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#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | kkreis/espressopp | testsuite/pickle_potential/testwarmup.py | Python | gpl-3.0 | 2,149 | [
"ESPResSo"
] | f1ecf82cf86ea9717bec3ff6ec316da28096220e858729a70627f2921acd260d |
"""
Downloads SDSS DR8 photometric and spectroscopic information.
:note: SamPy.db.sdss may need editing as this is the file where
the server is defined, and thus defines whether this script
calls DR7 or 8.
:requires: SamPy
:author: Sami-Matias Niemi
:contact: sniemi@unc.edu
:version: 0.1
"""
import sq... | sniemi/SamPy | resolve/catalogs/getSDSSphotandSpecDR8.py | Python | bsd-2-clause | 3,330 | [
"Galaxy"
] | 1440c56606ccac37f428e787ad80984b3d1d7e516b40c13424996c827891ff09 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | model_pruning/examples/cifar10/cifar10_pruning.py | Python | apache-2.0 | 13,794 | [
"Gaussian"
] | 054ee1aa0fdd0aae195746fc7a856138a172413db6d72c93f0a4d389122cf19f |
import util,collections,sys
import traceback
from copy import deepcopy,copy
from daytime import DayTimeRange
from termweek import TermWeek
import pparser
import tracker
# hours 1-7 -> 13-19
class PatternAtom(object):
dayname = ['M','Tu','W','Th','F','Sa','Su']
terms = ['Mi','Le','Ea']
def __init__(... | ieb/timetables | python/lib/patternatom.py | Python | agpl-3.0 | 7,447 | [
"BLAST"
] | 61629ce7e7bcf450d88eb3fdea092fe088e8a36804dcd96f688a2b437eebd2ad |
"""
Actions manager for transcripts ajax calls.
+++++++++++++++++++++++++++++++++++++++++++
Module do not support rollback (pressing "Cancel" button in Studio)
All user changes are saved immediately.
"""
import copy
import json
import logging
import os
import requests
from django.conf import settings
from django.cont... | procangroup/edx-platform | cms/djangoapps/contentstore/views/transcripts_ajax.py | Python | agpl-3.0 | 21,457 | [
"FEFF"
] | 1ebba7ad1ea55d45c44ae98f3c8b6e0f4e7d6d904367e766ccd05e9833bfd327 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2011 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the... | eevee/cocos2d-mirror | cocos/batch.py | Python | bsd-3-clause | 4,335 | [
"VisIt"
] | 80f3901b80fcf4aed399d4ad42394b217506e90f4f0d36f104ae88b9e22c758e |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-list-users
# Author : Adrian Casajus
########################################################################
"""
Lists the users in the Configuration. If no group is specified return all users.
Exam... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_list_users.py | Python | gpl-3.0 | 2,214 | [
"DIRAC"
] | 7972466f8c59256aa38843a3693d258079bc751b830c5ee8b65e1b6dcec3d856 |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | ahmadio/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 63,344 | [
"VisIt"
] | 9fd74216caf30cb3789b7044f15b04c05c5f5c593008dcf07c428d78eeb2428e |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""SpineML Bundle Module
This modual will form a convience class to bundle together related SpineML
objects into a single standard object which can be easily passed between
programs. The bundle will be able to interact with premade spineML objects
through the other suppor... | AdamRTomkins/libSpineML | libSpineML/smlBundle.py | Python | gpl-3.0 | 7,712 | [
"NEURON"
] | def63f6ee556d10c370c83a284807f0907a7a21be402286d275a1028e053ee7a |
#
# Copyright 2022 Lucas Frérot (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Founda... | libAtoms/matscipy | matscipy/calculators/manybody/explicit_forms/harmonic.py | Python | lgpl-2.1 | 14,227 | [
"ASE",
"Matscipy"
] | 730b4ff371fbc738573af222b00f4b97e5a37e7a06f610a2031684d9be070a0a |
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps
def here_anova1(Y, X, X0, Xi, X0i, df):
Y = np.matrix(Y)
### estimate parameters:
b = Xi*Y
eij = Y - X*b
R = eij.T*eij
### reduced design:
b0 = X0i*Y
eij0 = Y - X0*b0
R... | 0todd0000/rft1d | rft1d/examples/val_max_4_anova1_1d.py | Python | gpl-3.0 | 2,110 | [
"Gaussian"
] | 8b24e7bfa2ca7466e7ab335a7cf487150d18754dfdf80a693af35823d2154ce9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010--2014 Nico Schlömer
#
# This file is part of matplotlib2tikz.
#
# matplotlib2tikz 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 ver... | 0u812/matplotlib2tikz | test/testfunctions.py | Python | lgpl-3.0 | 10,698 | [
"Gaussian"
] | 81ccf1adc3d15d609caf52cb98ab5bae60caac8e9316f0a75c65f6f9a24df497 |
'''<h1> Figure of Merit (FOM)</h1>
The Figure of Merit (FOM) is the function that compares how well the simulation matches the measured data. Strictly speaking, for Gaussian errors, a chi squared (χ<sup>2</sup>) FOM is the most appropriate. However, the world is not perfect and many times the data can be fitted mor... | jackey-qiu/genx_pc_qiu | fom_funcs.py | Python | gpl-3.0 | 19,343 | [
"Gaussian"
] | cc981c5b5c5ea140e7d01b86b396cd75574b5fcc40eb0791a81ca7bb84ec560a |
# coding: utf-8
from __future__ import unicode_literals, division
from monty.os.path import zpath
import os
import time
import datetime
import operator
import shutil
from functools import reduce
from collections import Counter
import re
import numpy as np
from monty.dev import deprecated
from monty.serialization im... | specter119/custodian | custodian/vasp/handlers.py | Python | mit | 54,519 | [
"VASP",
"pymatgen"
] | 465bf2764da34d3fd4d2539c0f19ae5df39fce9ef83ef83883b7fc43dbcebccc |
from compositecore import Leaf
class DataPoint(Leaf):
"""
Class for components holding a single data point.
