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#!/usr/bin/env python
"""
Get the size of the given file or a list of files
Example:
$ dirac-dms-data-size /formation/user/v/vhamar/Example.txt
------------------------------
Files | Size (GB)
------------------------------
1 | 0.0
------------------------------
"""
f... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_data_size.py | Python | gpl-3.0 | 2,654 | [
"DIRAC"
] | 2670c7cade238c11b281d1664bc41a8191a73da301f0c5616eebe763d38678fe |
# -*- coding: utf-8 -*-
#
# structural_plasticity.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 L... | hakonsbm/nest-simulator | pynest/examples/structural_plasticity.py | Python | gpl-2.0 | 14,176 | [
"Gaussian",
"NEURON"
] | ce06c1c72854768535b68d86d2d73b63d67b61def71f8b84cf7e59cc624420bd |
from os import listdir
from os.path import isfile, join
from Bio.Align.Applications import ClustalOmegaCommandline
import os
path = "/Volumes/VATagliacollo/GitHub/Phyloworks/projects/VATagliacollo/phylo_of_gymn/sequences/Gymnotiformes"
fastas = [f for f in listdir(mypath) if isfile(join(mypath, f))]
os.chdir('/Vol... | Tagliacollo/Phyloworks | py_scripts/genbank_aln.py | Python | gpl-3.0 | 4,148 | [
"Bioconda"
] | b3debea8200c5a96e144c35a551ecdcfd7f869fa196d15bc3a16e323de54dc4c |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 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/player.py | Python | gpl-2.0 | 40,590 | [
"Brian"
] | 3c48c55b886f931a845c6ccce1fd5e2f4d7fefcf31eac7267dac3d74e031f420 |
#!/usr/bin/env python2.7
import argparse, sys
from collections import Counter, defaultdict
from string import maketrans
import re
from fast5tools.samclass import *
parser = argparse.ArgumentParser(description="""
DESCRIPTION
Input = samtools mpileup output.
Given sorted BAM/SAM do:
samtools mpi... | JohnUrban/fast5tools | bin/samRefPosAlnComposition.py | Python | mit | 14,084 | [
"BWA"
] | d0742e74f17c27773809bedc1f83085d5f059a15d12962b3d98323580a36f8b5 |
import pysam
import sys
import heapq
from collections import defaultdict
from operator import attrgetter
from itertools import tee
###################################################################################################
class Variant(object):
"""
Simple class to encapsulate variant information.
... | andyrimmer/Platypus | src/python/graph.py | Python | gpl-3.0 | 25,816 | [
"pysam"
] | def210890c54ca82d06638ad478dd0294e2bef84273860780d4460657be7d1ac |
from __future__ import print_function, division
import numpy as np
from ..utils.units import angstrom_to_bohr
#import pymatgen
__all__ = ['structure_to_abivars']
def structure_to_abivars(structure):
"""Get abinit variables from a pymatgen.Structure object."""
rprim = structure.lattice.matrix * angstrom_to_... | trangel/OPTpy | OPTpy/io/structures.py | Python | gpl-3.0 | 1,029 | [
"ABINIT",
"pymatgen"
] | 96d3a4118467fb2cdf320216c99a3d350f82adb8f03e28d432f7d318cc40acfb |
# accounts low-dimensional cases in 3D
# (NB the PW-based codes are forced to put vacuum in a "non-periodical" direction)
# extends ASE object(s)
# Author: Evgeny Blokhin
# TODO: account all "pseudo-periodic" cases for 1d and 0d
import math
from numpy.linalg import det
from ase.data import chemical_symbols, covalen... | tilde-lab/tilde | tilde/classifiers/dimensions.py | Python | mit | 2,192 | [
"ASE"
] | 7c0f8bf4e7d2384ba54da8d2428441a2be1b9ea213b24334a9c9a8e0d7a7546e |
# 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 a... | clarko1/Cramd | appengine/flexible/datastore/main.py | Python | apache-2.0 | 2,182 | [
"VisIt"
] | 690f7e05780cd6626049906b9c30abf8cc3c141f57de8e51d3fc142bce15334a |
# Copyright 2010-2020 Kurt McKee <contactme@kurtmckee.org>
# Copyright 2002-2008 Mark Pilgrim
# All rights reserved.
#
# This file is a part of feedparser.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistrib... | SickGear/SickGear | lib/feedparser_py3/http.py | Python | gpl-3.0 | 9,479 | [
"NetCDF"
] | 2fb873dd9606d19cb49a41c896bc35025cc96a684b5b0e363310355ecd250485 |
#!/usr/bin/env python
"""
DESCRIPTION
This script is provides helpful definitions for interactively visualizing
manufactured quantities within a Mayavi
(http://code.enthought.com/projects/mayavi/) or IPython session. It is
/not/ a standalone program and should be %run from within an 'python
-wthre... | nicholasmalaya/paleologos | disputatio/dissertation/mms/vizcoeffs.py | Python | mit | 5,930 | [
"Mayavi"
] | caa54ef8d51126755d01b430f07bdd8be9f09af82a37f88a34cc05bc5833af91 |
# -*- coding: utf-8 -*-
#
# El discurso de Zoe
#
# Copyright (C) 2015 GUL UC3M
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | rmed/discurso_zoe | scenarios/biblioteca_ai.py | Python | gpl-3.0 | 4,416 | [
"SIESTA"
] | 0ea6a8e3f16f34914d624d1221a4f1b812a897f13a85fad3a109868e2e3e1cb0 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/speech_generator.py | Python | gpl-3.0 | 77,119 | [
"ORCA"
] | efe6fe9101530f596d7ccc01c9c4f898378e20f6179908189046b430193787b5 |
# 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 (t... | apache/allura | Allura/allura/model/auth.py | Python | apache-2.0 | 40,227 | [
"VisIt"
] | b30acaad5635086ed986d2d13271c9d7bc066f22623412584956c2364905874e |
from collections import Counter
from logging import getLogger
from kademlia.node import Node, NodeHeap
from kademlia.utils import gather_dict
class SpiderCrawl(object):
"""
Crawl the network and look for given 160-bit keys.
