changed yml file to generate env, added kmedoids lib, added citations file
nicolas-zimmermann
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mlpy for use of k-medoid : D. Albanese, R. Visintainer, S. Merler, S. Riccadonna, G. Jurman, C. Furlanello. mlpy: Machine Learning Python, 2012. arXiv:1202.6548 [bib]
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name: projet-court
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channels:
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- defaults
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- bioconda
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- conda-forge
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dependencies:
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- numpy
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- pandas
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- scipy
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- jupyter
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- jupyterlab
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- pip
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- pip:
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- pbxplore
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name: projet-court
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channels:
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- defaults
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dependencies:
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- _libgcc_mutex=0.1=main
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- attrs=19.1.0=py37_1
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- backcall=0.1.0=py37_0
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- blas=1.0=mkl
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- bleach=3.1.0=py37_0
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- ca-certificates=2019.5.15=1
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- certifi=2019.6.16=py37_1
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- dbus=1.13.6=h746ee38_0
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- decorator=4.4.0=py37_1
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- defusedxml=0.6.0=py_0
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- entrypoints=0.3=py37_0
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- expat=2.2.6=he6710b0_0
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- fontconfig=2.13.0=h9420a91_0
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- freetype=2.9.1=h8a8886c_1
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- glib=2.56.2=hd408876_0
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- gmp=6.1.2=h6c8ec71_1
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- gst-plugins-base=1.14.0=hbbd80ab_1
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- gstreamer=1.14.0=hb453b48_1
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- icu=58.2=h9c2bf20_1
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- intel-openmp=2019.4=243
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- ipykernel=5.1.2=py37h39e3cac_0
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- ipython=7.8.0=py37h39e3cac_0
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- ipython_genutils=0.2.0=py37_0
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- ipywidgets=7.5.1=py_0
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- jedi=0.15.1=py37_0
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- jinja2=2.10.1=py37_0
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- jpeg=9b=h024ee3a_2
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- json5=0.8.5=py_0
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- jsonschema=3.0.2=py37_0
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- jupyter=1.0.0=py37_7
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- jupyter_client=5.3.1=py_0
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- jupyter_console=6.0.0=py37_0
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- jupyter_core=4.5.0=py_0
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- jupyterlab=1.1.3=pyhf63ae98_0
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- jupyterlab_server=1.0.0=py_1
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- libedit=3.1.20181209=hc058e9b_0
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- libffi=3.2.1=hd88cf55_4
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- libgcc-ng=9.1.0=hdf63c60_0
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- libgfortran-ng=7.3.0=hdf63c60_0
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- libpng=1.6.37=hbc83047_0
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- libsodium=1.0.16=h1bed415_0
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- libstdcxx-ng=9.1.0=hdf63c60_0
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- libuuid=1.0.3=h1bed415_2
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- libxcb=1.13=h1bed415_1
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- libxml2=2.9.9=hea5a465_1
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- markupsafe=1.1.1=py37h7b6447c_0
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- mistune=0.8.4=py37h7b6447c_0
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- mkl=2019.4=243
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- mkl-service=2.3.0=py37he904b0f_0
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- mkl_fft=1.0.14=py37ha843d7b_0
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- mkl_random=1.0.2=py37hd81dba3_0
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- nbconvert=5.5.0=py_0
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- nbformat=4.4.0=py37_0
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- ncurses=6.1=he6710b0_1
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- notebook=6.0.1=py37_0
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- numpy=1.16.5=py37h7e9f1db_0
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- numpy-base=1.16.5=py37hde5b4d6_0
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- openssl=1.1.1d=h7b6447c_1
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- pandas=0.25.1=py37he6710b0_0
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- pandoc=2.2.3.2=0
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- pandocfilters=1.4.2=py37_1
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- parso=0.5.1=py_0
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- pcre=8.43=he6710b0_0
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- pexpect=4.7.0=py37_0
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- pickleshare=0.7.5=py37_0
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- pip=19.2.2=py37_0
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- prometheus_client=0.7.1=py_0
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- prompt_toolkit=2.0.9=py37_0
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- ptyprocess=0.6.0=py37_0
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- pygments=2.4.2=py_0
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- pyqt=5.9.2=py37h05f1152_2
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- pyrsistent=0.14.11=py37h7b6447c_0
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- python=3.7.4=h265db76_1
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- python-dateutil=2.8.0=py37_0
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- pytz=2019.2=py_0
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- pyzmq=18.1.0=py37he6710b0_0
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- qt=5.9.7=h5867ecd_1
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- qtconsole=4.5.5=py_0
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- readline=7.0=h7b6447c_5
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- scipy=1.3.1=py37h7c811a0_0
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- send2trash=1.5.0=py37_0
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- setuptools=41.0.1=py37_0
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- sip=4.19.8=py37hf484d3e_0
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- six=1.12.0=py37_0
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- sqlite=3.29.0=h7b6447c_0
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- terminado=0.8.2=py37_0
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- testpath=0.4.2=py37_0
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- tk=8.6.8=hbc83047_0
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- tornado=6.0.3=py37h7b6447c_0
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- traitlets=4.3.2=py37_0
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- wcwidth=0.1.7=py37_0
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- webencodings=0.5.1=py37_1
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- wheel=0.33.4=py37_0
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- widgetsnbextension=3.5.1=py37_0
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- xz=5.2.4=h14c3975_4
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- zeromq=4.3.1=he6710b0_3
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- zlib=1.2.11=h7b6447c_3
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- pip:
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- biopython==1.74
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- cycler==0.10.0
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- griddataformats==0.5.0
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- gsd==1.8.1
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- joblib==0.13.2
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- kiwisolver==1.1.0
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- matplotlib==3.1.1
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- mdanalysis==0.20.1
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- mmtf-python==1.1.2
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- mock==3.0.5
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- msgpack==0.6.1
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- networkx==2.3
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- pbxplore==1.3.8
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- pillow==6.1.0
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- pyclustering==0.9.1
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- pyparsing==2.4.2
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prefix: /home/sdv/m2bi/nzimmermann/.conda/envs/projet-court
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@ -5,6 +5,7 @@ import numpy as np
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import pbxplore as pbx
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import sys
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from scipy.spatial.distance import squareform, pdist, jaccard
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from pyclustering.cluster.kmedoids import kmedoids # for kmedoids method
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class Conformations:
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"""
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