"""
def __init__(self, component_type, value, tags=[]):
super(DataPoint, self).__init__()
self.tags |= set(tags)
self.component_type = component_type
self.value =... | co/TheLastRogue | stats.py | Python | bsd-2-clause | 4,107 | [
"TINKER"
] | 62712b18fd7e8d67d70733046d13460093e8ea9bd9247741e9d2fadac2e61455 |
import csv
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import matplotlib.path as path
import matplotlib.dates as mdates
from dateutil.parser import parse
from datetime import datetime
from datetime import timedelta
# Python 2 and 3: easiest option
from future.stan... | bearing/dosenet-analysis | D3S_analysis/spectra_fitter.py | Python | mit | 25,763 | [
"Gaussian"
] | 12587b4d660d30bcad05c27d3461945a933d9aeb715c016b43e76851b005dd4d |
#!BPY
"""
Name: 'ASCII Scene (.ase) v0.16'
Blender: 249
Group: 'Import'
Tooltip: 'ASCII Scene import (*.ase)'
"""
__author__ = "Goofos & Plagman"
__version__ = "0.16"
# goofos at epruegel.de
#
# ***** BEGIN GPL LICENSE BLOCK *****
#
# This program is free software; you can redistribute it ... | masterfeizz/EDuke3D | build/src/util/ase_import.py | Python | gpl-2.0 | 15,337 | [
"ASE"
] | c29e34759baf6c30e0e87501e92cf594c354fd9423c0ffbf68ffe5dedac077ec |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import unittest
import os
import warnings
import numpy as np
from pymatgen.io.cif import CifParser, CifWriter, CifBlock
from pymatgen.io.vasp... | nisse3000/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 43,915 | [
"VASP",
"pymatgen"
] | 80ff38bec050403367af0d5b2ec010c00491abad627261c8ef2742496c83df7e |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 ver... | spring01/libPSI | lib/databases/S66.py | Python | gpl-2.0 | 148,284 | [
"Psi4"
] | c923dcde0c2631c468e69446294f729b634d82dc03f6fbfb9884dcf385cba730 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | flavioamieiro/pypln.web | pypln/web/core/tests/views/test_properties.py | Python | gpl-3.0 | 6,751 | [
"NAMD"
] | d82f7aacb39263e80432a955a8be1b93274261346f3b750b18ee63bb8ce7d415 |
import ocl
import pyocl
import camvtk
import time
import datetime
import vtk
import math
def main():
print ocl.revision()
myscreen = camvtk.VTKScreen()
myscreen.camera.SetPosition(2, 2, 5)
myscreen.camera.SetFocalPoint(0.5,0, 1)
# axis arrows
camvtk.drawArrows(myscreen,center=(-2,-2,0))... | tectronics/opencamlib | scripts/cutsim/cutsim_10_side_tris.py | Python | gpl-3.0 | 5,190 | [
"VTK"
] | afccd71350edd6c7a655c867317e1218544b20cc8321dce17c3f3ed6ad8a91d7 |
#!/usr/bin/env python
# mpirun -np 2 python test_ccsd.py
import numpy
from pyscf import lib
from pyscf import gto
from pyscf import scf
from pyscf import cc
from mpi4pyscf import cc as mpicc
from mpi4pyscf.tools import mpi
mol = gto.Mole()
mol.atom = [
[2 , (0. , 0. , 0.)],
[1 , (0. , -0.757 , 0.587)],
... | sunqm/mpi4pyscf | mpi4pyscf/cc/test/test_ccsd.py | Python | gpl-3.0 | 2,398 | [
"PySCF"
] | bb0277249d315eea32e0fcd132dbfbcf323cea643a7b02c6fb541cebc703bb80 |
#!/usr/bin/env python
import calendar
import netCDF4
import numpy as np
import os
import pandas as pd
import sys
import traceback
from cStringIO import StringIO
from datetime import datetime, timedelta
from .. import translator
# Return int with num days per year
def days_per_year(year):
if calendar.isleap(year):
... | RDCEP/psims | pysims/translators/dssat46/out2psimsdaily.py | Python | agpl-3.0 | 8,414 | [
"NetCDF"
] | 0380051462ce37394167452e8668ddffc7b16ec2d8e1e36d66cb3fe2971d0945 |
#!/usr/bin/env python
"""
given an input table with ra/dec, returns a culled list of ra/dec that are not near "DETECTED" pixels in an image.
This returns positions that are in blank regions of the image. The pixel radius necessary to consider a region blank is a command-line argument.
This can operate over a list of v... | HSC-Users/hscTools | clackner/bin/getBlankSources.py | Python | gpl-3.0 | 4,777 | [
"VisIt"
] | 9a81ccaeefb481aed1a0ca614503b5163ad38ec97ff23127edef8416e14c08e6 |
"""
The main client API you'll be working with most often. You'll need to
configure a dropbox.session.DropboxSession for this to work, but otherwise
it's fairly self-explanatory.