"""
def __init__(self, protocol, node, peers, ksize, alpha):
"""
... | faisalburhanudin/kademlia | kademlia/crawling.py | Python | mit | 6,286 | [
"exciting"
] | 5a03643c674d47100681e01816ac42b28cfa92c34630d8a79ad0b4e671026269 |
#coding:utf-8
from django.shortcuts import render
from django.http import HttpResponseRedirect
from django.http import HttpResponse
from .models import Accommodation,User,Room
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
import math,datetime
from django.utils import timezone
from django.db.m... | DingYuanfang/Django-simple-liwu | liwu/views.py | Python | mit | 6,517 | [
"VisIt"
] | 2721f8172173024d4d15791005f432a8f73e7925b72d46fa676ff615f1fe3604 |
from Cython.Compiler.Main import compile_single, CompilationOptions
from Cython.Compiler.TreeFragment import parse_from_strings
from Cython.Compiler.Visitor import TreeVisitor
from Cython.Compiler import Nodes
from Cython.Compiler.AutoDocTransforms import EmbedSignature
options = CompilationOptions()
options.include_p... | mcpv/PyAV | scratchpad/parse.py | Python | bsd-3-clause | 1,962 | [
"VisIt"
] | 397be079ece3171f2da0a4a7038850a9a5e56bee1c04d8646d7ffb5cc774b455 |
# ========================== Start Copyright Notice ========================== #
# #
# Copyright 2014 F.D.I.S. #
# This file is part of Kinetic Gunner: Gunner of Angst ... | CertainlyUncertain/Kinetic-Gunner-Gunner-of-Angst | engine.py | Python | gpl-3.0 | 4,816 | [
"VisIt"
] | 2028031442d82eb6c801af4738d655b00323643c07bbdb5b82f246bba5806125 |
# coding: utf-8
from __future__ import unicode_literals
import os
from unittest import TestCase
import unittest
from pymatgen.analysis.molecule_structure_comparator import \
MoleculeStructureComparator
from pymatgen.core.structure import Molecule
from pymatgen.io.qchemio import QcOutput
__author__ = 'xiaohuiqu'
... | Dioptas/pymatgen | pymatgen/analysis/tests/test_molecule_structure_comparator.py | Python | mit | 4,887 | [
"pymatgen"
] | 30a4f79ed9c5ef4055ea9ea192c728bb5dea27835580b434b24d565115431a54 |
# https://stackoverflow.com/a/30516254
import ast
import math
locals = {key: value for (key, value) in vars(math).items() if key[0] != '_'}
locals.update({"abs": abs, "complex": complex, "min": min, "max": max, "pow": pow, "round": round})
class Visitor(ast.NodeVisitor):
def visit(self, node):
if not isi... | redfast00/RCPU | RCPU/safe_eval.py | Python | mit | 1,105 | [
"VisIt"
] | a413bddfdbefe57642fb1511731b5baadc1e37bde4558864f5ca607c0e9fab6a |
#!/usr/bin/env python
"""Universal feed parser
Visit http://diveintomark.org/projects/feed_parser/ for the latest version
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom feeds
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: libxml2 <http://xmlsoft.org/python.html>
"""
__version__ = "3.0-fc... | qilicun/python | python2/PyMOTW-1.132/PyMOTW/Queue/feedparser.py | Python | gpl-3.0 | 87,457 | [
"VisIt"
] | b69c44e82e225282668aca92b1195864da6da127bcd280ade390b6b76006303b |
""" class Wannier provides the function get_wannier_localization_matrix and initial_wannier.
"""
import numpy as np
from Scientific.IO.NetCDF import NetCDFFile as netCDF
def dagger(matrix,copy=1):
# First change the axis: (Does not allocate a new array)
matrix_conj=np.swapaxes(matrix,0,1)
if c... | conwayje/ase-python | ase/calculators/jacapo/utils/wannier.py | Python | gpl-2.0 | 23,946 | [
"ASE",
"NetCDF"
] | 50c86e67f66648df000ee91cbe97e46ef7898191839e0498d5372d75b9d83d55 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | ened/scancode-toolkit | tests/cluecode/test_copyrights.py | Python | apache-2.0 | 182,899 | [
"Brian",
"VisIt"
] | b06e18101e05fdcde40a8ec549d73dcb7d63bc668b71adf061cc8d00dc70a65f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/topology/guessers.py | Python | gpl-2.0 | 12,275 | [
"Amber",
"CHARMM",
"GROMOS",
"MDAnalysis",
"VMD"
] | 8c491f99ad6a90ad5da0b58eae9b695f50ad3d27be22634a3bef05ad08d49f19 |
#!/usr/bin/env python3
# coding=utf-8
from __future__ import print_function, unicode_literals
import os
import os.path
import nose.tools as nose
from tests.utils import run_filter
def test_query_ignore_case():
"""should ignore case when querying playlists"""
results = run_filter('playplaylist', 'GuARDians... | caleb531/play-song | tests/test_playplaylist.py | Python | mit | 2,343 | [
"Galaxy"
] | b8c0b6a926fccc2cdeef959a13e198296c0017cde7c427ab0102d404600dc244 |
"""
Creates a precipitation time series for Charlottesville Airport using the NWS
AHPS precipitation data available here:
http://water.weather.gov/precip/download.php
Code will automtically download required files if files are not available within
the current working directory.
