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[NOP] add licence
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‎License.txt

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OpenMS is released under a 3 clause BSD license.
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The respective license file can be found in the LICENSE file
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The source code of OpenMS is available via our homepage http://www.OpenMS.de
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OpenMS depends on third party libraries which are listed below.
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The source code of these libraries is available from their website or can be
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obtained via a "contrib" package, which specifically configures these libraries
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for OpenMS and is available on our website.
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The respective license files for the contrib libraries can be found
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in the "contrib" package root directory or online (see below).
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libSVM
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- URL: http://www.csie.ntu.edu.tw/~cjlin/libsvm/
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- License available at http://www.csie.ntu.edu.tw/~cjlin/libsvm/COPYRIGHT
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GLPK
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- URL: http://www.gnu.org/s/glpk/
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- License available at http://www.gnu.org/copyleft/gpl.html
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Qt 4
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- URL: http://qt.nokia.com/
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- License available at http://www.gnu.org/licenses/old-licenses/lgpl-2.1.txt
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Xerces-C
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- URL: http://xerces.apache.org/xerces-c/index.html
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- License available at http://www.apache.org/licenses/LICENSE-2.0.html
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Boost (headers)
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- URL: http://www.boost.org/
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- License available at http://www.boost.org/more/license_info.html
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ZLib
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- URL: http://www.zlib.net
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- License available at http://www.zlib.net/zlib_license.html
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BZ2Lib
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- URL: http://www.bzip.org/
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- License.bzip2.txt
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Search engines:
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OMSSA
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- URL: http://pubchem.ncbi.nlm.nih.gov/omssa/
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- License: Public Domain
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X!Tandem:
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- URL and source code: http://www.thegpm.org/tandem/
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- License available at: http://www.perlfoundation.org/attachment/legal/artistic-2_0.txt
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MyriMatch:
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- URL and source code: http://fenchurch.mc.vanderbilt.edu/software.php
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- License available at: http://www.apache.org/licenses/LICENSE-2.0.txt
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‎README.md

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Installation
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=============
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Installation is best done through PyPI (the Python package index) where binary
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packages are provided for the release versions of OpenMS, covering
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Linux/Mac/Windows.
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Installation is best done through [PyPI](https://pypi.python.org/pypi/pyopenms)
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(the Python package index) where binary packages are provided for the release
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versions of OpenMS, covering Linux/Mac/Windows.
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‎src/examples/PhosphoScoring.py

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"""
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--------------------------------------------------------------------------
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OpenMS -- Open-Source Mass Spectrometry
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--------------------------------------------------------------------------
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Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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This software is released under a three-clause BSD license:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of any author or any participating institution
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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For a full list of authors, refer to the file AUTHORS.
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--------------------------------------------------------------------------
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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"""
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import pyopenms, re
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def convertToRichMSSpectrum(input_):

‎src/examples/convertToMGF.py

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"""
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--------------------------------------------------------------------------
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OpenMS -- Open-Source Mass Spectrometry
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--------------------------------------------------------------------------
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Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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This software is released under a three-clause BSD license:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of any author or any participating institution
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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For a full list of authors, refer to the file AUTHORS.
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--------------------------------------------------------------------------
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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"""
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###########################################################################
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## Example script to convert any file to MGF
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###########################################################################

‎src/examples/peakpicker_scipyFFT.py

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"""
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--------------------------------------------------------------------------
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OpenMS -- Open-Source Mass Spectrometry
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--------------------------------------------------------------------------
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Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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This software is released under a three-clause BSD license:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of any author or any participating institution
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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For a full list of authors, refer to the file AUTHORS.
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--------------------------------------------------------------------------
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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"""
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###########################################################################
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## Create peak-picking figure
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###########################################################################

‎src/examples/pymol_example.py

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"""
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--------------------------------------------------------------------------
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OpenMS -- Open-Source Mass Spectrometry
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--------------------------------------------------------------------------
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Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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This software is released under a three-clause BSD license:
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of any author or any participating institution
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may be used to endorse or promote products derived from this software
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without specific prior written permission.
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For a full list of authors, refer to the file AUTHORS.
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--------------------------------------------------------------------------
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
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INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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"""
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# Example of displaying a Streptococcal protein and showing peptide coverage
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import pymol
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import pyopenms

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