Before you can begin making requests to the dropbox API, you have to
authenticate your application with Dropbox and get the user to
autho... | azumimuo/family-xbmc-addon | script.xbmcbackup/resources/lib/dropbox/client.py | Python | gpl-2.0 | 40,015 | [
"VisIt"
] | 7368922a2e56f3f239ae2baae7ed76f66b9e497b88969d27332c25ffe647f72a |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/exodus/blocks/boundary_numeric.py | Python | lgpl-2.1 | 1,081 | [
"MOOSE",
"VTK"
] | 59e113629ab850b693b2217b403bec24806a4c152cb3682628bc03da32c470d6 |
import unittest
import os
import json
import scipy
from io import open
from pymatgen.phonon.dos import CompletePhononDos
from pymatgen.phonon.plotter import PhononDosPlotter, PhononBSPlotter, ThermoPlotter
from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
test_dir = os.path.join(os.path.dirname(__... | mbkumar/pymatgen | pymatgen/phonon/tests/test_plotter.py | Python | mit | 3,873 | [
"pymatgen"
] | f0fe99e1fb801b6553449e65bceb196690a1200413f435530d40b85a8e47b7a1 |
#
# @file TestPriority.py
# @brief SBML Priority unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatica... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestPriority.py | Python | gpl-3.0 | 4,795 | [
"VisIt"
] | eff3ac58e9c6e94bea7404b356173e4c672daf0fa8378805ebfb61f2ca17e201 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Test the button source
# The image to map on the button
r = vtk.vtkJPEGReader()
r.SetFileName(VTK_DATA_ROOT + "/Data/beach.jpg")
r.Update()
t = vtk.vtkTexture()
t.SetInputConnectio... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Sources/Testing/Python/TestButtonSource.py | Python | gpl-3.0 | 2,447 | [
"VTK"
] | 5bfda2690e12526ec6c701fce499e0e110a91ae0944eb9bf93eefe7ca310ef75 |
# -*- coding: utf-8 -*-
#
# canu documentation build configuration file, created by
# sphinx-quickstart on Wed Aug 26 18:41:08 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | sgblanch/canu | documentation/source/conf.py | Python | gpl-2.0 | 8,725 | [
"Brian"
] | 57a7acdbd23e77844dedd49bf4927ee48bc83a0a52c70701c4227b675ed9ea7c |
# -*- coding: utf-8 -*-
#
# The MIT License (MIT)
#
# Copyright (c) 2014 Edward Mountjoy
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation th... | edm1/error-aware-demultiplexer | src/fastqparser.py | Python | mit | 7,235 | [
"Biopython"
] | 6a1eb247c9503ec1699891f3393a4d7d213c7746e5d7b6cdb25d966456001923 |
########################################################################
# $HeadURL$
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. ... | calancha/DIRAC | WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 34,976 | [
"DIRAC"
] | b9044fa64eb879a23ebb598f335776f47708b89b93e9a84e81a51370e8396385 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | Livit/Livit.Learn.EdX | common/djangoapps/student/views.py | Python | agpl-3.0 | 109,663 | [
"VisIt"
] | 9e878bad9e84cf504cd9c601736d778215cc75b0bc4f81e11815c4da42d325fc |
"""
Subpackage ``LLSG`` contains the first version of our Local Low-rank plus Sparse
plus Gaussian-noise decomposition (Gomez Gonzalez et al. 2016) for ADI data.
"""
from __future__ import absolute_import
from .llsg import *
from .thresholding import * | henry-ngo/VIP | vip_hci/llsg/__init__.py | Python | mit | 253 | [
"Gaussian"
] | d7f1b3caf0042771708f047d2eef3122cdc10733a03e619df907346f3ca9cf5f |
########################################################################
# File : ResourcesDefaults.py
# Author : Ricardo Graciani
########################################################################
"""
Some Helper class to access Default options for Different Resources (CEs, SEs, Catalags,...)
"""
from __futur... | chaen/DIRAC | ConfigurationSystem/Client/Helpers/ResourcesDefaults.py | Python | gpl-3.0 | 3,078 | [
"DIRAC"
] | 608917cfc5d1e05a87eb666129e1bcd404e6895719d1c5c0f135980825d1229e |
#encoding:utf-8
""" Abstract classes to build Coord, Gr, Ax, AxGr and Field class.
Most classes inherit from the abstract base classes Named, Associative, Directional, Membered, Valued contained in abstract.py.
The abstract module contains the following classes:
Named
-----
Base class for most other sg classes, r... | willo12/spacegrids | spacegrids/abstract.py | Python | bsd-3-clause | 23,918 | [
"NetCDF"