To change the location, find the hrap... | goodalljl/hydroinformatics_class | Class24_GetPrecipTSForCville.py | Python | mit | 2,966 | [
"NetCDF"
] | 89f758ab97acdd1bbe9c396763940ba97ad3b58f50d502956bc774dd7d71f25a |
import os
import matplotlib
#matplotlib.use('Agg')
import seaborn
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import plotly.plotly as py
import plotly.graph_objs as go
import numpy
import scipy
import scipy.stats
import pandas
import itertools
import sklearn.manifold
import sklearn.decomposi... | phageghost/pg_tools | pgtools/myplots.py | Python | mit | 65,648 | [
"Bowtie"
] | 5735e2cfe09669990b4456072c3e05d40759552a197ff044193f079bdfaaf0a8 |
# -*- coding: utf-8 -*-
import cv2
import numpy as np
# import matplotlib.pyplot as plt
import math
from sample.grading.Box import Box
from sample.grading.AnswerSheet import AnswerSheet
from sample.grading.helperFunction import getNameFromDatabse, updateScore
import os
import time
import sys
# import Tkinter
import tki... | Hubert51/AutoGrading | sample/grading/main.py | Python | mit | 10,141 | [
"Gaussian"
] | 9993d5fa24523511d5cf9aeb642426c8c2d9bb576370802320cdef47d65ef345 |
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
#
""" Implements a class used to represent N-ary trees
"""
from __future__ import print_function
from rdkit.six.moves import cPickle
# FIX: the TreeNode class has not been updated to new-style classes
# (RD Issue380) because that would break all ... | rvianello/rdkit | rdkit/ML/DecTree/Tree.py | Python | bsd-3-clause | 7,583 | [
"RDKit"
] | f1926f63629b4ffd73be5d470cbfe5c6d235ed83621e1bb11f32cfae1cef0f4f |
"""
A fast implementation of the Voigt function.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from math import sqrt, pi
import numpy as np
__all__ = ['voigt_wofz', 'voigt']
sqrtpi = sqrt(pi)
# u values corresponding to H table values below
U = ... | cwfinn/igmtools | igmtools/calculations/voigt.py | Python | bsd-3-clause | 74,431 | [
"Gaussian"
] | 51fe1e277f04ca6145e68ba443448de526240f885f4e0a75d3fe3001fe8dea8d |
#
# Copyright (C) 2013,2014 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | sehrhardt/espresso | samples/python/slice_input.py | Python | gpl-3.0 | 2,771 | [
"ESPResSo"
] | 202b3ebcaca5e27835e63f4823e2a5e7128c87646d5e59dff00f854a35101fcb |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
import multiprocessing
import os
import unittest
import warnings
import pytest
import numpy as np
from monty.serialization import loadfn, dumpfn
from monty.tempfile import ScratchDir
from pymatgen.core import... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_pourbaix_diagram.py | Python | mit | 12,731 | [
"pymatgen"
] | 73b2e20a98c485264b38986d8116eda9ee7b69f91d615a591bb73f72e398dcaf |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 y... | jat255/hyperspy | hyperspy/tests/io/test_hdf5.py | Python | gpl-3.0 | 31,740 | [
"Gaussian"
] | 53d6dbc795ca75c90f8ed8c3f8a6fedbd49612069a48e437cf2ee77a2a22ff8c |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | jH0ward/psi4 | psi4/share/psi4/scripts/setenv.py | Python | lgpl-3.0 | 11,530 | [
"Psi4"
] | d74ffb78334410868093fe160d38cd4f501c85868e73b550898e52ee2974f044 |
#!/usr/bin/env python
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser G... | dilawar/moose-full | moose-examples/paper-2015/Fig6_NetMultiscale/Fig6BCDE.py | Python | gpl-2.0 | 38,642 | [
"Gaussian",
"MOOSE",
"NEURON"
] | 7a83ccc6611e238a2d90ad4d48258e6324dda892a36e307e5f25ba6a0f8d820b |
from Firefly import logging
from typing import Dict
GROUP = 'group'
ROOM = 'room'
ZONE = 'zone'
class DeviceGroups(object):
def __init__(self, firefly):
self.firefly = firefly
self._groups = Groups(self)
self._rooms = Rooms(self)
self._zones = Zones(self)
@property
def groups(self):
return... | Firefly-Automation/Firefly | Firefly/helpers/device_groups.py | Python | apache-2.0 | 4,448 | [
"Firefly"
] | 1bcab8f30aef0d5b7fe9e9061b958c26c3f3255e12f7125d6fbe32267421a1d1 |
#!/usr/bin/python
"""
change the contig indices to number corresponding to row and col.
This is for matlab plotting so use 1 indexed values
We want each contig to blast against many other contigs so we
do not take only the best match. Instead we take all matches
Edit History:
2015.05.25 Created
2015.05.28 Changed fil... | brianyu2010/Mini-Metagenomic_Analyses | snakehelper_contig_similarity.py | Python | gpl-3.0 | 1,961 | [
"BLAST"
] | f8992b706eeda2c1298eb41a64a0751885405ccf7aac49bb997808b4143a083c |
# $Id$
#
# Copyright (C) 2007 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.
#
import doctest
import unittest
from rdkit.VLib imp... | greglandrum/rdkit | rdkit/VLib/UnitTestVLib.py | Python | bsd-3-clause | 4,952 | [
"RDKit"
] | 6e611285e00ecb81f4eabfeba37a7f1c165420cc70fbef2c19bbc41e1e75f06c |
#!/usr/bin/env python3
import sys
import numpy as np
import argparse
import matplotlib.pyplot as plt
from plotTools import addContourf
from analysisTools import sensibleIds, groundOffset, quadrantAnalysis
from netcdfTools import read3dDataFromNetCDF
from utilities import filesFromList
from txtTools import openIOFile
''... | mjsauvinen/P4UL | pyNetCDF/quadrantHoleNetCdf.py | Python | mit | 6,023 | [
"NetCDF"
] | bfb625e609c96f39412cadf564ac15128fa6cc1fb29f8feb680dfa1c824dc170 |
import jsonpickle
from pathlib import Path
from intelhex import IntelHex
class CalibrationLog:
def __init__(self, path):
if path is None:
raise TypeError('path')
if not isinstance(path, Path):
path = Path(path)
if not path.is_dir():
raise ValueError('path', 'Calibration path needs to be a directory... | pete-restall/Cluck2Sesame | src/utilities/calibrator/calibration_log.py | Python | mit | 3,593 | [
"CRYSTAL"
] | 97629cc7bbc4c80a802eaeffab106d5cbdca13b83194fc63b08230b15e0a6aa2 |
import numpy as np
from scipy.ndimage.filters import gaussian_filter
from .util import (DescriptorExtractor, _mask_border_keypoints,
_prepare_grayscale_input_2D)
from .brief_cy import _brief_loop
class BRIEF(DescriptorExtractor):
"""BRIEF binary descriptor extractor.
