From 6f5fa0f1302746b5276cf0f1ef896238ab2b6f47 Mon Sep 17 00:00:00 2001
From: nicolas-zimmermann <nicolaszimmermann.snv@gmail.com>
Date: Tue, 17 Sep 2019 17:12:45 +0200
Subject: [PATCH] changed yml file to generate env, added kmedoids lib, added
 citations file

---
 doc/citations         |   1 +
 src/config_projet.yml |  14 -----
 src/environment.yml   | 120 ++++++++++++++++++++++++++++++++++++++++++
 src/projet8.py        |   1 +
 4 files changed, 122 insertions(+), 14 deletions(-)
 create mode 100644 doc/citations
 delete mode 100644 src/config_projet.yml
 create mode 100644 src/environment.yml

diff --git a/doc/citations b/doc/citations
new file mode 100644
index 0000000..bc297ca
--- /dev/null
+++ b/doc/citations
@@ -0,0 +1 @@
+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] 
diff --git a/src/config_projet.yml b/src/config_projet.yml
deleted file mode 100644
index ee5757a..0000000
--- a/src/config_projet.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-name: projet-court
-channels:
-        - defaults
-        - bioconda
-        - conda-forge
-dependencies:
-        - numpy
-        - pandas
-        - scipy
-        - jupyter
-        - jupyterlab
-        - pip
-        - pip:
-                - pbxplore
diff --git a/src/environment.yml b/src/environment.yml
new file mode 100644
index 0000000..069a6f1
--- /dev/null
+++ b/src/environment.yml
@@ -0,0 +1,120 @@
+name: projet-court
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - attrs=19.1.0=py37_1
+  - backcall=0.1.0=py37_0
+  - blas=1.0=mkl
+  - bleach=3.1.0=py37_0
+  - ca-certificates=2019.5.15=1
+  - certifi=2019.6.16=py37_1
+  - dbus=1.13.6=h746ee38_0
+  - decorator=4.4.0=py37_1
+  - defusedxml=0.6.0=py_0
+  - entrypoints=0.3=py37_0
+  - expat=2.2.6=he6710b0_0
+  - fontconfig=2.13.0=h9420a91_0
+  - freetype=2.9.1=h8a8886c_1
+  - glib=2.56.2=hd408876_0
+  - gmp=6.1.2=h6c8ec71_1
+  - gst-plugins-base=1.14.0=hbbd80ab_1
+  - gstreamer=1.14.0=hb453b48_1
+  - icu=58.2=h9c2bf20_1
+  - intel-openmp=2019.4=243
+  - ipykernel=5.1.2=py37h39e3cac_0
+  - ipython=7.8.0=py37h39e3cac_0
+  - ipython_genutils=0.2.0=py37_0
+  - ipywidgets=7.5.1=py_0
+  - jedi=0.15.1=py37_0
+  - jinja2=2.10.1=py37_0
+  - jpeg=9b=h024ee3a_2
+  - json5=0.8.5=py_0
+  - jsonschema=3.0.2=py37_0
+  - jupyter=1.0.0=py37_7
+  - jupyter_client=5.3.1=py_0
+  - jupyter_console=6.0.0=py37_0
+  - jupyter_core=4.5.0=py_0
+  - jupyterlab=1.1.3=pyhf63ae98_0
+  - jupyterlab_server=1.0.0=py_1
+  - libedit=3.1.20181209=hc058e9b_0
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc-ng=9.1.0=hdf63c60_0
+  - libgfortran-ng=7.3.0=hdf63c60_0
+  - libpng=1.6.37=hbc83047_0
+  - libsodium=1.0.16=h1bed415_0
+  - libstdcxx-ng=9.1.0=hdf63c60_0
+  - libuuid=1.0.3=h1bed415_2
+  - libxcb=1.13=h1bed415_1
+  - libxml2=2.9.9=hea5a465_1
+  - markupsafe=1.1.1=py37h7b6447c_0
+  - mistune=0.8.4=py37h7b6447c_0
+  - mkl=2019.4=243
+  - mkl-service=2.3.0=py37he904b0f_0
+  - mkl_fft=1.0.14=py37ha843d7b_0
+  - mkl_random=1.0.2=py37hd81dba3_0
+  - nbconvert=5.5.0=py_0
+  - nbformat=4.4.0=py37_0
+  - ncurses=6.1=he6710b0_1
+  - notebook=6.0.1=py37_0
+  - numpy=1.16.5=py37h7e9f1db_0
+  - numpy-base=1.16.5=py37hde5b4d6_0
+  - openssl=1.1.1d=h7b6447c_1
+  - pandas=0.25.1=py37he6710b0_0
+  - pandoc=2.2.3.2=0
+  - pandocfilters=1.4.2=py37_1
+  - parso=0.5.1=py_0
+  - pcre=8.43=he6710b0_0
+  - pexpect=4.7.0=py37_0
+  - pickleshare=0.7.5=py37_0
+  - pip=19.2.2=py37_0
+  - prometheus_client=0.7.1=py_0
+  - prompt_toolkit=2.0.9=py37_0
+  - ptyprocess=0.6.0=py37_0
+  - pygments=2.4.2=py_0
+  - pyqt=5.9.2=py37h05f1152_2
+  - pyrsistent=0.14.11=py37h7b6447c_0
+  - python=3.7.4=h265db76_1
+  - python-dateutil=2.8.0=py37_0
+  - pytz=2019.2=py_0
+  - pyzmq=18.1.0=py37he6710b0_0
+  - qt=5.9.7=h5867ecd_1
+  - qtconsole=4.5.5=py_0
+  - readline=7.0=h7b6447c_5
+  - scipy=1.3.1=py37h7c811a0_0
+  - send2trash=1.5.0=py37_0
+  - setuptools=41.0.1=py37_0
+  - sip=4.19.8=py37hf484d3e_0
+  - six=1.12.0=py37_0
+  - sqlite=3.29.0=h7b6447c_0
+  - terminado=0.8.2=py37_0
+  - testpath=0.4.2=py37_0
+  - tk=8.6.8=hbc83047_0
+  - tornado=6.0.3=py37h7b6447c_0
+  - traitlets=4.3.2=py37_0
+  - wcwidth=0.1.7=py37_0
+  - webencodings=0.5.1=py37_1
+  - wheel=0.33.4=py37_0
+  - widgetsnbextension=3.5.1=py37_0
+  - xz=5.2.4=h14c3975_4
+  - zeromq=4.3.1=he6710b0_3
+  - zlib=1.2.11=h7b6447c_3
+  - pip:
+    - biopython==1.74
+    - cycler==0.10.0
+    - griddataformats==0.5.0
+    - gsd==1.8.1
+    - joblib==0.13.2
+    - kiwisolver==1.1.0
+    - matplotlib==3.1.1
+    - mdanalysis==0.20.1
+    - mmtf-python==1.1.2
+    - mock==3.0.5
+    - msgpack==0.6.1
+    - networkx==2.3
+    - pbxplore==1.3.8
+    - pillow==6.1.0
+    - pyclustering==0.9.1
+    - pyparsing==2.4.2
+prefix: /home/sdv/m2bi/nzimmermann/.conda/envs/projet-court
+
diff --git a/src/projet8.py b/src/projet8.py
index b31bacb..578b2c9 100644
--- a/src/projet8.py
+++ b/src/projet8.py
@@ -5,6 +5,7 @@ import numpy as np
 import pbxplore as pbx
 import sys
 from scipy.spatial.distance import squareform, pdist, jaccard 
+from pyclustering.cluster.kmedoids import kmedoids # for kmedoids method
 
 class Conformations:
     """