] | 4732abda7b3eb2dc51a062d1ca52cb58a2a55e5c29ba53a8ab5a767244393f6c |
# Copyright 2016 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Generates reports base on bisect result data."""
import copy
import math
_BISECT_HEADER = """
=== BISECT JOB RESULTS ===
<b>%s</b>
"""
_BISECT_TO_RUN ... | sahiljain/catapult | dashboard/dashboard/bisect_report.py | Python | bsd-3-clause | 15,882 | [
"VisIt"
] | fb6225702dc463ec64afa1de04c02388a5e6eb267d5e396ac16e4ca7316db41e |
__author__ = 'amarch'
# -*- coding: utf-8 -*-
from utils import strutils as infoutils
import itertools
from scipy.integrate import *
from RotationCurve import *
from Galaxy import *
from utils import strutils as infoutils
import itertools
import copy
from RadialToAzimuthalRatioHandler import *
import scipy.optimize
... | Amarchuk/2FInstability | core/RadialToVerticalRatioHandler.py | Python | gpl-3.0 | 8,998 | [
"Galaxy"
] | 64b28a15e43cb96b7df13e8527fbe9ca6f672178f75339b407c01314cedf8df6 |
import numpy
from chainer.backends import cuda
from chainer import function_node
import chainer.functions
from chainer.utils import type_check
from chainer import variable
def _as_mat(x):
if x.ndim == 2:
return x
return x.reshape(len(x), -1)
def _matmul(a, b, xp):
if xp is numpy:
# nump... | aonotas/chainer | chainer/functions/noise/simplified_dropconnect.py | Python | mit | 6,999 | [
"Gaussian"
] | ef3b28d2200f7d86fa9cc8b625ddf7de710246bc501ca6afdac3e47bff75c406 |
"""
Dabble, a membrane protein system builder
Author: Robin Betz
Copyright (C) 2019 Robin Betz
This program is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your op... | Eigenstate/dabble | dabble/__main__.py | Python | gpl-2.0 | 13,843 | [
"Amber",
"CHARMM",
"VMD"
] | dcceebddf5003aa5bbbb42df7d9af7cb0b5e5f71b463e3e5c45f44f2297dbacb |
# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
from contextlib import contextmanager
from distutils.version import LooseVersion
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil imp... | Teekuningas/mne-python | mne/utils/_testing.py | Python | bsd-3-clause | 17,015 | [
"Mayavi",
"VTK"
] | 50dad377214cfd3d024b84bf9703d3c0efedb64280566acda4eed2a672a1afd9 |
""" Defines a series of scripts for running server and maintenance
FLASK_APP=manage.py flask --help
(bogus comment line added to triger build)
"""
import copy
from datetime import datetime
import json
import os
import sys
import alembic.config
import click
from flask import url_for
from flask_migrate import Migrate
... | uwcirg/true_nth_usa_portal | manage.py | Python | bsd-3-clause | 26,824 | [
"VisIt"
] | 335885586bbdde0d9e2e086282ede5938f0fe983ed364bf7dd5d246038aeaaed |
import numpy as np
import copy
import numpy.linalg as la
import summary_output as SUMMARY
import robust as ROBUST
import user_output as USER
from utils import spdot, sphstack, RegressionPropsY, RegressionPropsVM
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu, Jing Yao jingyao... | AlanZatarain/pysal | pysal/spreg/twosls.py | Python | bsd-3-clause | 18,699 | [
"COLUMBUS"
] | 62f2b2fc9582d09b878d7c243c42e798336ff5bd549e3c38159aae268e7b4c2d |
import gen_utils
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import wx
import vtk
import vtkdevide
class modifyHomotopySlow(NoConfigModuleMixin, ModuleBase):
"""
WARNING, WARNING, DANGER WILL ROBINSON: this filter exists purely
for experimental purp... | chrisidefix/devide | modules/user/experimental/modifyHomotopySlow.py | Python | bsd-3-clause | 12,547 | [
"VTK"
] | ff7da02eb472f6d72cb11da6b48f145352d27f82894a510f726eecc0913d45df |
''' http://www.biopython.org/DIST/docs/api/Bio.KDTree.KDTree%27-module.html '''
def photoz(list):
import sys, pyfits, os
file = os.environ['sne'] + '/cosmos/cosmos_zphot_mag25.nums.fits'
hdulist = pyfits.open(file)
table = hdulist["OBJECTS"].data
r = []
for i in list[0]:
r.append(... | deapplegate/wtgpipeline | non_essentials/kdtree/kdtree.py | Python | mit | 3,807 | [
"Biopython"
] | c36cea80fcc470476381367f34488d3aea0108e45eb29799377e16468ead4bf6 |
from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
atoms = nanotube(9,0)
angle = atoms.container.get('angle')
traj = PickleTrajectory('twisting.traj','w',atoms)
# twist without scaling
for twist in linspace(0,pi/10,100):
atoms.set_container(angle=angle+twist)
traj.writ... | pekkosk/hotbit | examples/twist_nanotube.py | Python | gpl-2.0 | 878 | [
"ASE"
] | 94a2e5d92d242b8dea1d239ec3b32e3ef8a306b37988542b9b4888c8cf731297 |
# Copyright 2004-2012 Tom Rothamel <pytom@bishoujo.us>
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modi... | MSEMJEJME/tkot | renpy/loadsave.py | Python | gpl-2.0 | 14,620 | [
"VisIt"
] | 4d685cd7428cb703b5fa42077dd49bc43f87034c2929f820d5d56e7820dfd2b4 |
from distutils.core import setup
from distutils.command.install_data import install_data
from distutils.command.install import INSTALL_SCHEMES
import os
import sys
class osx_install_data(install_data):