BRIEF (Binary Robus... | chintak/scikit-image | skimage/feature/brief.py | Python | bsd-3-clause | 7,030 | [
"Gaussian"
] | 49a18227c0ee7c953a4374f87d017239c8c38abbea89cfcda27db8090b71718c |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2013 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at yo... | kaplun/ops | modules/docextract/lib/refextract_regression_tests.py | Python | gpl-2.0 | 133,291 | [
"DIRAC"
] | b9149b8d6ab70fa8befb8ec6e7602e585db946247335cecff8ca30ee5cd051c3 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
import re
import miasm2.expression.expression as m2_expr
import miasm2.core.asmbloc as asmbloc
from miasm2.core.cpu import gen_base_expr, parse_ast
declarator = {'byte': 8,
'word': 16,
'dword': 32,
'qword': 64,
'long':... | amohanta/miasm | miasm2/core/parse_asm.py | Python | gpl-2.0 | 9,654 | [
"VisIt"
] | e5001b87be75087ac9ab9cc72959f7e935bbdfdcf64edf287fc4c7f1dc12cd77 |
# 2016-01-12 by teknohog
# Common functions for bittools Python scripts
import os.path
from math import ceil, exp
from time import ctime, time
# https://github.com/joshmarshall/jsonrpclib
from jsonrpclib import Server
from sys import exit, version_info
def ReadLines(f):
File = open(f, "r")
contents = File.... | teknohog/bittools | scripts/bittools.py | Python | gpl-3.0 | 8,388 | [
"DIRAC"
] | c9c4ad4f9f4c6b1c74097578eceec2d663b554f6e305a0bf7c2ccd5ab445920f |
import threading
import select
import time
import types
import socket
from DIRAC import gConfig, gMonitor, gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.private.TransportPool import getGlobalTransportPool
from DIRAC.Core.Utilities.ThreadPool import getGlobalThreadPool
from DIRAC.Core.Utilities.ReturnValues import isRe... | miloszz/DIRAC | Core/DISET/private/MessageBroker.py | Python | gpl-3.0 | 15,404 | [
"DIRAC"
] | 5bbf6efba4a033ae13da09fc09db8ee410563ad39099b2744d847c79c9fe82c1 |
from flask import Flask, jsonify, render_template, request
import nest
import os
import json
import anyjson
app = Flask(__name__)
def prep(data):
data_zipped = zip(*data)
return map(lambda x: {'x':x[0], 'y':x[1]}, data_zipped)
@app.template_filter('neurons')
def neurons_filter(nodes):
return filter(lambd... | babsey/nest-webapp | tryouts/flask/single_neuron.py | Python | mit | 3,637 | [
"NEURON"
] | a0518993bd678a7008c3ce95120befb0953a53c5892d388cf8a4b870aeb5bba4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract fasta sequences that are below a maximal length.
Usage:
%program <input_file> <output_file>"""
import sys
import re
try:
from Bio import SeqIO
except:
print "This program requires the Biopython library"
sys.exit(0)
try:
fasta_file = sys.a... | wkh124/wkh124 | fasta_extract_max_length.py | Python | gpl-3.0 | 728 | [
"Biopython"
] | a5e7adb32d9621bc271a474584170afd549b5650b531323bd308fa5adc8190d5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/share/psi4/databases/BASIC.py | Python | gpl-2.0 | 4,224 | [
"Psi4"
] | f2c33f73e9884a5e7ebd3b84bd8589df79d9e6765d48a69057df5ed873e0eb9b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Support for reading XCrysDen files.
"""
from pymatgen.core.periodic_table import Element
__author__ = "Matteo Giantomassi"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Mat... | vorwerkc/pymatgen | pymatgen/io/xcrysden.py | Python | mit | 3,826 | [
"CRYSTAL",
"pymatgen"
] | 1ee16355b7c31e83e197800611448ec0acfc5b5b11c988febb9e214ace1bdd7c |
import sys
import numpy as np
from ase.units import _hbar, _c, _e, Hartree
from gpaw.version import version
from gpaw.utilities.folder import Folder
def spectrum(exlist=None,
filename=None,
emin=None,
emax=None,
de=None,
energyunit='eV',
fo... | qsnake/gpaw | gpaw/lrtddft/spectrum.py | Python | gpl-3.0 | 3,487 | [
"ASE",
"GPAW"
] | aa1a1f7038f25b16ef16a1b139d82f6059b7272d0a62d95f8b0f405018dad9a3 |
#!/usr/bin/env python
################################################################################
# GIPS: Geospatial Image Processing System
#
# AUTHOR: Matthew Hanson
# EMAIL: matt.a.hanson@gmail.com
#
# Copyright (C) 2014-2018 Applied Geosolutions
#
# This program is free software; you can redist... | Applied-GeoSolutions/gips | gips/atmosphere.py | Python | gpl-3.0 | 26,265 | [
"NetCDF"
] | c8274d2b4bc56163cec20bbc2e9bee0ccb50f850fb16e90e459da69deac20d7a |
###########################################################################
# Sint Wind PI
# Copyright 2012 by Tonino Tarsi <tony.tarsi@gmail.com>
#
# USB comunication based pywws by 'Jim Easterbrook' <jim@jim-easterbrook.me.uk>
# Please refer to the LICENSE file for conditions
# Visit http://www.vo... | mspacca/CAIO_PLUGIN | caio_plugin_test.py | Python | gpl-2.0 | 8,089 | [
"VisIt"
] | 871b28d1f25b4d02ec09e7a105b4bceaecbad1b02d049445a241dcf190d77c55 |
from django.core.exceptions import ObjectDoesNotExist
from .metadata import Creator
class MetadataHandlerError(Exception):
pass
class MetadataObjectDoesNotExist(Exception):
pass
class MetadataHandler:
"""A class to get or create a CRF metadata model instance.
