diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..91ff313523277c176ae08c30e8c2af9c3bd61764 --- /dev/null +++ b/LICENSE @@ -0,0 +1,34 @@ +University of Illinois Open Source License +Copyright 2010-2016 Aksimentiev Group, +All rights reserved. + +Developed by: Aksimentiev Group +University of Illinois at Urbana-Champaign +http://bionano.phsyics.illinois.edu + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the Software), to deal with +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies +of the Software, and to permit persons to whom the Software is furnished to +do so, subject to the following conditions: + +- Redistributions of source code must retain the above copyright notice, +this list of conditions and the following disclaimers. + +- Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimers in the documentation +and/or other materials provided with the distribution. + +- Neither the names of the Aksimentiev Group, University of Illinois at +Urbana-Champaign, nor the names of its contributors may be used to endorse or +promote products derived from this Software without specific prior written +permission. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR +OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, +ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR +OTHER DEALINGS WITH THE SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..c325ac4440ce7524ff4ee13c12455cf00c7e776c --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +# DNArbd: multiresolution coarse-grained simulations of DNA nanotechnology + +... diff --git a/dnarbd/examples/segmentmodel_example.py b/dnarbd/examples/segmentmodel_example.py index 3da167b955fa0c6b50dcc48b2739409bf96f4e1d..4d22fc23d7747aa1f63021a67a84ebdecff38a88 100644 --- a/dnarbd/examples/segmentmodel_example.py +++ b/dnarbd/examples/segmentmodel_example.py @@ -1,12 +1,11 @@ import numpy as np -from segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment -from nbPot import nbDnaScheme +from dnarbd import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment """ Example of using segmentmodel to construct a CG -May need to execute after running: -PATH=/home/cmaffeo2/anaconda3/bin:$PATH; source activate cadnano +May need to update your shell PATH variable before running this script, e.g.: +PATH=/home/cmaffeo2/miniconda3/bin:$PATH """ diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..64a3c31f458a946e1b40d078615022885fa864ad --- /dev/null +++ b/setup.py @@ -0,0 +1,21 @@ +import setuptools + +with open("README.md", "r") as fh: + long_description = fh.read() + +setuptools.setup( + name="dnarbd", + version="0.1dev", + author="Christopher Maffeo", + author_email="cmaffeo2@illinois.edu", + description="Tools for simulating DNA nanotechnology with ARBD", + long_description=long_description, + long_description_content_type="text/markdown", + url="https://gitlab.engr.illinois.edu/tbgl/tools/dnarbd", + packages=setuptools.find_packages(), + classifiers=( + "Programming Language :: Python :: 3", + "License :: UIUC Open source License", + "Operating System :: OS Independent", + ), +)