# On MacOS, the platform-specific lib dir is /System/Library/Framework/Python/.../
# which is wrong. Python 2... | VPAC/lintory | setup.py | Python | gpl-3.0 | 3,062 | [
"Brian"
] | 33102aef787cf6213d10d61208574b63d01e5ad786b5bbe344e79b714e2a392d |
#!/usr/bin/env python
from ase.lattice.surface import fcc111
import ase
from kmos.utils import get_ase_constructor
from kmos.types import *
import numpy as np
slab = fcc111('Pt', [1,1,4], vacuum=10)
positions = slab.get_scaled_positions()
pt = Project()
pt.set_meta(model_name='pt111',
model_dimension='2... | mhoffman/kmos | examples/model_Pt111_surface.py | Python | gpl-3.0 | 1,724 | [
"ASE"
] | 9a05b30c6bdcdd5f43f70033674718ff093964897d7d867e6bc368302a2912ef |
#!/usr/bin/env python
import tkinter as Tk
from tkinter import ttk, messagebox
import matplotlib
import numpy as np
import numpy.ma as ma
import new_cmaps
import sys, traceback
from new_cnorms import PowerNormWithNeg, PowerNormFunc
import matplotlib.colors as mcolors
import matplotlib.gridspec as gridspec
import matplo... | pcrumley/Iseult | src/fields_plots.py | Python | gpl-3.0 | 84,898 | [
"Gaussian"
] | e4eb32a9aed2e23d094feae6272cdfabb3c89134be13ffde91e6f8f6ee7795a6 |
from neuron import h
import numpy as np
import matplotlib.pyplot as plt
def fetch_soma_sec(section_name):
cell_model = 'Hayton.hoc'
h.load_file(cell_model)
cell = h.L5PC
soma = cell.soma[0]
exec('sec = cell.' + section_name)
return soma, sec
def find_vrest(h, section_name):
h.load_file("... | ccluri/L5Pyr | agnesnrn.py | Python | gpl-3.0 | 3,121 | [
"NEURON"
] | fff076e74d08eef0c5de544549e1bfcdf1b024fde112323138687a20811cadc0 |
import numpy as np
# import FitsUtils
import FittingUtilities
import HelperFunctions
import matplotlib.pyplot as plt
import sys
import os
from astropy import units
from astropy.io import fits, ascii
import DataStructures
from scipy.interpolate import InterpolatedUnivariateSpline as interp
import MakeModel
import Helper... | kgullikson88/TS23-Scripts | Smooth.py | Python | gpl-3.0 | 6,248 | [
"Gaussian"
] | 7b35e0bfb87abfc6769a5a29407a856f918989efcfedaa23e89aadbcbd3a9d12 |
from dateutil.relativedelta import relativedelta
from edc_constants.constants import SCREENED
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED
from edc_meta_data.models import Requisitio... | TshepangRas/tshilo-dikotla | td_infant/tests/test_infant_birth_membership.py | Python | gpl-2.0 | 2,538 | [
"VisIt"
] | a49d0b2ce2e4693dfec63c1eae6302e3bb37bfd6a0723f6747c1363a461e121d |
# This file is part of ts_wep.
#
# Developed for the LSST Telescope and Site Systems.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
# This program is free software: you ... | lsst-ts/ts_wep | tests/task/test_estimateZernikesCwfsTask.py | Python | gpl-3.0 | 16,817 | [
"VisIt"
] | 07df71685b986158cf23733fde79cb57b25f3de400aa73da687abbcb1d4f8411 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import time
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware import CoursewarePage, CoursewareSequentialTabPage
from ...pages.lms.co... | martynovp/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 7,379 | [
"VisIt"
] | b16c8a3a8fabd3076864cca3af4ca88e2a0e9a6e48c289aafa55a325f882e340 |
import numpy as np
class sample(object):
"""
class to sample hyperparams
- randomly
- from the previous hyperparams
"""
def __init__(self):
# new : [n_couches, c1, c2, c3, learning_rate, reg_l1, reg_l2, moment, decay, nesterov, activation]
# space definition
self.values... | AntoinePrv/hyperNN | hyperLearn/sample.py | Python | mit | 2,893 | [
"Gaussian"
] | 4c1a7df7d07f7776b6ae9ddd31d6d0cd433b94e6ae84da084be745ae72f48e2e |
################################################################################
# Copyright (C) 2013 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for bayespy.utils.linalg module.
"""
import numpy as n... | jluttine/bayespy | bayespy/utils/tests/test_linalg.py | Python | mit | 6,200 | [
"Gaussian"
] | 5e0a19723d5611ed97f25d94f865c3b207d11b1600c28cbeda310bf8daf63125 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-protgenerics/package.py | Python | lgpl-2.1 | 1,700 | [
"Bioconductor"
] | c73c90b5b904c183aa8dd5d188463998847633dfde878ef28c92d4fb15a4591e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import json
from monty.json import MontyDecoder
import numpy as np
import matplotlib
matplotlib.use("pdf")
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.xas.s... | matk86/pymatgen | pymatgen/vis/tests/test_plotters.py | Python | mit | 1,629 | [
"pymatgen"
] | 5d6c83dac7431eed474d7b79873503f19ae521206318d7e2e3a1c3443a4ff7d0 |
# coding: utf-8
"""
This module provides classes to run and analyze boltztrap on pymatgen band
structure objects. Boltztrap is a software interpolating band structures and
computing materials properties from this band structure using Boltzmann
semi-classical transport theory.