"""
creator_cls = Creator
... | botswana-harvard/edc-entry | edc_metadata/metadata_handler.py | Python | gpl-2.0 | 1,562 | [
"VisIt"
] | e71bb861e7d5a8b84d0d2acf01a86c441eb3a6ecefa303c58aeff64ca6040c02 |
from __future__ import absolute_import, unicode_literals
from .base import TembaObject, SimpleField, IntegerField, DatetimeField, ObjectListField, ObjectField
class Broadcast(TembaObject):
id = IntegerField()
urns = SimpleField()
contacts = SimpleField()
groups = SimpleField()
text = SimpleField(... | caktus/rapidpro-python | temba_client/types.py | Python | bsd-3-clause | 4,747 | [
"VisIt"
] | 73687de2799edcbfb09ebbd62f7a8c3b13d972d15e023221b47cc4ff0522aa0a |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Leaker
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Standards.Recorders.Brianer"
DecorationModuleStr="ShareYourSystem.Standards.Classors.Classer"
S... | Ledoux/ShareYourSystem | Pythonlogy/build/lib/ShareYourSystem/Standards/Recorders/Leaker/__init__.py | Python | mit | 132,573 | [
"Brian"
] | c0aca80f80d39b46c3ab93f9cdc5aed3de92bdd83d86a42b4346b6abbbe4cb26 |
"""This module implements a class for (true) time-dependent density
functional theory calculations.
"""
import sys
import time
from math import log
import numpy as np
from ase.units import Bohr, Hartree
import gpaw.io
import gpaw.mpi as mpi
from gpaw.aseinterface import GPAW
from gpaw.mixer import DummyMixer
from g... | robwarm/gpaw-symm | gpaw/tddft/__init__.py | Python | gpl-3.0 | 24,018 | [
"ASE",
"GPAW",
"Gaussian"
] | f3ad8fb145f8b2915cab3b0e5cd0599189263880e57cd0dd71d25cc734b06689 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | Krigu/gif_optimizer | images2gif/images2gif.py | Python | gpl-3.0 | 37,279 | [
"NEURON"
] | b615470b2d7c442351e7421ede5ba7b0b2098d0fba8bae439192679cfe9eed96 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/internal.py | Python | gpl-3.0 | 12,106 | [
"Gaussian"
] | 3b2d36e1058e979d1cb195568cddf9bfcca5d5ae62dfcd79054f7b5ffc97a1c1 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-os-config | tests/unit/gapic/osconfig_v1/test_os_config_service.py | Python | apache-2.0 | 172,928 | [
"Octopus"
] | a732a5602971505c137adcdd181bf793577f1e058ce5e2bf5f4ec2087de10e21 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import sys
import platform
from setuptools import setup, find_packages, Extension
from setuptools.command.build_ext import build_ext as _build_ext
class build_ext(_build_ext):
def finalize_options(self):... | czhengsci/pymatgen | setup.py | Python | mit | 8,355 | [
"ABINIT",
"ASE",
"FEFF",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | a76c547ee931ed79513881e78523a4e83904a76c5bd100e43028dee5aaa18f4c |
from template import context, Template
from template.document import Document
from template.test import TestCase, main
from template.plugin.table import Table
class ContextTest(TestCase):
def testContext(self):
tt = Template({ 'INCLUDE_PATH': 'test/src:test/lib',
'TRIM': True,
... | gsnedders/Template-Python | t/context_test.py | Python | artistic-2.0 | 5,279 | [
"VisIt"
] | 7f383d57705f6743c8050fa02ebe4b137e3121298f0154354433beb54a3a50ee |
# Copyright 2019 Arie Bregman
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | bregman-arie/rhoci | rhoci/models/DFG.py | Python | apache-2.0 | 3,980 | [
"Elk"
] | 009c437ff3d87033197f6e1affb17f3a7b1aac0b3ea3166535c1134b72e5ff50 |
# http://djangosnippets.org/snippets/2121/
from django import template
import random
register = template.Library()
class AnyNode(template.Node):
def __init__(self, options, splitter="\n"):
self.options = options
self.splitter = splitter
def render(self, context):
raw_content = self.opt... | alabs/petateca | petateca/apps/core/templatetags/random_selection.py | Python | agpl-3.0 | 3,228 | [
"Galaxy"
] | 65f0c313cd6df89b951ff791e6c923b10f0edd8a68c433cf7f3102c254e44a09 |
#!/usr/bin/python
import numpy as np
import os
import sys
import math
import matplotlib
matplotlib.use('Pdf')
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.font_manager as fm
import logging
logging.basic... | plazas/wfirst-detectors-vnl | code/calculate_WFIRST_PSF_ellipticities.py | Python | mit | 6,749 | [
"Gaussian"
] | c7308d8141e37399b4a84ca43d2446e253f91445c79a2e3a2d7378771eaf5716 |
from typing import Any, Dict, Tuple
from .config import get_secret
################################################################
## Zulip Server settings.
##
## This file controls settings that affect the whole Zulip server.
## See our documentation at:
## https://zulip.readthedocs.io/en/latest/production/settin... | punchagan/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 31,444 | [
"VisIt"
] | cc275f736bb1f551e645181d2b2af7ad056747140f98d1d1e8035b41882e6c66 |
import sys, shutil
sys.path.insert(1, "../../../")
import h2o
import random
def milsong_checkpoint(ip,port):
milsong_train = h2o.upload_file(h2o.locate("bigdata/laptop/milsongs/milsongs-train.csv.gz"))
milsong_valid = h2o.upload_file(h2o.locate("bigdata/laptop/milsongs/milsongs-test.csv.gz"))
distribution... | mrgloom/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_milsongs_largeGBM.py | Python | apache-2.0 | 1,956 | [
"Gaussian"
] | 4846847e0656c6f051bf4997afb77a4a599b74043d7eec4860f8f136adfc25e6 |
from builtins import str
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
def pyunit_make_glm_model():
# TODO: PUBDEV-1717
pros = h2o.import_file(pyunit_utils.locate("smalldata/prostate/prostate.csv"))
model =... | mathemage/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_NOFEATURE_make_glm_model.py | Python | apache-2.0 | 1,137 | [
"Gaussian"
] | 7a4c3c2ebc5cfa28f30c75b7eac793f793b49140758241991faa5f7c51fed6f0 |
"""Support for the Amazon Polly text to speech service."""
