.0 | 3,047 | [
"ESPResSo",
"Quantum ESPRESSO",
"Wannier90"
] | 26a2072afb17a3846e764dc71283b2def6954b9c46c0ebb04a03c1848aa4292b |
import LFPy
import neuron # new
import numpy as np
import pickle
import os
def simulate_cells_serially(stimolo,
cell_ids,
data_name,
population_parameters,
cell_parameters,
... | espenhgn/LFPy | examples/mazzoni_example/single_cell.py | Python | gpl-3.0 | 7,625 | [
"NEURON"
] | 3bce907b0f726a62fbd349cd7c0c841876e9f4f656d30968216307d200e287c7 |
"""
Linter classes containing logic for checking various filetypes.
"""
import ast
import os
import re
import textwrap
from xsslint import visitors
from xsslint.reporting import ExpressionRuleViolation, FileResults, RuleViolation
from xsslint.rules import RuleSet
from xsslint.utils import Expression, ParseString, Stri... | gymnasium/edx-platform | scripts/xsslint/xsslint/linters.py | Python | agpl-3.0 | 61,116 | [
"VisIt"
] | 1d3739f4056e128ef9585b94d718229e0031cdc5a5c38ab267ea452e81ac62ee |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-add-resources
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Add resources from the BDII database for a given VO
"""
__RCSID... | coberger/DIRAC | ConfigurationSystem/scripts/dirac-admin-add-resources.py | Python | gpl-3.0 | 15,883 | [
"DIRAC"
] | c77e8cb225b1c8d2c5fc056e92ed3ca1b65d5dfc6d5798210c4239204e3b4e56 |
# -*- coding: utf-8 -*-
from datetime import (
datetime,
timedelta,
)
from inspect import isclass
import requests
from atomx.version import API_VERSION, VERSION
from atomx import models
from atomx.utils import (
get_model_name,
model_name_to_rest,
)
from atomx.exceptions import (
APIError,
Mode... | atomx/atomx-api-python | atomx/__init__.py | Python | isc | 18,863 | [
"VisIt"
] | c67dfaff3f62ba156263ebf78462c2cc050d681e353afcab538dfc96dcee5a35 |
##############################################################################
#
# Copyright (c) 2003 Zope Foundation and Contributors.
# All Rights Reserved.
#
# This software is subject to the provisions of the Zope Public License,
# Version 2.1 (ZPL). A copy of the ZPL should accompany this distribution.
# THIS SOF... | c0defreak/python-for-android | python-modules/zope/zope/interface/advice.py | Python | apache-2.0 | 7,245 | [
"VisIt"
] | 2fd76a01410f04bc11e363572a1e7c387f2a94f2dda88ab1a9501b68c5ada31b |
"""
Tests for transformer objects.
"""
from __future__ import division
from __future__ import unicode_literals
from deepchem.molnet import load_delaney
from deepchem.trans.transformers import FeaturizationTransformer
from deepchem.trans.transformers import DataTransforms
from tensorflow.examples.tutorials.mnist import... | ktaneishi/deepchem | deepchem/trans/tests/test_transformers.py | Python | mit | 24,790 | [
"Gaussian"
] | f1fa5e63bd736fd4da39ac9747c1a99c51c970544f085628ba5a0ba47fc836d4 |
# Copyright 2013 the V8 project authors. 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 copyright
# notice, this list of conditi... | x684867/nemesis | src/node/deps/v8/test/benchmarks/testcfg.py | Python | mit | 6,609 | [
"Gaussian"
] | b27fe37598af4c908cace8dbbe204208eab962e2c24ce0aa2cd3261ac149ddeb |
# ##### 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/object_add_chain.py | Python | gpl-3.0 | 5,456 | [
"Brian"
] | aca8d807e367e92183f029d83301c32a34eab1aba7521ee43b26bf1857b886c6 |
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# 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
... | espressopp/espressopp | src/integrator/LangevinThermostatOnGroup.py | Python | gpl-3.0 | 2,223 | [
"ESPResSo"
] | 83c3e60fd33ffa696b237305cb3acbb78af08b50591a17380952967c5ee74616 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
from scipy.stats import skew
import argparse
import copy
# evaluate the probed surface to get average values mapped to original segmentation
def Execute(args):
print("get average along line probes")
reader_lines = vmtkscri... | kayarre/Tools | vmtk/avg_probe_surface.py | Python | bsd-2-clause | 4,337 | [
"VTK"
] | c45f922f81d0f2691853aa2eecb9f5bf412c7728011bcba4fc14532b39132583 |
from __future__ import print_function, division
import os
import numpy as np
try:
asstr = np.compat.asstr
except AttributeError: # For Numpy 1.4.1
import sys
if sys.version_info[0] >= 3:
def asstr(s):
if isinstance(s, bytes):
return s.decode('latin1')
retu... | atpy/atpy | atpy/hdf5table.py | Python | mit | 11,069 | [
"VisIt"
] | 83f5b3e9dcb7eff96196b7b4b6499df0e993bbf2a282ef30cce85b76fb8fb178 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | rikima/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 50,292 | [
"Gaussian"
] | 22437810ccd0e2896959e12a4ba96e0747159990dee7d370654e891dd8d7ed85 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDeseq(RPackage):
"""Differential gene expression analysis based on the negative binomial
... | LLNL/spack | var/spack/repos/builtin/packages/r-deseq/package.py | Python | lgpl-2.1 | 1,546 | [
"Bioconductor"
] | 643543456af0faf95a016b4bfd4f1cfc0c9e5d004b2cb59d0835dc11a6c711f1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements abstract base classes for post-processing entries.