Boltztrap has been developed by Georg Mad... | mbkumar/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 107,107 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | e7ebf258456451eb3477d411fecd146d584999214bc84548448476cbf2cf7f39 |
#
# OldFSSource.py - Old-style basic file-system data source
# Copyright (C) 2004 - 2009 Tony Garnock-Jones <tonyg@kcbbs.gen.nz>
#
# 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 ... | tonyg/gyre | OldFSSource.py | Python | gpl-2.0 | 2,265 | [
"VisIt"
] | 1a0eb178bb508857e1f11c2db6e2675d0a64bb398d2b7a15897cefbe3929256f |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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 applicabl... | mikalstill/nova | nova/tests/unit/policy_fixture.py | Python | apache-2.0 | 6,072 | [
"TINKER"
] | 7913f1d2340bc9fac71e8dc7326cbf4386899b2eb973dce74252945bd625a96d |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tongwang01/tensorflow | tensorflow/python/ops/template.py | Python | apache-2.0 | 11,931 | [
"VisIt"
] | 89511314e7180a82fcfe1aeafd7eea8ccd9a9eccdd9a1994b25caf5bdc573c84 |
"""
StdoutBackend wrapper
"""
__RCSID__ = "$Id$"
import logging
import sys
from DIRAC.Resources.LogBackends.AbstractBackend import AbstractBackend
from DIRAC.FrameworkSystem.private.standardLogging.Formatter.ColoredBaseFormatter import ColoredBaseFormatter
class StdoutBackend(AbstractBackend):
"""
StdoutBacken... | Andrew-McNab-UK/DIRAC | Resources/LogBackends/StdoutBackend.py | Python | gpl-3.0 | 1,201 | [
"DIRAC"
] | 2231b84a04a655d4bfe94ac15f0c335318bb7aeb5a34b7d6a53a5f181e0ea95d |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'SurveyQuestionResponse.visit'
db.add_column(u'survey_surv... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0003_auto__add_field_surveyquestionresponse_visit.py | Python | bsd-2-clause | 13,605 | [
"VisIt"
] | 23b494e75c0fcff7fe193a57db6bdbdce98c0434f5ef6828e43087124bf84d4c |
#!/usr/bin/env python
# vim: ai ts=4 sts=4 et sw=4
import re
import rapidsms
from rapidsms.parsers import Matcher
from persistance.models import *
from models import *
from locations.models import *
from tags.models import *
from people.models import *
from rwanda.models import *
from rwanda.utils import *
class Ap... | adammck/rapidsms-community-apps | rwanda/app.py | Python | bsd-3-clause | 12,980 | [
"VisIt"
] | 9baafc05032bb559a05284056ec0a5d151d6b9726c1303e8adc0f69a0c57db23 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | peterbraden/tensorflow | tensorflow/contrib/bayesflow/__init__.py | Python | apache-2.0 | 1,307 | [
"Gaussian"
] | dd14c03d3d94a47714ab83af28ec994b49c8d5794d281183438a8f77582d513a |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import math
import numpy as np
from ..convolve import convolve, convolve_fft, convolve_models
from ...modeling import models, fitting
from ...test... | AustereCuriosity/astropy | astropy/convolution/tests/test_convolve_models.py | Python | bsd-3-clause | 4,056 | [
"Gaussian"
] | b78dd42ea91031bef903408052c864499a37df60511a99712dd09465575ce65b |
# 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.
# Maintainer: mphoward
R""" MPCD integration methods
Defines bounce-back methods for integrating solutes (MD particles) embedded in an MPCD
solvent. The integrat... | joaander/hoomd-blue | hoomd/mpcd/integrate.py | Python | bsd-3-clause | 8,782 | [
"HOOMD-blue"
] | 15cdca29ef62cd00740683f93ebac627335b7a7fda580b26f2b9e5ae79aa697c |
#-------------------------------------------------------------------------
# Name: pySaliencyMap
# Purpose: Extracting a saliency map from a single still image
#
# Author: Akisato Kimura <akisato@ieee.org>
#
# Created: April 24, 2014
# Copyright: (c) Akisato Kimura 2014-
# Licence: MIT
# URL: ... | tyarkoni/featureX | pliers/external/pysaliency/pySaliencyMap.py | Python | bsd-3-clause | 11,365 | [
"Gaussian"
] | cad0bbfa540f4467d2416854b5d99b6e89bdbf609a7e1d02de56d97a028cb173 |
"""
Tests of inference methods.
"""
# pylint: disable=no-member
# pylint: disable=missing-docstring
# future imports
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
# global imports
import numpy as np
import numpy.testing as nt
import scipy.optimize as spo... | mwhoffman/pygp | tests/test_inference.py | Python | bsd-2-clause | 7,224 | [
"Gaussian"
] | 99bee3bff0da7d6cd335a7a3b7ceefaa36da954a8ebb90bedef3e0c3a83ea31f |
""" This module loads all the classes from the VTK Imaging library into
its namespace. This is a required module."""
from vtkImagingPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/imaging.py | Python | bsd-3-clause | 150 | [
"VTK"
] | 41920ccd13f2e488c2cbb5f06efc85e23f09f614f48a0a03b5b872fd7826e9fe |
#!/usr/bin/env python
"""
hawaii.py
State Estimation and Analysis for PYthon
Utilities for dealing with data around Hawaii
Examples
--------
Assume you have longitude, latitude, and sst values:
>>> m=seapy.hawaii()
>>> m.pcolor(lon,lat,sst,vmin=22,vmax=26,cmap=plt.cm.bwr)
>>> m.land()... | dalepartridge/seapy | hawaii.py | Python | mit | 2,156 | [
"Brian"
] | 5a2ee97095a6c6e8769c091aeb84076386126a79eb7961018a70fa07adeef02c |
# coding=utf-8
from __future__ import absolute_import, division, print_function
import argparse
import antlr4
from conversion import *
from conversionLexer import *
from conversionVisitor import *
def add_indent(code, level):
retval = ''
for line in code:
if isinstance(line, list):
retv... | mwisslead/vfp2py | testbed/__main__.py | Python | mit | 3,092 | [
"VisIt"
] | d7050176410c43d9c995656ff5fc321a9476edf74b9d17fceaae15a8cc120fdc |
import os
import external.cclib as cclib
import logging
from subprocess import Popen, PIPE
import re
from rmgpy.molecule import Molecule
from qmdata import CCLibData
from molecule import QMMolecule
class Gaussian:
"""
A base class for all QM calculations that use Gaussian.