import logging
import boto3
import voluptuous as vol
from homeassistant.components.tts import PLATFORM_SCHEMA, Provider
import homeassistant.helpers.config_validation as cv
_LOGGER = logging.getLogger(__name__)
CONF_REGION = "region_name"
CONF_ACCESS_KEY_ID... | sdague/home-assistant | homeassistant/components/amazon_polly/tts.py | Python | apache-2.0 | 6,973 | [
"Brian"
] | 90faee9503a4d5f604a478129415babe187b7b45412a80036bc6f2763275dbdf |
#!/usr/bin/python
usage = """ a script that generates statistical tests of the algorithm, such as coverage plots """
#=================================================
import os
import sys
sys.path.append("/home/reed/LIGO/BAYESburst/bayesburst/")
import numpy as np
import healpy as hp
import utils
import detector_... | reedessick/bayesburst | statistical_tests.py | Python | gpl-2.0 | 17,602 | [
"Gaussian"
] | 6586af3aa170e01597c688503b7f9344d130ab338d2a485df1a4c367263d5bc7 |
##########################################################################
#
# Copyright 2008-2010 VMware, Inc.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software withou... | apitrace/apitrace | specs/stdapi.py | Python | mit | 29,667 | [
"VisIt"
] | 1ce2da3170de344c62c55e9bff2c2c371f376a76e975a31038d5208720c71cfc |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/orca_console_prefs.py | Python | lgpl-2.1 | 14,232 | [
"ORCA"
] | d16733753923d51e8e494c2a75421d9c1e5c73c58b41dc4c62aff200dd34c64f |
"""
The Flutter Shutter Code Calculator
"""
from lib import base_app, build, http
from lib.misc import ctime
from lib.base_app import init_app
import shutil
import cherrypy
from cherrypy import TimeoutError
import os.path
import time
import subprocess
class app(base_app):
""" The Flutter Shutter Code Calculator a... | juan-cardelino/matlab_demos | ipol_demo-light-1025b85/app_available/108/app.py | Python | gpl-2.0 | 13,183 | [
"Gaussian"
] | a5a97027a372ce4d8bea5e8cf51a8370e625dc1f5e808f8d5ad5fe4a3964ad80 |
import traceback
import string
import os.path
import sys
from FDO import *
import unittest
class ExpressionTest(unittest.TestCase):
def _parseExpression(self, exprText, exprResult = None, expectedType = None):
expr = FdoExpression.Parse(exprText)
self.assertIsNotNone(expr)
exprStr = expr.To... | jumpinjackie/fdo-swig | Lang/Python/UnitTest/Src/ExpressionTest.py | Python | lgpl-2.1 | 5,662 | [
"MOOSE"
] | 4a63d8b70bca652324cb2de46992ad43a2599ab643b02f6b856ef05f3300f37a |
""" Interface code for MOLDEN
assumes a somewhat doctored version of MOLDEN
"""
from objects.field import *
from jobmanager import *
from viewer.defaults import defaults
from viewer.paths import find_exe
import sys, os
class MoldenDriver:
def __init__(self, wavefunctionfile):
""" Initialise buy specify... | alexei-matveev/ccp1gui | interfaces/molden.py | Python | gpl-2.0 | 3,777 | [
"GAMESS"
] | 4d0ae8e589f6c9b9217b3fe39b594774313dd83c141f3b7967b85be550d0d158 |
# -*- coding: utf-8 -*-
# Author: Aziz Köksal
# License: zlib/libpng
from __future__ import unicode_literals
class Module:
def __init__(self, fqn):
self.pckg_fqn, sep, self.name = fqn.rpartition('.')
self.pckg = None
self.fqn = fqn
self.sym_dict = {}
def __cmp__(self, other):
result = cmp(self... | SiegeLord/dil | scripts/symbols.py | Python | gpl-3.0 | 6,177 | [
"VisIt"
] | 50c2c34df8b938dfd6331932bd01f3e7b6995a23d416befa5cceb7ced2d7f843 |
from __future__ import division
import six
from abc import ABCMeta, abstractmethod
import numpy as np
from numpy.random import choice, randint
from ...models.base import ModelMixin
from ...utils.common import Logger
from ..mdp_solvers import graph_policy_iteration
##################################################... | makokal/scalable-irl | sirl/algorithms/birl/base.py | Python | bsd-3-clause | 7,243 | [
"Gaussian"
] | a2ff9b0a3e52193185487c158d6d5341bfcc9b3ecd8b684c04cf881968c887fb |
from pyrobot.brain.conx import *
import math
__author__ = "George Dahl <gdahl1@swarthmore.edu>"
__version__ = "$Revision: 2409 $"
def findMax(seq):
"""
Returns the index of the maximum value in the sequence.