Any class which modifies entries should inherit these classes.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, ... | dongsenfo/pymatgen | pymatgen/entries/post_processors_abc.py | Python | mit | 1,391 | [
"pymatgen"
] | 76c909446890af1fee0f2cbbd9eb14b384a48f492b7ee71b1854fef06d894479 |
"""
ElasticSearch wrapper
"""
import logging
from cmreslogging.handlers import CMRESHandler
from DIRAC.Resources.LogBackends.AbstractBackend import AbstractBackend
class ElasticSearchBackend(AbstractBackend):
"""
ElasticsearchBackend is used to create an abstraction of the handler and the formatter concepts ... | DIRACGrid/DIRAC | src/DIRAC/Resources/LogBackends/ElasticSearchBackend.py | Python | gpl-3.0 | 3,113 | [
"DIRAC"
] | f661632aac3ed6781fe2bbc95573c710421e52bbf4493e1bf1132a8a1205ace4 |
# -*- coding:utf-8 -*-
# @author xupingmao
# @since 2016/12/09
# @modified 2021/12/05 11:23:34
"""xnote工具类总入口
xutils是暴露出去的统一接口，类似于windows.h一样
建议通过xutils暴露统一接口，其他的utils由xutils导入
"""
from __future__ import print_function
from __future__ import absolute_import
from threading import current_thread
from xutils.imports im... | xupingmao/xnote | xutils/__init__.py | Python | gpl-3.0 | 9,260 | [
"VisIt"
] | cb17872eb5c6ecc577a93bef69040bf95ebb31525209f05fad1a5924f49ea7c3 |
import numpy as np
from numpy.polynomial import Polynomial, Chebyshev, Legendre,\
Laguerre, Hermite, HermiteE
from scipy.misc import factorial
import pdb
from .core import ParamFunction, EMPTY_VAR
from .utils import fsign, dtype_c2r, dtype_r2c
__all__ = ['PReLU', 'Poly', 'Mobius', 'Georgiou1992', 'Gaussian', 'PMu... | GiggleLiu/poorman_nn | poornn/pfunctions.py | Python | mit | 10,358 | [
"Gaussian"
] | f3c2ce53668eddf57da22fc6902005cebfb3dfd14196f5e990e6be3a231ad831 |
import os
import subprocess
import pysam
from TestUtils import BAM_DATADIR, force_str
def build_fetch_with_samtoolsshell(fn):
retval = os.popen("samtools view {} 2> /dev/null | wc -l".format(fn)).read()
return int(retval.strip())
def build_fetch_with_samtoolspipe(fn):
FNULL = open(os.devnull, 'w')
w... | kyleabeauchamp/pysam | tests/AlignmentFileFetchTestUtils.py | Python | mit | 2,973 | [
"pysam"
] | 26c8a84b6583991118c129fae0639b8e975a166c2e4966eb16bba9f403ab2ae1 |
import numpy as np
from ase.units import Bohr, Hartree
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.eigensolvers.rmm_diis_old import RMM_DIIS
from gpaw.mixer import Mixer
from gpaw.response.df0 import DF
from gpaw.response.bse import BSE
GS = 1
df = 1
bse = 1
check_spectrum = 1
if GS:
a = 4.043
... | robwarm/gpaw-symm | gpaw/test/bse_aluminum.py | Python | gpl-3.0 | 1,837 | [
"ASE",
"GPAW"
] | fad548500b10af1189468f0b098271751aab36881b942ca4b474e1ef752619a4 |
# pre_NAMD.py
# Creates the files used for NAMD based on the .pdb file dowloaded from PDB bank
#
# Usage:
# python pre_NAMD.py $PDBID
#
# $PDBID=the 4 characters identification code of the .pdb file
#
# Input:
# $PDBID.pdb: .pdb file downloaded from PDB bank
#
# Output:
# $PDBID_p.pdb: .pdb file with water mole... | Xiaofei-Zhang/NAMD_Docking_pipeline | pre_NAMD/pre_NAMD.py | Python | mit | 2,553 | [
"NAMD",
"VMD"
] | 093fdf8733f3fa018279e1b2e4efd7f4a4550a1de0df8c03ef04567ed51c5f01 |
#!/usr/bin/env python
import sys
import os
import subprocess
#Local imports
from chemistry import elementdata, io
'''Usage: python make_isa_files.py'''
description='''
This program takes, as input, a generic template file, and creates
input files using geometries from all .gxyz files that are
located in the pwd and ... | mvanvleet/workflow-for-force-fields | scripts/make_isa_files.py | Python | gpl-3.0 | 4,328 | [
"GAMESS"
] | 19bf501d11ff1eae8d44918e3bf5f1e97a7b47a33b6ccf64c9947448b63a1831 |
#
# Python Design Patterns: Visitor
# Author: Jakub Vojvoda [github.com/JakubVojvoda]
# 2016
#
# Source code is licensed under MIT License
# (for more details see LICENSE)
#
import sys
#
# Visitor
# declares a Visit operation for each class of ConcreteElement
# in the object structure
#
class Visitor:
def visitEle... | JakubVojvoda/design-patterns-python | visitor/Visitor.py | Python | mit | 1,965 | [