Classes such as :class:`Ga... | KEHANG/RMG-Py | rmgpy/qm/gaussian.py | Python | mit | 18,505 | [
"Gaussian",
"MOPAC",
"cclib"
] | e18f1896394fe65b31c33402a6e885e9681ae5e579b2c193131c83557c7ed5ab |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# =======================... | rbejar/odrl-ogc-cache-policies | owslib/coverage/wcs110.py | Python | mit | 18,383 | [
"NetCDF"
] | ea79c42365bb5e69e36a176b346f3a37f0d166083d9cfd1f8c66c6d5ef3f301a |
#!/usr/bin/python
def enum(collection,st):
#just like "enumerate" but you define your own starting position.
#this returns indices RELATIVE TO ORIGINAL LIST
i = st
while i < len(collection):
yield (i,collection[i])
i += 1
def getfirstindex(L,st,value,K):
for pos,t in enum(L,st):
... | leekgroup/derfinder | countReads.py | Python | mit | 6,467 | [
"pysam"
] | 38d6b3dfa136987b13d0af6c4eae85062c0c53e8077b7dec314e1844ac4cc242 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/sources/tables.py | Python | agpl-3.0 | 7,113 | [
"Galaxy"
] | 65cd9ec5a328bd236f4ada9e8a24d467d9b0a8e41186b85c25847ef84e31b822 |
# -*- coding: utf-8 -*-
"""
celery.datastructures
~~~~~~~~~~~~~~~~~~~~~
Custom types and data structures.
"""
from __future__ import absolute_import, print_function, unicode_literals
import sys
import time
from collections import defaultdict, Mapping, MutableMapping, MutableSet
from heapq import heapify... | sivaprakashniet/push_pull | p2p/lib/python2.7/site-packages/celery/datastructures.py | Python | bsd-3-clause | 18,310 | [
"VisIt"
] | 031696865d814c7fc62c02d09b303d2dd26c6fb850b15b5aadaae3614d219703 |
"""
Learning functions for Projections.
For example, CFProjectionLearningFunctions compute a new set of
ConnectionFields when given an input and output pattern and a set of
ConnectionField objects.
"""
import numpy as np
import param
from topo.base.cf import CFPLearningFn
from topo.base.sheet import activity_type
f... | Tasignotas/topographica_mirror | topo/learningfn/projfn.py | Python | bsd-3-clause | 12,281 | [
"NEURON"
] | 6971e3751a5e3557455dcf23b51ac94d951d2343641c25385885b734284bb055 |
#!/usr/bin/env python
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Can... | adamcandy/qgis-plugins-meshing | dev/tests/gaussian_bump.py | Python | lgpl-2.1 | 4,413 | [
"Gaussian",
"NetCDF"
] | d14449e105b51f8978061b1cd1749f48c73ea8aff98f467355bfee38cecd41a0 |
"""Module symbol-table generator"""
from compiler import ast
from compiler.consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL, SC_UNKNOWN
from compiler.misc import mangle
import types
import sys
MANGLE_LEN = 256
class Scope:
# XXX how much information do I need about each name?
def __init__(self, name, mo... | xbmc/atv2 | xbmc/lib/libPython/Python/Lib/compiler/symbols.py | Python | gpl-2.0 | 14,591 | [
"VisIt"
] | 03a02b2c63b777f129b2223cc36159b3f8ec2582a74f6f1114040c9fd58a6ec0 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/naive_bayes.py | Python | mit | 28,917 | [
"Gaussian"
] | ae6ff96992e2da31797b17ce9dd01f79715257e68c9fd17ac75251f3e89844e9 |
#!/usr/bin/env python
import argparse
import pysam
def Parser():
parser = argparse.ArgumentParser(description='miRNAs counts and coverages')
parser.add_argument('-a', '--alignment', metavar='FILE', type=str,
dest='alignment_file', help='Alignment bam file')
parser.add_argument('--... | drosofff/tools-artbio | tools/mircounts/mircounts.py | Python | mit | 4,816 | [
"pysam"
] | 64c3f43e8790e2e269ad12e0cc6c794b2b43bfa5eb3d2e04a00db0a45523743a |
# -*- coding: utf-8 -*-
#
# Copyright © Spyder Project Contributors
# Licensed under the terms of the MIT License
# (see spyder/__init__.py for details)
"""
Spyder, the Scientific Python Development Environment
=====================================================
Developped and maintained by the Spyder Project
Contr... | sys-bio/tellurium | spyder_mod/Spyder 3.3.6/site-packages/spyder/app/mainwindow.py | Python | apache-2.0 | 138,222 | [
"CRYSTAL",
"VisIt"
] | 554aea01d8c41088f2aa1ee1cd9038850b6c9307a40a7933cf4be3228268dcb0 |
#=======================================================================
# sim_utils.py
#=======================================================================
import warnings
import greenlet
from ..ast_helpers import get_method_ast
from ...datatypes.SignalValue import SignalValue
from ast_visitor import... | Abhinav117/pymtl | pymtl/tools/simulation/sim_utils.py | Python | bsd-3-clause | 15,918 | [
"VisIt"
] | 47adcbd38401effc214b36ebb38d76fc509efcc4ba9bb7df7624f09cc3127da3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | pmghalvorsen/gramps_branch | gramps/gen/filters/rules/person/_hasassociation.py | Python | gpl-2.0 | 2,598 | [
"Brian"