"""
bestSoFar = 0
for i in range(len(seq)-1):
if seq[i+1] > seq[bestSoFar]:
... | emilydolson/forestcat | pyrobot/brain/cascor.py | Python | agpl-3.0 | 27,629 | [
"NEURON"
] | 1ab5023d05134ab7ebd51a4bbc20012dd5b837486e10165c045d6a6a7e2c6abd |
from sklearn.externals.joblib import dump
from sklearn.pipeline import _name_estimators, Pipeline as _Pipeline
from sklearn.utils.metaestimators import if_delegate_has_method
__all__ = ['make_pipeline', 'Pipeline']
def make_pipeline(*steps):
"""Construct a Pipeline from the given estimators. This is a shorthand ... | Y-oHr-N/kenchi | kenchi/pipeline.py | Python | bsd-3-clause | 10,490 | [
"Gaussian"
] | 6fc83e354cf8247e537f3439ba495fad5808902ba92e8dc7d30ec5c4fa0fb528 |
# -*- coding: utf-8 -*-
import json
from .common import CatmaidApiTestCase
class LogsApiTests(CatmaidApiTestCase):
log_rows = [
[
'test2',
'create_neuron',
'2012-07-22T16:50:57.758000+00:00',
5290... | tomka/CATMAID | django/applications/catmaid/tests/apis/test_logs.py | Python | gpl-3.0 | 3,460 | [
"NEURON"
] | 339573d86c46bb8d5effaf0704414163f7c0d4488f15fe3a0f64e14018bb82c5 |
#!/usr/bin/env python
"""
dirac-rss-list-status
Script that dumps the DB information for the elements into the standard output.
If returns information concerning the StatusType and Status attributes.
Usage:
dirac-rss-list-status
--element= Element family to be Synchroniz... | rajanandakumar/DIRAC | ResourceStatusSystem/scripts/dirac-rss-list-status.py | Python | gpl-3.0 | 6,200 | [
"DIRAC"
] | 8d0511982180241af11064ddc527b7f07d1477d18442ec2e9f3104d9aa90f459 |
""" TaskQueueDB class is a front-end to the task queues db
"""
__RCSID__ = "ebed3a8 (2012-07-06 20:33:11 +0200) Adri Casajs <adria@ecm.ub.es>"
import types
import random
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.private.SharesCorrector import SharesCorrector
from DIRAC.Wor... | Sbalbp/DIRAC | WorkloadManagementSystem/DB/TaskQueueDB.py | Python | gpl-3.0 | 53,584 | [
"DIRAC"
] | 35a63c5af6ded10d0dea9ed943c82ca18142098bbc02ce5dfadb793eb4eed1e4 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kobejean/tensorflow | tensorflow/python/autograph/converters/return_statements.py | Python | apache-2.0 | 11,411 | [
"VisIt"
] | 47661025ab1bf7590039e47dcb06ba1e9895940a2ff05175fcde4c8cfd1eb560 |
import logging
import os
import pysam
import subprocess
class AnnotationError(Exception):
pass
def ensureIndexed(bedPath, preset="bed", trySorting=True):
if not bedPath.endswith(".gz"):
if not os.path.exists(bedPath+".gz"):
logging.info("bgzf compressing {}".format(bedPath))
p... | svviz/svviz | src/svviz/tabix.py | Python | mit | 2,082 | [
"pysam"
] | 55959dc3d1eef93814d525d19af68f82fb00f93fb99be9f5fb96e7cf945edbc8 |
from lan.lan_ast import *
import copy
class Ids(NodeVisitor):
""" Finds all unique IDs, excluding function IDs"""
def __init__(self):
self.ids = set()
def visit_FuncDecl(self, node):
if node.compound.statements == []:
self.visit(node.arglist)
def visit_Id(self, node):
... | dikujepsen/OpenTran | v2.0/framework/unused/visitor_unused.py | Python | mit | 6,366 | [
"VisIt"
] | 8c6a9edbdcfe7133ba14e3d5a40bbbefeff83b623a350eec60580f3bedd16d09 |
# -*- coding: utf-8 -*-
"""Distributions used in the Kernel ICA paper of Bach and Jordan.
The program originally has been written by R. Bach as a part of
his kernel ICA software of MATLAB.
"""
# Copyright (c) Francis R. Bach, 2002.
# Author: Taku Yoshioka
import collections
import numpy as np
import scipy.stats as... | taku-y/bmlingam | bmlingam/utils/usr_distrib.py | Python | mit | 16,664 | [
"Gaussian"
] | 780562f53686f396b01704c7bb446e8780d36fec306a6cfc6b724d62d8e593a4 |
import json
import io
import numpy as np
from collections import OrderedDict
from PyQt5.QtWidgets import QFileDialog
class MyEncoder(json.JSONEncoder):
def default(self, obj):
if isinstance(obj, np.integer):
return int(obj)
elif isinstance(obj, np.floating):
return float(obj... | darioflute/sospex | sospex/inout.py | Python | gpl-3.0 | 25,396 | [
"Gaussian"
] | 516ac66385797be853e773c9846962f3130e4d1013f45c2fa224b648262b6783 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_programs
----------------------------------
Tests for `programs` module.
"""
import arcpy
import datetime
import dbseeder.resultmodels as resultmodel
import dbseeder.stationmodels as stationmodel
import os
import unittest
import SimpleHTTPServer
import SocketServ... | inkenbrandt/ugs-chemistry | scripts/dbseeder/tests/test_programs.py | Python | mit | 25,435 | [
"Brian"
] | 9cd3f885fb9cad7f3655c57fd711f35fae0afa1c0873fbe27fcbfd282a8b8ef3 |
#! /usr/bin/env python
import time
import os
import re
from quex.engine.misc.file_in import open_file_or_die, \
delete_comment, \
extract_identifiers_with_specific_prefix, \
get_include_guard_exte... | coderjames/pascal | quex-0.63.1/quex/output/cpp/token_id_maker.py | Python | bsd-2-clause | 13,556 | [
"VisIt"
] | a125e7cb25ee65d93444ea9e65674eb16d66e0d921600585ee66d9e6d79178bf |
import numpy as np
import matplotlib.pyplot as plt
def MockData(m, b, lnf=None, sigy=None, x=None, ndata=None, xep=[0.0, 0.0], yep=[0.0, 0.0]):
"""
Generate the mock data.
Parameters
----------
m : float
The slope.
b : float
The intercept.
lnf : float, optional (not with si... | darkbear9494/LinFit | linfit/mock.py | Python | mit | 4,123 | [
"Gaussian"
] | 549a8d9006dd52444cffc9d40a7624e2d20cb728a3723353010c61c0eee85beb |
"""
SolvationToolkit: Tools for setting up mixtures of small organic molecules for AMBER, GROMACS, OpenMM and others.