"VisIt"
] | edb6a9d057bbe80ea0976d7c0425cb48f0e7c28031656065a86e2165dd78e5bf |
#!/usr/bin/env python3
import os
import subprocess
from apt import liteapt
from gi.repository import Gtk
class SystrayApp(object):
def __init__(self):
self.apt = liteapt
self.tray = Gtk.StatusIcon()
self.menu = Gtk.Menu()
self.menu_about = Gtk.MenuItem()
self.menu_check_u... | darthlukan/liteupdater | usr/lib/python3/dist-packages/liteupdater/liteupdater.py | Python | gpl-2.0 | 2,842 | [
"Brian"
] | 9280841c64a8cd5b0eb906cf96492886738fca19ccdb8688de72a638c89583a4 |
class Visit:
visitList = {}
def __init__(self, date, cost, idNum=None):
if idNum == None:
self.idNum = len(Visit.visitList) + 1
else:
self.idNum = idNum
self.date = date
self.cost = cost
self.doctor = None
Visit.visitList[self.idNum] = se... | zhaladshar/HealthView | classes.py | Python | gpl-3.0 | 7,792 | [
"VisIt"
] | d4fb45150bd6f492057063663a4f4975c608eee15c0524f7f9e9203eee657704 |
# -*- coding: utf-8 -*-
"""Functions for FIR filter design."""
from math import ceil, log
import operator
import warnings
import numpy as np
from numpy.fft import irfft, fft, ifft
from scipy.special import sinc
from scipy.linalg import (toeplitz, hankel, solve, LinAlgError, LinAlgWarning,
ls... | scipy/scipy | scipy/signal/_fir_filter_design.py | Python | bsd-3-clause | 47,821 | [
"Brian"
] | 16236c68dd79598df0d04947c1a1682f20683069bd9ae74b4b2caf3884e0c092 |
import sys # Import sys to write to output files
print("#----------------------------------------------------------------------------------------------#")
print("#----------------------------------------------------------------------------------------------#")
print("# Script to Extract the Optimized Struc... | i4hashmi/Python_Scripts | Extract_Optimized_Molecule/Extract_Optimized_Molecule_Gaussian+ORCA.py | Python | gpl-3.0 | 13,194 | [
"Gaussian",
"ORCA"
] | e16f2e48c307a2dc2137d1c194678093f94074effff4916af23f06987b2eb86a |
#
# The OpenDiamond Platform for Interactive Search
#
# Copyright (c) 2011-2019 Carnegie Mellon University
# All rights reserved.
#
# This software is distributed under the terms of the Eclipse Public
# License, Version 1.0 which can be found in the file named LICENSE.
# ANY USE, REPRODUCTION OR DISTRIBUTION OF T... | cmusatyalab/opendiamond | opendiamond/server/server.py | Python | epl-1.0 | 12,962 | [
"BLAST"
] | abd79741b91a8cd6db1b36181cf40409da2cdd0676a2652ba7e770e4958f6216 |
#
# 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/test/zoo/orca/learn/test_utils.py | Python | apache-2.0 | 9,763 | [
"ORCA"
] | d0f6f780b3ef6bf3ef4a6392ff2f6a48740e0d6d49bda56f53581ac442181583 |
# Copyright 2015 datawire. 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 applicable law or agr... | bozzzzo/quark | quarkc/grammar.py | Python | apache-2.0 | 2,034 | [
"VisIt"
] | 6973741bcffe414a619c77c30d4f301412e055110927b34c6e384e1ece4aa05f |
# -*- coding: utf-8 -*-
"""
solace.application
~~~~~~~~~~~~~~~~~~
The WSGI application for Solace.
:copyright: (c) 2010 by the Solace Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
import os
from urlparse import urlparse, urlsplit, urljoin
from fnmatch import ... | mitsuhiko/solace | solace/application.py | Python | bsd-3-clause | 17,413 | [
"VisIt"
] | b562bf7aea007ceefe38c230bc2f5980fac6cf05aedcf86eedd0e22c0c2a15e8 |
##############################################################################
# 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 | lib/spack/spack/spec.py | Python | lgpl-2.1 | 139,193 | [
"VisIt"
] | a1d238a8b799e985e5f33571c0cf789ad18346557ebaadfea1e9a03a499c3c5b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains some utility functions and classes that are used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy Hautier"
_... | vorwerkc/pymatgen | pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py | Python | mit | 42,284 | [
"pymatgen"
] | cbf468c6076989b8de8311f8b5a32a746180ff6f84a9a28f8b2a259e1d9e0a7b |
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