] | ab94befef1bede0b4a1014abeecfe6927ed374d4b22f120a58111792c61cc29b |
from ase.db.core import connect
| suttond/MODOI | ase/db/__init__.py | Python | lgpl-3.0 | 32 | [
"ASE"
] | 86588af360e23b4b22c6cbcaa9618431783cc1131cd9521e6262e242e53f91ef |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK
from DIRAC.Core.Base.AgentModule import AgentModule
#from DIRAC.StorageManagementSystem.Client.StorageManagerClient import StorageManagerClient
from DIRAC.Core.Utilities.List import sor... | avedaee/DIRAC | StorageManagementSystem/Agent/StageRequestAgent.py | Python | gpl-3.0 | 24,204 | [
"DIRAC"
] | 47b41b10646823cad1cf16c3ce1d34c864db7cef5b95f7ccc966a6a531f287a7 |
from math import sqrt
import numpy as np
from ase.data import covalent_radii
from ase.atoms import Atoms
from ase.calculators.singlepoint import SinglePointCalculator
from ase.io import read, write, string2index
from ase.constraints import FixAtoms
from ase.gui.defaults import read_defaults
from ase.quaternions impor... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/images.py | Python | gpl-2.0 | 15,050 | [
"ASE"
] | d912e0b937b6db09f73e1b64573aafcef4905a841b593b42faabe3c0cad129c8 |
from gromacs.fileformats import TOP
import numpy as np
import math
import copy, argparse
def scale_angles(mol, angles):
new_angles = {}
for dh in mol.angles:
atypes = dh.atom1.get_atomtype(), dh.atom2.get_atomtype(), dh.atom3.get_atomtype()
atypes = [a.replace("_", "")... | jandom/GromacsWrapper | scripts/gw-forcefield.py | Python | gpl-3.0 | 5,792 | [
"Gromacs"
] | 938ac9949e3e68441a70d2ede64f5bb417ddfac63211ff5bc6f28905e9bc590b |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 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... | tiagocardosos/stoq | stoqlib/database/test/test_runtime.py | Python | gpl-2.0 | 12,115 | [
"VisIt"
] | 128236ef22fabbee7e068e26ec3050c5e9b0b2aa2903ecdc83326ff3af32a2ab |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | jtyr/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,473 | [
"Brian"
] | 892045c6c451842d1feedd2b78063b6a8774027f3dcf256c5423eab7ec804b03 |
#
# Copyright 2016-2017, 2020 Andreas Klemenz (Fraunhofer IWM)
# 2020 Thomas Reichenbach (Fraunhofer IWM)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the... | libAtoms/matscipy | matscipy/io/opls.py | Python | lgpl-2.1 | 20,447 | [
"ASE",
"LAMMPS",
"Matscipy"
] | 9b9e437ba5758ecea9b760b1f554ff83e86dd6f0a6815fc163a55a85338a33ac |
#!/usr/bin/env python
""" This script is used to submit the jobs on the grid.
It uses an executable (first argument), creates
a directory in which it will store all the job ids (<jobName> args),
and submit a configurable amount of jobs.
"""
from __future__ import print_function
from __future__ import abs... | ic-hep/DIRAC | tests/Performance/DFCPerformance/submitJobs.py | Python | gpl-3.0 | 1,320 | [
"DIRAC"
] | 0b477494304abb90185d863c12abaa50e18655e0e341fdc12562a35d756c64f0 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | si618/pi-time | node_modules/grunt-pylint/tasks/lib/pylint/lint.py | Python | gpl-3.0 | 57,921 | [
"VisIt"
] | 0d4b401aaa1e0062755cdf88529d5d16384dbdc143a4a6f8de523ca19c74c5ce |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | prculley/gramps | gramps/gen/filters/rules/event/_hasnote.py | Python | gpl-2.0 | 1,754 | [
"Brian"
] | 9a773b3860743a371eb7b61e8ebf6f8d636c7ff4ee5b4ec6535beec844e9f576 |
# DNSChef is a highly configurable DNS Proxy for Penetration Testers
# and Malware Analysts. Please visit http://thesprawl.org/projects/dnschef/
# for the latest version and documentation. Please forward all issues and
# concerns to iphelix [at] thesprawl.org.
# Copyright (C) 2015 Peter Kacherginsky, Marcello Salvati... | ru-faraon/MITMf | core/servers/DNS.py | Python | gpl-3.0 | 22,886 | [
"VisIt"
] | fc91c37175f6d2e2169592fb0703ba6ade739154eabd72ac5c314f77e9391a0c |
# Copyright 2016 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... | hfp/tensorflow-xsmm | tensorflow/contrib/distributions/python/ops/mvn_linear_operator.py | Python | apache-2.0 | 13,425 | [
"Gaussian"
] | e989ff467b23cb35ce6cb6e9f515efdac11b59bc056f5cccbd71b8ec883cb439 |
"""Perform streaming post-alignment preparation -- de-duplication and sorting.
Centralizes a pipelined approach to generating sorted, de-duplicated BAM output
from sequencer results.
samblaster: http://arxiv.org/pdf/1403.7486v1.pdf
biobambam bammarkduplicates: http://arxiv.org/abs/1306.0836
"""
import contextlib
impo... | brainstorm/bcbio-nextgen | bcbio/ngsalign/postalign.py | Python | mit | 10,135 | [
"BWA"
] | 7360707e2cd3a362fe4764b4acd58672555118851fb49c6bfaea13b39d94baf9 |
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