You can install SolvationTookit via
python setup.py install
"""
import sys
from setuptools import setup, find_packages
if sys.argv[-1] == 'setup.py':
print("To install, run 'python setup.py ins... | nividic/SolvationToolkit | setup.py | Python | lgpl-2.1 | 1,539 | [
"Amber",
"Gromacs",
"OpenMM"
] | 8c33105bf2a4022adc2b2b6f6ebe70dc1ed0c589ecaaf73429903282cddc8c25 |
#! /usr/bin/env python
import argparse
import operator
import os
import sys
from collections import namedtuple
from functools import lru_cache
from functools import reduce
from pathlib import Path
from typing import Any
from typing import Dict
from typing import List
import addict
import arrow
import googleapiclient.e... | ipwnponies/youtube-sort-playlist | playlist_updates.py | Python | unlicense | 13,622 | [
"VisIt"
] | ebf5283b36865303f65e8a09821b51f1a9f8a2162b10e3c06be5f6c8ba493a21 |
import math
import argparse
from string import maketrans
#Script used in order to obtain primers.
parser = argparse.ArgumentParser()
parser.add_argument('-file', action="store", dest = 'File', required = "True")
parser.add_argument('-fasta', action = "store", dest = "genome", required = "True")
parser.add_argument('-f... | davidwilson-85/easymap | primers/primer-generation.py | Python | gpl-3.0 | 17,494 | [
"Biopython"
] | 9e7056f018cfa3efdcc80eb6afe914cf0a970c44896dd19c04af2e65fa587c3d |
#!/usr/bin/env python
# PYTHON_ARGCOMPLETE_OK
from os.path import split
from math import log
from warnings import warn
from numpy import zeros, roll
try:
import pysam
except ImportError as e:
print(e);
def count_coverage(samfile, flip=False, include_insert=False):
"""counts coverage per base in a strand-... | dmccloskey/sequencing_utilities | sequencing_utilities/makegff.py | Python | mit | 10,488 | [
"pysam"
] | 3321be9dc694317f38e1813a1d6ecabca343849bb36508d783c3c3108b509c11 |
# -*-coding:utf-8-*-
# @auth ivan
# @time 2016-10-26 11:21:30
# @goal test for Visitor Pattern
class ComputerPart:
def __init__(self):
return
def accept(self, computerPartVisitor):
return
class Keyboard(ComputerPart):
def __init__(self):
ComputerPart.__init__(self)
retur... | IvanaXu/Test_Class_GOF | tPatterns/Behavioral_Patterns/test_Visitor_Pattern.py | Python | gpl-3.0 | 2,046 | [
"VisIt"
] | 046b5c12d67028c1510b95e435df70b844cc7b5f18bb23c0ba27b525ad46ba3a |
import re
from random import *
from collections import Counter
from pprint import pprint
# http://blog.echen.me/2011/08/22/introduction-to-latent-dirichlet-allocation/
# https://tedunderwood.com/2012/04/07/topic-modeling-made-just-simple-enough/
documents = [
# space
"Watching a bubble float effortlessly through the ... | mobarski/sandbox | topic/lda/lda.py | Python | mit | 3,767 | [
"COLUMBUS"
] | 09ac06756a4d21407be01860a0bb56aa4387278369b18c7e192d3061af177576 |
#!/usr/bin/env python
"""
create a directory in the FileCatalog
"""
import os
import DIRAC
from DIRAC.Core.Base import Script
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIRAC.Interfaces import createCatalog
from COMDIRAC.Interfaces import pathFromArguments
if __name__... | pigay/COMDIRAC | Interfaces/scripts/dmkdir.py | Python | gpl-3.0 | 1,488 | [
"DIRAC"
] | c7f08ceb42cfafbec2256b0a81eb0a690e988146ee68de0767e24411e37e96bc |
# Curves force analysis software
# JWA (c)2009
# Statistical functions for fitting
from numpy import *
import scipy.odr as odr
from scipy.interpolate.interpolate import interp1d
sqrt_2_pi = sqrt(2*pi)
# Fit model to x,y data, with choice of model, and returns
# callable function with fitted parameters
def fit(x,y,m... | jarmond/Curves | curves/stats.py | Python | gpl-3.0 | 3,224 | [
"Gaussian"
] | 7b9e629a543c0b2c2dddd729d7a40d51b21757bf51d716eb7fe3a9dd0b7e8d20 |
import lb_loader
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk.openmm import app
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
pdb = app.PDBFile("./sandbox/iamoeba.pdb")
forcefield = app.ForceField('iamoeba.xml')
n_s... | kyleabeauchamp/HMCNotes | code/old/hmr_iamoeba.py | Python | gpl-2.0 | 1,794 | [
"OpenMM"
] | 6959436c36f9031c41cd1bc753ab13f784d1c9058d68db64dc1ed7a1c1401dd5 |
#
# basic run through the PDB, test hydrogen addition and SMILES conversion
#
from glob import glob
import threading
import time
from pymol import cmd
import sys, os, os.path
from chempy.champ import Champ
ent_dir = "pdb"
def load():
cmd.set("valence")
r = 0
list = glob("pdb/*/*")
# list = ["pdb/... | gratefulfrog/lib | python/pymol/pymol_path/test/inp/B07.py | Python | gpl-2.0 | 1,026 | [
"ChemPy",
"PyMOL"
] | 41a0c45ed60c126e9e7d3aa95487144719b7111d7165db5e741d0647e1b25fba |
# -*- coding: utf-8 -*-
# $Id: manpage.py 8116 2017-06-18 19:09:40Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module is put into the public domain.
"""
Simple man page writer for reStructuredText.
Man pages (short for "manual pages") contain system documentation on unix-like... | burzillibus/RobHome | venv/lib/python2.7/site-packages/docutils/writers/manpage.py | Python | mit | 35,740 | [
"VisIt"
] | 2a99052f45c81078b2a6c6ccda2ff027b7d6ea3752f8af813255603e2ebf68b5 |
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