projet_court_nz

nzimmermann

Projet de classification de conformations de protéines par k-medoids

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Nicolas Zimmermann 88d52b8e8f added beginning of program, md.pdb as toy example and README		2019-09-15 18:54:19 +02:00
data	added beginning of program, md.pdb as toy example and README	2019-09-15 18:54:19 +02:00
doc	initial commit, repository structure and documentation	2019-09-10 10:52:07 +02:00
src	added beginning of program, md.pdb as toy example and README	2019-09-15 18:54:19 +02:00
README	added beginning of program, md.pdb as toy example and README	2019-09-15 18:54:19 +02:00

README

Make sure your current directory is projet_court_nz

Environment

1 - Recreate the conda environment with the config_projet.yml file avaible in the src repository 
	$ conda env create -f src/config_projet.yml
2 - Activate the generated environment
	$ conda activate projet-court

toy-example:
md.pdb contains structural information of 501 conformations of the calf-1 domain

3 - try the program on md.pdb
	$ python3 src/projet8 data/md.pdb 

This will generate a md.csv file in the results folder, representing a dataframe of the conformations, each row being a conformation and each column a PB position

Informations:

The pdb was obtained from .trr and .gro files available online (http://www.dsimb.inserm.fr/~tmp/DM_Calf-1_WT_production_long1.tar.gz)
pbd was generated using gromacs :
	$ trjconv -f md.trr -s md -o md.pdb